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Conserved domains on  [gi|2006036772|gb|QSW66468|]
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LysR family transcriptional regulator [Lactiplantibacillus plantarum]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 11426483)

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

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-194 4.69e-37

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 132.68  E-value: 4.69e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772   1 MDLDRLQTFLKVVQYGSFQQVAAREYRSQRTVSKQMTQLENELKVTLFDRGQNRIQLTPQGRLFWASAQDIVNNYMTALT 80
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772  81 ELRQFNVPTDQILRVGYFSAFEQRLLLPALYDLKQQHSELQLVVRQGSNEHLAQQVADGSLDLALsinygRPAVTPESQL 160
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAI-----RLGPPPDPGL 155

                         170       180       190
                  ....*....|....*....|....*....|....
gi 2006036772 161 TAVPIYHNQMVIGVSRLNPLSRLSQLPPSALATL 194
Cdd:COG0583   156 VARPLGEERLVLVASPDHPLARRAPLVNSLEALL 189
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 93-299 3.78e-21

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: 88.89  E-value: 3.78e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772  93 LRVGYFSAFEQRLLLPALYDLKQQHSELQLVVRQGSNEHLAQQVADGSLDLALSinYGRPavtPESQLTAVPIYHNQMVI 172
Cdd:pfam03466   4 LRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIR--RGPP---DDPGLEARPLGEEPLVL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772 173 GVSRLNPLSRLSQLPPSALATLPILYYSPESSTF-LLESFLASAPFiqNYEQIRRVPSAEQMHLLVALNQALAFYPAGLV 251
Cdd:pfam03466  79 VAPPDHPLARGEPVSLEDLADEPLILLPPGSGLRdLLDRALRAAGL--RPRVVLEVNSLEALLQLVAAGLGIALLPRSAV 156

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 2006036772 252 PTEHDE-QVAYLPITDAAQQgYDIVALLKSNRSR-PLIAKLVQRLKANAK 299
Cdd:pfam03466 157 ARELADgRLVALPLPEPPLP-RELYLVWRKGRPLsPAVRAFIEFLREALA 205
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-194 4.69e-37

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 132.68  E-value: 4.69e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772   1 MDLDRLQTFLKVVQYGSFQQVAAREYRSQRTVSKQMTQLENELKVTLFDRGQNRIQLTPQGRLFWASAQDIVNNYMTALT 80
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772  81 ELRQFNVPTDQILRVGYFSAFEQRLLLPALYDLKQQHSELQLVVRQGSNEHLAQQVADGSLDLALsinygRPAVTPESQL 160
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAI-----RLGPPPDPGL 155

                         170       180       190
                  ....*....|....*....|....*....|....
gi 2006036772 161 TAVPIYHNQMVIGVSRLNPLSRLSQLPPSALATL 194
Cdd:COG0583   156 VARPLGEERLVLVASPDHPLARRAPLVNSLEALL 189
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-172 1.17e-21

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: 92.29  E-value: 1.17e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772   1 MDLDRLQTFLKVVQYGSFQQVAAREYRSQRTVSKQMTQLENELKVTLFDRGQNRIQLTPQGRLFWASAQDIVNNYMTALT 80
Cdd:NF040786    1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772  81 ELRQFNVPTDQILRVGYFSafeqrllLPALYDL-------KQQHSELQLVVRQGSNEHLAQQVADGSLDLALSinyGrpA 153
Cdd:NF040786   81 EFDRYGKESKGVLRIGAST-------IPGQYLLpellkkfKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFT---G--T 148

                         170
                  ....*....|....*....
gi 2006036772 154 VTPESQLTAVPIYHNQMVI 172
Cdd:NF040786  149 KLEKKRLVYTPFYKDRLVL 167
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 93-299 3.78e-21

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: 88.89  E-value: 3.78e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772  93 LRVGYFSAFEQRLLLPALYDLKQQHSELQLVVRQGSNEHLAQQVADGSLDLALSinYGRPavtPESQLTAVPIYHNQMVI 172
Cdd:pfam03466   4 LRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIR--RGPP---DDPGLEARPLGEEPLVL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772 173 GVSRLNPLSRLSQLPPSALATLPILYYSPESSTF-LLESFLASAPFiqNYEQIRRVPSAEQMHLLVALNQALAFYPAGLV 251
Cdd:pfam03466  79 VAPPDHPLARGEPVSLEDLADEPLILLPPGSGLRdLLDRALRAAGL--RPRVVLEVNSLEALLQLVAAGLGIALLPRSAV 156

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 2006036772 252 PTEHDE-QVAYLPITDAAQQgYDIVALLKSNRSR-PLIAKLVQRLKANAK 299
Cdd:pfam03466 157 ARELADgRLVALPLPEPPLP-RELYLVWRKGRPLsPAVRAFIEFLREALA 205
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 93-289 3.80e-20

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: 86.11  E-value: 3.80e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772  93 LRVGYFSAFEQRLLLPALYDLKQQHSELQLVVRQGSNEHLAQQVADGSLDLALSInygrpAVTPESQLTAVPIYHNQMVI 172
Cdd:cd05466     2 LRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVA-----LPVDDPGLESEPLFEEPLVL 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772 173 GVSRLNPLSRLSQLPPSALATLPILYYSPESST-FLLESFLASAPFIQNYeqIRRVPSAEQMHLLVALNQALAFYPAGLV 251
Cdd:cd05466    77 VVPPDHPLAKRKSVTLADLADEPLILFERGSGLrRLLDRAFAEAGFTPNI--ALEVDSLEAIKALVAAGLGIALLPESAV 154

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 2006036772 252 PTEHDEQVAYLPITDAAQQgYDIVALLKSNRSRPLIAK 289
Cdd:cd05466   155 EELADGGLVVLPLEDPPLS-RTIGLVWRKGRYLSPAAR 191
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-62 7.54e-16

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 70.49  E-value: 7.54e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772   3 LDRLQTFLKVVQYGSFQQVAAREYRSQRTVSKQMTQLENELKVTLFDRGQNRIQLTPQGR 62
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 20-199 2.52e-12

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 66.22  E-value: 2.52e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772  20 QVAAREYRSQRTVSKQMTQLENELKVTLFDR-GQNRIQLTPQGRLFWASAQDIVNNYMTALTELRQFNVPTDQILRVGYF 98
Cdd:PRK12683   21 EVANALYTSQSGVSKQIKDLEDELGVEIFIRrGKRLTGLTEPGKELLQIVERMLLDAENLRRLAEQFADRDSGHLTVATT 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772  99 SAFEQRLLLPALYDLKQQHSELQLVVRQGSNEHLAQQVADGSLDLALSINygrpAVTPESQLTAVPIYHNQMVIGVSRLN 178
Cdd:PRK12683  101 HTQARYALPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGIATE----ALDREPDLVSFPYYSWHHVVVVPKGH 176

                         170       180
                  ....*....|....*....|.
gi 2006036772 179 PLSRLSQLPPSALATLPILYY 199
Cdd:PRK12683  177 PLTGRENLTLEAIAEYPIITY 197
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 1-85 5.09e-07

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: 50.12  E-value: 5.09e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772   1 MDLDRLQTFLKVVQYGSFQQVAAREYRSQRTVSKQMTQLENELKVTLFDRGQNRIQLTPQGRLFWASAQDIVNNYMTALT 80
Cdd:NF041036    1 METRYLKTLVIVAEEGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRILDIEDSLMD 80


                  ....*
gi 2006036772  81 ELRQF 85
Cdd:NF041036   81 ELKSF 85
PBP2_TdcA cd08418
The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is ...
 98-296 3.72e-04

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


Pssm-ID: 176110 [Multi-domain]  Cd Length: 201  Bit Score: 40.80  E-value: 3.72e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772  98 FSAFEQRLLLPA-LYDLKQQHSELQLVVRQGSNEHLAQQVADGSLDLALSINYGRPavtPESQLTAVPIYHNQMVIGVSR 176
Cdd:cd08418     6 VSSLIAHTLMPAvINRFKEQFPDVQISIYEGQLSSLLPELRDGRLDFAIGTLPDEM---YLKELISEPLFESDFVVVARK 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772 177 LNPLSRLSQLP--PSALATLPILYYSPESstFLLESFLASAPFIQNyeqIRRVPSAEQMHLLVALNQALAFYPAGLVPTE 254
Cdd:cd08418    83 DHPLQGARSLEelLDASWVLPGTRMGYYN--NLLEALRRLGYNPRV---AVRTDSIVSIINLVEKADFLTILSRDMGRGP 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 2006036772 255 -HDEQVAYLPITDaaQQGYDIVALLKSNRSR--PLIAKLVQRLKA 296
Cdd:cd08418   158 lDSFRLITIPVEE--PLPSADYYLIYRKKSRltPLAEQLVELFRR 200
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-194 4.69e-37

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 132.68  E-value: 4.69e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772   1 MDLDRLQTFLKVVQYGSFQQVAAREYRSQRTVSKQMTQLENELKVTLFDRGQNRIQLTPQGRLFWASAQDIVNNYMTALT 80
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772  81 ELRQFNVPTDQILRVGYFSAFEQRLLLPALYDLKQQHSELQLVVRQGSNEHLAQQVADGSLDLALsinygRPAVTPESQL 160
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAI-----RLGPPPDPGL 155

                         170       180       190
                  ....*....|....*....|....*....|....
gi 2006036772 161 TAVPIYHNQMVIGVSRLNPLSRLSQLPPSALATL 194
Cdd:COG0583   156 VARPLGEERLVLVASPDHPLARRAPLVNSLEALL 189
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-172 1.17e-21

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: 92.29  E-value: 1.17e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772   1 MDLDRLQTFLKVVQYGSFQQVAAREYRSQRTVSKQMTQLENELKVTLFDRGQNRIQLTPQGRLFWASAQDIVNNYMTALT 80
Cdd:NF040786    1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772  81 ELRQFNVPTDQILRVGYFSafeqrllLPALYDL-------KQQHSELQLVVRQGSNEHLAQQVADGSLDLALSinyGrpA 153
Cdd:NF040786   81 EFDRYGKESKGVLRIGAST-------IPGQYLLpellkkfKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFT---G--T 148

                         170
                  ....*....|....*....
gi 2006036772 154 VTPESQLTAVPIYHNQMVI 172
Cdd:NF040786  149 KLEKKRLVYTPFYKDRLVL 167
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 93-299 3.78e-21

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: 88.89  E-value: 3.78e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772  93 LRVGYFSAFEQRLLLPALYDLKQQHSELQLVVRQGSNEHLAQQVADGSLDLALSinYGRPavtPESQLTAVPIYHNQMVI 172
Cdd:pfam03466   4 LRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIR--RGPP---DDPGLEARPLGEEPLVL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772 173 GVSRLNPLSRLSQLPPSALATLPILYYSPESSTF-LLESFLASAPFiqNYEQIRRVPSAEQMHLLVALNQALAFYPAGLV 251
Cdd:pfam03466  79 VAPPDHPLARGEPVSLEDLADEPLILLPPGSGLRdLLDRALRAAGL--RPRVVLEVNSLEALLQLVAAGLGIALLPRSAV 156

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 2006036772 252 PTEHDE-QVAYLPITDAAQQgYDIVALLKSNRSR-PLIAKLVQRLKANAK 299
Cdd:pfam03466 157 ARELADgRLVALPLPEPPLP-RELYLVWRKGRPLsPAVRAFIEFLREALA 205
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 93-289 3.80e-20

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: 86.11  E-value: 3.80e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772  93 LRVGYFSAFEQRLLLPALYDLKQQHSELQLVVRQGSNEHLAQQVADGSLDLALSInygrpAVTPESQLTAVPIYHNQMVI 172
Cdd:cd05466     2 LRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVA-----LPVDDPGLESEPLFEEPLVL 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772 173 GVSRLNPLSRLSQLPPSALATLPILYYSPESST-FLLESFLASAPFIQNYeqIRRVPSAEQMHLLVALNQALAFYPAGLV 251
Cdd:cd05466    77 VVPPDHPLAKRKSVTLADLADEPLILFERGSGLrRLLDRAFAEAGFTPNI--ALEVDSLEAIKALVAAGLGIALLPESAV 154

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 2006036772 252 PTEHDEQVAYLPITDAAQQgYDIVALLKSNRSRPLIAK 289
Cdd:cd05466   155 EELADGGLVVLPLEDPPLS-RTIGLVWRKGRYLSPAAR 191
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 93-294 3.31e-16

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: 75.24  E-value: 3.31e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772  93 LRVGYFSAFEQRLLLPALYDLKQQHSELQLVVRQGSNEHLAQQVADGSLDLALsinyGRPAVTPESqLTAVPIYHNQMVI 172
Cdd:cd08414     2 LRIGFVGSALYGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGF----VRPPPDPPG-LASRPLLREPLVV 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772 173 GVSRLNPLSRLSQLPPSALATLPILYYSPESSTFL---LESFLASAPFiqnyeQIRRVPSAEQMHL---LVALNQALAFY 246
Cdd:cd08414    77 ALPADHPLAARESVSLADLADEPFVLFPREPGPGLydqILALCRRAGF-----TPRIVQEASDLQTllaLVAAGLGVALV 151

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 2006036772 247 PAGLVPTEHDEqVAYLPITDAAQQgYDIVALLKSNRSRPLIAKLVQRL 294
Cdd:cd08414   152 PASVARLQRPG-VVYRPLADPPPR-SELALAWRRDNASPALRAFLELA 197
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-62 7.54e-16

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 70.49  E-value: 7.54e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772   3 LDRLQTFLKVVQYGSFQQVAAREYRSQRTVSKQMTQLENELKVTLFDRGQNRIQLTPQGR 62
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 20-199 2.52e-12

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 66.22  E-value: 2.52e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772  20 QVAAREYRSQRTVSKQMTQLENELKVTLFDR-GQNRIQLTPQGRLFWASAQDIVNNYMTALTELRQFNVPTDQILRVGYF 98
Cdd:PRK12683   21 EVANALYTSQSGVSKQIKDLEDELGVEIFIRrGKRLTGLTEPGKELLQIVERMLLDAENLRRLAEQFADRDSGHLTVATT 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772  99 SAFEQRLLLPALYDLKQQHSELQLVVRQGSNEHLAQQVADGSLDLALSINygrpAVTPESQLTAVPIYHNQMVIGVSRLN 178
Cdd:PRK12683  101 HTQARYALPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGIATE----ALDREPDLVSFPYYSWHHVVVVPKGH 176

                         170       180
                  ....*....|....*....|.
gi 2006036772 179 PLSRLSQLPPSALATLPILYY 199
Cdd:PRK12683  177 PLTGRENLTLEAIAEYPIITY 197
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
1-199 3.04e-12

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 65.77  E-value: 3.04e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772   1 MDLDRLQTFLKVVQYG-SFQQVAAREYRSQRTVSKQMTQLENELKVTLFDRGQNRIQ-LTPQGRLFWASAQDIvnnymta 78
Cdd:PRK12684    1 MNLHQLRFVREAVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRgLTEPGRIILASVERI------- 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772  79 lteLRQfnvpTDQILRVGY-FSAFEQ------------RLLLP-ALYDLKQQHSELQLVVRQGSNEHLAQQVADGSLDLA 144
Cdd:PRK12684   74 ---LQE----VENLKRVGKeFAAQDQgnltiatthtqaRYALPaAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLA 146

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2006036772 145 LSINygrpAVTPESQLTAVPIYH-NQMVIgVSRLNPLSRLSQLPPSALATLPILYY 199
Cdd:PRK12684  147 IATE----AIADYKELVSLPCYQwNHCVV-VPPDHPLLERKPLTLEDLAQYPLITY 197
rbcR CHL00180
LysR transcriptional regulator; Provisional
 3-145 3.96e-12

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 65.43  E-value: 3.96e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772   3 LDRLQTFLKVVQYGSFQQVAAREYRSQRTVSKQMTQLENELKVTLFDRGQNRIQLTPQGRLFWASAQDIV---NNYMTAL 79
Cdd:CHL00180    7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILalcEETCRAL 86

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2006036772  80 TELRQFNVPTdqiLRVGYfSAFEQRLLLPALYDL-KQQHSELQLVVRQGSNEHLAQQVADGSLDLAL 145
Cdd:CHL00180   87 EDLKNLQRGT---LIIGA-SQTTGTYLMPRLIGLfRQRYPQINVQLQVHSTRRIAWNVANGQIDIAI 149
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
1-143 2.15e-11

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 63.11  E-value: 2.15e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772   1 MDLDRLQTFLKVVQYGSFQQVAAREYRSQRTVSKQMTQLENELKVTLFDRGQNRIQLTPQGRLFWASAQDIVNNYMTALT 80
Cdd:PRK03601    1 MDTELLKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYAETLMNTWQAAKK 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2006036772  81 EL---RQFNVptdqiLRVGYFSAFEQRLLLPALYDLKQQHSELQLVVRQGSNEHLAQQVADGSLDL 143
Cdd:PRK03601   81 EVahtSQHNE-----LSIGASASLWECMLTPWLGRLYQNQEALQFEARIAQRQSLVKQLHERQLDL 141
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 1-201 2.48e-11

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 63.09  E-value: 2.48e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772   1 MDLDRLQTFLKVVQYG-SFQQVAAREYRSQRTVSKQMTQLENELKVTLFDR-GQNRIQLTPQGRLFWASAQDIVNNYMTA 78
Cdd:PRK12682    1 MNLQQLRFVREAVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRhGKRLKGLTEPGKAVLDVIERILREVGNI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772  79 LTELRQFNVPTDQILRVgYFSAFEQRLLLP-ALYDLKQQHSELQLVVRQGSNEHLAQQVADGSLDLALSINygrpAVTPE 157
Cdd:PRK12682   81 KRIGDDFSNQDSGTLTI-ATTHTQARYVLPrVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGIATE----SLADD 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 2006036772 158 SQLTAVPIYHNQMVIGVSRLNPLSRLSQLPPSALATLPILYYSP 201
Cdd:PRK12682  156 PDLATLPCYDWQHAVIVPPDHPLAQEERITLEDLAEYPLITYHP 199
PRK09801 PRK09801
LysR family transcriptional regulator;
6-148 9.86e-11

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 61.59  E-value: 9.86e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772   6 LQTFLKVVQYGSFQQVAAREYRSQRTVSKQMTQLENELKVTLFDRGQNRIQLTPQGRLFWASAQDIVNNYMTALTELRQF 85
Cdd:PRK09801   11 LQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVTQI 90

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2006036772  86 NVPTDQILRVGYFSAFEQRLLLPALYDLKQQHSELQLVVrqgsnEHLAQQV--ADGSLDLALSIN 148
Cdd:PRK09801   91 KTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHF-----ELFDRQIdlVQDNIDLDIRIN 150
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 1-205 1.64e-10

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 60.74  E-value: 1.64e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772   1 MDLDRLQTFLKVVQYGSFQQVAAREYRSQRTVSKQMTQLENELKVTLFDRGQNRIQLTPQGRLFWASAQdivnnymTALT 80
Cdd:PRK11242    1 MLLRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYAR-------RALQ 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772  81 EL----RQFNVPTD---QILRVGYFSAFEQRLLLPALYDLKQQHSELQLVVRQGSNEHLAQQVADGSLDLALSINygrPA 153
Cdd:PRK11242   74 DLeagrRAIHDVADlsrGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMSQERIEALLADDELDVGIAFA---PV 150

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2006036772 154 VTPEsqLTAVPIYHNQMVIGVSRLNPL-SRLSQLPPSALATLPILYYSPESST 205
Cdd:PRK11242  151 HSPE--IEAQPLFTETLALVVGRHHPLaARRKALTLDELADEPLVLLSAEFAT 201
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
1-204 5.41e-10

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 59.26  E-value: 5.41e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772   1 MDLDRLQTFLKVVQYGSFQQVAAREYRSQRTVSKQMTQLENELKVTLFDRGQNRIQLTPQGRLFWASAQDIVNNYMTAlt 80
Cdd:PRK15421    2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQA-- 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772  81 eLRQFNVPTDQILRVGYFSAFEQRLLLPALYDLKQQHSELQLVVRQGSNEHLAQQVADGSLDLALSINygrpaVTPESQL 160
Cdd:PRK15421   80 -LQACNEPQQTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSD-----ILPRSGL 153

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 2006036772 161 TAVPIYHNQMVIGVSRLNPLSRLSQLPPSALATLPILYYSPESS 204
Cdd:PRK15421  154 HYSPMFDYEVRLVLAPDHPLAAKTRITPEDLASETLLIYPVQRS 197
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 1-294 7.85e-10

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 58.63  E-value: 7.85e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772   1 MDLDRLQTFLKVVQYGSFQQVAAREYRSQRTVSKQMTQLENELKVTLFDRGQNRIQLTPQGRLFWASAQDIVNNYMTALT 80
Cdd:PRK09906    1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772  81 ELRQFnVPTDQILRVGYFSAFEQRLLLPALYDLKQQHSELQLVVRQGSNEHLAQQVADGSLDLALSinygRPAVTPESqL 160
Cdd:PRK09906   81 RARKI-VQEDRQLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFM----RHPVYSDE-I 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772 161 TAVPIYHNQMVIGVSRLNPLSRLSQLPPSALATLPILYYSPESSTFLLESFLASapFIQNYEQIRRVPSAEQMHL---LV 237
Cdd:PRK09906  155 DYLELLDEPLVVVLPVDHPLAHEKEITAAQLDGVNFISTDPAYSGSLAPIIKAW--FAQHNSQPNIVQVATNILVtmnLV 232

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2006036772 238 ALNQALAFYPaGLVPTEHDEQVAYLPItDAAQQGYDIVALLKSNRSRPLIAKLVQRL 294
Cdd:PRK09906  233 GMGLGCTIIP-GYMNNFNTGQVVFRPL-AGNVPSIALLMAWKKGEMKPALRDFIAIV 287
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
3-153 8.97e-10

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 58.47  E-value: 8.97e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772   3 LDRLQTFLKVVQYGSFQQVAAREYRSQRTVSKQMTQLENELKVTLFDRGQNRIQLTPQG-RLFWAsaqdiVNNYMTALTE 81
Cdd:PRK10086   16 LSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGkRVFWA-----LKSSLDTLNQ 90

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2006036772  82 --LRQFNVPTDQILRVGYFSAFEQRLLLPALYDLKQQHSELQLVVRQGsNEHLAQQVAdgSLDLALSINYGRPA 153
Cdd:PRK10086   91 eiLDIKNQELSGTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTILTG-NENVNFQRA--GIDLAIYFDDAPSA 161
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
3-120 2.93e-09

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 57.08  E-value: 2.93e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772   3 LDRLQTFLKVVQYGSFQQVAAREYRSQRTVSKQMTQLENELKVTLFDRGQNRIQLTPQGRLFWASAQDIVNNYMTALTEL 82
Cdd:PRK10632    4 LKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQL 83

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 2006036772  83 RQFNVPTDQILRVGYFSAFEQRLLLPALYDLKQQHSEL 120
Cdd:PRK10632   84 YAFNNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGL 121
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 106-197 9.99e-09

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: 54.42  E-value: 9.99e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772 106 LLPA-LYDLKQQHSELQLVVRQGSNEHLAQQVADGSLDLALsInyGRPAVTPEsqLTAVPIYHNQMVIGVSRLNPLSRLS 184
Cdd:cd08420    14 LLPRlLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGL-V--EGPVDHPD--LIVEPFAEDELVLVVPPDHPLAGRK 88

                          90
                  ....*....|...
gi 2006036772 185 QLPPSALATLPIL 197
Cdd:cd08420    89 EVTAEELAAEPWI 101
PRK12680 PRK12680
LysR family transcriptional regulator;
22-205 2.60e-08

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 54.24  E-value: 2.60e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772  22 AAREYRSQRTVSKQMTQLENELKVTLFDR-GQNRIQLTPQGRLFWASAQDI---VNNYMTALTELR-----QFNVPTDQI 92
Cdd:PRK12680   23 AARVHATQPGLSKQLKQLEDELGFLLFVRkGRSLESVTPAGVEVIERARAVlseANNIRTYAANQRresqgQLTLTTTHT 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772  93 lrvgyfsafEQRLLL-PALYDLKQQHSELQLVVRQGSNEHLAQQVADGSLDLALSINYGRpavTPESQLtAVPIYHNQMV 171
Cdd:PRK12680  103 ---------QARFVLpPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVSTAGG---EPSAGI-AVPLYRWRRL 169

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 2006036772 172 IGVSRLNPLSRLSQLPP-SALATLPILYYspESST 205
Cdd:PRK12680  170 VVVPRGHALDTPRRAPDmAALAEHPLISY--ESST 202
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-267 3.25e-08

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


Pssm-ID: 176127 [Multi-domain]  Cd Length: 194  Bit Score: 52.60  E-value: 3.25e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772  93 LRVGYFSAFEQRLLLPALYDLKQQHSELQLVVRQGSNEHLAQQVADGSLDLALsinYGRPAVTPEsQLTAVPIYHNQMVI 172
Cdd:cd08436     2 LAIGTITSLAAVDLPELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAF---VGLPERRPP-GLASRELAREPLVA 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772 173 GVSRLNPLSRLSQLPPSALATLPILYYSPESST-FLLESFLASApfiqnyeQIRR-----VPSAEQMHLLVALNQALAFY 246
Cdd:cd08436    78 VVAPDHPLAGRRRVALADLADEPFVDFPPGTGArRQVDRAFAAA-------GVRRrvafeVSDVDLLLDLVARGLGVALL 150

                         170       180
                  ....*....|....*....|.
gi 2006036772 247 PAGLVPteHDEQVAYLPITDA 267
Cdd:cd08436   151 PASVAA--RLPGLAALPLEPA 169
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 106-197 1.36e-07

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: 50.99  E-value: 1.36e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772 106 LLPALY-DLKQQHSELQLVVRQGSNEHLAQQVADGSLDLALSinygrPAVTPESQLTAVPIYHNQMVIGVSRLNPLSRLS 184
Cdd:cd08411    15 LLPRLLpALRQAYPKLRLYLREDQTERLLEKLRSGELDAALL-----ALPVDEPGLEEEPLFDEPFLLAVPKDHPLAKRK 89

                          90
                  ....*....|...
gi 2006036772 185 QLPPSALATLPIL 197
Cdd:cd08411    90 SVTPEDLAGERLL 102
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 1-165 1.39e-07

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 51.99  E-value: 1.39e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772   1 MDLDRLQTFLKVVQYGSFQQVAAREYRSQRTVSKQMTQLENELKVTLFDRGQNRIQLTPQGRLFWASAQDIvnnymtalt 80
Cdd:PRK11233    1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAI--------- 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772  81 eLRQFNVPTDQILRVGYFSAFE-----------QRLLLPALYDLKQQHSELQLVVRQGSNEHLAQQVADGSLDLAlsINY 149
Cdd:PRK11233   72 -LRQCEQAQLAVHNVGQALSGQvsiglapgtaaSSLTMPLLQAVRAEFPGIVLYLHENSGATLNEKLMNGQLDMA--VIY 148

                         170
                  ....*....|....*.
gi 2006036772 150 GRpavTPESQLTAVPI 165
Cdd:PRK11233  149 EH---SPVAGLSSQPL 161
PRK09986 PRK09986
LysR family transcriptional regulator;
1-206 1.65e-07

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 51.65  E-value: 1.65e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772   1 MDLDRLQTFLKVVQYGSFQQVAAREYRSQRTVSKQMTQLENELKVTLFDRGQNRIQLTPQGRLFWASAQDIVNNYMTALT 80
Cdd:PRK09986    7 IDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLA 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772  81 ELRQFNVPTDQILRVGYFSAFEQRLLLPALYDLKQQHSELQLVVRQGSNehlAQQVAdGSLDLALSINYGRPAVT-PESQ 159
Cdd:PRK09986   87 RVEQIGRGEAGRIEIGIVGTALWGRLRPAMRHFLKENPNVEWLLRELSP---SMQMA-ALERRELDAGIWRMADLePNPG 162

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 2006036772 160 LTAVPIYHNQMVIGVSRLNPLSRLSQLPPSALATLPILYYSPESSTF 206
Cdd:PRK09986  163 FTSRRLHESAFAVAVPEEHPLASRSSVPLKALRNEYFITLPFVHSDW 209
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 104-268 1.77e-07

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: 50.63  E-value: 1.77e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772 104 RLLLPALYDLKQQHS--ELQLVVRqGSNEhLAQQVADGSLDLALSINygrPAVtpESQLTAVPIYHNQMVIGVSRLNPLS 181
Cdd:cd08438    13 LLFAPLLAAFRQRYPniELELVEY-GGKK-VEQAVLNGELDVGITVL---PVD--EEEFDSQPLCNEPLVAVLPRGHPLA 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772 182 RLSQLPPSALATLP-ILYyspeSSTFLLESFLasapfIQNYEQIRRVP-----SAeQMHLLVAL---NQALAFYPAGLVP 252
Cdd:cd08438    86 GRKTVSLADLADEPfILF----NEDFALHDRI-----IDACQQAGFTPniaarSS-QWDFIAELvaaGLGVALLPRSIAQ 155

                         170
                  ....*....|....*.
gi 2006036772 253 TEHDEQVAYLPITDAA 268
Cdd:cd08438   156 RLDNAGVKVIPLTDPD 171
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-294 2.17e-07

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


Pssm-ID: 176115 [Multi-domain]  Cd Length: 200  Bit Score: 50.29  E-value: 2.17e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772  93 LRVGYFSAFEQRLLLPALYDLKQQHSELQLVVRQGSNEHLAQQVADGSLDLALSINYGRPAVTPESQLTAVPIYHNQMVI 172
Cdd:cd08423     2 LRVGAFPTAAAALLPPALAALRARHPGLEVRLREAEPPESLDALRAGELDLAVVFDYPVTPPPDDPGLTRVPLLDDPLDL 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772 173 GVSRLNPLSRLSQLPPSALATLP-ILyySPESSTF--LLESFLASAPFIQNYE-QIRRVPSAEQMhllVALNQALAFYPA 248
Cdd:cd08423    82 VLPADHPLAGREEVALADLADEPwIA--GCPGSPChrWLVRACRAAGFTPRIAhEADDYATVLAL---VAAGLGVALVPR 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 2006036772 249 gLVPTEHDEQVAYLPITDAAQQgYDIVALLKSNRSRPLIAKLVQRL 294
Cdd:cd08423   157 -LALGARPPGVVVRPLRPPPTR-RIYAAVRAGAARRPAVAAALEAL 200
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
1-86 3.72e-07

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 50.58  E-value: 3.72e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772   1 MDLDRLQTFLKVVQYGSFQQVAAREYRSQRTVSKQMTQLENELKVTLFDRGQNRIQLTPQGRLFWASAQDIVNNYMTALT 80
Cdd:PRK10094    2 FDPETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPS 81


                  ....*.
gi 2006036772  81 ELRQFN 86
Cdd:PRK10094   82 ELQQVN 87
cysB PRK12681
HTH-type transcriptional regulator CysB;
26-199 4.96e-07

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 50.28  E-value: 4.96e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772  26 YRSQRTVSKQMTQLENELKVTLFDR-GQNRIQLTPQGRLFWASAQDIVNNYMTALTELRQFNVPTDQILRVGYFSAFEQR 104
Cdd:PRK12681   27 YTSQPGISKQVRMLEDELGIQIFARsGKHLTQVTPAGEEIIRIAREILSKVESIKSVAGEHTWPDKGSLYIATTHTQARY 106

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772 105 LLLPALYDLKQQHSELQLVVRQGSNEHLAQQVADGSLDLalsinygrpAVTPESQ-----LTAVPIYH-NQMVIgVSRLN 178
Cdd:PRK12681  107 ALPPVIKGFIERYPRVSLHMHQGSPTQIAEAAAKGNADF---------AIATEALhlyddLIMLPCYHwNRSVV-VPPDH 176

                         170       180
                  ....*....|....*....|.
gi 2006036772 179 PLSRLSQLPPSALATLPILYY 199
Cdd:PRK12681  177 PLAKKKKLTIEELAQYPLVTY 197
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 1-85 5.09e-07

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: 50.12  E-value: 5.09e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772   1 MDLDRLQTFLKVVQYGSFQQVAAREYRSQRTVSKQMTQLENELKVTLFDRGQNRIQLTPQGRLFWASAQDIVNNYMTALT 80
Cdd:NF041036    1 METRYLKTLVIVAEEGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRILDIEDSLMD 80


                  ....*
gi 2006036772  81 ELRQF 85
Cdd:NF041036   81 ELKSF 85
PBP2_CysB_like cd08413
The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains ...
 104-202 7.77e-07

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


Pssm-ID: 176105 [Multi-domain]  Cd Length: 198  Bit Score: 48.77  E-value: 7.77e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772 104 RLLLP-ALYDLKQQHSELQLVVRQGSNEHLAQQVADGSLDLALSINygrpAVTPESQLTAVPIYHNQMVIGVSRLNPLSR 182
Cdd:cd08413    12 RYVLPpVIAAFRKRYPKVKLSLHQGTPSQIAEMVLKGEADIAIATE----ALDDHPDLVTLPCYRWNHCVIVPPGHPLAD 87

                          90       100
                  ....*....|....*....|
gi 2006036772 183 LSQLPPSALATLPILYYSPE 202
Cdd:cd08413    88 LGPLTLEDLAQYPLITYDFG 107
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 3-182 1.42e-06

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 48.92  E-value: 1.42e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772   3 LDRLQTFLKVVQYGSFQQVAAREYRSQRTVSKQMTQLENELKVTLFDRGQNRIQLTPQGRLFWASAQDIvnnyMTALTEL 82
Cdd:PRK10837    5 LRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALAL----LEQAVEI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772  83 RQFNVPTDQILRVGYFSAFEQRLLLPALYDLKQQHSELQLVVRQGSNEHLAQQVADGSLDLALsinYGRPAVTPEsqLTA 162
Cdd:PRK10837   81 EQLFREDNGALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNSQDVINAVLDFRVDIGL---IEGPCHSPE--LIS 155

                         170       180
                  ....*....|....*....|
gi 2006036772 163 VPIYHNQMVIGVSRLNPLSR 182
Cdd:PRK10837  156 EPWLEDELVVFAAPDSPLAR 175
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 17-151 3.69e-06

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 47.53  E-value: 3.69e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772  17 SFQQVAAREYRSQRTVSKQMTQLENELKVTLFDRGQNRIQLTPQGRLFWASAQDIVNNYMTALTELRQFNvpTDQILRVG 96
Cdd:PRK11139   22 SFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEATRKLRARS--AKGALTVS 99

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2006036772  97 YFSAFEQRLLLPALYDLKQQHSELQlvVR-QGSNEHLAQqvADGSLDLAlsINYGR 151
Cdd:PRK11139  100 LLPSFAIQWLVPRLSSFNEAHPDID--VRlKAVDRLEDF--LRDDVDVA--IRYGR 149
PBP2_LTTR_aromatics_like_1 cd08447
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-291 4.24e-06

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


Pssm-ID: 176138 [Multi-domain]  Cd Length: 198  Bit Score: 46.49  E-value: 4.24e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772  93 LRVGYFSAFEQRLLLPALYDLKQQHSELQLVVRQGSNEHLAQQVADGSLDLALsinyGRPAVTPESqLTAVPIYHNQMVI 172
Cdd:cd08447     2 LRIGFTAASAYSFLPRLLAAARAALPDVDLVLREMVTTDQIEALESGRIDLGL----LRPPFARPG-LETRPLVREPLVA 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772 173 GVSRLNPLSRLSQLPPSALATLPILYYSP-ESSTF--LLESFLASAPFIQNYEQirrvpSAEQMHLLVALNQA---LAFY 246
Cdd:cd08447    77 AVPAGHPLAGAERLTLEDLDGQPFIMYSPtEARYFhdLVVRLFASAGVQPRYVQ-----YLSQIHTMLALVRAglgVALV 151

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 2006036772 247 PA---GLVPtehdEQVAYLPITDAAQQGYDIVALLKSNRSRPLIAKLV 291
Cdd:cd08447   152 PAsasRLRF----EGVVFRPLDLPRDVPVELHLAWRRDNDNPALRALL 195
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 9-128 6.61e-06

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 46.91  E-value: 6.61e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772   9 FLKVVQYGSFQQVAAREYRSQRTVSKQMTQLENELKVTLFDRGQNRIQLTPQG-RLF------WASAQDIVNnymtALTE 81
Cdd:PRK11013   12 FHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGlRLFeevqrsYYGLDRIVS----AAES 87

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 2006036772  82 LRQFNvptDQILRVGYFSAFEQRLLLPALYDLKQQHSELQL-VVRQGS 128
Cdd:PRK11013   88 LREFR---QGQLSIACLPVFSQSLLPGLCQPFLARYPDVSLnIVPQES 132
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 12-144 6.88e-06

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 46.86  E-value: 6.88e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772  12 VVQYGSFQQVAAREYRSQRTVSKQMTQLENELKVTLFDRGQNRIQLTPQGRLFWASAQDIVNNymtaLTELR-------- 83
Cdd:PRK11074   13 VARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKK----MQETRrqcqqvan 88

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2006036772  84 ----QFNVPTDQILRvgyfsafEQRlLLPALYDLKQQHSELQLVVRQ----GSNEHLaqqvADGSLDLA 144
Cdd:PRK11074   89 gwrgQLSIAVDNIVR-------PDR-TRQLIVDFYRHFDDVELIIRQevfnGVWDAL----ADGRVDIA 145
cbl PRK12679
HTH-type transcriptional regulator Cbl;
20-199 6.91e-06

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 46.73  E-value: 6.91e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772  20 QVAAREYRSQRTVSKQMTQLENELKVTLF-DRGQNRIQLTPQGRLFWASAQDIVN--NYMTALTELrqFNVPTDQILRVG 96
Cdd:PRK12679   21 EVANMLFTSQSGVSRHIRELEDELGIEIFiRRGKRLLGMTEPGKALLVIAERILNeaSNVRRLADL--FTNDTSGVLTIA 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772  97 YFSAFEQRLLLPALYDLKQQHSELQLVVRQGSNEHLAQQVADGSLDLALSinygRPAVTPESQLTAVPIYHNQMVIGVSR 176
Cdd:PRK12679   99 TTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIA----SERLSNDPQLVAFPWFRWHHSLLVPH 174

                         170       180
                  ....*....|....*....|...
gi 2006036772 177 LNPLSRLSQLPPSALATLPILYY 199
Cdd:PRK12679  175 DHPLTQITPLTLESIAKWPLITY 197
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 106-203 7.24e-06

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: 45.60  E-value: 7.24e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772 106 LLPAL-YDLKQQHSELQLVVRQGSNEHLAQQVADGSLDLALSinygrPAVTPESQLTAVPIYHNQMVIGVSRLNPLSRLS 184
Cdd:cd08434    14 LVPDLiRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLALC-----SPVPDEPDIEWIPLFTEELVLVVPKDHPLAGRD 88

                          90
                  ....*....|....*....
gi 2006036772 185 QLPPSALATLPILYYSPES 203
Cdd:cd08434    89 SVDLAELADEPFVLLSPGF 107
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 1-146 7.34e-06

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 46.56  E-value: 7.34e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772   1 MDLDRLQTFLKVVQYGSFQQVAAREYRSQRTVSKQMTQLENELKVTLFDR-GQNRIqLTPQGRLFWASAQDIVNNYMTAL 79
Cdd:PRK15092   11 LDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARhGRNKL-LTEHGIQLLGYARKILRFNDEAC 89

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2006036772  80 TELRQFNVptDQILRVGYfSAFEQRLLLPALYD-LKQQHSELQLVVRQGSNEHLAQQVADGSLDLALS 146
Cdd:PRK15092   90 SSLMYSNL--QGVLTIGA-SDDTADTILPFLLNrVSSVYPKLALDVRVKRNAFMMEMLESQEVDLAVT 154
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
31-158 1.26e-05

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 45.58  E-value: 1.26e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772  31 TVSKQMTQLENELKVTLFDRGQNRIQLTPQGRLFWASAQDIVNNYMTALTELRQfnvPTDQI---LRVgYFSAFEQRLLL 107
Cdd:PRK11716    7 TLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQ---QGPSLsgeLSL-FCSVTAAYSHL 82

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2006036772 108 PALYD-LKQQHSELQLVVRQGSNEHLAQQVADGSLDLALSinyGRPAVTPES 158
Cdd:PRK11716   83 PPILDrFRAEHPLVEIKLTTGDAADAVEKVQSGEADLAIA---AKPETLPAS 131
PBP2_LTTR_like_2 cd08427
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-200 1.48e-05

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


Pssm-ID: 176118 [Multi-domain]  Cd Length: 195  Bit Score: 44.87  E-value: 1.48e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772  93 LRVGYFSAFEQRLLLPALYDLKQQHSELQLVVRQGSNEHLAQQVADGSLDLALSInygRPAVTPESQLTAVPIYHNQMVI 172
Cdd:cd08427     2 LRLGAIATVLTGLLPRALARLRRRHPDLEVHIVPGLSAELLARVDAGELDAAIVV---EPPFPLPKDLVWTPLVREPLVL 78

                          90       100
                  ....*....|....*....|....*...
gi 2006036772 173 GVSRLNPLSRLSQLppsaLATLPILYYS 200
Cdd:cd08427    79 IAPAELAGDDPREL----LATQPFIRYD 102
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
6-83 3.01e-05

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 44.66  E-value: 3.01e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2006036772   6 LQTFLKVVQYGSFQQVAAREYRSQRTVSKQMTQLENELKVTLFDRGQNRIQLTPQGRLFWASAQDIVNNYMTALTELR 83
Cdd:PRK10082   16 LYDFLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESNLAELR 93
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 93-215 5.13e-05

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: 43.42  E-value: 5.13e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772  93 LRVGYFSAFEQRLLLPALYDLKQQHSELQLVVRQGSNEHLAQQVADGSLDLALsinyGRpaVTPESQ---LTAVPIYHNQ 169
Cdd:cd08435     2 VRVGAVPAAAPVLLPPAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAI----GR--LADDEQppdLASEELADEP 75

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2006036772 170 MVIGVSRLNPLSRLSQLPPSALATLP-ILYYSPESSTFLLESFLASA 215
Cdd:cd08435    76 LVVVARPGHPLARRARLTLADLADYPwVLPPPGTPLRQRLEQLFAAA 122
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 92-205 6.20e-05

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: 42.93  E-value: 6.20e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772  92 ILRVGYFSAFEQRLLLPALYDLKQQHSELQLVVRQGSNEHLAQQVADGSLDLALSINygrPAVTPesQLTAVPIYHNQMV 171
Cdd:cd08415     1 TLRIAALPALALSLLPRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASL---PLDHP--GLESEPLASGRAV 75

                          90       100       110
                  ....*....|....*....|....*....|....
gi 2006036772 172 IGVSRLNPLSRLSQLPPSALATLPILYYSPESST 205
Cdd:cd08415    76 CVLPPGHPLARKDVVTPADLAGEPLISLGRGDPL 109
PRK10341 PRK10341
transcriptional regulator TdcA;
6-186 8.63e-05

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 43.31  E-value: 8.63e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772   6 LQTFLKVVQYGSFQQVAAREYRSQRTVSKQMTQLENELKVTLFDRGQNRIQLTPQGRLFWASAQDIVNNYMTALTELRQF 85
Cdd:PRK10341   12 LVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEINGM 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772  86 NVPTDQILRVGYFSAFEQRLLLPALYDLKQQHSELQLVVRQGSNEHLAQQVADGSLDLALSinygrpAVTPESQ---LTA 162
Cdd:PRK10341   92 SSEAVVDVSFGFPSLIGFTFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIG------TLSNEMKlqdLHV 165

                         170       180
                  ....*....|....*....|....
gi 2006036772 163 VPIYHNQMVIGVSRLNPLSRLSQL 186
Cdd:PRK10341  166 EPLFESEFVLVASKSRTCTGTTTL 189
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 104-266 8.73e-05

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: 42.51  E-value: 8.73e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772 104 RLLLPALYDLKQQHSELQLVVRQGSNEHLAQQVADGSLDLALSInygrpAVTPESQLTAVPIYHNQMVIGVSRLNPLSRL 183
Cdd:cd08440    13 TLLPPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGS-----EPEADPDLEFEPLLRDPFVLVCPKDHPLARR 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772 184 SQLPPSALATLPILYYSPESST-FLLESFLASAPfiqnyeqIRRVPS--AEQMHLLVALNQA---LAFYPAGLVPTEHDE 257
Cdd:cd08440    88 RSVTWAELAGYPLIALGRGSGVrALIDRALAAAG-------LTLRPAyeVSHMSTALGMVAAglgVAVLPALALPLADHP 160


                  ....*....
gi 2006036772 258 QVAYLPITD 266
Cdd:cd08440   161 GLVARPLTE 169
PBP2_XapR cd08449
The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved ...
 92-294 9.09e-05

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


Pssm-ID: 176140 [Multi-domain]  Cd Length: 197  Bit Score: 42.64  E-value: 9.09e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772  92 ILRVGYFSAFEQRLLLPALYDLKQQHSELQLVVRQGSNEHLAQQVADGSLDLALSINYGRPAVTPesqLTAVPIYHNQMV 171
Cdd:cd08449     1 HLNIGMVGSVLWGGLGPALRRFKRQYPNVTVRFHELSPEAQKAALLSKRIDLGFVRFADTLNDPP---LASELLWREPMV 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772 172 IGVSRLNPLSRLSQLPPSALATLPILYYSPESSTFllesflasAPFIQNYEQ--------IRRVPSAEQMHLLVALNQAL 243
Cdd:cd08449    78 VALPEEHPLAGRKSLTLADLRDEPFVFLRLANSRF--------ADFLINCCLqagftpqiTQEVVEPQTLMALVAAGFGV 149

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2006036772 244 AFYPAGlVPTEHDEQVAYLPITDAAQQgyDIVALLKSNRSRPLIAKLVQRL 294
Cdd:cd08449   150 ALVPES-YARLPWPGVRFIPLKQAISA--DLYAVYHPDSATPVIQAFLALL 197
PBP2_BudR cd08451
The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is ...
 93-268 1.05e-04

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: 42.55  E-value: 1.05e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772  93 LRVGYFS--AFeQRLLLPALYDLKQQHSELQLVVRQGSNEHLAQQVADGSLDLALsinyGRPAVTPESQLTAVPIYHNQM 170
Cdd:cd08451     2 LRVGFTSsaAF-HPLVPGLIRRFREAYPDVELTLEEANTAELLEALREGRLDAAF----VRPPVARSDGLVLELLLEEPM 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772 171 VIGVSRLNPLSRLSQLPPSALATLPILYYSPESSTFLLESFLAS---APFiqnyeQIRRVPSAEQMhlLVALNQALAFYP 247
Cdd:cd08451    77 LVALPAGHPLARERSIPLAALADEPFILFPRPVGPGLYDAIIAAcrrAGF-----TPRIGQEAPQM--ASAINLVAAGLG 149

                         170       180
                  ....*....|....*....|....*
gi 2006036772 248 AGLVPTE----HDEQVAYLPITDAA 268
Cdd:cd08451   150 VSIVPASmrqlQAPGVVYRPLAGAP 174
SBP_bac_11 pfam13531
Bacterial extracellular solute-binding protein; This family includes bacterial extracellular ...
 115-295 3.49e-04

Bacterial extracellular solute-binding protein; This family includes bacterial extracellular solute-binding proteins.


Pssm-ID: 463911 [Multi-domain]  Cd Length: 225  Bit Score: 41.10  E-value: 3.49e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772 115 QQHSELQLVVRQGSNEHLAQQVADG-SLDLALSINYGRPAVTPESQL----TAVPIYHNQMVIGVSRLNPlsrlsqLPPS 189
Cdd:pfam13531  20 EAETGVKVVVSYGGSGKLAKQIANGaPADVFISADSAWLDKLAAAGLvvpgSRVPLAYSPLVIAVPKGNP------KDIS 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772 190 ALATL--P---ILYYSPESST--FLLESFLASAPFIQNYEQ--IRRVPSAEQMHLLVALNQAlafyPAGLVP------TE 254
Cdd:pfam13531  94 GLADLlkPgvrLAVADPKTAPsgRAALELLEKAGLLKALEKkvVVLGENVRQALTAVASGEA----DAGIVYlsealfPE 169

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 2006036772 255 HDEQVAYLPITDAAQQGYDI-VALLKSNRSRPLIAKLVQRLK 295
Cdd:pfam13531 170 NGPGLEVVPLPEDLNLPLDYpAAVLKKAAHPEAARAFLDFLL 211
PBP2_TdcA cd08418
The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is ...
 98-296 3.72e-04

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


Pssm-ID: 176110 [Multi-domain]  Cd Length: 201  Bit Score: 40.80  E-value: 3.72e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772  98 FSAFEQRLLLPA-LYDLKQQHSELQLVVRQGSNEHLAQQVADGSLDLALSINYGRPavtPESQLTAVPIYHNQMVIGVSR 176
Cdd:cd08418     6 VSSLIAHTLMPAvINRFKEQFPDVQISIYEGQLSSLLPELRDGRLDFAIGTLPDEM---YLKELISEPLFESDFVVVARK 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772 177 LNPLSRLSQLP--PSALATLPILYYSPESstFLLESFLASAPFIQNyeqIRRVPSAEQMHLLVALNQALAFYPAGLVPTE 254
Cdd:cd08418    83 DHPLQGARSLEelLDASWVLPGTRMGYYN--NLLEALRRLGYNPRV---AVRTDSIVSIINLVEKADFLTILSRDMGRGP 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 2006036772 255 -HDEQVAYLPITDaaQQGYDIVALLKSNRSR--PLIAKLVQRLKA 296
Cdd:cd08418   158 lDSFRLITIPVEE--PLPSADYYLIYRKKSRltPLAEQLVELFRR 200
PBP2_MleR cd08437
The substrate binding domain of LysR-type transcriptional regulator MleR which required for ...
 105-294 4.48e-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: 40.39  E-value: 4.48e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772 105 LLLPALYDLKQQHSELQLVVRQGSNEHLAQQVADGSLDLALsinYGRPAVTPESQLTAVPIYHNQMVIGVSRLNPLSRLS 184
Cdd:cd08437    14 YFPKLAKDLIKTGLMIQIDTYEGGSAELLEQLLQGDLDIAL---LGSLTPLENSALHSKIIKTQHFMIIVSKDHPLAKAK 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772 185 QLppsALATLpilyySPESSTFLLESFLASAPFI----QNYEQIRRVPSAEQMHL---LVALNQALAFYPAGLVPTEHDe 257
Cdd:cd08437    91 KV---NFADL-----KKENFILLNEHFVHPKAFDslcqQANFQPNIVYRTNDIHIlksMVRENVGIGFLTDIAVKPDDH- 161

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 2006036772 258 qVAYLPITDAAQQGYDI-VALLKSNRSRPLIAKLVQRL 294
Cdd:cd08437   162 -LVAIPLLDNEQPTFYIsLAHRKDQLLTPAQKKLLDLL 198
PBP2_CysB cd08443
The C-terminal substrate domain of LysR-type transcriptional regulator CysB contains type 2 ...
 106-199 6.86e-04

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


Pssm-ID: 176134  Cd Length: 198  Bit Score: 39.85  E-value: 6.86e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772 106 LLPALYDLKQQHSELQLVVRQGSNEHLAQQVADGSLDLALSINygrpAVTPESQLTAVPIYHNQMVIGVSRLNPLSRLSQ 185
Cdd:cd08443    15 LPPVIKGFIERYPRVSLQMHQGSPTQIAEMVSKGLVDFAIATE----ALHDYDDLITLPCYHWNRCVVVKRDHPLADKQS 90

                          90
                  ....*....|....
gi 2006036772 186 LPPSALATLPILYY 199
Cdd:cd08443    91 ISIEELATYPIVTY 104
PBP2_DntR_like_3 cd08461
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 102-277 1.51e-03

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


Pssm-ID: 176150 [Multi-domain]  Cd Length: 198  Bit Score: 38.80  E-value: 1.51e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772 102 EQRLLLPALYDLKQQHSELQLVVRQGSNEHLAQQVADGSLDLALSInygrPAVTPESqLTAVPIYHNQMVIGVSRLNPLS 181
Cdd:cd08461    11 QKAILPPLLAALRQEAPGVRVAIRDLESDNLEAQLERGEVDLALTT----PEYAPDG-LRSRPLFEERYVCVTRRGHPLL 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772 182 R----LSQlppsaLATLPILYYSPESSTFllesflaSAPFIQNYEQI---RRV----PSAEQMHLLVALNQALAFYPAGL 250
Cdd:cd08461    86 QgplsLDQ-----FCALDHIVVSPSGGGF-------AGSTDEALAALgltRNVvlsvPSFLVVPEILAATDMVAFVPSRL 153

                         170       180
                  ....*....|....*....|....*..
gi 2006036772 251 VPteHDEQVAYLPItDAAQQGYDIVAL 277
Cdd:cd08461   154 VP--NLEGLQEVEL-PLEPPGFDVVMA 177
PBP2_ToxR cd08465
The C-terminal substrate binding domain of LysR-type transcriptional regulator ToxR regulates ...
 104-145 1.96e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulator ToxR regulates the expression of the toxoflavin biosynthesis genes; contains the type 2 periplasmic bindinig fold; In soil bacterium Burkholderia glumae, ToxR regulates the toxABCDE and toxFGHI operons in the presence of toxoflavin as a coinducer. Additionally, the expression of both operons requires a transcriptional activator, ToxJ, whose expression is regulated by the TofI or TofR quorum-sensing system. The biosynthesis of toxoflavin is suggested to be synthesized in a pathway common to the synthesis of riboflavin. 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: 176154  Cd Length: 200  Bit Score: 38.44  E-value: 1.96e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 2006036772 104 RLLLPALY-DLKQQHSELQLVVRQGSNEHLAQQVADGSLDLAL 145
Cdd:cd08465    12 RLVLPALMrQLRAEAPGIDLAVSQASREAMLAQVADGEIDLAL 54
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
2-62 2.32e-03

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 38.80  E-value: 2.32e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2006036772   2 DLDRLQTFLKVVQYGSFQQVAAREYRSQRTVSKQMTQLENELKVTLFDRGQNrIQLTPQGR 62
Cdd:PRK13348    3 DYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRGRP-CRPTPAGQ 62
PBP2_Cbl cd08444
The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is ...
 114-199 4.11e-03

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: 37.48  E-value: 4.11e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006036772 114 KQQHSELQLVVRQGSNEHLAQQVADGSLDLALSINygrpAVTPESQLTAVPIYHNQMVIGVSRLNPLSRLSQLPPSALAT 193
Cdd:cd08444    23 KEQFPNVHLVLHQGSPEEIASMLANGQADIGIATE----ALENHPELVSFPYYDWHHHIIVPVGHPLESITPLTIETIAK 98


                  ....*.
gi 2006036772 194 LPILYY 199
Cdd:cd08444    99 WPIITY 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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