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Conserved domains on  [gi|28202359|gb|AAO34805|]
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transcriptional regulatory protein [Clostridium tetani E88]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 11426483)

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

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
3-292 2.43e-56

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 181.99  E-value: 2.43e-56
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359   3 IKLDLYKIFSEVAKHKSFSKAAKSLYMTQPAVSQAIMQLENELEIRLFTRTSRGVILTNEGELLFEYTNSAINLINVAEK 82
Cdd:COG0583   1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359  83 KLIESKNLLMGDLKLGVGDTISRYFLLPYLEKFHSSYPNIKLKIINRTTLELCVMLKSGEIDIAICNLPINDPSLEVTEL 162
Cdd:COG0583  81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359 163 TDIHDIFVCGKKYknkisksislkelskfPLILLESKSNsrqyvekymlskgipftpeielgSHDLLLEFAKINLGISCV 242
Cdd:COG0583 161 GEERLVLVASPDH----------------PLARRAPLVN-----------------------SLEALLAAVAAGLGIALL 201

                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|
gi 28202359 243 IKEFSQDYLKSKELYEIQTNEVIPKRNIGVCFLKSVSLSPSSTKFVDILK 292
Cdd:COG0583 202 PRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLR 251
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
3-292 2.43e-56

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 181.99  E-value: 2.43e-56
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359   3 IKLDLYKIFSEVAKHKSFSKAAKSLYMTQPAVSQAIMQLENELEIRLFTRTSRGVILTNEGELLFEYTNSAINLINVAEK 82
Cdd:COG0583   1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359  83 KLIESKNLLMGDLKLGVGDTISRYFLLPYLEKFHSSYPNIKLKIINRTTLELCVMLKSGEIDIAICNLPINDPSLEVTEL 162
Cdd:COG0583  81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359 163 TDIHDIFVCGKKYknkisksislkelskfPLILLESKSNsrqyvekymlskgipftpeielgSHDLLLEFAKINLGISCV 242
Cdd:COG0583 161 GEERLVLVASPDH----------------PLARRAPLVN-----------------------SLEALLAAVAAGLGIALL 201

                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|
gi 28202359 243 IKEFSQDYLKSKELYEIQTNEVIPKRNIGVCFLKSVSLSPSSTKFVDILK 292
Cdd:COG0583 202 PRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLR 251
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 9-293 6.60e-46

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: 156.62  E-value: 6.60e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359    9 KIFSEVAKHKSFSKAAKSLYMTQPAVSQAIMQLENELEIRLFTRTSRGVILTNEGELLFEYTNSAINLINVAEKKLIESK 88
Cdd:NF040786   7 EAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEEEFDRYG 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359   89 NLLMGDLKLGVGDTISRYFLLPYLEKFHSSYPNIKLKII---NRTTLELcvmLKSGEIDIAICNLPINDPSLEVTELtdI 165
Cdd:NF040786  87 KESKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMisdSIKVIEL---LLEGEVDIGFTGTKLEKKRLVYTPF--Y 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359  166 HDIFV----CGKKYKNKISKSISLKELSKFPLILLESKSNSRQYVEKYMLSKGIPfTPEI----ELGSHDLLLEFAKINL 237
Cdd:NF040786 162 KDRLVlitpNGTEKYRMLKEEISISELQKEPFIMREEGSGTRKEAEKALKSLGIS-LEDLnvvaSLGSTEAIKQSVEAGL 240

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 28202359  238 GIScVIKEFS-QDYLKSKELYEIQTNEVIPKRNIGVCFLKSVSLSPSSTKFVDILKK 293
Cdd:NF040786 241 GIS-VISELAaEKEVERGRVLIFPIPGLPKNRDFYLVYNKNRQLSPTAEAFLQFVKE 296
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 95-291 2.75e-40

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: 138.89  E-value: 2.75e-40
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359  95 LKLGVGDTISRYFLLPYLEKFHSSYPNIKLKIINRTTLELCVMLKSGEIDIAICNLPINDPSLEVTELTDIHDIFVCGKK 174
Cdd:cd05466   2 LRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPPD 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359 175 YKNKISKSISLKELSKFPLILLESKSNSRQYVEKYMLSKGIPFTPEIELGSHDLLLEFAKINLGISCVIKEFSQDyLKSK 254
Cdd:cd05466  82 HPLAKRKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEE-LADG 160

                       170       180       190
                ....*....|....*....|....*....|....*..
gi 28202359 255 ELYEIQTNEVIPKRNIGVCFLKSVSLSPSSTKFVDIL 291
Cdd:cd05466 161 GLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 11-223 1.88e-33

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 123.91  E-value: 1.88e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359   11 FSEVAKHKSFSKAAKSLYMTQPAVSQAIMQLENELEIRLFTRTSRGVILTNEGELLFEYTNSAINLINVAEKKLIESKNL 90
Cdd:PRK11242   9 FLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRRAIHDVADL 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359   91 LMGDLKLGVGDTISRYFLLPYLEKFHSSYPNIKLKIINRTTLELCVMLKSGEIDIAICNLPINDPSLEVTELTDIHDIFV 170
Cdd:PRK11242  89 SRGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMSQERIEALLADDELDVGIAFAPVHSPEIEAQPLFTETLALV 168

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 28202359  171 CGKKYK-NKISKSISLKELSKFPLILLESKSNSRQYVEKYMLSKGIpfTPEIEL 223
Cdd:PRK11242 169 VGRHHPlAARRKALTLDELADEPLVLLSAEFATREQIDRYFRRHGV--TPRVAI 220
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 93-293 8.96e-30

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: 111.61  E-value: 8.96e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359    93 GDLKLGVGDTISRYFLLPYLEKFHSSYPNIKLKIINRTTLELCVMLKSGEIDIAICNLPINDPSLEVTELTDIHDIFVCG 172
Cdd:pfam03466   2 GRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVAP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359   173 KKYKNKISKSISLKELSKFPLILLESKSNSRQYVEKYMLSKGIPFTPEIELGSHDLLLEFAKINLGISCVIKEFSQDYLK 252
Cdd:pfam03466  82 PDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARELA 161

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 28202359   253 SKELYEIQTNEVIPKRNIGVCFLKSVSLSPSSTKFVDILKK 293
Cdd:pfam03466 162 DGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLRE 202
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 14-258 6.08e-09

multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, including founding member GSU2202 from Geobacter sulfurreducens PCA, are LysR family transcriptional regulators found regularly in the vicinity of multiheme cytochromes such as GSU2203, a decaheme c-type cytochrome.


Pssm-ID: 468965 [Multi-domain]  Cd Length: 301  Bit Score: 55.90  E-value: 6.08e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359   14 VAKHKSFSKAAKSLYMTQPAVSQAIMQLENELEIRLFTRTSRGVILTNEGELLFEytnSAINLINVaEKKLIESKNLLMG 93
Cdd:NF041036  12 VAEEGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLE---KARRILDI-EDSLMDELKSFKG 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359   94 DLKLGVGDTISryFLLPYLEK----FHSSYPNI-KLKIINRTTLELCVMLKSGEIDIAICNLPINDP--SLEVTELTDIH 166
Cdd:NF041036  88 RQRLSICCTPT--FGMAHLPGvlnrFMLRNADVvDLKFLFHSPAQALEGIQNKEFDLAIIEHCADLDlgRFHTYPLPQDE 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359  167 DIFVCGKKYkNKISKSISLKELSKFPLILLESKSNSRQYVEKYMLSKGIP---FTPEIELGSHDLLLEFAKINLGISCVI 243
Cdd:NF041036 166 LVFVSAPSL-GLPTPNVTLERLLELCLITRRDGCSSRDLLRRNLAEQGRDlddFRRVVVSDDLRLTIQTVLDGGGISFVS 244

                        250
                 ....*....|....*
gi 28202359  244 KEFSQDYLKSKELYE 258
Cdd:NF041036 245 RSLVCEYLKNGQLRE 259
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
3-292 2.43e-56

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 181.99  E-value: 2.43e-56
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359   3 IKLDLYKIFSEVAKHKSFSKAAKSLYMTQPAVSQAIMQLENELEIRLFTRTSRGVILTNEGELLFEYTNSAINLINVAEK 82
Cdd:COG0583   1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359  83 KLIESKNLLMGDLKLGVGDTISRYFLLPYLEKFHSSYPNIKLKIINRTTLELCVMLKSGEIDIAICNLPINDPSLEVTEL 162
Cdd:COG0583  81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359 163 TDIHDIFVCGKKYknkisksislkelskfPLILLESKSNsrqyvekymlskgipftpeielgSHDLLLEFAKINLGISCV 242
Cdd:COG0583 161 GEERLVLVASPDH----------------PLARRAPLVN-----------------------SLEALLAAVAAGLGIALL 201

                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|
gi 28202359 243 IKEFSQDYLKSKELYEIQTNEVIPKRNIGVCFLKSVSLSPSSTKFVDILK 292
Cdd:COG0583 202 PRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLR 251
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 9-293 6.60e-46

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: 156.62  E-value: 6.60e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359    9 KIFSEVAKHKSFSKAAKSLYMTQPAVSQAIMQLENELEIRLFTRTSRGVILTNEGELLFEYTNSAINLINVAEKKLIESK 88
Cdd:NF040786   7 EAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEEEFDRYG 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359   89 NLLMGDLKLGVGDTISRYFLLPYLEKFHSSYPNIKLKII---NRTTLELcvmLKSGEIDIAICNLPINDPSLEVTELtdI 165
Cdd:NF040786  87 KESKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMisdSIKVIEL---LLEGEVDIGFTGTKLEKKRLVYTPF--Y 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359  166 HDIFV----CGKKYKNKISKSISLKELSKFPLILLESKSNSRQYVEKYMLSKGIPfTPEI----ELGSHDLLLEFAKINL 237
Cdd:NF040786 162 KDRLVlitpNGTEKYRMLKEEISISELQKEPFIMREEGSGTRKEAEKALKSLGIS-LEDLnvvaSLGSTEAIKQSVEAGL 240

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 28202359  238 GIScVIKEFS-QDYLKSKELYEIQTNEVIPKRNIGVCFLKSVSLSPSSTKFVDILKK 293
Cdd:NF040786 241 GIS-VISELAaEKEVERGRVLIFPIPGLPKNRDFYLVYNKNRQLSPTAEAFLQFVKE 296
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 95-291 2.75e-40

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: 138.89  E-value: 2.75e-40
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359  95 LKLGVGDTISRYFLLPYLEKFHSSYPNIKLKIINRTTLELCVMLKSGEIDIAICNLPINDPSLEVTELTDIHDIFVCGKK 174
Cdd:cd05466   2 LRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPPD 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359 175 YKNKISKSISLKELSKFPLILLESKSNSRQYVEKYMLSKGIPFTPEIELGSHDLLLEFAKINLGISCVIKEFSQDyLKSK 254
Cdd:cd05466  82 HPLAKRKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEE-LADG 160

                       170       180       190
                ....*....|....*....|....*....|....*..
gi 28202359 255 ELYEIQTNEVIPKRNIGVCFLKSVSLSPSSTKFVDIL 291
Cdd:cd05466 161 GLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 11-223 1.88e-33

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 123.91  E-value: 1.88e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359   11 FSEVAKHKSFSKAAKSLYMTQPAVSQAIMQLENELEIRLFTRTSRGVILTNEGELLFEYTNSAINLINVAEKKLIESKNL 90
Cdd:PRK11242   9 FLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRRAIHDVADL 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359   91 LMGDLKLGVGDTISRYFLLPYLEKFHSSYPNIKLKIINRTTLELCVMLKSGEIDIAICNLPINDPSLEVTELTDIHDIFV 170
Cdd:PRK11242  89 SRGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMSQERIEALLADDELDVGIAFAPVHSPEIEAQPLFTETLALV 168

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 28202359  171 CGKKYK-NKISKSISLKELSKFPLILLESKSNSRQYVEKYMLSKGIpfTPEIEL 223
Cdd:PRK11242 169 VGRHHPlAARRKALTLDELADEPLVLLSAEFATREQIDRYFRRHGV--TPRVAI 220
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 93-293 8.96e-30

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: 111.61  E-value: 8.96e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359    93 GDLKLGVGDTISRYFLLPYLEKFHSSYPNIKLKIINRTTLELCVMLKSGEIDIAICNLPINDPSLEVTELTDIHDIFVCG 172
Cdd:pfam03466   2 GRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVAP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359   173 KKYKNKISKSISLKELSKFPLILLESKSNSRQYVEKYMLSKGIPFTPEIELGSHDLLLEFAKINLGISCVIKEFSQDYLK 252
Cdd:pfam03466  82 PDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARELA 161

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 28202359   253 SKELYEIQTNEVIPKRNIGVCFLKSVSLSPSSTKFVDILKK 293
Cdd:pfam03466 162 DGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLRE 202
rbcR CHL00180
LysR transcriptional regulator; Provisional
 5-225 1.86e-27

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 108.18  E-value: 1.86e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359    5 LDLYKIFSEVAKHKSFSKAAKSLYMTQPAVSQAIMQLENELEIRLFTRTSRGVILTNEGELLFEYTNSAINLINVAEKKL 84
Cdd:CHL00180   7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRAL 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359   85 IESKNLLMGDLKLGVGDTISRYFLLPYLEKFHSSYPNIKLKIINRTTLELCVMLKSGEIDIAIC--NLPIN-DPSLEVTE 161
Cdd:CHL00180  87 EDLKNLQRGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVggEVPTElKKILEITP 166

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 28202359  162 LTDIHDIFVCGKKYKNKISKSISLKELSKFPLILLESKSNSRQYVEKYMLSKGIP---FTPEIELGS 225
Cdd:CHL00180 167 YVEDELALIIPKSHPFAKLKKIQKEDLYRLNFITLDSNSTIRKVIDNILIQNGIDskrFKIEMELNS 233
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
5-64 1.13e-23

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 91.29  E-value: 1.13e-23
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359     5 LDLYKIFSEVAKHKSFSKAAKSLYMTQPAVSQAIMQLENELEIRLFTRTSRGVILTNEGE 64
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 95-291 1.68e-23

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: 94.87  E-value: 1.68e-23
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359  95 LKLGVGDTISRYFLLPYLEKFHSSYPNIKLKIINRTTLELCVMLKSGEIDIAICNLPINDPSLEVTELTDIHDIFVCGKK 174
Cdd:cd08420   2 LRIGASTTIGEYLLPRLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLVEGPVDHPDLIVEPFAEDELVLVVPPD 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359 175 YKNKISKSISLKELSKFPLILLESKSNSRQYVEKYMLSKGIP---FTPEIELGSHDLLLEFAKINLGISCVIKEFSQDYL 251
Cdd:cd08420  82 HPLAGRKEVTAEELAAEPWILREPGSGTREVFERALAEAGLDgldLNIVMELGSTEAIKEAVEAGLGISILSRLAVRKEL 161

                       170       180       190       200
                ....*....|....*....|....*....|....*....|
gi 28202359 252 KSKELYEIQTNEVIPKRNIGVCFLKSVSLSPSSTKFVDIL 291
Cdd:cd08420 162 ELGRLVALPVEGLRLTRPFSLIYHKDKYLSPAAEAFLEFL 201
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 9-207 5.81e-23

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 95.68  E-value: 5.81e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359    9 KIFSEVAKHKSFSKAAKSLYMTQPAVSQAIMQLENELEIRLFTRTSRGVILTNEGELLFEYTNSAINLINVAEKKLIESK 88
Cdd:PRK11139  12 RAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEATRKLRARS 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359   89 NllMGDLKLGVGDTISRYFLLPYLEKFHSSYPNIKLKIinRTTLELcVMLKSGEIDIAICNLPINDPSLEVTELTDIHDI 168
Cdd:PRK11139  92 A--KGALTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRL--KAVDRL-EDFLRDDVDVAIRYGRGNWPGLRVEKLLDEYLL 166

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 28202359  169 FVCGKKYKNKISKSISLKELSKFPLILLESKSNSRQYVE 207
Cdd:PRK11139 167 PVCSPALLNGGKPLKTPEDLARHTLLHDDSREDWRAWFR 205
PRK09791 PRK09791
LysR family transcriptional regulator;
2-147 1.27e-22

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 94.83  E-value: 1.27e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359    2 SIKLDLYKIFSEVAKHKSFSKAAKSLYMTQPAVSQAIMQLENELEIRLFTRTSRGVILTNEGELLFEYTNSAINLINVAE 81
Cdd:PRK09791   4 QVKIHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQ 83

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 28202359   82 KKLIESKNLLMGDLKLGVGDTISRYFLLPYLEKFHSSYPNIKLKIINRTTLELCVMLKSGEIDIAI 147
Cdd:PRK09791  84 EDIRQRQGQLAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDFTI 149
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 1-259 2.55e-21

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 91.29  E-value: 2.55e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359    1 MSIKLDLYKIFSEVAKHKSFSKAAKSLYMTQPAVSQAIMQLENELEIRLFTRTSRGVILTNEGELLFEytnSAINLINVA 80
Cdd:PRK10837   1 MHITLRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYP---RALALLEQA 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359   81 ekklIESKNLLMGD---LKLGVGDTISRYFLLPYLEKFHSSYPNIKLKIINRTTLELCVMLKSGEIDIAICNLPINDPSL 157
Cdd:PRK10837  78 ----VEIEQLFREDngaLRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNSQDVINAVLDFRVDIGLIEGPCHSPEL 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359  158 eVTELTDIHDIFVCGKKYKNKISKSISLKELSKFPLILLESKSNSRQYVEKYMLSKGIPFTPEIELGSHDLLLEFAKINL 237
Cdd:PRK10837 154 -ISEPWLEDELVVFAAPDSPLARGPVTLEQLAAAPWILRERGSGTREIVDYLLLSHLPRFELAMELGNSEAIKHAVRHGL 232

                        250       260
                 ....*....|....*....|..
gi 28202359  238 GISCVIKEFSQDYLKSKELYEI 259
Cdd:PRK10837 233 GISCLSRRVIADQLQAGTLVEV 254
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
11-148 2.95e-21

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 91.22  E-value: 2.95e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359   11 FSEVAKHKSFSKAAKSLYMTQPAVSQAIMQLENELEIRLFTRTSRGVILTNEGELLFEYTNSAINLINvaeKKLIESKNL 90
Cdd:PRK10086  22 FEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLDTLN---QEILDIKNQ 98

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 28202359   91 -LMGDLKLGVGDTISRYFLLPYLEKFHSSYPNIKLKIinRTTLELcVMLKSGEIDIAIC 148
Cdd:PRK10086  99 eLSGTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTI--LTGNEN-VNFQRAGIDLAIY 154
cbl PRK12679
HTH-type transcriptional regulator Cbl;
9-261 1.72e-19

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 86.40  E-value: 1.72e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359    9 KIFSEVAK-HKSFSKAAKSLYMTQPAVSQAIMQLENELEIRLFTRtsrgviltnEGELLFEYTNSAINLINVAEKKLIES 87
Cdd:PRK12679   7 KIIREAARqDYNLTEVANMLFTSQSGVSRHIRELEDELGIEIFIR---------RGKRLLGMTEPGKALLVIAERILNEA 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359   88 KNL----------LMGDLKLGVGDTISRYFLLPYLEKFHSSYPNIKLKIINRTTLELCVMLKSGEIDIAICN-LPINDPS 156
Cdd:PRK12679  78 SNVrrladlftndTSGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASeRLSNDPQ 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359  157 LEVTELTDIHDIFVCGKKYKNKISKSISLKELSKFPLILLESKSNSRQYVEKYMLSKGIpfTPEIELGSH--DLLLEFAK 234
Cdd:PRK12679 158 LVAFPWFRWHHSLLVPHDHPLTQITPLTLESIAKWPLITYRQGITGRSRIDDAFARKGL--LADIVLSAQdsDVIKTYVA 235

                        250       260       270
                 ....*....|....*....|....*....|....
gi 28202359  235 INLGISCVIKEFSQDY-------LKSKELYEIQT 261
Cdd:PRK12679 236 LGLGIGLVAEQSSGEQeesnlirLDTRHLFDANT 269
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 3-227 2.38e-19

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 86.20  E-value: 2.38e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359    3 IKLDLYKIFSEVAKHK-SFSKAAKSLYMTQPAVSQAIMQLENELEIRLFTR--------TSRGVILTNEGELLFeytNSA 73
Cdd:PRK12682   1 MNLQQLRFVREAVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRhgkrlkglTEPGKAVLDVIERIL---REV 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359   74 INLINVAEKKLIESKnllmGDLKLGVGDTISRYFLLPYLEKFHSSYPNIKLKIINRTTLELCVMLKSGEIDIAICNLPI- 152
Cdd:PRK12682  78 GNIKRIGDDFSNQDS----GTLTIATTHTQARYVLPRVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGIATESLa 153

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 28202359  153 NDPSLEVTELTDIHDIFVCGKKYKNKISKSISLKELSKFPLILLESKSNSRQYVEKYMLSKGIpfTPEIELGSHD 227
Cdd:PRK12682 154 DDPDLATLPCYDWQHAVIVPPDHPLAQEERITLEDLAEYPLITYHPGFTGRSRIDRAFAAAGL--QPDIVLEAID 226
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
4-223 5.37e-18

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 82.33  E-value: 5.37e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359    4 KLDLYKIFSEVAKHK-SFSKAAKSLYMTQPAVSQAIMQLENELEIRLFTRT-SRGVILTNEGELLFEytnsainlinVAE 81
Cdd:PRK12684   2 NLHQLRFVREAVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHgKRLRGLTEPGRIILA----------SVE 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359   82 KKLIESKNLL----------MGDLKLGVGDTISRYFLLPYLEKFHSSYPNIKLKIINRTTLELCVMLKSGEIDIAICNLP 151
Cdd:PRK12684  72 RILQEVENLKrvgkefaaqdQGNLTIATTHTQARYALPAAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAIATEA 151

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 28202359  152 I-NDPSLEVTELTDIHDIFVCGKKYKNKISKSISLKELSKFPLILLESKSNSRQYVEKYMLSKGIpfTPEIEL 223
Cdd:PRK12684 152 IaDYKELVSLPCYQWNHCVVVPPDHPLLERKPLTLEDLAQYPLITYDFAFAGRSKINKAFALRGL--KPDIVL 222
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 102-291 5.91e-18

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


Pssm-ID: 176131 [Multi-domain]  Cd Length: 197  Bit Score: 79.88  E-value: 5.91e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359 102 TISRYFLLPYLEKFHSSYPNIKLKIINRTTLELCVMLKSGEIDIAICNLPINDPSLEVTELTDihDIFVC--------GK 173
Cdd:cd08440   9 SLAATLLPPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEADPDLEFEPLLR--DPFVLvcpkdhplAR 86

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359 174 KyknkisKSISLKELSKFPLILLESKSNSRQYVEKYMLSKGIPFTPEIELGSHDLLLEFAKINLGISCV----IKEFSQD 249
Cdd:cd08440  87 R------RSVTWAELAGYPLIALGRGSGVRALIDRALAAAGLTLRPAYEVSHMSTALGMVAAGLGVAVLpalaLPLADHP 160

                       170       180       190       200
                ....*....|....*....|....*....|....*....|..
gi 28202359 250 YLKSKELyeiqTNEVIpKRNIGVCFLKSVSLSPSSTKFVDIL 291
Cdd:cd08440 161 GLVARPL----TEPVV-TRTVGLIRRRGRSLSPAAQAFLDLL 197
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 11-243 8.59e-17

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 78.66  E-value: 8.59e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359   11 FSEVAKHKSFSKAAKSLYMTQPAVSQAIMQLENELEIRLFTRTSRGVILTNEGELLFEYtnsAINLINVAEKKLIESKNL 90
Cdd:PRK09906   9 FVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQD---ARAILEQAEKAKLRARKI 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359   91 LMGDLKLGVGDT-ISRYFLLPY-LEKFHSSYPNIKLKIINRTTLELCVMLKSGEIDIAICNLPINDPSLEVTELTDIHDI 168
Cdd:PRK09906  86 VQEDRQLTIGFVpSAEVNLLPKvLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPVYSDEIDYLELLDEPLV 165

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 28202359  169 FVCGKKYKNKISKSISLKELSKFPLILLES-KSNS-RQYVEKYMLSKGIpfTPEIELGSHDLLLEFAKINLGISCVI 243
Cdd:PRK09906 166 VVLPVDHPLAHEKEITAAQLDGVNFISTDPaYSGSlAPIIKAWFAQHNS--QPNIVQVATNILVTMNLVGMGLGCTI 240
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
6-132 1.12e-16

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 78.14  E-value: 1.12e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359    6 DLYKIFSEVAKHKSFSKAAKSLYMTQPAVSQAIMQLENELEIRLFTRTSRGVILTNEGELLFEYTNSAINLINVAEKKLI 85
Cdd:PRK03601   4 ELLKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYAETLMNTWQAAKKEVA 83

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 28202359   86 ESKNllmgDLKLGVGDTISRY--FLLPYLEKFHSSYPNIKL--KIINRTTL 132
Cdd:PRK03601  84 HTSQ----HNELSIGASASLWecMLTPWLGRLYQNQEALQFeaRIAQRQSL 130
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 15-147 3.45e-16

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 76.99  E-value: 3.45e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359   15 AKHKSFSKAAKSLYMTQPAVSQAIMQLENELEIRLFTRTSRGVILTNEGELLFEYtnsainlinvAEKKLIESKNL---- 90
Cdd:PRK11151  13 AEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQ----------ARTVLREVKVLkema 82

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 28202359   91 ------LMGDLKLGVGDTISRYfLLPY-LEKFHSSYPNIKLKIINRTTLELCVMLKSGEIDIAI 147
Cdd:PRK11151  83 sqqgetMSGPLHIGLIPTVGPY-LLPHiIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCAI 145
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 1-216 5.74e-16

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 76.61  E-value: 5.74e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359    1 MSIKLDLYKIFSEVAKHKSFSKAAKSLYMTQPAVSQAIMQLENELEIRLFTRTSRGVILTNEGELLFEYTNSAINLINVA 80
Cdd:PRK15092   9 INLDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEA 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359   81 EKKLIESKnlLMGDLKLGV----GDTIsryflLPY-LEKFHSSYPNIKLKIINRTTLELCVMLKSGEIDIAICNLPIND- 154
Cdd:PRK15092  89 CSSLMYSN--LQGVLTIGAsddtADTI-----LPFlLNRVSSVYPKLALDVRVKRNAFMMEMLESQEVDLAVTTHRPSSf 161

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359  155 --------PSLevteltdihdiFVCGKKYKNKISKSIslkelskfPLILLESKSNSRQYVEKYMLSKGIP 216
Cdd:PRK15092 162 palnlrtsPTL-----------WYCAAEYVLQKGEPI--------PLVLLDEPSPFRDMALATLNAAGIP 212
PRK09986 PRK09986
LysR family transcriptional regulator;
3-240 6.76e-15

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 73.22  E-value: 6.76e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359    3 IKLDLYKIFSEVAKHKSFSKAAKSLYMTQPAVSQAIMQLENELEIRLFTRTSRGVILTNEGELLFEYTNsaiNLINVAEK 82
Cdd:PRK09986   7 IDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESR---RLLDNAEQ 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359   83 KLIESKNLLMGD---LKLGVGDTISRYFLLPYLEKFHSSYPNIKLKIINRTTLELCVMLKSGEIDIAICNLPINDPSLEV 159
Cdd:PRK09986  84 SLARVEQIGRGEagrIEIGIVGTALWGRLRPAMRHFLKENPNVEWLLRELSPSMQMAALERRELDAGIWRMADLEPNPGF 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359  160 TELTDIHDIFVCGKKYKNKIS--KSISLKELSKFPLILLES-KSNSRQYVEKYMLSKGipFTPEI--ELGSHDLLLEFAK 234
Cdd:PRK09986 164 TSRRLHESAFAVAVPEEHPLAsrSSVPLKALRNEYFITLPFvHSDWGKFLQRVCQQAG--FSPQIirQVNEPQTVLAMVS 241


                 ....*.
gi 28202359  235 INLGIS 240
Cdd:PRK09986 242 MGIGIT 247
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 95-241 6.41e-14

The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold; This CD includes the substrate binding domain of CidR which positively up-regulates the expression of cidABC operon in the presence of acetic acid produced by the metabolism of excess glucose. The CidR affects the control of murein hydrolase activity by enhancing cidABC expression in the presence of acetic acid. Thus, up-regulation of cidABC expression results in increased murein hydrolase activity. This substrate binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176129 [Multi-domain]  Cd Length: 197  Bit Score: 68.74  E-value: 6.41e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359  95 LKLGVGDTISRYFLLPYLEKFHSSYPNIKLKIINRTTLELCVMLKSGEIDIAICNLPINDPSLEVTELTDiHDIFVCGKK 174
Cdd:cd08438   2 LRLGLPPLGGSLLFAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVLPVDEEEFDSQPLCN-EPLVAVLPR 80

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 28202359 175 yKNKIS--KSISLKELSKFPLILLESKSNSRQYVEKYMLSKGipFTPEI--ELGSHDLLLEFAKINLGISC 241
Cdd:cd08438  81 -GHPLAgrKTVSLADLADEPFILFNEDFALHDRIIDACQQAG--FTPNIaaRSSQWDFIAELVAAGLGVAL 148
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
 95-225 2.06e-13

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: 67.53  E-value: 2.06e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359  95 LKLGVGDTiSRYFLLPYLEKFHSSYPNI--KLKIINRTtlELCVMLKSGEIDIAICNLPINDPSLEVTELTDiHDIFV-- 170
Cdd:cd08419   2 LRLAVVST-AKYFAPRLLGAFCRRHPGVevSLRVGNRE--QVLERLADNEDDLAIMGRPPEDLDLVAEPFLD-NPLVVia 77

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 28202359 171 ------CGKKyknkiskSISLKELSKFPLILLESKSNSRQYVEKYMLSKGIPFTPEIELGS 225
Cdd:cd08419  78 ppdhplAGQK-------RIPLERLAREPFLLREPGSGTRLAMERFFAEHGVTLRVRMELGS 131
PRK10341 PRK10341
transcriptional regulator TdcA;
10-150 7.98e-13

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 67.58  E-value: 7.98e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359   10 IFSEVAKHKSFSKAAKSLYMTQPAVSQAIMQLENELEIRLFTRTSRGVILTNEGELLFEYTNSAINLInvaeKKLIESKN 89
Cdd:PRK10341  14 VFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREM----KNMVNEIN 89

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 28202359   90 LLMG----DLKLGVGDTISRYFLLPYLEKFHSSYPNIKLKIINRTTLELCVMLKSGEIDIAICNL 150
Cdd:PRK10341  90 GMSSeavvDVSFGFPSLIGFTFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIGTL 154
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 5-291 6.32e-12

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 64.63  E-value: 6.32e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359    5 LDLYKIFSEVAKHKSFSKAAKSLYMTQPAVSQAIMQLENELEIRLFTRTSRGVILTNEGELLFEYTNSAINLINVAEKKL 84
Cdd:PRK14997   4 LNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDAI 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359   85 IESKNLLMGDLKLGVGDTISRYFLLPYLEKFHSSYPNIKLKiINRTTLELCVMLKSGEIDIAICNLPINDPSLEVTELTD 164
Cdd:PRK14997  84 AALQVEPRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQ-LEATNRRVDVVGEGVDVAIRVRPRPFEDSDLVMRVLAD 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359  165 IHDIFVCGKKYKNKISKSISLKELSKFPLILLESKsnsrQYVEKYMLS------KGIPFTPEIELGSHDLLLEFAKINLG 238
Cdd:PRK14997 163 RGHRLFASPDLIARMGIPSAPAELSHWPGLSLASG----KHIHRWELYgpqgarAEVHFTPRMITTDMLALREAAMAGVG 238

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....
gi 28202359  239 ISCVIKEFSQDYLKSKELyEIQTNEVIPKRN-IGVCFLKSVSLSPSSTKFVDIL 291
Cdd:PRK14997 239 LVQLPVLMVKEQLAAGEL-VAVLEEWEPRREvIHAVFPSRRGLLPSVRALVDFL 291
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 21-242 1.31e-11

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 63.91  E-value: 1.31e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359   21 SKAAKSLYMTQPAVSQAIMQLENELEIRLFTRtsrgviltnEGELLFEYTNSAINLINVAEKKLIESKNLL--------- 91
Cdd:PRK12683  20 TEVANALYTSQSGVSKQIKDLEDELGVEIFIR---------RGKRLTGLTEPGKELLQIVERMLLDAENLRrlaeqfadr 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359   92 -MGDLKLGVGDTISRYFLLPYLEKFHSSYPNIKLKIINRTTLELCVMLKSGEIDIAICNLPIND-PSLEVTELTDIHDIF 169
Cdd:PRK12683  91 dSGHLTVATTHTQARYALPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGIATEALDRePDLVSFPYYSWHHVV 170

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 28202359  170 VCGKKYKNKISKSISLKELSKFPLILLESKSNSRQYVEKYMLSKGIpfTPEIELGS--HDLLLEFAKINLGISCV 242
Cdd:PRK12683 171 VVPKGHPLTGRENLTLEAIAEYPIITYDQGFTGRSRIDQAFAEAGL--VPDIVLTAldADVIKTYVELGMGVGIV 243
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 108-289 1.71e-11

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: 62.17  E-value: 1.71e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359 108 LLPYL-EKFHSSYPNIKLKIINRTTLELCVMLKSGEIDIAICNLPINDPSLEVTELTDiHDIFV--------CGKKyknk 178
Cdd:cd08434  14 LVPDLiRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLALCSPVPDEPDIEWIPLFT-EELVLvvpkdhplAGRD---- 88

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359 179 iskSISLKELSKFPLILLESKSNSRQYVEKymLSKGIPFTPEIELGSHDL--LLEFAKINLGIScVIKEFSQ-DYLKSKE 255
Cdd:cd08434  89 ---SVDLAELADEPFVLLSPGFGLRPIVDE--LCAAAGFTPKIAFEGEEDstIAGLVAAGLGVA-ILPEMTLlNPPGVKK 162

                       170       180       190
                ....*....|....*....|....*....|....
gi 28202359 256 lyeIQTNEVIPKRNIGVCFLKSVSLSPSSTKFVD 289
Cdd:cd08434 163 ---IPIKDPDAERTIGLAWLKDRYLSPAARRFKD 193
PBP2_CynR cd08425
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, ...
 93-234 2.27e-11

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: 61.58  E-value: 2.27e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359  93 GDLKLGVGDTISRYFLLPYLEKFHSSYPNIKLKIINRTTLELCVMLKSGEIDIAICNLPINDPSLEVTELTDIHDIFVCG 172
Cdd:cd08425   1 GSLRLAMTPTFTAYLIGPLIDRFHARYPGIALSLREMPQERIEAALADDRLDLGIAFAPVRSPDIDAQPLFDERLALVVG 80

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 28202359 173 KKYKNKISK-SISLKELSKFPLILLESKSNSRQYVEKYMLSKGIPFTPEIELGSHDLLLEFAK 234
Cdd:cd08425  81 ATHPLAQRRtALTLDDLAAEPLALLSPDFATRQHIDRYFQKQGIKPRIAIEANSISAVLEVVR 143
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
28-221 2.33e-11

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 62.91  E-value: 2.33e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359   28 YMTQPAVSQAIMQLENELEIRLFTRTSRGVILTNEGELLFEYTNSAINLINVAEKKLIESKNLLMGDLKLGVGDTISRYF 107
Cdd:PRK11716   2 HVSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSLFCSVTAAYSH 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359  108 LLPYLEKFHSSYPNIKLKI--------INRttlelcvmLKSGEIDIAICNLPINDP-SLEVTELTDIHDIFVcGKKYKNK 178
Cdd:PRK11716  82 LPPILDRFRAEHPLVEIKLttgdaadaVEK--------VQSGEADLAIAAKPETLPaSVAFSPIDEIPLVLI-APALPCP 152

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 28202359  179 ISKSISLKEL--SKFPLILLESkSNSRQYVEKYMLSKGIpfTPEI 221
Cdd:PRK11716 153 VRQQLSQEKPdwSRIPFILPEH-GPARRRIDLWFRRHKI--KPNI 194
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 93-197 3.63e-11

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: 61.00  E-value: 3.63e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359  93 GDLKLGVGDTISRYfLLPY-LEKFHSSYPNIKLKIINRTTLELCVMLKSGEIDIAICNLPINDPSLEVTELTDihDIF-- 169
Cdd:cd08411   1 GPLRLGVIPTIAPY-LLPRlLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAALLALPVDEPGLEEEPLFD--EPFll 77

                        90       100
                ....*....|....*....|....*...
gi 28202359 170 VCGKKYKNKISKSISLKELSKFPLILLE 197
Cdd:cd08411  78 AVPKDHPLAKRKSVTPEDLAGERLLLLE 105
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
19-147 1.17e-10

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 61.19  E-value: 1.17e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359   19 SFSKAAKSLYMTQPAVSQAIMQLENELEIRLFTRTSRGVILTNEGELLFEYTNSAINLINVAEKKLIESKNLlmgDLKLG 98
Cdd:PRK15421  18 SLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQACNEPQQT---RLRIA 94

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 28202359   99 VGDTISRYFLLPYLEKFHSSYPNIKLKIINRTTLELCVMLKSGEIDIAI 147
Cdd:PRK15421  95 IECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVM 143
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
10-127 1.18e-10

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 60.93  E-value: 1.18e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359   10 IFSEVAKHKSFSKAAKSLYMTQPAVSQAIMQLENELEIRLFTRTSRGVILTNEGELLFEYTNSAINLINVAEKKLIESKN 89
Cdd:PRK10632   9 VFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQLYAFNN 88

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 28202359   90 LLMGDLKLGVGDTISRYFLLPYLEKFHSSYPNIKLKII 127
Cdd:PRK10632  89 TPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLV 126
cysB PRK12681
HTH-type transcriptional regulator CysB;
13-148 2.02e-10

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 60.30  E-value: 2.02e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359   13 EVAKHK-SFSKAAKSLYMTQPAVSQAIMQLENELEIRLFTR--------TSRGV-ILTNEGELLFEytnsAINLINVAEk 82
Cdd:PRK12681  11 EVVNHNlNVSATAEGLYTSQPGISKQVRMLEDELGIQIFARsgkhltqvTPAGEeIIRIAREILSK----VESIKSVAG- 85

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 28202359   83 kliESKNLLMGDLKLGVGDTISRYFLLPYLEKFHSSYPNIKLKIINRTTLELCVMLKSGEIDIAIC 148
Cdd:PRK12681  86 ---EHTWPDKGSLYIATTHTQARYALPPVIKGFIERYPRVSLHMHQGSPTQIAEAAAKGNADFAIA 148
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
9-68 2.31e-10

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 60.21  E-value: 2.31e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359    9 KIFSEVAKHKSFSKAAKSLYMTQPAVSQAIMQLENELEIRLFTRTSRGVILTNEGELLFE 68
Cdd:PRK10094   8 RTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLS 67
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 107-291 4.46e-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: 176117 [Multi-domain]  Cd Length: 199  Bit Score: 58.09  E-value: 4.46e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359 107 FLLPYLEKFHSSYPNIKLKIINRTTLELCVMLKSGEIDIAICNLPINDPSLEVTELTDIHDIFVCGKKYKNKISKSISLK 186
Cdd:cd08426  14 LLPSLIARFRQRYPGVFFTVDVASTADVLEAVLSGEADIGLAFSPPPEPGIRVHSRQPAPIGAVVPPGHPLARQPSVTLA 93

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359 187 ELSKFPLILLESKSNSRQYVEKYMLSKGIPFTPEIELGSHDLLLEFAKINLGIS-----CVIKEFSQDYLKSKELYEIQT 261
Cdd:cd08426  94 QLAGYPLALPPPSFSLRQILDAAFARAGVQLEPVLISNSIETLKQLVAAGGGISlltelAVRREIRRGQLVAVPLADPHM 173

                       170       180       190
                ....*....|....*....|....*....|
gi 28202359 262 NEvipkRNIGVCFLKSVSLSPSSTKFVDIL 291
Cdd:cd08426 174 NH----RQLELQTRAGRQLPAAASAFLQLL 199
PRK12680 PRK12680
LysR family transcriptional regulator;
23-242 5.90e-10

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 59.25  E-value: 5.90e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359   23 AAKSLYMTQPAVSQAIMQLENELEIRLFTRTSRGV-ILTNEGELLFEYTNSAINLINVAEKKLIESKNLLMGDLKLGVGD 101
Cdd:PRK12680  22 AAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLeSVTPAGVEVIERARAVLSEANNIRTYAANQRRESQGQLTLTTTH 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359  102 TISRYFLLPYLEKFHSSYPNIKLKIINRTTLELCVMLKSGEIDIAICNLPINDPSLEV-TELTDIHDIFVCGKKYK-NKI 179
Cdd:PRK12680 102 TQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVSTAGGEPSAGIaVPLYRWRRLVVVPRGHAlDTP 181

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 28202359  180 SKSISLKELSKFPLILLESKSNSRQYVEKYMLSKGIpfTPEIELGS--HDLLLEFAKINLGISCV 242
Cdd:PRK12680 182 RRAPDMAALAEHPLISYESSTRPGSSLQRAFAQLGL--EPSIALTAldADLIKTYVRAGLGVGLL 244
PRK09801 PRK09801
LysR family transcriptional regulator;
9-190 2.78e-09

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 56.97  E-value: 2.78e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359    9 KIFSEVAKHKSFSKAAKSLYMTQPAVSQAIMQLENELEIRLFTRTSRGVILTNEGELLFEYTNSAINLINVAEKKLIESK 88
Cdd:PRK09801  12 QVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVTQIK 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359   89 NLLMGDLKLGVGDTISRYFLLPYLEKFHSSYPNIKL--KIINRTtlelcVMLKSGEIDIaicNLPIND--PSLEVTE-LT 163
Cdd:PRK09801  92 TRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVhfELFDRQ-----IDLVQDNIDL---DIRINDeiPDYYIAHlLT 163

                        170       180
                 ....*....|....*....|....*..
gi 28202359  164 DIHDIFVCGKKYKNKISKSISLKELSK 190
Cdd:PRK09801 164 KNKRILCAAPEYLQKYPQPQSLQELSR 190
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
11-143 4.17e-09

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 56.52  E-value: 4.17e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359   11 FSEVAKHKSFSKAAKSLYMTQPAVSQAIMQLENELEIRLFTRTsRGVILTNEGELLFEYTnSAINLINVAEKKLIESKNL 90
Cdd:PRK13348  10 LAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRG-RPCRPTPAGQRLLRHL-RQVALLEADLLSTLPAERG 87

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 28202359   91 LMGDLKLGV-GDTISRYFlLPYLEKFHSSyPNIKLKII---NRTTLELcvmLKSGEI 143
Cdd:PRK13348  88 SPPTLAIAVnADSLATWF-LPALAAVLAG-ERILLELIvddQDHTFAL---LERGEV 139
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 14-258 6.08e-09

multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, including founding member GSU2202 from Geobacter sulfurreducens PCA, are LysR family transcriptional regulators found regularly in the vicinity of multiheme cytochromes such as GSU2203, a decaheme c-type cytochrome.


Pssm-ID: 468965 [Multi-domain]  Cd Length: 301  Bit Score: 55.90  E-value: 6.08e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359   14 VAKHKSFSKAAKSLYMTQPAVSQAIMQLENELEIRLFTRTSRGVILTNEGELLFEytnSAINLINVaEKKLIESKNLLMG 93
Cdd:NF041036  12 VAEEGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLE---KARRILDI-EDSLMDELKSFKG 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359   94 DLKLGVGDTISryFLLPYLEK----FHSSYPNI-KLKIINRTTLELCVMLKSGEIDIAICNLPINDP--SLEVTELTDIH 166
Cdd:NF041036  88 RQRLSICCTPT--FGMAHLPGvlnrFMLRNADVvDLKFLFHSPAQALEGIQNKEFDLAIIEHCADLDlgRFHTYPLPQDE 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359  167 DIFVCGKKYkNKISKSISLKELSKFPLILLESKSNSRQYVEKYMLSKGIP---FTPEIELGSHDLLLEFAKINLGISCVI 243
Cdd:NF041036 166 LVFVSAPSL-GLPTPNVTLERLLELCLITRRDGCSSRDLLRRNLAEQGRDlddFRRVVVSDDLRLTIQTVLDGGGISFVS 244

                        250
                 ....*....|....*
gi 28202359  244 KEFSQDYLKSKELYE 258
Cdd:NF041036 245 RSLVCEYLKNGQLRE 259
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 19-147 6.62e-09

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 55.84  E-value: 6.62e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359   19 SFSKAAKSLYMTQPAVSQAIMQLENELEIRLFTRTSRGVILTNEGELLFEYTNSAINLINVAEKKLIESKNLLMGDLKLG 98
Cdd:PRK11233  17 SLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQLAVHNVGQALSGQVSIG 96

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 28202359   99 VG-DTISRYFLLPYLEKFHSSYPNIKLkIINR---TTLELCVMlkSGEIDIAI 147
Cdd:PRK11233  97 LApGTAASSLTMPLLQAVRAEFPGIVL-YLHEnsgATLNEKLM--NGQLDMAV 146
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 14-202 8.50e-08

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 52.64  E-value: 8.50e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359   14 VAKHKSFSKAAKSLYMTQPAVSQAIMQLENELEIRLFTRTSRGVILTNEGELLFEYTNSAInlinvaeKKLIESK----- 88
Cdd:PRK11074  13 VARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVI-------KKMQETRrqcqq 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359   89 --NLLMGDLKLGVgDTISR-YFLLPYLEKFHSSYPNIKLKIinrtTLElcVM------LKSGEIDIAI---CNLPINDpS 156
Cdd:PRK11074  86 vaNGWRGQLSIAV-DNIVRpDRTRQLIVDFYRHFDDVELII----RQE--VFngvwdaLADGRVDIAIgatRAIPVGG-R 157

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 28202359  157 LEVTELTDIHDIFVCGKKYK-NKISKSISLKELSKFPLILLESKSNS 202
Cdd:PRK11074 158 FAFRDMGMLSWACVVSSDHPlASMDGPLSDDELRPYPSLCLEDTSRT 204
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 95-242 1.15e-07

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: 50.97  E-value: 1.15e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359  95 LKLGVGDTISRYFLLPYLEKFHSSYPNIKLKIINRTTLELCVMLKSGEIDIAICNLPINDPSLEVTELTDiHDIFVC--- 171
Cdd:cd08414   2 LRIGFVGSALYGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPPPDPPGLASRPLLR-EPLVVAlpa 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359 172 -----GKkyknkisKSISLKELSKFPLILLESKSNS--RQYVEKYMLSKGipFTPEI--ELGSHDLLLEFAKINLGISCV 242
Cdd:cd08414  81 dhplaAR-------ESVSLADLADEPFVLFPREPGPglYDQILALCRRAG--FTPRIvqEASDLQTLLALVAAGLGVALV 151
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 95-228 1.79e-07

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


Pssm-ID: 176104 [Multi-domain]  Cd Length: 198  Bit Score: 50.62  E-value: 1.79e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359  95 LKLGVGDTISRYFLLPYLEKFHSSYPNIKLKIINRTTLELCVMLKSGEIDIAIC---NLPindPSLEVTELTDIH----- 166
Cdd:cd08412   2 LRIGCFSTLAPYYLPGLLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALTydlDLP---EDIAFEPLARLPpyvwl 78

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 28202359 167 --DIFVCGKkyknkisKSISLKELSKFPLILLESKSnSRQYVEKYMLSKGIpfTPEIELGSHDL 228
Cdd:cd08412  79 paDHPLAGK-------DEVSLADLAAEPLILLDLPH-SREYFLSLFAAAGL--TPRIAYRTSSF 132
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 105-291 1.44e-06

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: 48.04  E-value: 1.44e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359 105 RYFLLP-YLEKFHSSYPNIKLKIINRTTLELCVMLKSGEIDIAICNLP--INDPSLEVTELTDIHDIFVCGKKYKNKISK 181
Cdd:cd08435  11 APVLLPpAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAIGRLAddEQPPDLASEELADEPLVVVARPGHPLARRA 90

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359 182 SISLKELSKFPLILLESKSNSRQYVEKYMLSKGIPF-TPEIELGSHDLLLEFAKINLGISCVIKEFSQDYLKSKELYEIQ 260
Cdd:cd08435  91 RLTLADLADYPWVLPPPGTPLRQRLEQLFAAAGLPLpRNVVETASISALLALLARSDMLAVLPRSVAEDELRAGVLRELP 170

                       170       180       190
                ....*....|....*....|....*....|.
gi 28202359 261 TNEVIPKRNIGVCFLKSVSLSPSSTKFVDIL 291
Cdd:cd08435 171 LPLPTSRRPIGITTRRGGPLSPAARALLDAL 201
PBP2_CysB cd08443
The C-terminal substrate domain of LysR-type transcriptional regulator CysB contains type 2 ...
 95-290 1.55e-06

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: 47.94  E-value: 1.55e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359  95 LKLGVGDTISRYFLLPYLEKFHSSYPNIKLKIINRTTLELCVMLKSGEIDIAICNLPINDPSLEVTeltdihdiFVCGKK 174
Cdd:cd08443   2 LYVATTHTQARYVLPPVIKGFIERYPRVSLQMHQGSPTQIAEMVSKGLVDFAIATEALHDYDDLIT--------LPCYHW 73

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359 175 YKNKISK---------SISLKELSKFPLILLESKSNSRQYVEKYMLSKGIpfTPEIELGSH--DLLLEFAKINLGIScVI 243
Cdd:cd08443  74 NRCVVVKrdhpladkqSISIEELATYPIVTYTFGFTGRSELDTAFNRAGL--TPNIVLTATdaDVIKTYVRLGLGVG-VI 150

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*..
gi 28202359 244 KEFSQDYLKSKELYEIQTNEVIPKRNIGVCFLKSVSLSPSSTKFVDI 290
Cdd:cd08443 151 ASMAYDPVDDPDLVIRDARDLFPWSVTKIAFRRGTFLRSYMYDFIQR 197
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 97-215 1.91e-06

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


Pssm-ID: 176109 [Multi-domain]  Cd Length: 200  Bit Score: 47.59  E-value: 1.91e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359  97 LGVGDTISRYFLLPYLEKFHSSYPNIKLKIINRTTLELCVMLKSGEIDIAICNLPINDPSLEVTELTDIHDIFVCGKKYK 176
Cdd:cd08417   4 IAASDYLEALLLPPLLARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELPPGLRSQPLFEDRFVCVARKDHP 83

                        90       100       110
                ....*....|....*....|....*....|....*....
gi 28202359 177 nKISKSISLKELSKFPLILLESKSNSRQYVEKYMLSKGI 215
Cdd:cd08417  84 -LAGGPLTLEDYLAAPHVLVSPRGRGHGLVDDALAELGL 121
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 95-242 2.61e-06

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: 47.17  E-value: 2.61e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359  95 LKLGVGDTISRYFLLPYLEKFHSSYPNIKLKIINRTTLELCVMLKSGEIDIAICNLPINDPSLEVTELTDIHdiFVC--- 171
Cdd:cd08415   2 LRIAALPALALSLLPRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPLDHPGLESEPLASGR--AVCvlp 79

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 28202359 172 ------GKkyknkisKSISLKELSKFPLILLESKSNSRQYVEKYMLSKGIPFTPEIELGSHDLLLEFAKINLGISCV 242
Cdd:cd08415  80 pghplaRK-------DVVTPADLAGEPLISLGRGDPLRQRVDAAFERAGVEPRIVIETQLSHTACALVAAGLGVAIV 149
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
11-66 7.51e-06

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 46.69  E-value: 7.51e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 28202359   11 FSEVAKHKSFSKAAKSLYMTQPAVSQAIMQLENELEIRLFTRTsRGVILTNEGELL 66
Cdd:PRK03635  10 LAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVRT-QPCRPTEAGQRL 64
PBP2_Cbl cd08444
The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is ...
 102-267 7.86e-06

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: 45.57  E-value: 7.86e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359 102 TISRYFLLPYLEKFHSSYPNIKLKIINRTTLELCVMLKSGEIDIAICNLPI-NDPSLEVTELTDIHDIFVCGKKYKNKIS 180
Cdd:cd08444   9 TQARYALPWVVQAFKEQFPNVHLVLHQGSPEEIASMLANGQADIGIATEALeNHPELVSFPYYDWHHHIIVPVGHPLESI 88

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359 181 KSISLKELSKFPLILLESKSNSRQYVEKYMLSKGIpfTPEIELGS--HDLLLEFAKINLGIScVIKEFSQDYLKSKELYE 258
Cdd:cd08444  89 TPLTIETIAKWPIITYHGGFTGRSRIDRAFSRAEL--TPNIVLSAldADVIKTYVGLGMGIG-IVAEMAFEGQRDTNLIK 165


                ....*....
gi 28202359 259 IQTNEVIPK 267
Cdd:cd08444 166 LDTSHLFGK 174
nhaR PRK11062
transcriptional activator NhaR; Provisional
 11-76 8.60e-06

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 46.54  E-value: 8.60e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 28202359   11 FSEVAKHKSFSKAAKSLYMTQPAVSQAIMQLENELEIRLFTRTSRGVILTNEGELLFEYTNSAINL 76
Cdd:PRK11062  12 FWMVCKEGSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGELVFRYADKMFTL 77
PBP2_CysB_like cd08413
The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains ...
 102-194 1.82e-05

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: 44.54  E-value: 1.82e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359 102 TISRYFLLPYLEKFHSSYPNIKLKIINRTTLELCVMLKSGEIDIAICNLPINDPSlevtELTDI------HDIFV-CGKK 174
Cdd:cd08413   9 TQARYVLPPVIAAFRKRYPKVKLSLHQGTPSQIAEMVLKGEADIAIATEALDDHP----DLVTLpcyrwnHCVIVpPGHP 84

                        90       100
                ....*....|....*....|
gi 28202359 175 YKNKisKSISLKELSKFPLI 194
Cdd:cd08413  85 LADL--GPLTLEDLAQYPLI 102
PBP2_DntR_NahR_LinR_like cd08459
The C-terminal substrate binding domain of LysR-type transcriptional regulators that are ...
 106-216 2.15e-05

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: 44.49  E-value: 2.15e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359 106 YFLLPYLEKFHSSYPNIKLKIINRTTLELCVMLKSGEIDIAICNLPINDPSLEVTELtdIHDIFVC-GKKYKNKISKSIS 184
Cdd:cd08459  13 YFLPRLLAALREVAPGVRIETVRLPVDELEEALESGEIDLAIGYLPDLGAGFFQQRL--FRERYVClVRKDHPRIGSTLT 90

                        90       100       110
                ....*....|....*....|....*....|..
gi 28202359 185 LKELSKFPLILLESKSNSRQYVEKYMLSKGIP 216
Cdd:cd08459  91 LEQFLAARHVVVSASGTGHGLVEQALREAGIR 122
leuO PRK09508
leucine transcriptional activator; Reviewed
 2-77 2.15e-05

leucine transcriptional activator; Reviewed


Pssm-ID: 181918 [Multi-domain]  Cd Length: 314  Bit Score: 45.40  E-value: 2.15e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 28202359    2 SIKLDLYKIFSEVAKHKSFSKAAKSLYMTQPAVSQAIMQLENELEIRLFTRTSRGVILTNEGELLFEYTNSAINLI 77
Cdd:PRK09508  21 MVDLNLLTVFDAVMQEQNITRAAHNLGMSQPAVSNAVARLKVMFNDELFVRYGRGIQPTARARQLFGPVRQALQLV 96
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 97-238 2.42e-05

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: 44.12  E-value: 2.42e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359  97 LGVGDTISRYFLLPYLEKFHSSYPNIKLKIIN---RTTLElcvMLKSGEIDIAICNLPINDPSLEVTELTdIHDIFVCGK 173
Cdd:cd08433   4 VGLPPSAASVLAVPLLRAVRRRYPGIRLRIVEglsGHLLE---WLLNGRLDLALLYGPPPIPGLSTEPLL-EEDLFLVGP 79

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 28202359 174 KYKNKIS-KSISLKELSKFPLILLESKSNSRQYVEKYMLSKGIPFTPEIELGSHDLLLEFAKINLG 238
Cdd:cd08433  80 ADAPLPRgAPVPLAELARLPLILPSRGHGLRRLVDEAAARAGLTLNVVVEIDSVATLKALVAAGLG 145
PBP2_LrhA_like cd08439
The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of ...
 95-240 3.26e-05

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: 43.86  E-value: 3.26e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359  95 LKLGVGDTISRYFLLPYLEKFHSSYPNIKLKIINRTTLELCVMLKSGEIDIAICNLPINDPSLEVTELTDIHdiFVCGKK 174
Cdd:cd08439   2 LRIGCPDDYADTILPFLLNRFASVYPRLAIEVVCKRTPRLMEMLERGEVDLALITHPPPGASATILRRSPTV--WYCAAG 79

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 28202359 175 YKNKISKSIslkelskfPLILLESKSNSRQYVEKYMLSKGIPFTPEIELGSHDLLLEFAKINLGIS 240
Cdd:cd08439  80 YILAPGEPL--------PLALLDEPTLDRRAALAALDAAGIPWRIAYAASSLSGLRAAVRAGLGIT 137
PBP2_OccR cd08457
The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the ...
 95-242 1.02e-04

The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the catabolism of octopine, contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulator OccR, which is involved in the catabolism of octopine. Opines are low molecular weight compounds found in plant crown gall tumors produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. In Agrobacterium tumefaciens, OccR protein activates the occQ operon of the Ti plasmid in response to octopine. This operon encodes proteins required for the uptake and catabolism of octopine, an arginine derivative. The occ operon also encodes the TraR protein, which is a quorum-sensing transcriptional regulator of the Ti plasmid tra regulon. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176146 [Multi-domain]  Cd Length: 196  Bit Score: 42.48  E-value: 1.02e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359  95 LKLGVGDTISRYFLLPYLEKFHSSYPNIKLKIINRTTLELCVMLKSGEIDIAICNLPINDPSLEVTELTDIHDIFVCGKK 174
Cdd:cd08457   2 LRIAAMPALANGFLPRFLAAFLRLRPNLHLSLMGLSSSQVLEAVASGRADLGIADGPLEERQGFLIETRSLPAVVAVPMG 81

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 28202359 175 YKNKISKSISLKELSKFPLILLESKSNSRQYVEKYMLSKGIPFTPEIELGSHDLLLEFAKINLGISCV 242
Cdd:cd08457  82 HPLAQLDVVSPQDLAGERIITLENGYLFRMRVEVALGKIGVKRRPIIEVNLSHTALSLVREGLGIAII 149
PBP2_MleR cd08437
The substrate binding domain of LysR-type transcriptional regulator MleR which required for ...
 95-291 1.07e-04

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


Pssm-ID: 176128  Cd Length: 198  Bit Score: 42.32  E-value: 1.07e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359  95 LKLGVGDTISRYFLLPYLEKFHSSYPNIKLKIINRTTLELCVMLKSGEIDIA--ICNLPINDPSLEVTELTDIHDIFVCG 172
Cdd:cd08437   2 LRFGLPPIIGNYYFPKLAKDLIKTGLMIQIDTYEGGSAELLEQLLQGDLDIAllGSLTPLENSALHSKIIKTQHFMIIVS 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359 173 KKYKNKISKSISLKELSKFPLILLEskSNSRQYVEKYMLSKGIPFTPEIELGSHD--LLLEFAKINLGISCVIkEFS--- 247
Cdd:cd08437  82 KDHPLAKAKKVNFADLKKENFILLN--EHFVHPKAFDSLCQQANFQPNIVYRTNDihILKSMVRENVGIGFLT-DIAvkp 158

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....
gi 28202359 248 QDYLKSKELyeiqTNEVIPKRNIGVCFLKSVSLSPSSTKFVDIL 291
Cdd:cd08437 159 DDHLVAIPL----LDNEQPTFYISLAHRKDQLLTPAQKKLLDLL 198
PRK11482 PRK11482
DNA-binding transcriptional regulator;
3-69 1.83e-04

DNA-binding transcriptional regulator;


Pssm-ID: 183159 [Multi-domain]  Cd Length: 317  Bit Score: 42.40  E-value: 1.83e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 28202359    3 IKLDLYKIFSEVAKHKSFSKAAKSLYMTQPAVSQAIMQLENELEIRLFTRTSRGVILTNEGELLFEY 69
Cdd:PRK11482  29 IDLNLLTIFEAVYVHKGIVNAAKILNLTPSAISQSIQKLRVIFPDPLFIRKGQGVTPTAYATHLHEY 95
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 1-127 1.90e-04

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 42.29  E-value: 1.90e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359    1 MSIKLDLYKIFSEVAKHKSFSKAAKSLYMTQPAVSQAIMQLENELEIRLFTRTsRGVIL-TNEGELLFEYTNSAI----N 75
Cdd:PRK11013   2 AAVSLRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERV-RGRLHpTVQGLRLFEEVQRSYygldR 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 28202359   76 LINVAEkkliESKNLLMGDLKLGVGDTISRYFLLPYLEKFHSSYPNIKLKII 127
Cdd:PRK11013  81 IVSAAE----SLREFRQGQLSIACLPVFSQSLLPGLCQPFLARYPDVSLNIV 128
PBP2_GcdR_like cd08481
The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, ...
 95-256 1.02e-03

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


Pssm-ID: 176170 [Multi-domain]  Cd Length: 194  Bit Score: 39.20  E-value: 1.02e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359  95 LKLGVGDTISRYFLLPYLEKFHSSYPNIKLKIINRTtleLCVMLKSGEIDIAICNLPINDPSLEVTELTDIHDIFVCGKK 174
Cdd:cd08481   2 LELAVLPTFGTRWLIPRLPDFLARHPDITVNLVTRD---EPFDFSQGSFDAAIHFGDPVWPGAESEYLMDEEVVPVCSPA 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359 175 YKNKiSKSISLKELSKFPLILLESKSNS-RQYVEKYMLSKGIPFT-PEIELGShdLLLEFAKINLGISCVIKEFSQDYLK 252
Cdd:cd08481  79 LLAG-RALAAPADLAHLPLLQQTTRPEAwRDWFEEVGLEVPTAYRgMRFEQFS--MLAQAAVAGLGVALLPRFLIEEELA 155


                ....
gi 28202359 253 SKEL 256
Cdd:cd08481 156 RGRL 159
PRK15243 PRK15243
virulence genes transcriptional activator SpvR;
9-84 1.69e-03

virulence genes transcriptional activator SpvR;


Pssm-ID: 185155 [Multi-domain]  Cd Length: 297  Bit Score: 39.27  E-value: 1.69e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 28202359    9 KIFSEVAKHKSFSKAAKSLYMTQPAVSQAIMQLENELEIRLFTRTSRGVILTNEGELLFEYTNSAINLINVAEKKL 84
Cdd:PRK15243  10 KIFITLMETGSFSIATSVLYITRTPLSRVISDLERELKQRLFIRKNGTLIPTEFAQTIYRKVKSHYIFLHALEQEI 85
PBP2_BenM_CatM_CatR cd08445
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 99-195 1.80e-03

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: 38.75  E-value: 1.80e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359  99 VGDTIsrYFLLPYL-EKFHSSYPNIKLKIINRTTLELCVMLKSGEIDIAICNLPINDPSLE---------VTELTDIHDI 168
Cdd:cd08445   8 VPSTL--YGLLPELiRRFRQAAPDVEIELIEMTTVQQIEALKEGRIDVGFGRLRIEDPAIRrivlreeplVVALPAGHPL 85

                        90       100
                ....*....|....*....|....*..
gi 28202359 169 fvcgkkykNKISKSISLKELSKFPLIL 195
Cdd:cd08445  86 --------AQEKAPLTLAQLADEPLIL 104
PBP2_IlvY cd08430
The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates ...
 102-221 2.43e-03

The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates the expression of ilvC gene that encoding acetohydroxy acid isomeroreductase for the biosynthesis of branched amino acids; contains the type 2 periplasmic bindin; In Escherichia coli, IlvY is required for the regulation of ilvC gene expression that encodes acetohydroxy acid isomeroreductase (AHIR), a key enzyme in the biosynthesis of branched-chain amino acids (isoleucine, valine, and leucine). The ilvGMEDA operon genes encode remaining enzyme activities required for the biosynthesis of these amino acids. Activation of ilvC transcription by IlvY requires the additional binding of a co-inducer molecule (either alpha-acetolactate or alpha-acetohydoxybutyrate, the substrates for AHIR) to a preformed complex of IlvY protein-DNA. Like many other LysR-family members, IlvY negatively auto-regulates the transcription of its own divergently transcribed ilvY gene in an inducer-independent manner. This substrate-binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176121  Cd Length: 199  Bit Score: 38.33  E-value: 2.43e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359 102 TISRYFLLPYLEKFHSSYPNIKLKIINRTTLELCVMLKSGEIDIAICNLPINDPS-LEVTELTDIHDIFvCGKKYKNKIS 180
Cdd:cd08430   9 TASYSFLPPILERFRAQHPQVEIKLHTGDPADAIDKVLNGEADIAIAARPDKLPArLAFLPLATSPLVF-IAPNIACAVT 87

                        90       100       110       120
                ....*....|....*....|....*....|....*....|...
gi 28202359 181 KSISLKEL--SKFPLILLESKSnSRQYVEKYMLSKGIPftPEI 221
Cdd:cd08430  88 QQLSQGEIdwSRLPFILPERGL-ARERLDQWFRRRGIK--PNI 127
PBP2_AlsR cd08452
The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which ...
 95-262 2.96e-03

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: 37.87  E-value: 2.96e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359  95 LKLGVGDTISRYFLLPYLEKFHSSYPNIKLKIINRTTLELCVMLKSGEIDIAICNLPINDPSLEVTELTDIHDIFVCGKK 174
Cdd:cd08452   2 LVIGFVGAAIYEFLPPIVREYRKKFPSVKVELRELSSPDQVEELLKGRIDIGFLHPPIQHTALHIETVQSSPCVLALPKQ 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359 175 YKNKISKSISLKELSKFPLILLESKSNSRQYVEKYMLSKGIPFTPEI--ELGSHDLLLEFAKINLGISCV---IKEFSQD 249
Cdd:cd08452  82 HPLASKEEITIEDLRDEPIITVAREAWPTLYDEIIQLCEQAGFRPKIvqEATEYQTVIGLVSAGIGVTFVpssAKKLFNL 161

                       170
                ....*....|...
gi 28202359 250 YLKSKELYEIQTN 262
Cdd:cd08452 162 EVAYRKIDQINLN 174
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
11-66 3.96e-03

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 38.11  E-value: 3.96e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 28202359   11 FSEVAKHKSFSKAAKSLYMTQPAVSQAIMQLENELEIRLFTRTSRGVILTNEGELL 66
Cdd:PRK10082  19 FLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIF 74
PBP2_BudR cd08451
The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is ...
 115-195 4.32e-03

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: 37.54  E-value: 4.32e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28202359 115 FHSSYPNIKLKIINRTTLELCVMLKSGEIDIAICNLPINDP-SLEVTELTDIHDIFVCGKKYKNKISKSISLKELSKFPL 193
Cdd:cd08451  23 FREAYPDVELTLEEANTAELLEALREGRLDAAFVRPPVARSdGLVLELLLEEPMLVALPAGHPLARERSIPLAALADEPF 102


                ..
gi 28202359 194 IL 195
Cdd:cd08451 103 IL 104
 
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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