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Conserved domains on  [gi|1553259162|gb|AZZ95119|]
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LysR family transcriptional regulator [Hahella sp. KA22]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 10444012)

LysR family transcriptional regulator may function as a transcriptional activator or repressor of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, among others

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 92-285 2.63e-62

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: 195.51  E-value: 2.63e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  92 EVRVGVPSMLGSFYFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGVIVAEFVPEELEARPFLREQMLVTVSQ 171
Cdd:cd05466     1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 172 EHPFAKQESVTPEQFFQEELVMFKEGYFHRKVVDRLAKAAGVTPNIGFETNLLPLIKSIIKQGFGISTLLGMVVEE--NE 249
Cdd:cd05466    81 DHPLAKRKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEElaDG 160

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1553259162 250 SLVTIPF-DTPIWLDLSIAWRRNGYLSRANQAFVEFL 285
Cdd:cd05466   161 GLVVLPLeDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-61 9.06e-14

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


:

Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 64.71  E-value: 9.06e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1553259162   3 IKSLRYFYEVARLGSFTRAAESLGVAQPAVSMALRKLETELTLTLLHRNDRRISLTDEG 61
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
 
Name Accession Description Interval E-value
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 92-285 2.63e-62

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: 195.51  E-value: 2.63e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  92 EVRVGVPSMLGSFYFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGVIVAEFVPEELEARPFLREQMLVTVSQ 171
Cdd:cd05466     1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 172 EHPFAKQESVTPEQFFQEELVMFKEGYFHRKVVDRLAKAAGVTPNIGFETNLLPLIKSIIKQGFGISTLLGMVVEE--NE 249
Cdd:cd05466    81 DHPLAKRKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEElaDG 160

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1553259162 250 SLVTIPF-DTPIWLDLSIAWRRNGYLSRANQAFVEFL 285
Cdd:cd05466   161 GLVVLPLeDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-291 1.20e-61

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 195.86  E-value: 1.20e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162   1 MDIKSLRYFYEVARLGSFTRAAESLGVAQPAVSMALRKLETELTLTLLHRNDRRISLTDEGAILYRHAEKILRAADDAAL 80
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  81 EMSELKGLTRGEVRVGVPSMLGSFYFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGVIVAEFVPEELEARPF 160
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 161 LREQMLVTVSQEHPFAKQESVtpeqffqeelvmfkegyfhrkvvdrlakaagvtpnigfeTNLLPLIKSIIKQGFGISTL 240
Cdd:COG0583   161 GEERLVLVASPDHPLARRAPL---------------------------------------VNSLEALLAAVAAGLGIALL 201

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1553259162 241 LGMVVE---ENESLVTIPF-DTPIWLDLSIAWRRNGYLSRANQAFVEFLLEHSGR 291
Cdd:COG0583   202 PRFLAAdelAAGRLVALPLpDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 90-288 7.84e-51

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: 166.31  E-value: 7.84e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  90 RGEVRVGVPSMLGSFYFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGVIVAEFVPEELEARPFLREQMLVTV 169
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 170 SQEHPFAKQESVTPEQFFQEELVMFKEGYFHRKVVDRLAKAAGVTPNIGFETNLLPLIKSIIKQGFGISTLLGMVVEE-- 247
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARel 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1553259162 248 -NESLVTIPF-DTPIWLDLSIAWRRNGYLSRANQAFVEFLLEH 288
Cdd:pfam03466 161 aDGRLVALPLpEPPLPRELYLVWRKGRPLSPAVRAFIEFLREA 203
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 1-291 7.25e-45

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 153.57  E-value: 7.25e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162   1 MDIKSLRYFYEVARLGSFTRAAESLGVAQPAVSMALRKLETELTLTLLHRNDRRISLTDEGAILYRHAEKILRAADDAAL 80
Cdd:PRK11242    1 MLLRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  81 EMSELKGLTRGEVRVGVPSMLGSFYFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGVIVAEFVPEELEARPF 160
Cdd:PRK11242   81 AIHDVADLSRGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMSQERIEALLADDELDVGIAFAPVHSPEIEAQPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 161 LREQMLVTVSQEHPFA-KQESVTPEQFFQEELVMFKEGYFHRKVVDRLAKAAGVTPNIGFETNLLPLIKSIIKQGfGIST 239
Cdd:PRK11242  161 FTETLALVVGRHHPLAaRRKALTLDELADEPLVLLSAEFATREQIDRYFRRHGVTPRVAIEANSISAVLEIVRRG-RLAT 239

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1553259162 240 LL-GMVVEENESLVTIPFDTPIwLDLSIA--WRRNGYLSRANQAFVEFLLEHSGR 291
Cdd:PRK11242  240 LLpAAIAREHDGLCAIPLDPPL-PQRTAAllRRKGAYRSAAARAFIELALERRAE 293
phn_lysR TIGR03339
aminoethylphosphonate catabolism associated LysR family transcriptional regulator; This group ...
 6-256 1.50e-37

aminoethylphosphonate catabolism associated LysR family transcriptional regulator; This group of sequences represents a number of related clades with numerous examples of members adjacent to operons for the degradation of 2-aminoethylphosphonate (AEP) in Pseudomonas, Ralstonia, Bordetella and Burkholderia species. These are transcriptional regulators of the LysR family which contain a helix-turn-helix (HTH) domain (pfam00126) and a periplasmic substrate-binding protein-like domain (pfam03466). [Regulatory functions, DNA interactions]


Pssm-ID: 132382 [Multi-domain]  Cd Length: 279  Bit Score: 134.09  E-value: 1.50e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162   6 LRYFYEVARLGSFTRAAESLGVAQPAVSMALRKLETELTLTLLHRNDRRISLTDEGAILYRHAEKILRAADDAALEMSEL 85
Cdd:TIGR03339   2 LKAFHAVARCGSFTRAAERLGLSQPTVTDQVRKLEERYGVELFHRNGRRLELTDAGHRLLPIVERLFQQEAEAEFLLRES 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  86 KGLTRGEVRVGVPsmlGSFYFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGVIVAEFVPEELEARPFLREQM 165
Cdd:TIGR03339  82 GALREGSLRIAAT---APYYVLDLVARFRQRYPGIEVSVRIGNSQEVLQALQSYRVDVAVSSEVVDDPRLDRVVLGNDPL 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 166 LVTVSQEHPFAKQESVTPEQFFQEELVMFKEGYFHRKVVDRLAKAAGVTPNIGFETNLLPLIKSIIKQGFGISTLLGMVV 245
Cdd:TIGR03339 159 VAVVHRQHPLAERESVTLEELAGQPLLMREPGSVTRQTTEEALAAAGVAPRPALEIGSREAIREAVLAGLGVSVVSAAEV 238

                         250
                  ....*....|.
gi 1553259162 246 EENESLVTIPF 256
Cdd:TIGR03339 239 GRDPRLRVLPI 249
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-287 4.96e-32

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: 120.03  E-value: 4.96e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162   1 MDIKSLRYFYEVARLGSFTRAAESLGVAQPAVSMALRKLETELTLTLLHRNDRRISLTDEGAILYRHAEKILRAADDAAL 80
Cdd:NF040786    1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  81 EMSELKGLTRGEVRVGVPSMLGSFYFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGVIVAEFVPEELEARPF 160
Cdd:NF040786   81 EFDRYGKESKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKKRLVYTPF 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 161 LREQMLVTVSQEHPF--AKQESVTPEQFFQEELVMFKEGYFHRKVVDRLAKAAGVTP---NIGFETNLLPLIKSIIKQGF 235
Cdd:NF040786  161 YKDRLVLITPNGTEKyrMLKEEISISELQKEPFIMREEGSGTRKEAEKALKSLGISLedlNVVASLGSTEAIKQSVEAGL 240

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1553259162 236 GISTLLGMVVEENES---LVTIPFDT-PIWLDLSIAWRRNGYLSRANQAFVEFLLE 287
Cdd:NF040786  241 GISVISELAAEKEVErgrVLIFPIPGlPKNRDFYLVYNKNRQLSPTAEAFLQFVKE 296
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-61 9.06e-14

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 64.71  E-value: 9.06e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1553259162   3 IKSLRYFYEVARLGSFTRAAESLGVAQPAVSMALRKLETELTLTLLHRNDRRISLTDEG 61
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 1-97 1.20e-05

transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity. [Cellular processes, Toxin production and resistance, DNA metabolism, DNA replication, recombination, and repair, Regulatory functions, DNA interactions]


Pssm-ID: 274509 [Multi-domain]  Cd Length: 292  Bit Score: 45.68  E-value: 1.20e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162   1 MDIKSLRYFYEVARLGSFTRAAESLGVAQPAVSMALRKLETELTLTLLHRNdRRISLTDEGAILYRHAEKILRAADDAAL 80
Cdd:TIGR03298   1 LDYRQLAALAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVRT-QPCRATEAGQRLLRHARQVRLLEAELLA 79

                          90
                  ....*....|....*..
gi 1553259162  81 EMSELKGLTRGEVRVGV 97
Cdd:TIGR03298  80 ELPGLAPGAPTRLTIAV 96
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
2-116 6.04e-05

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 43.81  E-value: 6.04e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162   2 DIKSLRYFYEVARLGSFTRAAESLGVAQPAVSMALRKLETELTLTLLHRnDRRISLTDEGAILYRHAEKI-LRAADDAAL 80
Cdd:PRK13348    3 DYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQRLLRHLRQVaLLEADLLST 81

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1553259162  81 EMSELKGLTRGEVRVGVPSmLGSfYFPPILMAFRHR 116
Cdd:PRK13348   82 LPAERGSPPTLAIAVNADS-LAT-WFLPALAAVLAG 115
 
Name Accession Description Interval E-value
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 92-285 2.63e-62

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: 195.51  E-value: 2.63e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  92 EVRVGVPSMLGSFYFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGVIVAEFVPEELEARPFLREQMLVTVSQ 171
Cdd:cd05466     1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 172 EHPFAKQESVTPEQFFQEELVMFKEGYFHRKVVDRLAKAAGVTPNIGFETNLLPLIKSIIKQGFGISTLLGMVVEE--NE 249
Cdd:cd05466    81 DHPLAKRKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEElaDG 160

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1553259162 250 SLVTIPF-DTPIWLDLSIAWRRNGYLSRANQAFVEFL 285
Cdd:cd05466   161 GLVVLPLeDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-291 1.20e-61

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 195.86  E-value: 1.20e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162   1 MDIKSLRYFYEVARLGSFTRAAESLGVAQPAVSMALRKLETELTLTLLHRNDRRISLTDEGAILYRHAEKILRAADDAAL 80
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  81 EMSELKGLTRGEVRVGVPSMLGSFYFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGVIVAEFVPEELEARPF 160
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 161 LREQMLVTVSQEHPFAKQESVtpeqffqeelvmfkegyfhrkvvdrlakaagvtpnigfeTNLLPLIKSIIKQGFGISTL 240
Cdd:COG0583   161 GEERLVLVASPDHPLARRAPL---------------------------------------VNSLEALLAAVAAGLGIALL 201

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1553259162 241 LGMVVE---ENESLVTIPF-DTPIWLDLSIAWRRNGYLSRANQAFVEFLLEHSGR 291
Cdd:COG0583   202 PRFLAAdelAAGRLVALPLpDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 90-288 7.84e-51

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: 166.31  E-value: 7.84e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  90 RGEVRVGVPSMLGSFYFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGVIVAEFVPEELEARPFLREQMLVTV 169
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 170 SQEHPFAKQESVTPEQFFQEELVMFKEGYFHRKVVDRLAKAAGVTPNIGFETNLLPLIKSIIKQGFGISTLLGMVVEE-- 247
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARel 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1553259162 248 -NESLVTIPF-DTPIWLDLSIAWRRNGYLSRANQAFVEFLLEH 288
Cdd:pfam03466 161 aDGRLVALPLpEPPLPRELYLVWRKGRPLSPAVRAFIEFLREA 203
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 92-285 4.26e-46

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: 153.87  E-value: 4.26e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  92 EVRVGVPSMLGSFYFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGVIVAEFVPEELEARPFLREQMLVTVSQ 171
Cdd:cd08438     1 HLRLGLPPLGGSLLFAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVLPVDEEEFDSQPLCNEPLVAVLPR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 172 EHPFAKQESVTPEQFFQEELVMFKEGY-FHRKVVDrLAKAAGVTPNIGFETNLLPLIKSIIKQGFGISTLLGMVVEE--N 248
Cdd:cd08438    81 GHPLAGRKTVSLADLADEPFILFNEDFaLHDRIID-ACQQAGFTPNIAARSSQWDFIAELVAAGLGVALLPRSIAQRldN 159

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 1553259162 249 ESLVTIPFDTP--IWlDLSIAWRRNGYLSRANQAFVEFL 285
Cdd:cd08438   160 AGVKVIPLTDPdlRW-QLALIWRKGRYLSHAARAWLALL 197
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 1-291 7.25e-45

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 153.57  E-value: 7.25e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162   1 MDIKSLRYFYEVARLGSFTRAAESLGVAQPAVSMALRKLETELTLTLLHRNDRRISLTDEGAILYRHAEKILRAADDAAL 80
Cdd:PRK11242    1 MLLRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  81 EMSELKGLTRGEVRVGVPSMLGSFYFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGVIVAEFVPEELEARPF 160
Cdd:PRK11242   81 AIHDVADLSRGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMSQERIEALLADDELDVGIAFAPVHSPEIEAQPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 161 LREQMLVTVSQEHPFA-KQESVTPEQFFQEELVMFKEGYFHRKVVDRLAKAAGVTPNIGFETNLLPLIKSIIKQGfGIST 239
Cdd:PRK11242  161 FTETLALVVGRHHPLAaRRKALTLDELADEPLVLLSAEFATREQIDRYFRRHGVTPRVAIEANSISAVLEIVRRG-RLAT 239

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1553259162 240 LL-GMVVEENESLVTIPFDTPIwLDLSIA--WRRNGYLSRANQAFVEFLLEHSGR 291
Cdd:PRK11242  240 LLpAAIAREHDGLCAIPLDPPL-PQRTAAllRRKGAYRSAAARAFIELALERRAE 293
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 92-285 6.23e-38

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: 132.66  E-value: 6.23e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  92 EVRVGVPSMLGSFYFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGVIVAEFVPEELEARPFLREQMLVTVSQ 171
Cdd:cd08434     1 TVRLGFLHSLGTSLVPDLIRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLALCSPVPDEPDIEWIPLFTEELVLVVPK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 172 EHPFAKQESVTPEQFFQEELVMFKEGYFHRKVVDRLAKAAGVTPNIGFETNLLPLIKSIIKQGFGISTLLGMVVEENESL 251
Cdd:cd08434    81 DHPLAGRDSVDLAELADEPFVLLSPGFGLRPIVDELCAAAGFTPKIAFEGEEDSTIAGLVAAGLGVAILPEMTLLNPPGV 160

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 1553259162 252 VTIPFDTPIWL-DLSIAWRRNGYLSRANQAFVEFL 285
Cdd:cd08434   161 KKIPIKDPDAErTIGLAWLKDRYLSPAARRFKDFV 195
phn_lysR TIGR03339
aminoethylphosphonate catabolism associated LysR family transcriptional regulator; This group ...
 6-256 1.50e-37

aminoethylphosphonate catabolism associated LysR family transcriptional regulator; This group of sequences represents a number of related clades with numerous examples of members adjacent to operons for the degradation of 2-aminoethylphosphonate (AEP) in Pseudomonas, Ralstonia, Bordetella and Burkholderia species. These are transcriptional regulators of the LysR family which contain a helix-turn-helix (HTH) domain (pfam00126) and a periplasmic substrate-binding protein-like domain (pfam03466). [Regulatory functions, DNA interactions]


Pssm-ID: 132382 [Multi-domain]  Cd Length: 279  Bit Score: 134.09  E-value: 1.50e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162   6 LRYFYEVARLGSFTRAAESLGVAQPAVSMALRKLETELTLTLLHRNDRRISLTDEGAILYRHAEKILRAADDAALEMSEL 85
Cdd:TIGR03339   2 LKAFHAVARCGSFTRAAERLGLSQPTVTDQVRKLEERYGVELFHRNGRRLELTDAGHRLLPIVERLFQQEAEAEFLLRES 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  86 KGLTRGEVRVGVPsmlGSFYFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGVIVAEFVPEELEARPFLREQM 165
Cdd:TIGR03339  82 GALREGSLRIAAT---APYYVLDLVARFRQRYPGIEVSVRIGNSQEVLQALQSYRVDVAVSSEVVDDPRLDRVVLGNDPL 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 166 LVTVSQEHPFAKQESVTPEQFFQEELVMFKEGYFHRKVVDRLAKAAGVTPNIGFETNLLPLIKSIIKQGFGISTLLGMVV 245
Cdd:TIGR03339 159 VAVVHRQHPLAERESVTLEELAGQPLLMREPGSVTRQTTEEALAAAGVAPRPALEIGSREAIREAVLAGLGVSVVSAAEV 238

                         250
                  ....*....|.
gi 1553259162 246 EENESLVTIPF 256
Cdd:TIGR03339 239 GRDPRLRVLPI 249
rbcR CHL00180
LysR transcriptional regulator; Provisional
 6-287 2.59e-35

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 128.98  E-value: 2.59e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162   6 LRYFYEVARLGSFTRAAESLGVAQPAVSMALRKLETELTLTLLHRNDRRISLTDEGAILYRHAEKILRAADDAALEMSEL 85
Cdd:CHL00180   10 LRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRALEDL 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  86 KGLTRGEVRVGVPSMLGSFYFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGVIVAEfVPEE----LEARPFL 161
Cdd:CHL00180   90 KNLQRGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVGGE-VPTElkkiLEITPYV 168

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 162 REQMLVTVSQEHPFAKQESVTPEQFFQEELVMFKEGYFHRKVVDRLAKAAGVTPN---IGFETNLLPLIKSIIKQGFGIS 238
Cdd:CHL00180  169 EDELALIIPKSHPFAKLKKIQKEDLYRLNFITLDSNSTIRKVIDNILIQNGIDSKrfkIEMELNSIEAIKNAVQSGLGAA 248

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1553259162 239 TLLGMVVEENESL-----VTIPfDTPIWLDLSIAWRRNGYLSRANQAFVEFLLE 287
Cdd:CHL00180  249 FVSVSAIEKELELgllhwIKIE-NITIKRMLSIITNPNRYKSKASETFYNEILT 301
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 92-285 5.66e-35

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: 125.30  E-value: 5.66e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  92 EVRVGVPSMLGSFYFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGVIVAEFVPEELEARPFLREQMLVTVSQ 171
Cdd:cd08420     1 TLRIGASTTIGEYLLPRLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLVEGPVDHPDLIVEPFAEDELVLVVPP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 172 EHPFAKQESVTPEQFFQEELVMFKEGYFHRKVVDRLAKAAGVTP---NIGFETNLLPLIKSIIKQGFGISTLLGMVVE-- 246
Cdd:cd08420    81 DHPLAGRKEVTAEELAAEPWILREPGSGTREVFERALAEAGLDGldlNIVMELGSTEAIKEAVEAGLGISILSRLAVRke 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1553259162 247 -ENESLVTIPF-DTPIWLDLSIAWRRNGYLSRANQAFVEFL 285
Cdd:cd08420   161 lELGRLVALPVeGLRLTRPFSLIYHKDKYLSPAAEAFLEFL 201
PBP2_MleR cd08437
The substrate binding domain of LysR-type transcriptional regulator MleR which required for ...
 92-285 4.73e-34

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: 122.83  E-value: 4.73e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  92 EVRVGVPSMLGSFYFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGVIVA--EFVPEELEARPFLREQMLVTV 169
Cdd:cd08437     1 KLRFGLPPIIGNYYFPKLAKDLIKTGLMIQIDTYEGGSAELLEQLLQGDLDIALLGSltPLENSALHSKIIKTQHFMIIV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 170 SQEHPFAKQESVTPEQFFQEELVMFKEGYFHRKVVDRLAKAAGVTPNIGFETNLLPLIKSIIKQGFGISTLLGMVVEENE 249
Cdd:cd08437    81 SKDHPLAKAKKVNFADLKKENFILLNEHFVHPKAFDSLCQQANFQPNIVYRTNDIHILKSMVRENVGIGFLTDIAVKPDD 160

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 1553259162 250 SLVTIPFD---TPIWLdLSIAWRRNGYLSRANQAFVEFL 285
Cdd:cd08437   161 HLVAIPLLdneQPTFY-ISLAHRKDQLLTPAQKKLLDLL 198
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-287 4.96e-32

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: 120.03  E-value: 4.96e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162   1 MDIKSLRYFYEVARLGSFTRAAESLGVAQPAVSMALRKLETELTLTLLHRNDRRISLTDEGAILYRHAEKILRAADDAAL 80
Cdd:NF040786    1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  81 EMSELKGLTRGEVRVGVPSMLGSFYFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGVIVAEFVPEELEARPF 160
Cdd:NF040786   81 EFDRYGKESKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKKRLVYTPF 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 161 LREQMLVTVSQEHPF--AKQESVTPEQFFQEELVMFKEGYFHRKVVDRLAKAAGVTP---NIGFETNLLPLIKSIIKQGF 235
Cdd:NF040786  161 YKDRLVLITPNGTEKyrMLKEEISISELQKEPFIMREEGSGTRKEAEKALKSLGISLedlNVVASLGSTEAIKQSVEAGL 240

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1553259162 236 GISTLLGMVVEENES---LVTIPFDT-PIWLDLSIAWRRNGYLSRANQAFVEFLLE 287
Cdd:NF040786  241 GISVISELAAEKEVErgrVLIFPIPGlPKNRDFYLVYNKNRQLSPTAEAFLQFVKE 296
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-285 5.27e-31

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: 114.54  E-value: 5.27e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  93 VRVGVPSMLGSFYFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGVIVAEFVPEELEARPFLREQMLVTVSQE 172
Cdd:cd08440     2 VRVAALPSLAATLLPPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEADPDLEFEPLLRDPFVLVCPKD 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 173 HPFAKQESVTPEQFFQEELVMFKEGYFHRKVVDRLAKAAGVTPNIGFETNLLPLIKSIIKQGFGISTLLGMVVE--ENES 250
Cdd:cd08440    82 HPLARRRSVTWAELAGYPLIALGRGSGVRALIDRALAAAGLTLRPAYEVSHMSTALGMVAAGLGVAVLPALALPlaDHPG 161

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1553259162 251 LVTIPFDTP-IWLDLSIAWRRNGYLSRANQAFVEFL 285
Cdd:cd08440   162 LVARPLTEPvVTRTVGLIRRRGRSLSPAAQAFLDLL 197
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 92-285 2.08e-27

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: 105.28  E-value: 2.08e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  92 EVRVG-VPSMLGSFyFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGVIVAEFVPEELEARPFLREQMLVTVS 170
Cdd:cd08414     1 RLRIGfVGSALYGL-LPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPPPDPPGLASRPLLREPLVVALP 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 171 QEHPFAKQESVTPEQFFQEELVMFKEG---YFHRKVVDRLAkAAGVTPNIGFETNLLPLIKSIIKQGFGIsTLL--GMVV 245
Cdd:cd08414    80 ADHPLAARESVSLADLADEPFVLFPREpgpGLYDQILALCR-RAGFTPRIVQEASDLQTLLALVAAGLGV-ALVpaSVAR 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1553259162 246 EENESLVTIPF-DTPIWLDLSIAWRRNGyLSRANQAFVEFL 285
Cdd:cd08414   158 LQRPGVVYRPLaDPPPRSELALAWRRDN-ASPALRAFLELA 197
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 92-284 4.93e-27

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: 104.16  E-value: 4.93e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  92 EVRVGVPSMLGSFYFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGVIVAEFVPEELEARPFLREQMLVTVSQ 171
Cdd:cd08412     1 TLRIGCFSTLAPYYLPGLLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALTYDLDLPEDIAFEPLARLPPYVWLPA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 172 EHPFAKQESVTPEQFFQEELVM----FKEGYFHrkvvdRLAKAAGVTPNIGFETNLLPLIKSIIKQGFGISTLLGMVV-- 245
Cdd:cd08412    81 DHPLAGKDEVSLADLAAEPLILldlpHSREYFL-----SLFAAAGLTPRIAYRTSSFEAVRSLVANGLGYSLLNDRPYrp 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1553259162 246 --EENESLVTIPF-DTPIWLDLSIAWRRNGYLSRANQAFVEF 284
Cdd:cd08412   156 wsYDGKRLVRRPLaDPVPPLRLGLAWRRGARLTRAARAFVDF 197
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-285 2.05e-26

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: 102.68  E-value: 2.05e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  93 VRVGVPSMLGSFYFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGVI-VAEFVPEELEARPFLREQMLVTVSQ 171
Cdd:cd08436     2 LAIGTITSLAAVDLPELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAFVgLPERRPPGLASRELAREPLVAVVAP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 172 EHPFAKQESVTPEQFFQEELVMFKEGYFHRKVVDRLAKAAGVTPNIGFETNLLPLIKSIIKQGFGISTLLGMVVEENESL 251
Cdd:cd08436    82 DHPLAGRRRVALADLADEPFVDFPPGTGARRQVDRAFAAAGVRRRVAFEVSDVDLLLDLVARGLGVALLPASVAARLPGL 161

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 1553259162 252 VTIPF-DTPIWLdLSIAWRRNGYlSRANQAFVEFL 285
Cdd:cd08436   162 AALPLePAPRRR-LYLAWSAPPP-SPAARAFLELL 194
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 91-285 6.49e-26

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: 101.45  E-value: 6.49e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  91 GEVRVGVPSMLGSFYFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGVIVAEFVPEELEARPFLREQMLVTVS 170
Cdd:cd08411     1 GPLRLGVIPTIAPYLLPRLLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAALLALPVDEPGLEEEPLFDEPFLLAVP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 171 QEHPFAKQESVTPEQFFQEELVMFKEGY-FHRKVVDrLAKAAGVTPNIGFETNLLPLIKSIIKQGFGISTLLGMVVE--- 246
Cdd:cd08411    81 KDHPLAKRKSVTPEDLAGERLLLLEEGHcLRDQALE-LCRLAGAREQTDFEATSLETLRQMVAAGLGITLLPELAVPsee 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1553259162 247 -ENESLVTIPFDTPI-WLDLSIAWRRNGYLSRANQAFVEFL 285
Cdd:cd08411   160 lRGDRLVVRPFAEPApSRTIGLVWRRSSPRAAAFEALAELI 200
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 1-288 6.57e-25

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 101.22  E-value: 6.57e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162   1 MDIKSLRYFYEVARLG-SFTRAAESLGVAQPAVSMALRKLETELTLTLLHRNDRRI-SLTDEGAILYRHAEKILRaadda 78
Cdd:PRK12682    1 MNLQQLRFVREAVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLkGLTEPGKAVLDVIERILR----- 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  79 alEMSELKGLTR-------GEVRVGVPSMLGSFYFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGvIVAEFV 151
Cdd:PRK12682   76 --EVGNIKRIGDdfsnqdsGTLTIATTHTQARYVLPRVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIG-IATESL 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 152 P--EELEARPFLREQMLVTVSQEHPFAKQESVTPEQFFQEELVMFKEGYFHRKVVDRLAKAAGVTPNIGFETNLLPLIKS 229
Cdd:PRK12682  153 AddPDLATLPCYDWQHAVIVPPDHPLAQEERITLEDLAEYPLITYHPGFTGRSRIDRAFAAAGLQPDIVLEAIDSDVIKT 232

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1553259162 230 IIKQGFGISTLLGMVVEE--NESLVTIP----FDT-PIWldlsIAWRRNGYLSRANQAFVEFLLEH 288
Cdd:PRK12682  233 YVRLGLGVGIVAEMAYRPdrDGDLVALPaghlFGPnTAW----VALKRGAYLRNYVYKFIELCAPH 294
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 92-285 3.83e-24

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: 96.48  E-value: 3.83e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  92 EVRVGVPSMLGSFYFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGVIVAEFVPEELEARPFLREQMLVTVSQ 171
Cdd:cd08415     1 TLRIAALPALALSLLPRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPLDHPGLESEPLASGRAVCVLPP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 172 EHPFAKQESVTPEQFFQEELVMFKEGYFHRKVVDRLAKAAGVTPNIGFETNLLPLIKSIIKQGFGISTLLGMVVEEN--E 249
Cdd:cd08415    81 GHPLARKDVVTPADLAGEPLISLGRGDPLRQRVDAAFERAGVEPRIVIETQLSHTACALVAAGLGVAIVDPLTAAGYagA 160

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1553259162 250 SLVTIPFDTPIWLDLSIAWRRNGYLSRANQAFVEFL 285
Cdd:cd08415   161 GLVVRPFRPAIPFEFALVRPAGRPLSRLAQAFIDLL 196
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
1-291 8.75e-24

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 98.13  E-value: 8.75e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162   1 MDIKSLRYFYEVARLG-SFTRAAESLGVAQPAVSMALRKLETELTLTLLHRNDRRI-SLTDEGAILYRHAEKILRAADDA 78
Cdd:PRK12684    1 MNLHQLRFVREAVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLrGLTEPGRIILASVERILQEVENL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  79 ALEMSELKGLTRGEVRVGVPSMLGSFYFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGVI---VAEFvpEEL 155
Cdd:PRK12684   81 KRVGKEFAAQDQGNLTIATTHTQARYALPAAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAIAteaIADY--KEL 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 156 EARPFLREQMLVTVSQEHPFAKQESVTPEQFFQEELVMFKEGYFHRKVVDRLAKAAGVTPNIGFETNLLPLIKSIIKQGF 235
Cdd:PRK12684  159 VSLPCYQWNHCVVVPPDHPLLERKPLTLEDLAQYPLITYDFAFAGRSKINKAFALRGLKPDIVLEAIDADVIKTYVELGL 238

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1553259162 236 GISTLLGMVV--EENESLVTIP----FDTPIwldLSIAWRRNGYLSRANQAFVEFLLEHSGR 291
Cdd:PRK12684  239 GVGIVADMAFdpERDRNLRAIDaghlFGSST---TRLGLRRGAYLRGYVYTFIELFAPTLNR 297
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 1-260 2.44e-23

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 97.02  E-value: 2.44e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162   1 MDIKSLRYFYEVARLGSFTRAAESLGVAQPAVSMALRKLETELTLTLLHRNDRRISLTDEGAILYRHAEKILRAAdDAAL 80
Cdd:PRK11151    1 MNIRDLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREV-KVLK 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  81 EMSELKGLT-RGEVRVGVPSMLGSFYFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLgVIVAeFVPeelEARP 159
Cdd:PRK11151   80 EMASQQGETmSGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDC-AILA-LVK---ESEA 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 160 FLR-----EQMLVTVSQEHPFAKQESVTPEQFFQEELVMFKEGYFHRKVVDRLAKAAGVTPNIGFETNLLPLIKSIIKQG 234
Cdd:PRK11151  155 FIEvplfdEPMLLAVYEDHPWANRDRVPMSDLAGEKLLMLEDGHCLRDQAMGFCFEAGADEDTHFRATSLETLRNMVAAG 234

                         250       260
                  ....*....|....*....|....*....
gi 1553259162 235 FGISTLLGMVV---EENESLVTIPFDTPI 260
Cdd:PRK11151  235 SGITLLPALAVpneRKRDGVCYLPCIKPE 263
PBP2_CynR cd08425
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, ...
 91-284 3.01e-23

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: 94.32  E-value: 3.01e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  91 GEVRVGVPSMLGSFYFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGVIVAEFVPEELEARPFLREQMLVTVS 170
Cdd:cd08425     1 GSLRLAMTPTFTAYLIGPLIDRFHARYPGIALSLREMPQERIEAALADDRLDLGIAFAPVRSPDIDAQPLFDERLALVVG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 171 QEHPFAKQE-SVTPEQFFQEELVMFKEGYFHRKVVDRLAKAAGVTPNIGFETNLLPLIKSIIKQGfGISTLL-GMVVEEN 248
Cdd:cd08425    81 ATHPLAQRRtALTLDDLAAEPLALLSPDFATRQHIDRYFQKQGIKPRIAIEANSISAVLEVVRRG-RLATILpDAIAREQ 159

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1553259162 249 ESLVTIPFDTPI-WLDLSIAWRRNGYLSRANQAFVEF 284
Cdd:cd08425   160 PGLCAVALEPPLpGRTAALLRRKGAYRSAAARAFAAL 196
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 3-287 4.03e-23

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 95.91  E-value: 4.03e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162   3 IKSLRYFYEVARLGSFTRAAESLGVAQPAVSMALRKLETELTLTLLHRNDRRISLTDEGAILYRHAEKILraadDAALEM 82
Cdd:PRK10837    5 LRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALL----EQAVEI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  83 SELKGLTRGEVRVGVPSMLGSFYFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGVIVAEFVPEELEARPFLR 162
Cdd:PRK10837   81 EQLFREDNGALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNSQDVINAVLDFRVDIGLIEGPCHSPELISEPWLE 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 163 EQMLVTVSQEHPFAKQEsVTPEQFFQEELVMFKEGYFHRKVVDRLAKAAGVTPNIGFETNLLPLIKSIIKQGFGISTLLG 242
Cdd:PRK10837  161 DELVVFAAPDSPLARGP-VTLEQLAAAPWILRERGSGTREIVDYLLLSHLPRFELAMELGNSEAIKHAVRHGLGISCLSR 239

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*....
gi 1553259162 243 MVVEE---NESLVTIPFDTP-IWLDLSIAWRRNGYLSRANQAFVEFLLE 287
Cdd:PRK10837  240 RVIADqlqAGTLVEVAVPLPrLMRTLYRIHHRQKHLSNALQRFLSYCQE 288
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 1-271 1.19e-22

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 94.84  E-value: 1.19e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162   1 MDIKSLRYFYEVARLGSFTRAAESLGVAQPAVSMALRKLETELTLTLLHRNDRRISLTDEGAILYRHAEKILRAADDAAL 80
Cdd:PRK09906    1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  81 eMSELKGLTRGEVRVG-VPSMLGSFyFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGVIVAEFVPEELEARP 159
Cdd:PRK09906   81 -RARKIVQEDRQLTIGfVPSAEVNL-LPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPVYSDEIDYLE 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 160 FLREQMLVTVSQEHPFAKQESVTPEQFFQEELVM---FKEGYFHRKVVDrLAKAAGVTPNIGFETNLLPLIKSIIKQGFG 236
Cdd:PRK09906  159 LLDEPLVVVLPVDHPLAHEKEITAAQLDGVNFIStdpAYSGSLAPIIKA-WFAQHNSQPNIVQVATNILVTMNLVGMGLG 237

                         250       260       270
                  ....*....|....*....|....*....|....*..
gi 1553259162 237 ISTLLGMVVEEN-ESLVTIPFDTPI-WLDLSIAWRRN 271
Cdd:PRK09906  238 CTIIPGYMNNFNtGQVVFRPLAGNVpSIALLMAWKKG 274
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 1-287 2.45e-21

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 91.28  E-value: 2.45e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162   1 MDIKSLRYFYEVARLGSFTRAAESLGVAQPAVSMALRKLETELTLTLLHRNDRRISLTDEGAILYRHAEKILRAADDAAL 80
Cdd:PRK11233    1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  81 EMSELKGLTRGEVRVGV-PSMLGSFYFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGVIVAEFVPEELEARP 159
Cdd:PRK11233   81 AVHNVGQALSGQVSIGLaPGTAASSLTMPLLQAVRAEFPGIVLYLHENSGATLNEKLMNGQLDMAVIYEHSPVAGLSSQP 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 160 FLREQMLVTVSQEHPfakQESVTPEQFFQEELVMFKEGYFHRKVVDRLAKAAGVTPNIGFETNLLPLIKSIIKQGFGIST 239
Cdd:PRK11233  161 LLKEDLFLVGTQDCP---GQSVDLAAVAQMNLFLPRDYSAVRLRVDEAFSLRRLTAKVIGEIESIATLTAAIASGMGVTV 237

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1553259162 240 LL-----GMVVEENESLVTIpfDTP-IWLDLSIAWRRNGYLSRANQAFVEFLLE 287
Cdd:PRK11233  238 LPesaarSLCGAVNGWMARI--TTPsMSLSLSLNLSARLPLSPQAQAVKEILLS 289
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-285 3.93e-21

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: 88.42  E-value: 3.93e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  92 EVRVGVPSMLGSFYFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGVIVA-----EFVPEELEARPFLREQML 166
Cdd:cd08423     1 TLRVGAFPTAAAALLPPALAALRARHPGLEVRLREAEPPESLDALRAGELDLAVVFDypvtpPPDDPGLTRVPLLDDPLD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 167 VTVSQEHPFAKQESVTPEQFFQEELVMFKEGYFHRKVVDRLAKAAGVTPNIGFETNLLPLIKSIIKQGFGISTLLGMVVE 246
Cdd:cd08423    81 LVLPADHPLAGREEVALADLADEPWIAGCPGSPCHRWLVRACRAAGFTPRIAHEADDYATVLALVAAGLGVALVPRLALG 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 1553259162 247 -ENESLVTIPFDTPIWLDLSIAWRRNGYLSRANQAFVEFL 285
Cdd:cd08423   161 aRPPGVVVRPLRPPPTRRIYAAVRAGAARRPAVAAALEAL 200
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 92-285 8.33e-21

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


Pssm-ID: 176124  Cd Length: 198  Bit Score: 87.65  E-value: 8.33e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  92 EVRVGVPSMLGSFYFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGVIvaeFVPEE---LEARPFLREQMLVT 168
Cdd:cd08433     1 RVSVGLPPSAASVLAVPLLRAVRRRYPGIRLRIVEGLSGHLLEWLLNGRLDLALL---YGPPPipgLSTEPLLEEDLFLV 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 169 VSQEHPFAKQESVTPEQFFQEELVMFKEGYFHRKVVDRLAKAAGVTPNIGFETNLLPLIKSIIKQGFGiSTLL--GMVVE 246
Cdd:cd08433    78 GPADAPLPRGAPVPLAELARLPLILPSRGHGLRRLVDEAAARAGLTLNVVVEIDSVATLKALVAAGLG-YTILpaSAVAA 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1553259162 247 ENES--LVTIPFDTP-IWLDLSIAWRRNGYLSRANQAFVEFL 285
Cdd:cd08433   157 EVAAgrLVAAPIVDPaLTRTLSLATPRDRPLSPAALAVRDLL 198
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 1-288 1.16e-19

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 87.02  E-value: 1.16e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162   1 MDIKSLRYFYEVARLG-SFTRAAESLGVAQPAVSMALRKLETELTLTLLHRNDRRIS-LTDEGAILYRHAEKILRAADDA 78
Cdd:PRK12683    1 MNFQQLRIIREAVRQNfNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTgLTEPGKELLQIVERMLLDAENL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  79 ALEMSELKGLTRGEVRVGVPSMLGSFYFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGvIVAEFVPEE--LE 156
Cdd:PRK12683   81 RRLAEQFADRDSGHLTVATTHTQARYALPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIG-IATEALDREpdLV 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 157 ARPFLREQMLVTVSQEHPFAKQESVTPEQFFQEELVMFKEGYFHRKVVDRLAKAAGVTPNIGFETNLLPLIKSIIKQGFG 236
Cdd:PRK12683  160 SFPYYSWHHVVVVPKGHPLTGRENLTLEAIAEYPIITYDQGFTGRSRIDQAFAEAGLVPDIVLTALDADVIKTYVELGMG 239

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1553259162 237 ISTLLGMVV--EENESLVTIpfDTPIWLDLSIAW---RRNGYLSRANQAFVEFLLEH 288
Cdd:PRK12683  240 VGIVAAMAYdpQRDTGLVAL--DTDHLFEANTTRvglRRGAYLRGYAYRFIELFAPH 294
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
 92-285 1.84e-19

The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO operon, which is involved in the carbon dioxide fixation, contains the type 2 periplasmic binding fold; CbbR, a LysR-type transcriptional regulator, is required to activate expression of RubisCO, one of two unique enzymes in the Calvin-Benson-Bassham (CBB) cycle pathway. All plants, cyanobacteria, and many autotrophic bacteria use the CBB cycle to fix carbon dioxide. Thus, this cycle plays an essential role in assimilating CO2 into organic carbon on earth. The key CBB cycle enzyme is ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO), which catalyzes the actual CO2 fixation reaction. The CO2 concentration affects the expression of RubisCO genes. It has also shown that NADPH enhances the DNA-binding ability of the CbbR. RubisCO is composed of eight large (CbbL) and eight small subunits (CbbS). The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176111  Cd Length: 197  Bit Score: 84.10  E-value: 1.84e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  92 EVRVGVPSMlgSFYF-PPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGVIVAefVPEEL--EARPFLREQMLVT 168
Cdd:cd08419     1 RLRLAVVST--AKYFaPRLLGAFCRRHPGVEVSLRVGNREQVLERLADNEDDLAIMGR--PPEDLdlVAEPFLDNPLVVI 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 169 VSQEHPFAKQESVTPEQFFQEELVMFKEGYFHRKVVDRLAKAAGVTPNIGFETNLLPLIKSIIKQGFGISTL--LGMVVE 246
Cdd:cd08419    77 APPDHPLAGQKRIPLERLAREPFLLREPGSGTRLAMERFFAEHGVTLRVRMELGSNEAIKQAVMAGLGLSVLslHTLALE 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1553259162 247 -ENESLVTIPF-DTPIWLDLSIAWRRNGYLSRANQAFVEFL 285
Cdd:cd08419   157 lATGRLAVLDVeGFPIRRQWYVVHRKGKRLSPAAQAFLDFL 197
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
1-289 2.30e-19

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 86.22  E-value: 2.30e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162   1 MDIKSLRYFYEVARLGSFTRAAESLGVAQPAVSMALRKLETELTLTLLHRNDRRISLTDEGAILYRHAEKILRAADDAAL 80
Cdd:PRK15421    2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQ 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  81 EMSELKgltRGEVRVGVPSMLGSFYFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLgVIVAEFVPEE-LEARP 159
Cdd:PRK15421   82 ACNEPQ---QTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDL-VMTSDILPRSgLHYSP 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 160 FLREQMLVTVSQEHPFAKQESVTPEQFFQEELVMFKEGYFHRKVVDRLAKAAGVTPNIGFETNLLPLIKsIIKQGFGIST 239
Cdd:PRK15421  158 MFDYEVRLVLAPDHPLAAKTRITPEDLASETLLIYPVQRSRLDVWRHFLQPAGVSPSLKSVDNTLLLIQ-MVAARMGIAA 236

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1553259162 240 LLGMVVEENES---LVTIPFDTPIWLDLSIAWRRNGYLSRANQAFVEFLLEHS 289
Cdd:PRK15421  237 LPHWVVESFERqglVVTKTLGEGLWSRLYAAVRDGEQRQPVTEAFIRSARNHA 289
PBP2_LTTR_aromatics_like_2 cd08448
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-285 2.40e-19

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: 83.86  E-value: 2.40e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  92 EVRVG-VPSMLGSFyFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGVIVAEFVPEELEARPFLREQMLVTVS 170
Cdd:cd08448     1 RLRIGfVGSMLYRG-LPRILRAFRAEYPGIEVALHEMSSAEQIEALLRGELDLGFVHSRRLPAGLSARLLHREPFVCCLP 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 171 QEHPFAKQESVTPEQFFQEELVMFKEGY---FHRKVVDRLAkAAGVTPNIGFETNLLPLIKSIIKQGFGISTL-LGMVVE 246
Cdd:cd08448    80 AGHPLAARRRIDLRELAGEPFVLFSREVspdYYDQIIALCM-DAGFHPKIRHEVRHWLTVVALVAAGMGVALVpRSLARA 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 1553259162 247 ENESLVTIPF-DTPIWLDLSIAWRRNGYlSRANQAFVEFL 285
Cdd:cd08448   159 GLAGVRFLPLkGATQRSELYAAWKASAP-NPALQAFLAAL 197
PBP2_CysB_like cd08413
The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains ...
 107-283 1.40e-17

The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; CysB is a transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the regulation of transcription in response to sulfur source is attributed to two transcriptional regulators, CysB and Cbl. CysB, in association with Cbl, downregulates the expression of ssuEADCB operon which is required for the utilization of sulfur from aliphatic sulfonates, in the presence of cysteine. Also, Cbl and CysB together directly function as transcriptional activators of tauABCD genes, which are required for utilization of taurine as sulfur source for growth. Like many other members of the LTTR family, CysB is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 176105 [Multi-domain]  Cd Length: 198  Bit Score: 78.82  E-value: 1.40e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 107 PPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGvIVAEFV--PEELEARPFLREQMLVTVSQEHPFAKQESVTPE 184
Cdd:cd08413    16 PPVIAAFRKRYPKVKLSLHQGTPSQIAEMVLKGEADIA-IATEALddHPDLVTLPCYRWNHCVIVPPGHPLADLGPLTLE 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 185 QFFQEELVMFKEGYFHRKVVDRLAKAAGVTPNIGFETNLLPLIKSIIKQGFGISTLLGMVV--EENESLVTIPFDTPIwl 262
Cdd:cd08413    95 DLAQYPLITYDFGFTGRSSIDRAFARAGLEPNIVLTALDADVIKTYVRLGLGVGIIAEMAYdpQRDADLVALDAGHLF-- 172

                         170       180
                  ....*....|....*....|....
gi 1553259162 263 DLSIAW---RRNGYLSRANQAFVE 283
Cdd:cd08413   173 GPNTTRialRRGTYLRSYAYDFIE 196
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-285 1.41e-17

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


Pssm-ID: 176117 [Multi-domain]  Cd Length: 199  Bit Score: 78.89  E-value: 1.41e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  92 EVRVGVPSMLGSFYFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGVIVAEFVPEELEARPFLREQMLVTVSQ 171
Cdd:cd08426     1 RVRVATGEGLAAELLPSLIARFRQRYPGVFFTVDVASTADVLEAVLSGEADIGLAFSPPPEPGIRVHSRQPAPIGAVVPP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 172 EHPFAKQESVTPEQFFQEELVMFKEGYFHRKVVDRLAKAAGVTPNIGFETNLLPLIKSIIKQGFGISTLLGM-VVEENES 250
Cdd:cd08426    81 GHPLARQPSVTLAQLAGYPLALPPPSFSLRQILDAAFARAGVQLEPVLISNSIETLKQLVAAGGGISLLTELaVRREIRR 160

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 1553259162 251 --LVTIPFDTP--IWLDLSIAWRRNGYLSRANQAFVEFL 285
Cdd:cd08426   161 gqLVAVPLADPhmNHRQLELQTRAGRQLPAAASAFLQLL 199
PRK10341 PRK10341
transcriptional regulator TdcA;
4-289 1.86e-17

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 80.68  E-value: 1.86e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162   4 KSLRYFYEVARLGSFTRAAESLGVAQPAVSMALRKLETELTLTLLHRNDRRISLTDEGAILYRHAEKILRAADDAALEMS 83
Cdd:PRK10341   10 QHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEIN 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  84 ELKGLTRGEVRVGVPSMLGSFYFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELD--LGVIVAEFVPEELEARPFL 161
Cdd:PRK10341   90 GMSSEAVVDVSFGFPSLIGFTFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDfaIGTLSNEMKLQDLHVEPLF 169

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 162 REQMLVTVSQEHPFAKQ---ESVTPEQFFQEELVMfkeGYF---------HRKVVDRLAKAAGVTP--NIGFETNLLPLI 227
Cdd:PRK10341  170 ESEFVLVASKSRTCTGTttlESLKNEQWVLPQTNM---GYYsellttlqrNGISIENIVKTDSVVTiyNLVLNADFLTVI 246

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1553259162 228 KSIIKQGFGISTLLGMVVEEneslvtipfDTPIwLDLSIAWRRNGYLSRANQAFVEFLLEHS 289
Cdd:PRK10341  247 PCDMTSPFGSNQFITIPIEE---------TLPV-AQYAAVWSKNYRIKKAASVLVELAKEYS 298
cbl PRK12679
HTH-type transcriptional regulator Cbl;
1-268 4.21e-17

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 79.85  E-value: 4.21e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162   1 MDIKSLRYFYEVARLG-SFTRAAESLGVAQPAVSMALRKLETELTLTLLHRNDRRI-SLTDEGAILYRHAEKILRAADDA 78
Cdd:PRK12679    1 MNFQQLKIIREAARQDyNLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRLlGMTEPGKALLVIAERILNEASNV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  79 ALEMSELKGLTRGEVRVGVPSMLGSFYFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGVIVAEFVP-EELEA 157
Cdd:PRK12679   81 RRLADLFTNDTSGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASERLSNdPQLVA 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 158 RPFLREQMLVTVSQEHPFAKQESVTPEQFFQEELVMFKEGYFHRKVVDRLAKAAGVTPNIGFETNLLPLIKSIIKQGFGI 237
Cdd:PRK12679  161 FPWFRWHHSLLVPHDHPLTQITPLTLESIAKWPLITYRQGITGRSRIDDAFARKGLLADIVLSAQDSDVIKTYVALGLGI 240

                         250       260       270
                  ....*....|....*....|....*....|.
gi 1553259162 238 STLLGMVVEENESLVTIPFDTPIWLDLSIAW 268
Cdd:PRK12679  241 GLVAEQSSGEQEESNLIRLDTRHLFDANTVW 271
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 93-285 1.53e-16

The C-terminal substrate binding domain of galactose-binding protein regulator contains the type 2 periplasmic binding fold; Galactose-binding protein regulator (GbpR), a member of the LysR family of bacterial transcriptional regulators, regulates the expression of chromosomal virulence gene chvE. The chvE gene is involved in the uptake of specific sugars, in chemotaxis to these sugars, and in the VirA-VirG two-component signal transduction system. In the presence of an inducing sugar such as L-arabinose, D-fucose, or D-galactose, GbpR activates chvE expression, while in the absence of an inducing sugar, GbpR represses expression. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176126 [Multi-domain]  Cd Length: 201  Bit Score: 76.16  E-value: 1.53e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  93 VRVGVPSMLGSFYFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDL--GVIVAEFVPEELEARPFLREQMLVTVS 170
Cdd:cd08435     2 VRVGAVPAAAPVLLPPAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLaiGRLADDEQPPDLASEELADEPLVVVAR 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 171 QEHPFAKQESVTPEQFFQEELVMFKEGYFHRKVVDRLAKAAGV-TPNIGFETNLLPLIKSIIKQGFGISTLLGMVVEENE 249
Cdd:cd08435    82 PGHPLARRARLTLADLADYPWVLPPPGTPLRQRLEQLFAAAGLpLPRNVVETASISALLALLARSDMLAVLPRSVAEDEL 161

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 1553259162 250 S---LVTIPFDTPIWL-DLSIAWRRNGYLSRANQAFVEFL 285
Cdd:cd08435   162 RagvLRELPLPLPTSRrPIGITTRRGGPLSPAARALLDAL 201
PBP2_LTTR_aromatics_like_1 cd08447
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-271 1.48e-15

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


Pssm-ID: 176138 [Multi-domain]  Cd Length: 198  Bit Score: 73.45  E-value: 1.48e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  93 VRVGVPSMLGSFYFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGVIVAEFVPEELEARPFLREQMLVTVSQE 172
Cdd:cd08447     2 LRIGFTAASAYSFLPRLLAAARAALPDVDLVLREMVTTDQIEALESGRIDLGLLRPPFARPGLETRPLVREPLVAAVPAG 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 173 HPFAKQESVTPEQFFQEELVMF---KEGYFHrKVVDRLAKAAGVTPNIGFETNLLPLIKSIIKQGFGIS------TLLGM 243
Cdd:cd08447    82 HPLAGAERLTLEDLDGQPFIMYsptEARYFH-DLVVRLFASAGVQPRYVQYLSQIHTMLALVRAGLGVAlvpasaSRLRF 160

                         170       180
                  ....*....|....*....|....*...
gi 1553259162 244 vveENESLVTIPFDTPIWLDLSIAWRRN 271
Cdd:cd08447   161 ---EGVVFRPLDLPRDVPVELHLAWRRD 185
PBP2_Cbl cd08444
The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is ...
 104-283 3.28e-15

The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is required for expression of sulfate starvation-inducible (ssi) genes, contains the type 2 periplasmic binding fold; Cbl is a member of the LysR transcriptional regulators that comprise the largest family of prokaryotic transcription factor. Cbl shows high sequence similarity to CysB, the LysR-type transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the function of Cbl is required for expression of sulfate starvation-inducible (ssi) genes, coupled with the biosynthesis of cysteine from the organic sulfur sources (sulfonates). The ssi genes include the ssuEADCB and tauABCD operons encoding uptake systems for organosulfur compounds, aliphatic sulfonates, and taurine. The genes in these operons encode an ABC-type transport system required for uptake of aliphatic sulfonates and a desulfonation enzyme. Both Cbl and CysB require expression of the tau and ssu genes. Like many other members of the LTTR family, the Cbl 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: 176135  Cd Length: 198  Bit Score: 72.54  E-value: 3.28e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 104 FYFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGVIVAEFVPE-ELEARPFLREQMLVTVSQEHPFAKQESVT 182
Cdd:cd08444    13 YALPWVVQAFKEQFPNVHLVLHQGSPEEIASMLANGQADIGIATEALENHpELVSFPYYDWHHHIIVPVGHPLESITPLT 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 183 PEQFFQEELVMFKEGYFHRKVVDRLAKAAGVTPNIGFETNLLPLIKSIIKQGFGISTLLGMVVEENESLVTIPFDTPIWL 262
Cdd:cd08444    93 IETIAKWPIITYHGGFTGRSRIDRAFSRAELTPNIVLSALDADVIKTYVGLGMGIGIVAEMAFEGQRDTNLIKLDTSHLF 172

                         170       180
                  ....*....|....*....|....
gi 1553259162 263 DLSIAW---RRNGYLSRANQAFVE 283
Cdd:cd08444   173 GKNTTWialRRGGDLRNFAYRFIE 196
PRK09986 PRK09986
LysR family transcriptional regulator;
1-268 3.43e-15

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 73.99  E-value: 3.43e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162   1 MDIKSLRYFYEVARLGSFTRAAESLGVAQPAVSMALRKLETELTLTLLHRNDRRISLTDEGAILYRHAEKILRAADDAal 80
Cdd:PRK09986    7 IDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQS-- 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  81 eMSELKGLTRGEVRVGVPSMLGSFYFPPILMAFRHrYPTLNLSVieggTWRL------QQM--LEQGELDLGV--IVAEF 150
Cdd:PRK09986   85 -LARVEQIGRGEAGRIEIGIVGTALWGRLRPAMRH-FLKENPNV----EWLLrelspsMQMaaLERRELDAGIwrMADLE 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 151 VPEELEARPFLREQMLVTVSQEHPFAKQESVTPEQFFQEELVM--FKEGYFHRKvVDRLAKAAGVTPNIGFETNLLPLIK 228
Cdd:PRK09986  159 PNPGFTSRRLHESAFAVAVPEEHPLASRSSVPLKALRNEYFITlpFVHSDWGKF-LQRVCQQAGFSPQIIRQVNEPQTVL 237

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|.
gi 1553259162 229 SIIKQGFGISTLLGMVVEENESLVT-IPFDTPIWLDLSIAW 268
Cdd:PRK09986  238 AMVSMGIGITLLPDSYAQIPWPGVVfRPLKERIPADLYAVY 278
PBP2_LysR cd08456
The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine ...
 92-285 4.90e-15

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: 72.07  E-value: 4.90e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  92 EVRVG-VPSMLGSFyFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGVIVAEFVPEELEARPFLREQMLVTVS 170
Cdd:cd08456     1 ELRIAvLPALSQSF-LPRAIKAFLQRHPDVTISIHTRDSPTVEQWLSAQQCDLGLVSTLHEPPGIERERLLRIDGVCVLP 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 171 QEHPFAKQESVTPEQFFQEELVMFKEGYFHRKVVDRLAKAAGVTPNIGFETNLLPLIKSIIKQGFGISTLLGMVVEE--N 248
Cdd:cd08456    80 PGHRLAVKKVLTPSDLEGEPFISLARTDGTRQRVDALFEQAGVKRRIVVETSYAATICALVAAGVGVSVVNPLTALDyaA 159

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1553259162 249 ESLVTIPFDTPIWLDLSIAWRRNGYLSRANQAFVEFL 285
Cdd:cd08456   160 AGLVVRRFSPAVPFEVSLIRPKHRPSSALVAAFSACL 196
PRK09791 PRK09791
LysR family transcriptional regulator;
6-260 5.28e-15

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 73.64  E-value: 5.28e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162   6 LRYFYEVARLGSFTRAAESLGVAQPAVSMALRKLETELTLTLLHRNDRRISLTDEGAILYRHAEKILRAADDAALEMSEL 85
Cdd:PRK09791   10 IRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQEDIRQR 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  86 KGLTRGEVRVGVPSMLGSFYFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDL-------GVIVAEFVPEELEAR 158
Cdd:PRK09791   90 QGQLAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDFtintyyqGPYDHEFTFEKLLEK 169

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 159 PFlreqmLVTVSQEHPFAKQESVtpEQFFQEELVM-FKEGYFHRKVVDRLAKaAGVTPNIGFETNLLPLIKSIIKQGFGI 237
Cdd:PRK09791  170 QF-----AVFCRPGHPAIGARSL--KQLLDYSWTMpTPHGSYYKQLSELLDD-QAQTPQVGVVCETFSACISLVAKSDFL 241

                         250       260
                  ....*....|....*....|....*.
gi 1553259162 238 STLLGMVVEE---NESLVTIPFDTPI 260
Cdd:PRK09791  242 SILPEEMGCDplhGQGLVMLPVSEIL 267
PBP2_CysB cd08443
The C-terminal substrate domain of LysR-type transcriptional regulator CysB contains type 2 ...
 93-283 1.96e-14

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: 70.28  E-value: 1.96e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  93 VRVGVPSMLGSFYFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGvIVAEFVPEE--LEARPFLREQMLVTVS 170
Cdd:cd08443     2 LYVATTHTQARYVLPPVIKGFIERYPRVSLQMHQGSPTQIAEMVSKGLVDFA-IATEALHDYddLITLPCYHWNRCVVVK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 171 QEHPFAKQESVTPEQFFQEELVMFKEGYFHRKVVDRLAKAAGVTPNIGFETNLLPLIKSIIKQGFGISTLLGMVVE--EN 248
Cdd:cd08443    81 RDHPLADKQSISIEELATYPIVTYTFGFTGRSELDTAFNRAGLTPNIVLTATDADVIKTYVRLGLGVGVIASMAYDpvDD 160

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1553259162 249 ESLVTIPF-DTPIWLDLSIAWRRNGYLSRANQAFVE 283
Cdd:cd08443   161 PDLVIRDArDLFPWSVTKIAFRRGTFLRSYMYDFIQ 196
PBP2_BudR cd08451
The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is ...
 107-283 4.94e-14

The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is responsible for activation of the expression of the butanediol operon genes; contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of BudR regulator, which is responsible for induction of the butanediol formation pathway under fermentative growth conditions. Three enzymes are involved in the production of 1 mol of 2,3 butanediol from the condensation of 2 mol of pyruvate with acetolactate and acetoin as intermediates: acetolactate synthetase, acetolactate decarboxylase, and acetoin reductase. In Klebsiella terrigena, BudR regulates the expression of the budABC operon genes, encoding these three enzymes of the butanediol pathway. In many bacterial species, the use of this pathway can prevent intracellular acidification by diverting metabolism from acid production to the formation of neutral compounds (acetoin and butanediol). This substrate-binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176142 [Multi-domain]  Cd Length: 199  Bit Score: 69.13  E-value: 4.94e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 107 PPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGVIVAEFV-PEELEARPFLREQMLVTVSQEHPFAKQESVTPEQ 185
Cdd:cd08451    17 PGLIRRFREAYPDVELTLEEANTAELLEALREGRLDAAFVRPPVArSDGLVLELLLEEPMLVALPAGHPLARERSIPLAA 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 186 FFQEELVMFKegyfhRKV----VDRLAKA---AGVTPNIGFETNLLPLIKSIIKQGFGISTL-LGMVVEENESLVTIPF- 256
Cdd:cd08451    97 LADEPFILFP-----RPVgpglYDAIIAAcrrAGFTPRIGQEAPQMASAINLVAAGLGVSIVpASMRQLQAPGVVYRPLa 171

                         170       180
                  ....*....|....*....|....*..
gi 1553259162 257 DTPIWLDLSIAWRRNGyLSRANQAFVE 283
Cdd:cd08451   172 GAPLTAPLALAYRRGE-RSPAVRNFIA 197
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 94-270 7.59e-14

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


Pssm-ID: 176109 [Multi-domain]  Cd Length: 200  Bit Score: 68.78  E-value: 7.59e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  94 RVGVPSMLGSFYFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGVIVAEFVPEELEARPFLREQMLVTVSQEH 173
Cdd:cd08417     3 RIAASDYLEALLLPPLLARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELPPGLRSQPLFEDRFVCVARKDH 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 174 PFAKQEsVTPEQFFQEELVMFK-EGYFHRkVVDRLAKAAGVTPNIGFETNLLPLIKSIIKQGFGISTLLGMVVEENES-- 250
Cdd:cd08417    83 PLAGGP-LTLEDYLAAPHVLVSpRGRGHG-LVDDALAELGLSRRVALTVPHFLAAPALVAGTDLIATVPRRLAEALAErl 160

                         170       180
                  ....*....|....*....|...
gi 1553259162 251 ---LVTIPFDTPIwLDLSIAWRR 270
Cdd:cd08417   161 glrVLPLPFELPP-FTVSLYWHP 182
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-61 9.06e-14

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 64.71  E-value: 9.06e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1553259162   3 IKSLRYFYEVARLGSFTRAAESLGVAQPAVSMALRKLETELTLTLLHRNDRRISLTDEG 61
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
PBP2_YofA_SoxR_like cd08442
The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, ...
 107-285 6.30e-13

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: 66.09  E-value: 6.30e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 107 PPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDlGVIVAEFV-PEELEARPFLREQMLVTVSQEHPfakqESVTPEQ 185
Cdd:cd08442    16 PPLLAAYHARYPKVDLSLSTGTTGALIQAVLEGRLD-GAFVAGPVeHPRLEQEPVFQEELVLVSPKGHP----PVSRAED 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 186 FFQEELVMFKEGYFHRKVVDRLAKAAGVTPNIGFETNLLPLIKSIIKQGFGI-----STLLGMVVEENESLVTIPF---D 257
Cdd:cd08442    91 LAGSTLLAFRAGCSYRRRLEDWLAEEGVSPGKIMEFGSYHAILGCVAAGMGIallprSVLDSLQGRGSVSIHPLPEpfaD 170

                         170       180
                  ....*....|....*....|....*...
gi 1553259162 258 TPIWLdlsiAWRRnGYLSRANQAFVEFL 285
Cdd:cd08442   171 VTTWL----VWRK-DSFTAALQAFLDLL 193
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 1-237 1.67e-12

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 66.59  E-value: 1.67e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162   1 MDIKSLRYFYEVARLGSFTRAAESLGVAQPAVSMALRKLETELTLTLLHRNDRRISLTDEGAILYRHAEKILRAADDAAl 80
Cdd:PRK15092   11 LDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEAC- 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  81 eMSELKGLTRGEVRVGVPSMLGSFYFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGVIVAEfvPEELEaRPF 160
Cdd:PRK15092   90 -SSLMYSNLQGVLTIGASDDTADTILPFLLNRVSSVYPKLALDVRVKRNAFMMEMLESQEVDLAVTTHR--PSSFP-ALN 165

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1553259162 161 LREQ-MLVTVSQEHPFAKQESVTpeqffqeeLVMFKEGYFHRKVVDRLAKAAGVTPNIGFETNLLPLIKSIIKQGFGI 237
Cdd:PRK15092  166 LRTSpTLWYCAAEYVLQKGEPIP--------LVLLDEPSPFRDMALATLNAAGIPWRIAYVASTLSAVRAAVKAGLGV 235
PBP2_LTTR_like_2 cd08427
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-285 1.85e-12

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


Pssm-ID: 176118 [Multi-domain]  Cd Length: 195  Bit Score: 64.52  E-value: 1.85e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  92 EVRVG-VPSMLGSFyFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGVIV-AEF-VPEELEARPFLREQMLVT 168
Cdd:cd08427     1 RLRLGaIATVLTGL-LPRALARLRRRHPDLEVHIVPGLSAELLARVDAGELDAAIVVePPFpLPKDLVWTPLVREPLVLI 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 169 VSQEHPFAkqesvTPEQFFQEE-LVMFKEGYFHRKVVDRLAKAAGVTPNIGFETNLLPLIKSIIKQGFGIST--LLGMVV 245
Cdd:cd08427    80 APAELAGD-----DPRELLATQpFIRYDRSAWGGRLVDRFLRRQGIRVREVMELDSLEAIAAMVAQGLGVAIvpDIAVPL 154

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1553259162 246 EENESLVTIPF-DTPIWLDLSIAWRRNGYLSRANQAFVEFL 285
Cdd:cd08427   155 PAGPRVRVLPLgDPAFSRRVGLLWRRSSPRSRLIQALLEAL 195
PBP2_TdcA cd08418
The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is ...
 92-288 3.06e-12

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


Pssm-ID: 176110 [Multi-domain]  Cd Length: 201  Bit Score: 64.30  E-value: 3.06e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  92 EVRVGVPSMLGSFYFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDL--GVIVAEFVPEELEARPFLREQMLVTV 169
Cdd:cd08418     1 KVSIGVSSLIAHTLMPAVINRFKEQFPDVQISIYEGQLSSLLPELRDGRLDFaiGTLPDEMYLKELISEPLFESDFVVVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 170 SQEHPFAKQESVtpEQFFQEELVM--FKEGYFHrKVVDRLaKAAGVTPNIGFETNLLPLIKSIIKQGFGISTLLGMVVEE 247
Cdd:cd08418    81 RKDHPLQGARSL--EELLDASWVLpgTRMGYYN-NLLEAL-RRLGYNPRVAVRTDSIVSIINLVEKADFLTILSRDMGRG 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 1553259162 248 ---NESLVTIPFDTPIWL-DLSIAWRRNGYLSRANQAFVEFLLEH 288
Cdd:cd08418   157 pldSFRLITIPVEEPLPSaDYYLIYRKKSRLTPLAEQLVELFRRY 201
PBP2_DntR_like_3 cd08461
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 107-268 5.53e-12

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


Pssm-ID: 176150 [Multi-domain]  Cd Length: 198  Bit Score: 63.45  E-value: 5.53e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 107 PPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGVIVAEFVPEELEARPFLREQMLVTVSQEHPFAkQESVTPEQF 186
Cdd:cd08461    16 PPLLAALRQEAPGVRVAIRDLESDNLEAQLERGEVDLALTTPEYAPDGLRSRPLFEERYVCVTRRGHPLL-QGPLSLDQF 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 187 FQEELVM--FKEGYFhRKVVDRLAKAAGVTPNIGFETNLLPLIKSIIKQgfgiSTLLGMV----VEENESLVTIPFDTPI 260
Cdd:cd08461    95 CALDHIVvsPSGGGF-AGSTDEALAALGLTRNVVLSVPSFLVVPEILAA----TDMVAFVpsrlVPNLEGLQEVELPLEP 169


                  ....*....
gi 1553259162 261 -WLDLSIAW 268
Cdd:cd08461   170 pGFDVVMAW 178
PBP2_LrhA_like cd08439
The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of ...
 92-238 6.07e-12

The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of closely related homologs, contains the type 2 periplasmic binding fold; This CD represents the LrhA subfamily of LysR-like bacterial transcriptional regulators, including LrhA, HexA, PecT, and DgdR. LrhA is involved in control of the transcription of flagellar, motility, and chemotaxis genes by regulating the synthesis and concentration of FlhD(2)C(2), the master regulator for the expression of flagellar and chemotaxis genes. The LrhA protein has strong homology to HexA and PecT from plant pathogenic bacteria, in which HexA and PecT act as repressors of motility and of virulence factors, such as exoenzymes required for lytic reactions. DgdR also shares similar characteristics to those of LrhA, HexA and PecT. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176130  Cd Length: 185  Bit Score: 63.12  E-value: 6.07e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  92 EVRVGVPSMLGSFYFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGVIVAEfvPEELEARPFLREQMLVTVSQ 171
Cdd:cd08439     1 TLRIGCPDDYADTILPFLLNRFASVYPRLAIEVVCKRTPRLMEMLERGEVDLALITHP--PPGASATILRRSPTVWYCAA 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1553259162 172 EHPFAKQESVtpeqffqeELVMFKE-GYFHRKVVDRLaKAAGVTPNIGFETNLLPLIKSIIKQGFGIS 238
Cdd:cd08439    79 GYILAPGEPL--------PLALLDEpTLDRRAALAAL-DAAGIPWRIAYAASSLSGLRAAVRAGLGIT 137
PBP2_IlvR cd08453
The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved ...
 107-285 7.47e-12

The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved in the biosynthesis of isoleucine, leucine and valine; contains type 2 periplasmic binding fold; The IlvR is an activator of the upstream and divergently transcribed ilvD gene, which encodes dihydroxy acid dehydratase that participates in isoleucine, leucine, and valine biosynthesis. As in the case of other members of the LysR family, the expression of ilvR gene is repressed in the presence of its own gene product. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176144 [Multi-domain]  Cd Length: 200  Bit Score: 63.15  E-value: 7.47e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 107 PPILMAFRHRYPTLNLSVIEGgTWRLQ-QMLEQGELDLGVIVA---EFVPEELEARPFLREQMLVTVSQEHPFAKQESVT 182
Cdd:cd08453    16 PELVRRFREAYPDVELQLREA-TSDVQlEALLAGEIDAGIVIPppgASAPPALAYRPLLSEPLVLAVPAAWAAEGGAPLA 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 183 PEQFFQEELVMFKEGY---FHrKVVDRLAKAAGVTPNIGFETNLLPLIKSIIKQGFGIStllgMVVEENESL-----VTI 254
Cdd:cd08453    95 LAAVAAEPLVIFPRRIapaFH-DAVTGYYRAAGQTPRIAQEAIQMQTIISLVSAGMGVA----LVPASLRNLarpgvVYR 169

                         170       180       190
                  ....*....|....*....|....*....|..
gi 1553259162 255 PFDTPI-WLDLSIAWRRNGyLSRANQAFVEFL 285
Cdd:cd08453   170 ELADPApVLETGLVWRRDD-ASPVLARFLDLV 200
cysB PRK12681
HTH-type transcriptional regulator CysB;
1-254 1.36e-11

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 63.76  E-value: 1.36e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162   1 MDIKSLRYFYEVARLG-SFTRAAESLGVAQPAVSMALRKLETELTLTLLHRNDRRIS-LTDEGAILYRHAEKILRAADDA 78
Cdd:PRK12681    1 MKLQQLRYIVEVVNHNlNVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTqVTPAGEEIIRIAREILSKVESI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  79 ALEMSELKGLTRGEVRVGVPSMLGSFYFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGVIV-AEFVPEELEA 157
Cdd:PRK12681   81 KSVAGEHTWPDKGSLYIATTHTQARYALPPVIKGFIERYPRVSLHMHQGSPTQIAEAAAKGNADFAIATeALHLYDDLIM 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 158 RPFLREQMLVTVSQEHPFAKQESVTPEQFFQEELVMFKEGYFHRKVVDRLAKAAGVTPNIGFETNLLPLIKSIIKQGFGI 237
Cdd:PRK12681  161 LPCYHWNRSVVVPPDHPLAKKKKLTIEELAQYPLVTYVFGFTGRSELDTAFNRAGLTPRIVFTATDADVIKTYVRLGLGV 240

                         250
                  ....*....|....*....
gi 1553259162 238 STLLGMVVEENE--SLVTI 254
Cdd:PRK12681  241 GVIASMAVDPVAdpDLVAI 259
PRK12680 PRK12680
LysR family transcriptional regulator;
1-268 1.49e-11

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 63.87  E-value: 1.49e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162   1 MDIKSLRYFYEVARLG-SFTRAAESLGVAQPAVSMALRKLETELTLTLLHRNDRRI-SLTDEGAILYRHAEKILRAADDA 78
Cdd:PRK12680    1 MTLTQLRYLVAIADAElNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLeSVTPAGVEVIERARAVLSEANNI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  79 ALEMSELKGLTRGEVRVGVPSMLGSFYFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGVI-VAEFVPEELEA 157
Cdd:PRK12680   81 RTYAANQRRESQGQLTLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVsTAGGEPSAGIA 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 158 RPFLREQMLVTVSQEHPFaKQESVTPE--QFFQEELVMFKEGYFHRKVVDRLAKAAGVTPNIGFETNLLPLIKSIIKQGF 235
Cdd:PRK12680  161 VPLYRWRRLVVVPRGHAL-DTPRRAPDmaALAEHPLISYESSTRPGSSLQRAFAQLGLEPSIALTALDADLIKTYVRAGL 239

                         250       260       270
                  ....*....|....*....|....*....|....
gi 1553259162 236 GISTLLGMVVEEN-ESLVTIPFDTPIwlDLSIAW 268
Cdd:PRK12680  240 GVGLLAEMAVNANdEDLRAWPAPAPI--AECIAW 271
PBP2_HcaR cd08450
The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in ...
 106-270 5.26e-11

The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in involved in 3-phenylpropionic acid catabolism, contains the type2 periplasmic binding fold; HcaR, a member of the LysR family of transcriptional regulators, controls the expression of the hcA1, A2, B, C, and D operon, encoding for the 3-phenylpropionate dioxygenase complex and 3-phenylpropionate-2',3'-dihydrodiol dehydrogenase, that oxidizes 3-phenylpropionate to 3-(2,3-dihydroxyphenyl) propionate. Dioxygenases play an important role in protecting the cell against the toxic effects of dioxygen. The expression of hcaR is negatively auto-regulated, as for other members of the LysR family, and is strongly repressed in the presence of glucose. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176141 [Multi-domain]  Cd Length: 196  Bit Score: 60.47  E-value: 5.26e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 106 FPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGVIVAEFVPEELEARPFLREQMLVTVSQEHPFAKQESVTPEQ 185
Cdd:cd08450    15 LPEVLPILREEHPDLDVELSSLFSPQLAEALMRGKLDVAFMRPEIQSDGIDYQLLLKEPLIVVLPADHRLAGREKIPPQD 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 186 FFQEELVMF--KEGYFHrKVVDRLAKAAGVTPNIGFETNLLPLIKSIIKQGFGISTLLGMVVEEN-ESLVTIPFD--TPI 260
Cdd:cd08450    95 LAGENFISPapTAPVLQ-QVIENYAAQHNIQPNIIQEADNLLSAMSLVASTLGCALLPLYANNLLpPSVVARPLSgeTPT 173

                         170
                  ....*....|
gi 1553259162 261 wLDLSIAWRR 270
Cdd:cd08450   174 -IDLVMGYNK 182
PBP2_XapR cd08449
The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved ...
 106-238 8.23e-11

The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved in xanthosine catabolism, contains the type 2 periplasmic binding fold; In Escherichia coli, XapR is a positive regulator for the expression of xapA gene, encoding xanthosine phosphorylase, and xapB gene, encoding a polypeptide similar to the nucleotide transport protein NupG. As an operon, the expression of both xapA and xapB is fully dependent on the presence of both XapR and the inducer xanthosine. Expression of the xapR is constitutive but not auto-regulated, unlike many other LysR family proteins. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176140 [Multi-domain]  Cd Length: 197  Bit Score: 59.98  E-value: 8.23e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 106 FPPILMAFRHRYPTLnlsvieggTWRLQQM--------LEQGELDLGVI--VAEFVPEELEARPFLREQMLVTVSQEHPF 175
Cdd:cd08449    15 LGPALRRFKRQYPNV--------TVRFHELspeaqkaaLLSKRIDLGFVrfADTLNDPPLASELLWREPMVVALPEEHPL 86

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1553259162 176 AKQESVTPEQFFQEELVMFK-EGYFHRKVVDRLAKAAGVTPNIGFETNLLPLIKSIIKQGFGIS 238
Cdd:cd08449    87 AGRKSLTLADLRDEPFVFLRlANSRFADFLINCCLQAGFTPQITQEVVEPQTLMALVAAGFGVA 150
PBP2_LTTR_like_1 cd08421
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 105-285 9.32e-10

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


Pssm-ID: 176113  Cd Length: 198  Bit Score: 57.15  E-value: 9.32e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 105 YFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGVIVAEFVPEELEARPFLREQMLVTVSQEHPFAKQESVTPE 184
Cdd:cd08421    14 FLPEDLASFLAAHPDVRIDLEERLSADIVRAVAEGRADLGIVAGNVDAAGLETRPYRTDRLVVVVPRDHPLAGRASVAFA 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 185 QFFQEELVMFKEGYFHRKVVDRLAKAAGVTPNI-----GFETnllplIKSIIKQGFGISTLLGMVVEENES---LVTIPF 256
Cdd:cd08421    94 DTLDHDFVGLPAGSALHTFLREAAARLGRRLRLrvqvsSFDA-----VCRMVAAGLGIGIVPESAARRYARalgLRVVPL 168

                         170       180       190
                  ....*....|....*....|....*....|.
gi 1553259162 257 DTPiWLD--LSIAWRRNGYLSRANQAFVEFL 285
Cdd:cd08421   169 DDA-WARrrLLLCVRSFDALPPAARALVDHL 198
PBP2_MetR cd08441
The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which ...
 108-192 3.11e-09

The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which regulates the expression of methionine biosynthetic genes, contains type 2 periplasmic binding fold; MetR, a member of the LysR family, is a positive regulator for the metA, metE, metF, and metH genes. The sulfur-containing amino acid methionine is the universal initiator of protein synthesis in all known organisms and its derivative S-adenosylmethionine (SAM) and autoinducer-2 (AI-2) are involved in various cellular processes. SAM plays a central role as methyl donor in methylation reactions, which are essential for the biosynthesis of phospholipids, proteins, DNA and RNA. The interspecies signaling molecule AI-2 is involved in cell-cell communication process (quorum sensing) and gene regulation in bacteria. Although methionine biosynthetic enzymes and metabolic pathways are well conserved in bacteria, the regulation of methionine biosynthesis involves various regulatory mechanisms. In Escherichia coli and Salmonella enterica serovar Typhimurium, MetJ and MetR regulate the expression of methionine biosynthetic genes. The MetJ repressor negatively regulates the E. coli met genes, except for metH. Several of these genes are also under the positive control of MetR with homocysteine as a co-inducer. In Bacillus subtilis, the met genes are controlled by S-box termination-antitermination system. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176132  Cd Length: 198  Bit Score: 55.65  E-value: 3.11e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 108 PILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLgVIVAEFVP-EELEARPFLREQMLVTVSQEHPFAKQESVTPEQF 186
Cdd:cd08441    17 PVLDQFRERWPDVELDLSSGFHFDPLPALLRGELDL-VITSDPLPlPGIAYEPLFDYEVVLVVAPDHPLAAKEFITPEDL 95


                  ....*.
gi 1553259162 187 FQEELV 192
Cdd:cd08441    96 ADETLI 101
PRK09801 PRK09801
LysR family transcriptional regulator;
4-196 3.64e-09

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 56.58  E-value: 3.64e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162   4 KSLRYFYEVARLGSFTRAAESLGVAQPAVSMALRKLETELTLTLLHRNDRRISLTDEGAILYRHAEKILRAADDAALEMS 83
Cdd:PRK09801    9 KDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVT 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  84 ELKGLTRGEVRVGVPSMLGSFYFPPILMAFRHRYPTLNlsvIEGGTWRLQQMLEQGELDLGVIVAEFVPEELEARPFLRE 163
Cdd:PRK09801   89 QIKTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQ---VHFELFDRQIDLVQDNIDLDIRINDEIPDYYIAHLLTKN 165

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1553259162 164 QMLVTVSQEHPFAKQESVTPEQFFQEELVMFKE 196
Cdd:PRK09801  166 KRILCAAPEYLQKYPQPQSLQELSRHDCLVTKE 198
PBP2_OccR cd08457
The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the ...
 94-285 6.08e-09

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: 54.80  E-value: 6.08e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  94 RVGVPSMLGSFYFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGVIVAEFVPEELEARPFLREQMLVTVSQEH 173
Cdd:cd08457     3 RIAAMPALANGFLPRFLAAFLRLRPNLHLSLMGLSSSQVLEAVASGRADLGIADGPLEERQGFLIETRSLPAVVAVPMGH 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 174 PFAKQESVTPEQFFQEELVMFKEGYFHRKVVDRLAKAAGVTPNIGFETNLLPLIKSIIKQGFGISTLLGMVVEEN--ESL 251
Cdd:cd08457    83 PLAQLDVVSPQDLAGERIITLENGYLFRMRVEVALGKIGVKRRPIIEVNLSHTALSLVREGLGIAIIDPATAIGLplDGI 162

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1553259162 252 VTIPFDTPIWLDLSIAWRRNGYLSRANQAFVEFL 285
Cdd:cd08457   163 VIRPFDTFIDAGFLVVRAANGPPSTMVDRFIDEF 196
PBP2_MdcR cd08416
The C-terminal substrate-binding domian of LysR-type transcriptional regulator MdcR, which ...
 101-244 7.48e-09

The C-terminal substrate-binding domian of LysR-type transcriptional regulator MdcR, which involved in the malonate catabolism contains the type 2 periplasmic binding fold; This family includes the C-terminal substrate binding domain of LysR-type transcriptional regulator (LTTR) MdcR that controls the expression of the malonate decarboxylase (mdc) genes. Like other members of the LTTRs, MdcR is a positive regulatory protein for its target promoter and composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins (PBP2). The PBP2 are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate- binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 176108  Cd Length: 199  Bit Score: 54.66  E-value: 7.48e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 101 LGSFY------FPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGVIV--AEFVPEELEARPFLREQMLVTVSQE 172
Cdd:cd08416     4 LGSLYsltvntVPRIIMGLKLRRPELDIELTLGSNKDLLKKLKDGELDAILVAtpEGLNDPDFEVVPLFEDDIFLAVPAT 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1553259162 173 HPFAKQESVTPEQFFQEELVMFKEGYFHRKVVDRLAKAAGVTPNIGFETNLLPLIKSIIKQGFGISTLLGMV 244
Cdd:cd08416    84 SPLAASSEIDLRDLKDEKFVTLSEGFATYRGFDEAFEIAGFEPNVVMRVNDIFSLMSMVSGGVGYALLPGRI 155
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 5-118 9.29e-09

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 55.23  E-value: 9.29e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162   5 SLRYFYEVARLGSFTRAAESLGVAQPAVSMALRKLETELTLTLLHRNDRRISLTDEGAILYRHAEKILRAADDAALEMse 84
Cdd:PRK11139   10 ALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEATRKL-- 87

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1553259162  85 lkgLTRGEVRVGVPSMLGSF---YFPPILMAFRHRYP 118
Cdd:PRK11139   88 ---RARSAKGALTVSLLPSFaiqWLVPRLSSFNEAHP 121
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
1-184 3.15e-08

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 53.66  E-value: 3.15e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162   1 MDIKSLRYFYEVARLGSFTRAAESLGVAQPAVSMALRKLETELTLTLLHRNDRRISLTDEGAILYRHAEKILRAADDAAL 80
Cdd:PRK10094    2 FDPETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPS 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  81 EMSELKGLTRGEVRVGVPSMLGSFYFPPILMAFRH-RYPTLNLSV---IEGGTWrlQQML-EQGELDLGVIVAEFVPEEL 155
Cdd:PRK10094   82 ELQQVNDGVERQVNIVINNLLYNPQAVAQLLAWLNeRYPFTQFHIsrqIYMGVW--DSLLyEGFSLAIGVTGTEALANTF 159

                         170       180
                  ....*....|....*....|....*....
gi 1553259162 156 EARPFLREQMLVTVSQEHPFAKQESVTPE 184
Cdd:PRK10094  160 SLDPLGSVQWRFVMAADHPLANVEEPLTE 188
PBP2_AlsR cd08452
The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which ...
 105-285 3.77e-08

The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which regulates acetoin formation under stationary phase growth conditions; contains the type 2 periplasmic binding fold; AlsR is responsible for activating the expression of the acetoin operon (alsSD) in response to inducing signals such as glucose and acetate. Like many other LysR family proteins, AlsR is transcribed divergently from the alsSD operon. The alsS gene encodes acetolactate synthase, an enzyme involved in the production of acetoin in cells of stationary-phase. AlsS catalyzes the conversion of two pyruvate molecules to acetolactate and carbon dioxide. Acetolactate is then converted to acetoin at low pH by acetolactate decarboxylase which encoded by the alsD gene. Acetoin is an important physiological metabolite excreted by many microorganisms grown on glucose or other fermentable carbon sources. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176143 [Multi-domain]  Cd Length: 197  Bit Score: 52.50  E-value: 3.77e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 105 YFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGVIVAEFVPEELEARPFLREQMLVTVSQEHPFAKQESVTPE 184
Cdd:cd08452    14 FLPPIVREYRKKFPSVKVELRELSSPDQVEELLKGRIDIGFLHPPIQHTALHIETVQSSPCVLALPKQHPLASKEEITIE 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 185 QFFQEELVMFKEGYFHRKVVD--RLAKAAGVTPNIGFETNLLPLIKSIIKQGFGIsTLLGMVVEE--NESLVTIPFDTP- 259
Cdd:cd08452    94 DLRDEPIITVAREAWPTLYDEiiQLCEQAGFRPKIVQEATEYQTVIGLVSAGIGV-TFVPSSAKKlfNLEVAYRKIDQIn 172

                         170       180
                  ....*....|....*....|....*.
gi 1553259162 260 IWLDLSIAWRRNgylsRANQAFVEFL 285
Cdd:cd08452   173 LNAEWSIAYRKD----NHNPLLKHFI 194
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 5-238 4.17e-08

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 53.46  E-value: 4.17e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162   5 SLRY---FYEVARLGSFTRAAESLGVAQPAVSMALRKLETELTLTLLHRNDRRISLTDEGAIL-------YRHAEKILRA 74
Cdd:PRK11013    5 SLRHieiFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLfeevqrsYYGLDRIVSA 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  75 ADDaalemseLKGLTRGEVRVGVPSMLGSFYFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGVIVAEFVPEE 154
Cdd:PRK11013   85 AES-------LREFRQGQLSIACLPVFSQSLLPGLCQPFLARYPDVSLNIVPQESPLLEEWLSAQRHDLGLTETLHTPAG 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 155 LEARPFLREQMLVTVSQEHPFAKQESVTPEQFFQEELVMFKEGYFHRKVVDRLAKAAGVTPNIGFETNLLPLIKSIIKQG 234
Cdd:PRK11013  158 TERTELLTLDEVCVLPAGHPLAAKKVLTPDDFAGENFISLSRTDSYRQLLDQLFAEHGVKRRMVVETHSAASVCAMVRAG 237


                  ....
gi 1553259162 235 FGIS 238
Cdd:PRK11013  238 VGVS 241
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 1-124 1.09e-07

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 52.30  E-value: 1.09e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162   1 MDIKSLRYFYEVARLGSFTRAAESLGVAQPAVSMALRKLETELTLTLLHRNDRRISLTDEGAILYRHAEKILRAADDAAL 80
Cdd:PRK14997    2 TDLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQD 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1553259162  81 EMSELKGLTRGEVRVGVPSMLGSFYFPPILMAFRHRYPTLNLSV 124
Cdd:PRK14997   82 AIAALQVEPRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQL 125
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 91-285 1.58e-07

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


Pssm-ID: 176114 [Multi-domain]  Cd Length: 197  Bit Score: 50.52  E-value: 1.58e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  91 GEVRVGVPSMLGSFYFPPILMAFRHRYP--TLNLSVieggTWRLQQMLEQGeLDLGVIVAEFVPEELEARPFLREQMLVT 168
Cdd:cd08422     1 GRLRISAPVSFGRLHLAPLLAEFLARYPdvRLELVL----SDRLVDLVEEG-FDLAIRIGELPDSSLVARRLGPVRRVLV 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 169 VS----QEHPfakqESVTPEQFFQEELVMFkeGYFHRKVVDRLAKAAG---VTPNIGFETNLLPLIKSIIKQGFGISTLL 241
Cdd:cd08422    76 ASpaylARHG----TPQTPEDLARHRCLGY--RLPGRPLRWRFRRGGGeveVRVRGRLVVNDGEALRAAALAGLGIALLP 149

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1553259162 242 GMVVEE---NESLVTI-----PFDTPIWLdlsiAWRRNGYLSRANQAFVEFL 285
Cdd:cd08422   150 DFLVAEdlaSGRLVRVlpdwrPPPLPIYA----VYPSRRHLPAKVRAFIDFL 197
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
3-127 2.10e-07

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 51.30  E-value: 2.10e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162   3 IKSLRYFYEVARLGSFTRAAESLGVAQPAVSMALRKLETELTLTLLHRNDRRISLTDEGAILYRHAEKILRAADDAALEM 82
Cdd:PRK10632    4 LKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQL 83

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1553259162  83 SELKGLTRGEVRVGVPSMLGSFYFPPILMAFRHRYPTLNLSVIEG 127
Cdd:PRK10632   84 YAFNNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTG 128
PBP2_DntR_like_4 cd08463
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-217 4.54e-07

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


Pssm-ID: 176152 [Multi-domain]  Cd Length: 203  Bit Score: 49.23  E-value: 4.54e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  94 RVGVPSMLGSFYFPPILMAFRHRYPTLNLsVIE--GGTWRLQQMLEQGELDLGVIVAEFVPEELEARPFLREQMLVTVSQ 171
Cdd:cd08463     3 RIAAPDYLNALFLPELVARFRREAPGARL-EIHplGPDFDYERALASGELDLVIGNWPEPPEHLHLSPLFSDEIVCLMRA 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1553259162 172 EHPFAKQESVTPEQFFQEE-LVMFKEGYFHRKVVD-RLAKaAGVTPNI 217
Cdd:cd08463    82 DHPLARRGLMTLDDYLEAPhLAPTPYSVGQRGVIDsHLAR-LGLKRNI 128
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
5-127 5.52e-07

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 50.00  E-value: 5.52e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162   5 SLRYFYEVARLGSFTRAAESLGVAQPAVSMALRKLETELTLTLLHRNDRRISLTDEGAILYrHAEKilRAADDAALEMSE 84
Cdd:PRK10086   18 KLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVF-WALK--SSLDTLNQEILD 94

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1553259162  85 LKGL-TRGEVRVGVPSMLGSFYFPPILMAFRHRYPTLNLSVIEG 127
Cdd:PRK10086   95 IKNQeLSGTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTILTG 138
PBP2_Chlorocatechol cd08446
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 91-217 1.63e-06

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: 47.66  E-value: 1.63e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  91 GEVRVGVpsmLGSFYF---PPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGVivAEFVPEE--LEARPFLREQM 165
Cdd:cd08446     1 GELDVGY---FGSAILdtvPRLLRAFLTARPDVTVSLHNMTKDEQIEALRAGRIHIGF--GRFYPVEpdIAVENVAQERL 75

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1553259162 166 LVTVSQEHPFAKQESVTPEQFFQEELVMFKEGY---FHRKVVdRLAKAAGVTPNI 217
Cdd:cd08446    76 YLAVPKSHPLAARPAVSLADLRNEPLILFPRGGrpsFADEVL-GLFRRAGVEPRV 129
PBP2_DntR_like_2 cd08464
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-230 8.38e-06

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


Pssm-ID: 176153 [Multi-domain]  Cd Length: 200  Bit Score: 45.69  E-value: 8.38e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  93 VRVGVPSMLGSFYFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGVIVAEFVPEELEARPfLREQMLVTVSQE 172
Cdd:cd08464     2 FRIGLSDDVESWLAPPLLAALRAEAPGVRLVFRQVDPFNVGDMLDRGEIDLAIGVFGELPAWLKREV-LYTEGYACLFDP 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1553259162 173 HPFAKQESVTPEQFFQEE--LVMFKEGyfHRKVVDRLAKAAGVTPNIGFET----NLLPLIKSI 230
Cdd:cd08464    81 QQLSLSAPLTLEDYVARPhvLVSYRGG--LRGFVDDALAELGRSRRVVASTphfaALPALLRGT 142
PBP2_LeuO cd08466
The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an ...
 94-195 8.59e-06

The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an activator of leucine synthesis operon, contains the type 2 periplasmic binding fold; LeuO, a LysR-type transcriptional regulator, was originally identified as an activator of the leucine synthesis operon (leuABCD). Subsequently, LeuO was found to be not a specific regulator of the leu gene but a global regulator of unrelated various genes. LeuO activates bglGFB (utilization of beta-D-glucoside) and represses cadCBA (lysine decarboxylation) and dsrA (encoding a regulatory small RNA for translational control of rpoS and hns). LeuO also regulates the yjjQ-bglJ operon which coding for a LuxR-type transcription factor. In Salmonella enterica serovar Typhi, LeuO is a positive regulator of ompS1 (encoding an outer membrane), ompS2 (encoding a pathogenicity determinant), and assT, while LeuO represses the expression of OmpX and Tpx. Both osmS1 and osmS2 influence virulence in the mouse model of Salmonella. In Vibrio cholerae, LeuO is involved in control of biofilm formation and in the stringent response. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176155 [Multi-domain]  Cd Length: 200  Bit Score: 45.71  E-value: 8.59e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  94 RVGVPSMLGSFYFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGVIVAEFVPEELEARPFLREQMLVTVSQEH 173
Cdd:cd08466     3 NIAANETLDLLLLPRLLARLKQLAPNISLRESPSSEEDLFEDLRLQEVDLVIDYVPFRDPSFKSELLFEDELVCVARKDH 82

                          90       100
                  ....*....|....*....|..
gi 1553259162 174 PfAKQESVTPEQFFQEELVMFK 195
Cdd:cd08466    83 P-RIQGSLSLEQYLAEKHVVLS 103
PBP2_DntR_NahR_LinR_like cd08459
The C-terminal substrate binding domain of LysR-type transcriptional regulators that are ...
 101-255 8.71e-06

The C-terminal substrate binding domain of LysR-type transcriptional regulators that are involved in the catabolism of dinitrotoluene, naphthalene and gamma-hexachlorohexane; contains the type 2 periplasmic binding fold; This CD includes LysR-like bacterial transcriptional regulators, DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. DntR from Burkholderia species controls genes encoding enzymes for oxidative degradation of the nitro-aromatic compound 2,4-dinitrotoluene. The active form of DntR is homotetrameric, consisting of a dimer of dimers. NahR is a salicylate-dependent transcription activator of the nah and sal operons for naphthalene degradation. Salicylic acid is an intermediate of the oxidative degradation of the aromatic ring in soil bacteria. LinR positively regulates expression of the genes (linD and linE) encoding enzymes for gamma-hexachlorocyclohexane (a haloorganic insecticide) degradation. Expression of linD and linE are induced by their substrates, 2,5-dichlorohydroquinone (2,5-DCHQ) and chlorohydroquinone (CHQ). 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: 176148 [Multi-domain]  Cd Length: 201  Bit Score: 45.65  E-value: 8.71e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 101 LGSFYF-PPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGVIVAEFVPEELEARPFLREQMLVTVSQEHPFAKQE 179
Cdd:cd08459     9 IGEMYFlPRLLAALREVAPGVRIETVRLPVDELEEALESGEIDLAIGYLPDLGAGFFQQRLFRERYVCLVRKDHPRIGST 88

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1553259162 180 sVTPEQFFQEELVMFK-EGYFHRKVVDRLAKaAGVTPNIGFETnllpliksiikQGFGistLLGMVVEENESLVTIP 255
Cdd:cd08459    89 -LTLEQFLAARHVVVSaSGTGHGLVEQALRE-AGIRRRIALRV-----------PHFL---ALPLIVAQTDLVATVP 149
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 1-97 1.20e-05

transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity. [Cellular processes, Toxin production and resistance, DNA metabolism, DNA replication, recombination, and repair, Regulatory functions, DNA interactions]


Pssm-ID: 274509 [Multi-domain]  Cd Length: 292  Bit Score: 45.68  E-value: 1.20e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162   1 MDIKSLRYFYEVARLGSFTRAAESLGVAQPAVSMALRKLETELTLTLLHRNdRRISLTDEGAILYRHAEKILRAADDAAL 80
Cdd:TIGR03298   1 LDYRQLAALAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVRT-QPCRATEAGQRLLRHARQVRLLEAELLA 79

                          90
                  ....*....|....*..
gi 1553259162  81 EMSELKGLTRGEVRVGV 97
Cdd:TIGR03298  80 ELPGLAPGAPTRLTIAV 96
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
2-116 6.04e-05

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 43.81  E-value: 6.04e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162   2 DIKSLRYFYEVARLGSFTRAAESLGVAQPAVSMALRKLETELTLTLLHRnDRRISLTDEGAILYRHAEKI-LRAADDAAL 80
Cdd:PRK13348    3 DYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQRLLRHLRQVaLLEADLLST 81

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1553259162  81 EMSELKGLTRGEVRVGVPSmLGSfYFPPILMAFRHR 116
Cdd:PRK13348   82 LPAERGSPPTLAIAVNADS-LAT-WFLPALAAVLAG 115
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
1-72 2.99e-04

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 41.54  E-value: 2.99e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1553259162   1 MDIKSLRYFYEVARLGSFTRAAESLGVAQPAVSMALRKLETE--LTLTLLHRNDrrISLTDEGAILYRHAEKIL 72
Cdd:PRK03601    1 MDTELLKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQlgVNLFTRHRNN--IRLTAAGERLLPYAETLM 72
PBP2_BenM_CatM_CatR cd08445
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 97-194 3.03e-04

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


Pssm-ID: 176136  Cd Length: 203  Bit Score: 41.06  E-value: 3.03e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  97 VPSMLGSFyFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGVIVAEFVPEELEaRPFLR-EQMLVTVSQEHPF 175
Cdd:cd08445     8 VPSTLYGL-LPELIRRFRQAAPDVEIELIEMTTVQQIEALKEGRIDVGFGRLRIEDPAIR-RIVLReEPLVVALPAGHPL 85

                          90       100
                  ....*....|....*....|
gi 1553259162 176 AK-QESVTPEQFFQEELVMF 194
Cdd:cd08445    86 AQeKAPLTLAQLADEPLILY 105
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 12-186 5.44e-04

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 40.70  E-value: 5.44e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  12 VARLGSFTRAAESLGVAQPAVSMALRKLETELTLTLLHRNDRRISLTDEGAILYRHAEKILRaaddaalEMSELKGLT-- 89
Cdd:PRK11074   13 VARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIK-------KMQETRRQCqq 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  90 -----RGEVRVGVPSMLGSFYFPPILMAFRHRYPTLNLSV-IE--GGTWrlqQMLEQGELDLGVIVAEFVP--EELEARP 159
Cdd:PRK11074   86 vangwRGQLSIAVDNIVRPDRTRQLIVDFYRHFDDVELIIrQEvfNGVW---DALADGRVDIAIGATRAIPvgGRFAFRD 162

                         170       180
                  ....*....|....*....|....*..
gi 1553259162 160 FLREQMLVTVSQEHPFAKQESVTPEQF 186
Cdd:PRK11074  163 MGMLSWACVVSSDHPLASMDGPLSDDE 189
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
1-281 5.62e-04

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 40.81  E-value: 5.62e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162   1 MDIKSLRYFYEVARLGSFTRAAESLGVAQPAVSMALRKLETELTLTLLHRNDRRISLTDEGAILYRHAEKILRAADDaal 80
Cdd:PRK10082   11 IETKWLYDFLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLES--- 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162  81 EMSELKG---LTRGEVRVGVPSMLGSFYFPPILmafrHRYPTLNLSVIEG-GTWRLQQMLEQGELDLgviVAEFVPEELE 156
Cdd:PRK10082   88 NLAELRGgsdYAQRKIKIAAAHSLSLGLLPSII----SQMPPLFTWAIEAiDVDEAVDKLREGQSDC---IFSFHDEDLL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 157 ARPF----LREQML--VTVSQEHPFAKQESVTPeqffQEELVMFKEGYFHRKVVDR-LAKAAGVTPNIGFETNLLPLIKS 229
Cdd:PRK10082  161 EAPFdhirLFESQLfpVCASDEHGEALFNLAQP----HFPLLNYSRNSYMGRLINRtLTRHSELSFSTFFVSSMSELLKQ 236

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1553259162 230 IIKQGFGISTLLGMVVEE---NESLVTIPFDTPIWLDLSIAWRRNGYLSRANQAF 281
Cdd:PRK10082  237 VALDGCGIAWLPEYAIQQeirSGQLVVLNRDELVIPIQAYAYRMNTRMNPVAERF 291
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
1-95 2.45e-03

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 38.60  E-value: 2.45e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162   1 MDIKSLRYFYEVARLGSFTRAAESLGVAQPAVSMALRKLETELTLTLLHRnDRRISLTDEGAILYRHAEKIlraaddAAL 80
Cdd:PRK03635    2 LDYKQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRLLRHARQV------RLL 74

                          90
                  ....*....|....*...
gi 1553259162  81 E---MSELKGLTRGEVRV 95
Cdd:PRK03635   75 EaelLGELPALDGTPLTL 92
PBP2_PnbR cd08469
The C-terminal substrate binding domain of LysR-type transcriptional regulator PnbR, which is ...
 105-187 5.39e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulator PnbR, which is involved in regulating the pnb genes encoding enzymes for 4-nitrobenzoate catabolism, contains the type 2 periplasmic binding fold; PnbR is the regulator of one or both of the two pnb genes that encoding enzymes for 4-nitrobenzoate catabolism. In Pseudomonas putida strain, pnbA encodes a 4-nitrobenzoate reductase, which is responsible for catalyzing the direct reduction of 4-nitrobenzoate to 4-hydroxylaminobenzoate, and pnbB encodes a 4-hydroxylaminobenzoate lyase, which catalyzes the conversion of 4-hydroxylaminobenzoate to 3, 4-dihydroxybenzoic acid and ammonium. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176158  Cd Length: 221  Bit Score: 37.38  E-value: 5.39e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1553259162 105 YFPPILMAFRHRYPTLNLSVIEGGTWRLQQMLEQGELDLGVIVAEFVPEELEARPFLREQMLVTVSQEHPFAKQEsVTPE 184
Cdd:cd08469    14 LLPALVRRLETEAPGIDLRIRPVTRLDLAEQLDLGRIDLVIGIFEQIPPRFRRRTLFDEDEVWVMRKDHPAARGA-LTIE 92


                  ...
gi 1553259162 185 QFF 187
Cdd:cd08469    93 TLA 95
 
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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