NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|345535007|gb|AEO04448|]
View 

transcriptional regulator [Listeria monocytogenes J0161]

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-287 2.07e-55

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 180.06  E-value: 2.07e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007   1 MEFRTIKTFYTVVNTGSFQRAAEVLNYSQPTISMRIKQLEQDLDVQLFER-GKTLKLTHAGRLFYERAGQLIAQYEVLDH 79
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERtGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007  80 TIFDLKNGNAGLIKVGISEPSASLILPKILKAFLADFPKLMVNVSVDDANTCSQKLIDGEIDFAICGEPELILENFYFPF 159
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007 160 FHDTLDLIVSESHPLASRTSVelrdlrdecfiftpancpiriqieqhlkraigsdykkmeLTSSMSHKYFVRENVGVSIF 239
Cdd:COG0583  161 GEERLVLVASPDHPLARRAPL---------------------------------------VNSLEALLAAVAAGLGIALL 201

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|
gi 345535007 240 -TSTAHSELLDGTVRIL-IENLPISPPIGLLTnQKEKDFDSTTKELIDRI 287
Cdd:COG0583  202 pRFLAADELAAGRLVALpLPDPPPPRPLYLVW-RRRRHLSPAVRAFLDFL 250
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-287 2.07e-55

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 180.06  E-value: 2.07e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007   1 MEFRTIKTFYTVVNTGSFQRAAEVLNYSQPTISMRIKQLEQDLDVQLFER-GKTLKLTHAGRLFYERAGQLIAQYEVLDH 79
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERtGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007  80 TIFDLKNGNAGLIKVGISEPSASLILPKILKAFLADFPKLMVNVSVDDANTCSQKLIDGEIDFAICGEPELILENFYFPF 159
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007 160 FHDTLDLIVSESHPLASRTSVelrdlrdecfiftpancpiriqieqhlkraigsdykkmeLTSSMSHKYFVRENVGVSIF 239
Cdd:COG0583  161 GEERLVLVASPDHPLARRAPL---------------------------------------VNSLEALLAAVAAGLGIALL 201

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|
gi 345535007 240 -TSTAHSELLDGTVRIL-IENLPISPPIGLLTnQKEKDFDSTTKELIDRI 287
Cdd:COG0583  202 pRFLAADELAAGRLVALpLPDPPPPRPLYLVW-RRRRHLSPAVRAFLDFL 250
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-295 6.34e-44

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: 151.62  E-value: 6.34e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007   1 MEFRTIKTFYTVVNTGSFQRAAEVLNYSQPTISMRIKQLEQDLDVQLFER-GKTLKLTHAGRLFYERAGQLIAQYEVLDH 79
Cdd:NF040786   1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRnTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007  80 TIFDLKNGNAGLIKVGISEPSASLILPKILKAFLADFPKLMVNVSVDDANTCSQKLIDGEIDFAICGEPeliLEN---FY 156
Cdd:NF040786  81 EFDRYGKESKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTK---LEKkrlVY 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007 157 FPFFHDTLDLIVSESHPLASRTSVE--LRDLRDECFIFTPANCPIRIQIEQHLKRAiGSDYKKMELTSSMSH----KYFV 230
Cdd:NF040786 158 TPFYKDRLVLITPNGTEKYRMLKEEisISELQKEPFIMREEGSGTRKEAEKALKSL-GISLEDLNVVASLGSteaiKQSV 236

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 345535007 231 RENVGVSIFTS-TAHSELLDGTVRIL-IENLPISPPIGLLTNQKEKdfdstTKELIDRIIYYFDDKK 295
Cdd:NF040786 237 EAGLGISVISElAAEKEVERGRVLIFpIPGLPKNRDFYLVYNKNRQ-----LSPTAEAFLQFVKERY 298
rbcR CHL00180
LysR transcriptional regulator; Provisional
 4-283 4.56e-40

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 141.70  E-value: 4.56e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007   4 RTIKTFYTVVNTGSFQRAAEVLNYSQPTISMRIKQLEQDLDVQLFERGK-TLKLTHAGRLFYERAGQLIAQYEVLDHTIF 82
Cdd:CHL00180   8 DQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKnKASLTEAGELLLRYGNRILALCEETCRALE 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007  83 DLKNGNAGLIKVGISEPSASLILPKILKAFLADFPKLMVNVSVDDANTCSQKLIDGEIDFAICG---EPEL--ILEnfYF 157
Cdd:CHL00180  88 DLKNLQRGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVGgevPTELkkILE--IT 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007 158 PFFHDTLDLIVSESHPLASRTSVELRDLRDECFIFTPANCPIRIQIEQHLKR-AIGSDYKK--MELTSSMSHKYFVRENV 234
Cdd:CHL00180 166 PYVEDELALIIPKSHPFAKLKKIQKEDLYRLNFITLDSNSTIRKVIDNILIQnGIDSKRFKieMELNSIEAIKNAVQSGL 245

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....
gi 345535007 235 GVSIFTSTA-HSELLDGTVRIL-IENLPISPPIGLLTN---QKEKDFDSTTKEL 283
Cdd:CHL00180 246 GAAFVSVSAiEKELELGLLHWIkIENITIKRMLSIITNpnrYKSKASETFYNEI 299
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 92-285 7.76e-35

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: 125.02  E-value: 7.76e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007  92 IKVGISEPSASLILPKILKAFLADFPKLMVNVSVDDANTCSQKLIDGEIDFAICGEPELILENFYFPFFHDTLDLIVSES 171
Cdd:cd05466    2 LRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPPD 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007 172 HPLASRTSVELRDLRDECFIFTPANCPIRIQIEQHLKRAIGSDYKKMELTSSMSHKYFVRENVGVSIFTSTAHSELLDGT 251
Cdd:cd05466   82 HPLAKRKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEELADGG 161

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 345535007 252 VRIL-IENLPISPPIGLLTNqKEKDFDSTTKELID 285
Cdd:cd05466  162 LVVLpLEDPPLSRTIGLVWR-KGRYLSPAARAFLE 195
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 89-287 5.33e-33

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: 120.47  E-value: 5.33e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007   89 AGLIKVGISEPSASLILPKILKAFLADFPKLMVNVSVDDANTCSQKLIDGEIDFAICGEPELILENFYFPFFHDTLDLIV 168
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007  169 SESHPLASRTSVELRDLRDECFIFTPANCPIRIQIEQHLKRAIGSDYKKMELTSSMSHKYFVRENVGVSIF-TSTAHSEL 247
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLpRSAVAREL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 345535007  248 LDGTVRIL-IENLPISPPIGLLTnQKEKDFDSTTKELIDRI 287
Cdd:pfam03466 161 ADGRLVALpLPEPPLPRELYLVW-RKGRPLSPAVRAFIEFL 200
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 1-208 3.41e-13

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: 68.61  E-value: 3.41e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007   1 MEFRTIKTFYTVVNTGSFQRAAEVLNYSQPTISMRIKQLEQDLDVQLFER-GKTLKLTHAGRLFYERAGQLIAQYEVLDH 79
Cdd:NF041036   1 METRYLKTLVIVAEEGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRsGPSLEPTAAGEMVLEKARRILDIEDSLMD 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007  80 TIFDLKngnaGLIKVGI-SEPSASLI-LPKILKAFladfpkLMVNVSVDDA----NTCSQKLI---DGEIDFAICGEPE- 149
Cdd:NF041036  81 ELKSFK----GRQRLSIcCTPTFGMAhLPGVLNRF------MLRNADVVDLkflfHSPAQALEgiqNKEFDLAIIEHCAd 150

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007 150 LILENFY-FPFFHDTLDLIVSESHPLASrTSVELRDLRDECFIFTPANCPIRIQIEQHLK 208
Cdd:NF041036 151 LDLGRFHtYPLPQDELVFVSAPSLGLPT-PNVTLERLLELCLITRRDGCSSRDLLRRNLA 209
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 1-149 1.63e-11

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


Pssm-ID: 274509 [Multi-domain]  Cd Length: 292  Bit Score: 63.40  E-value: 1.63e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007    1 MEFRTIKTFYTVVNTGSFQRAAEVLNYSQPTISMRIKQLEQDLDVQLFERGKTLKLTHAGRL---FYERAGQLIAQyevL 77
Cdd:TIGR03298   1 LDYRQLAALAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVRTQPCRATEAGQRllrHARQVRLLEAE---L 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 345535007   78 DHTIFDLKNGNAGLIKVGISEPS-ASLILPkILKAFLADfPKLMVNVSVDDANTCSQKLIDGEIDFAICGEPE 149
Cdd:TIGR03298  78 LAELPGLAPGAPTRLTIAVNADSlATWFLP-ALAPVLAR-EGVLLDLVVEDQDHTAELLRSGEVLGAVTTEAK 148
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-287 2.07e-55

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 180.06  E-value: 2.07e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007   1 MEFRTIKTFYTVVNTGSFQRAAEVLNYSQPTISMRIKQLEQDLDVQLFER-GKTLKLTHAGRLFYERAGQLIAQYEVLDH 79
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERtGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007  80 TIFDLKNGNAGLIKVGISEPSASLILPKILKAFLADFPKLMVNVSVDDANTCSQKLIDGEIDFAICGEPELILENFYFPF 159
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007 160 FHDTLDLIVSESHPLASRTSVelrdlrdecfiftpancpiriqieqhlkraigsdykkmeLTSSMSHKYFVRENVGVSIF 239
Cdd:COG0583  161 GEERLVLVASPDHPLARRAPL---------------------------------------VNSLEALLAAVAAGLGIALL 201

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|
gi 345535007 240 -TSTAHSELLDGTVRIL-IENLPISPPIGLLTnQKEKDFDSTTKELIDRI 287
Cdd:COG0583  202 pRFLAADELAAGRLVALpLPDPPPPRPLYLVW-RRRRHLSPAVRAFLDFL 250
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-295 6.34e-44

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: 151.62  E-value: 6.34e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007   1 MEFRTIKTFYTVVNTGSFQRAAEVLNYSQPTISMRIKQLEQDLDVQLFER-GKTLKLTHAGRLFYERAGQLIAQYEVLDH 79
Cdd:NF040786   1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRnTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007  80 TIFDLKNGNAGLIKVGISEPSASLILPKILKAFLADFPKLMVNVSVDDANTCSQKLIDGEIDFAICGEPeliLEN---FY 156
Cdd:NF040786  81 EFDRYGKESKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTK---LEKkrlVY 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007 157 FPFFHDTLDLIVSESHPLASRTSVE--LRDLRDECFIFTPANCPIRIQIEQHLKRAiGSDYKKMELTSSMSH----KYFV 230
Cdd:NF040786 158 TPFYKDRLVLITPNGTEKYRMLKEEisISELQKEPFIMREEGSGTRKEAEKALKSL-GISLEDLNVVASLGSteaiKQSV 236

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 345535007 231 RENVGVSIFTS-TAHSELLDGTVRIL-IENLPISPPIGLLTNQKEKdfdstTKELIDRIIYYFDDKK 295
Cdd:NF040786 237 EAGLGISVISElAAEKEVERGRVLIFpIPGLPKNRDFYLVYNKNRQ-----LSPTAEAFLQFVKERY 298
rbcR CHL00180
LysR transcriptional regulator; Provisional
 4-283 4.56e-40

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 141.70  E-value: 4.56e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007   4 RTIKTFYTVVNTGSFQRAAEVLNYSQPTISMRIKQLEQDLDVQLFERGK-TLKLTHAGRLFYERAGQLIAQYEVLDHTIF 82
Cdd:CHL00180   8 DQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKnKASLTEAGELLLRYGNRILALCEETCRALE 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007  83 DLKNGNAGLIKVGISEPSASLILPKILKAFLADFPKLMVNVSVDDANTCSQKLIDGEIDFAICG---EPEL--ILEnfYF 157
Cdd:CHL00180  88 DLKNLQRGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVGgevPTELkkILE--IT 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007 158 PFFHDTLDLIVSESHPLASRTSVELRDLRDECFIFTPANCPIRIQIEQHLKR-AIGSDYKK--MELTSSMSHKYFVRENV 234
Cdd:CHL00180 166 PYVEDELALIIPKSHPFAKLKKIQKEDLYRLNFITLDSNSTIRKVIDNILIQnGIDSKRFKieMELNSIEAIKNAVQSGL 245

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....
gi 345535007 235 GVSIFTSTA-HSELLDGTVRIL-IENLPISPPIGLLTN---QKEKDFDSTTKEL 283
Cdd:CHL00180 246 GAAFVSVSAiEKELELGLLHWIkIENITIKRMLSIITNpnrYKSKASETFYNEI 299
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 92-285 7.76e-35

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: 125.02  E-value: 7.76e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007  92 IKVGISEPSASLILPKILKAFLADFPKLMVNVSVDDANTCSQKLIDGEIDFAICGEPELILENFYFPFFHDTLDLIVSES 171
Cdd:cd05466    2 LRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPPD 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007 172 HPLASRTSVELRDLRDECFIFTPANCPIRIQIEQHLKRAIGSDYKKMELTSSMSHKYFVRENVGVSIFTSTAHSELLDGT 251
Cdd:cd05466   82 HPLAKRKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEELADGG 161

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 345535007 252 VRIL-IENLPISPPIGLLTNqKEKDFDSTTKELID 285
Cdd:cd05466  162 LVVLpLEDPPLSRTIGLVWR-KGRYLSPAARAFLE 195
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 89-287 5.33e-33

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: 120.47  E-value: 5.33e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007   89 AGLIKVGISEPSASLILPKILKAFLADFPKLMVNVSVDDANTCSQKLIDGEIDFAICGEPELILENFYFPFFHDTLDLIV 168
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007  169 SESHPLASRTSVELRDLRDECFIFTPANCPIRIQIEQHLKRAIGSDYKKMELTSSMSHKYFVRENVGVSIF-TSTAHSEL 247
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLpRSAVAREL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 345535007  248 LDGTVRIL-IENLPISPPIGLLTnQKEKDFDSTTKELIDRI 287
Cdd:pfam03466 161 ADGRLVALpLPEPPLPRELYLVW-RKGRPLSPAVRAFIEFL 200
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 1-209 8.06e-26

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 103.50  E-value: 8.06e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007   1 MEFRTIKTFYTVVNTGSFQRAAEVLNYSQPTISMRIKQLEQDLDVQLFER-GKTLKLTHAGRLFYERAGQLIAQYEVLDH 79
Cdd:PRK11242   1 MLLRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRsGRTVRLTDAGEVYLRYARRALQDLEAGRR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007  80 TIFDLKNGNAGLIKVGISeP--SASLILPkILKAFLADFPKLMVNV---SVDDANTcsqKLIDGEIDFAICGEPELILEN 154
Cdd:PRK11242  81 AIHDVADLSRGSLRLAMT-PtfTAYLIGP-LIDAFHARYPGITLTIremSQERIEA---LLADDELDVGIAFAPVHSPEI 155

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 345535007 155 FYFPFFHDTLDLIVSESHPLAS-RTSVELRDLRDECFIFTPANCPIRIQIEQHLKR 209
Cdd:PRK11242 156 EAQPLFTETLALVVGRHHPLAArRKALTLDELADEPLVLLSAEFATREQIDRYFRR 211
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 4-260 1.46e-23

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 97.45  E-value: 1.46e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007   4 RTIKTFYTVVNTGSFQRAAEVLNYSQPTISMRIKQLEQDLDVQLFER-GKTLKLTHAGRLFYERAGQLIAQYEvldhTIF 82
Cdd:PRK10837   6 RQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRvGKRLVVNEHGRLLYPRALALLEQAV----EIE 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007  83 DLKNGNAGLIKVGISEPSASLILPKILKAFLADFPKLMVNVSVddANTcsQKLIDGEIDFAI--------CGEPELILEn 154
Cdd:PRK10837  82 QLFREDNGALRIYASSTIGNYILPAMIARYRRDYPQLPLELSV--GNS--QDVINAVLDFRVdigliegpCHSPELISE- 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007 155 fyfPFFHDTLDLIVSESHPLASRTsVELRDLRDECFIFTPANCPIRIQIEQ----HLKR-AIGsdykkMELTSSMSHKYF 229
Cdd:PRK10837 157 ---PWLEDELVVFAAPDSPLARGP-VTLEQLAAAPWILRERGSGTREIVDYlllsHLPRfELA-----MELGNSEAIKHA 227

                        250       260       270
                 ....*....|....*....|....*....|..
gi 345535007 230 VRENVGVSIFTSTAHSELLD-GTVRILIENLP 260
Cdd:PRK10837 228 VRHGLGISCLSRRVIADQLQaGTLVEVAVPLP 259
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 104-262 3.31e-22

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: 91.78  E-value: 3.31e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007 104 ILPKILKAFLADFPKLMVNVSVDDANTCSQKLIDGEIDFAI----CGEPELILEnfyfPFFHDTLDLIVSESHPLASRTS 179
Cdd:cd08420   14 LLPRLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLvegpVDHPDLIVE----PFAEDELVLVVPPDHPLAGRKE 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007 180 VELRDLRDECFIFTPANCPIRIQIEQHLKRAI--GSDYK-KMELTSSMSHKYFVRENVGVSIF-TSTAHSELLDGTVRIL 255
Cdd:cd08420   90 VTAEELAAEPWILREPGSGTREVFERALAEAGldGLDLNiVMELGSTEAIKEAVEAGLGISILsRLAVRKELELGRLVAL 169


                 ....*...
gi 345535007 256 -IENLPIS 262
Cdd:cd08420  170 pVEGLRLT 177
PRK09986 PRK09986
LysR family transcriptional regulator;
4-196 3.62e-22

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 93.63  E-value: 3.62e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007   4 RTIKTFYTVVNTGSFQRAAEVLNYSQPTISMRIKQLEQDLDVQLFER-GKTLKLTHAGRLFYERAGQLIAQYEVLDHTIF 82
Cdd:PRK09986  10 KLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRhSRSVVLTHAGKILMEESRRLLDNAEQSLARVE 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007  83 DLKNGNAGLIKVGISEPSA-SLILPKiLKAFLADFPKlmVNVSVDDANTCSQ--KLIDGEIDFAI--CGEPElILENFYF 157
Cdd:PRK09986  90 QIGRGEAGRIEIGIVGTALwGRLRPA-MRHFLKENPN--VEWLLRELSPSMQmaALERRELDAGIwrMADLE-PNPGFTS 165

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 345535007 158 PFFH-DTLDLIVSESHPLASRTSVELRDLRDECFIFTPAN 196
Cdd:PRK09986 166 RRLHeSAFAVAVPEEHPLASRSSVPLKALRNEYFITLPFV 205
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-61 1.70e-21

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 85.51  E-value: 1.70e-21
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007    3 FRTIKTFYTVVNTGSFQRAAEVLNYSQPTISMRIKQLEQDLDVQLFER-GKTLKLTHAGR 61
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERtTRGVRLTEAGE 60
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 99-269 1.13e-18

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


Pssm-ID: 176131 [Multi-domain]  Cd Length: 197  Bit Score: 82.19  E-value: 1.13e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007  99 PS-ASLILPKILKAFLADFPKlmVNVSVDDANT--CSQKLIDGEIDFAICGEPELiLENFYF-PFFHDTLDLIVSESHPL 174
Cdd:cd08440    8 PSlAATLLPPVLAAFRRRHPG--IRVRLRDVSAeqVIEAVRSGEVDFGIGSEPEA-DPDLEFePLLRDPFVLVCPKDHPL 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007 175 ASRTSVELRDLRDECFIFTPANCPIRIQIEQHLKRAIGSDYKKME---LTSSMShkyFVRENVGVSIFTSTAHsELLD-- 249
Cdd:cd08440   85 ARRRSVTWAELAGYPLIALGRGSGVRALIDRALAAAGLTLRPAYEvshMSTALG---MVAAGLGVAVLPALAL-PLADhp 160

                        170       180
                 ....*....|....*....|
gi 345535007 250 GTVRILIENLPISPPIGLLT 269
Cdd:cd08440  161 GLVARPLTEPVVTRTVGLIR 180
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 18-188 3.61e-17

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 80.07  E-value: 3.61e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007  18 FQRAAEVLNYSQPTISMRIKQLEQDLDVQLFERG--KTLkLTHAGRLFYERAGQLIAQYEVLDhtifDLKNGN----AGL 91
Cdd:PRK11151  18 FRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTsrKVL-FTQAGLLLVDQARTVLREVKVLK----EMASQQgetmSGP 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007  92 IKVGISEPSASLILPKILKAFLADFPKLmvNVSVDDANTcsQKLID----GEIDFAICG---EPELILEnfyFPFFHDTL 164
Cdd:PRK11151  93 LHIGLIPTVGPYLLPHIIPMLHQTFPKL--EMYLHEAQT--HQLLAqldsGKLDCAILAlvkESEAFIE---VPLFDEPM 165

                        170       180
                 ....*....|....*....|....
gi 345535007 165 DLIVSESHPLASRTSVELRDLRDE 188
Cdd:PRK11151 166 LLAVYEDHPWANRDRVPMSDLAGE 189
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 4-238 7.53e-17

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 79.27  E-value: 7.53e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007   4 RTIKTFYTVVNTGSFQRAAEVLNYSQPTISMRIKQLEQDLDVQLFERGK-TLKLTHAG-RLFYE---------------- 65
Cdd:PRK11013   7 RHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRgRLHPTVQGlRLFEEvqrsyygldrivsaae 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007  66 -----RAGQL-IAQYEVLDHTifdlkngnaglikvgisepsaslILPKILKAFLADFPKLMVNVSVDDANTCSQKLIDGE 139
Cdd:PRK11013  87 slrefRQGQLsIACLPVFSQS-----------------------LLPGLCQPFLARYPDVSLNIVPQESPLLEEWLSAQR 143

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007 140 IDFAIC--------GEPELILenfyfpffhdTLD--LIVSESHPLASRTSVELRDLRDECFIFTPANCPIRIQIEQHLKR 209
Cdd:PRK11013 144 HDLGLTetlhtpagTERTELL----------TLDevCVLPAGHPLAAKKVLTPDDFAGENFISLSRTDSYRQLLDQLFAE 213

                        250       260
                 ....*....|....*....|....*....
gi 345535007 210 AIGSDYKKMELTSSMSHKYFVRENVGVSI 238
Cdd:PRK11013 214 HGVKRRMVVETHSAASVCAMVRAGVGVSI 242
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
 100-261 2.31e-16

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


Pssm-ID: 176111  Cd Length: 197  Bit Score: 75.62  E-value: 2.31e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007 100 SASLILPKILKAFLADFPKLMVNVSVDDANTCSQKLIDGEIDFAICGEPELILENFYFPFFHDTLDLIVSESHPLASRTS 179
Cdd:cd08419    9 TAKYFAPRLLGAFCRRHPGVEVSLRVGNREQVLERLADNEDDLAIMGRPPEDLDLVAEPFLDNPLVVIAPPDHPLAGQKR 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007 180 VELRDLRDECFIFTPANCPIRIQIEQHLKRAIGSDYKKMELTSSMSHKYFVRENVGVSIFT-STAHSELLDGTVRIL-IE 257
Cdd:cd08419   89 IPLERLAREPFLLREPGSGTRLAMERFFAEHGVTLRVRMELGSNEAIKQAVMAGLGLSVLSlHTLALELATGRLAVLdVE 168


                 ....
gi 345535007 258 NLPI 261
Cdd:cd08419  169 GFPI 172
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 21-191 2.65e-16

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 77.72  E-value: 2.65e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007  21 AAEVLNYSQPTISMRIKQLEQDLDVQLFER-GKTLK-LTHAGRLFYERAGQLIAQYEVLDHTIFDLKNGNAGLIKVGISE 98
Cdd:PRK12682  22 AAKALHTSQPGVSKAIIELEEELGIEIFIRhGKRLKgLTEPGKAVLDVIERILREVGNIKRIGDDFSNQDSGTLTIATTH 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007  99 PSASLILPKILKAFLADFPKlmVNVSVDDAN--TCSQKLIDGEIDFAICGE-----PELILenfyFPFFHDTLDLIVSES 171
Cdd:PRK12682 102 TQARYVLPRVVAAFRKRYPK--VNLSLHQGSpdEIARMVISGEADIGIATEsladdPDLAT----LPCYDWQHAVIVPPD 175

                        170       180
                 ....*....|....*....|
gi 345535007 172 HPLASRTSVELRDLRDECFI 191
Cdd:PRK12682 176 HPLAQEERITLEDLAEYPLI 195
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 92-191 3.11e-16

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: 75.29  E-value: 3.11e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007  92 IKVGISEPSASLILPKILKAFLADFPKLMVNVSVDDANTCSQKLIDGEIDFAICGEPeLILENF-YFPFFHDTLDLIVSE 170
Cdd:cd08438    2 LRLGLPPLGGSLLFAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVLP-VDEEEFdSQPLCNEPLVAVLPR 80

                         90       100
                 ....*....|....*....|.
gi 345535007 171 SHPLASRTSVELRDLRDECFI 191
Cdd:cd08438   81 GHPLAGRKTVSLADLADEPFI 101
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 92-195 8.11e-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: 74.08  E-value: 8.11e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007  92 IKVGISEPSASLILPKILKAFLADFPklMVNVSVDDANTCSQ--KLIDGEIDFAI----CGEPELILEnfyfPFFHDTLD 165
Cdd:cd08414    2 LRIGFVGSALYGLLPRLLRRFRARYP--DVELELREMTTAEQleALRAGRLDVGFvrppPDPPGLASR----PLLREPLV 75

                         90       100       110
                 ....*....|....*....|....*....|
gi 345535007 166 LIVSESHPLASRTSVELRDLRDECFIFTPA 195
Cdd:cd08414   76 VALPADHPLAARESVSLADLADEPFVLFPR 105
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 1-195 9.43e-16

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 75.96  E-value: 9.43e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007   1 MEFRTIKTFYTVVNTGSFQRAAEVLNYSQPTISMRIKQLEQDLDVQLFERGK-TLKLTHAGRLFYERAGQLIAQYEvldh 79
Cdd:PRK09906   1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKrKVALTAAGEVFLQDARAILEQAE---- 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007  80 tifdlkngNAGLIKVGISE----------PSASL-ILPKILKAFLADFPKLMVNVSVDDANTCSQKLIDGEIDFAICGEP 148
Cdd:PRK09906  77 --------KAKLRARKIVQedrqltigfvPSAEVnLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHP 148

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 345535007 149 ELILENFYFPFFHDTLDLIVSESHPLASRTSVELRDLRDECFIFTPA 195
Cdd:PRK09906 149 VYSDEIDYLELLDEPLVVVLPVDHPLAHEKEITAAQLDGVNFISTDP 195
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 21-185 1.09e-15

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 75.85  E-value: 1.09e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007  21 AAEVLNYSQPTISMRIKQLEQDLDVQLFER-GKTLK-LTHAGRLFYERAGQLIAQYEVLDHTIFDLKNGNAGLIKVGISE 98
Cdd:PRK12683  22 VANALYTSQSGVSKQIKDLEDELGVEIFIRrGKRLTgLTEPGKELLQIVERMLLDAENLRRLAEQFADRDSGHLTVATTH 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007  99 PSASLILPKILKAFLADFPKLMVNVSVDDANTCSQKLIDGEIDFAICGE-----PELILenfyFPFFHDTLDLIVSESHP 173
Cdd:PRK12683 102 TQARYALPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGIATEaldrePDLVS----FPYYSWHHVVVVPKGHP 177

                        170
                 ....*....|..
gi 345535007 174 LASRTSVELRDL 185
Cdd:PRK12683 178 LTGRENLTLEAI 189
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
7-151 1.17e-15

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 75.39  E-value: 1.17e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007   7 KTFYTVVNTGSFQRAAEVLNYSQPTISMRIKQLEQDLDVQLFERGKTLKLTHAGrlfyERAGQLIAQYEVLDHTIF-DLK 85
Cdd:PRK13348   8 EALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRGRPCRPTPAG----QRLLRHLRQVALLEADLLsTLP 83

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 345535007  86 NGNAGLIKVGISEPSASL---ILPkILKAFLADfPKLMVNVSVDDANTCSQKLIDGEIDFAICGEPELI 151
Cdd:PRK13348  84 AERGSPPTLAIAVNADSLatwFLP-ALAAVLAG-ERILLELIVDDQDHTFALLERGEVVGCVSTQPKPM 150
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 1-144 1.35e-15

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 75.49  E-value: 1.35e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007   1 MEFRTIKTFYTVVNTGSFQRAAEVLNYSQPTISMRIKQLEQDLDVQLFERGKT-LKLTHAGRLFYERAGQLIAQYEVLDH 79
Cdd:PRK11233   1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRgVTPTEAGKILYTHARAILRQCEQAQL 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 345535007  80 TIFDLKNGNAGLIKVGISEPSA--SLILPkILKAFLADFPKLMVNVSVDDANTCSQKLIDGEIDFAI 144
Cdd:PRK11233  81 AVHNVGQALSGQVSIGLAPGTAasSLTMP-LLQAVRAEFPGIVLYLHENSGATLNEKLMNGQLDMAV 146
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 105-267 1.55e-15

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: 73.34  E-value: 1.55e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007 105 LPKILKAFLADFPKLMVNVSVDDANTCSQKLIDGEIDFAICGEPELILENFYFPFFHDTLDLIVSESHPLASRTSVELRD 184
Cdd:cd08434   15 VPDLIRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLALCSPVPDEPDIEWIPLFTEELVLVVPKDHPLAGRDSVDLAE 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007 185 LRDECFIFTPANCPIRiQIEQHLKRAIGSDYK-KMELTSSMSHKYFVRENVGVSIFTSTAhSELLDGTVRILIENLPISP 263
Cdd:cd08434   95 LADEPFVLLSPGFGLR-PIVDELCAAAGFTPKiAFEGEEDSTIAGLVAAGLGVAILPEMT-LLNPPGVKKIPIKDPDAER 172


                 ....
gi 345535007 264 PIGL 267
Cdd:cd08434  173 TIGL 176
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
5-180 2.09e-15

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 74.84  E-value: 2.09e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007   5 TIKTFYTVVNTGSFQRAAEVLNYSQPTISMRIKQLEQDLDVQLFER-GKTLKLTHAGRLFYERAGQLIaqyEVLDHTIFD 83
Cdd:PRK10094   6 TLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRtTRSVTLTAAGEHLLSQARDWL---SWLESMPSE 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007  84 LKNGNAGLikvgisEPSASLIL------PKILKAFLA----DFPKLMVNVS------VDDAntcsqkLIDGEIDFAIcGE 147
Cdd:PRK10094  83 LQQVNDGV------ERQVNIVInnllynPQAVAQLLAwlneRYPFTQFHISrqiymgVWDS------LLYEGFSLAI-GV 149

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 345535007 148 P--ELILENF-YFPFFHDTLDLIVSESHPLASRTSV 180
Cdd:PRK10094 150 TgtEALANTFsLDPLGSVQWRFVMAADHPLANVEEP 185
cysB PRK12681
HTH-type transcriptional regulator CysB;
21-185 2.84e-15

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 74.93  E-value: 2.84e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007  21 AAEVLNYSQPTISMRIKQLEQDLDVQLFER-GKTLK-LTHAGRLFYERAGQLIAQYEVLDHTIFDLKNGNAGLIKVGISE 98
Cdd:PRK12681  22 TAEGLYTSQPGISKQVRMLEDELGIQIFARsGKHLTqVTPAGEEIIRIAREILSKVESIKSVAGEHTWPDKGSLYIATTH 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007  99 PSASLILPKILKAFLADFPKLMVNVSVDDANTCSQKLIDGEIDFAICGEP-----ELILenfyFPFFHDTLDLIVSESHP 173
Cdd:PRK12681 102 TQARYALPPVIKGFIERYPRVSLHMHQGSPTQIAEAAAKGNADFAIATEAlhlydDLIM----LPCYHWNRSVVVPPDHP 177

                        170
                 ....*....|..
gi 345535007 174 LASRTSVELRDL 185
Cdd:PRK12681 178 LAKKKKLTIEEL 189
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
21-185 3.60e-15

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 74.24  E-value: 3.60e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007  21 AAEVLNYSQPTISMRIKQLEQDLDVQLFER-GKTLK-LTHAGRLFYERAGQLIAQYEVLDHTIFDLKNGNAGLIKVGISE 98
Cdd:PRK12684  22 AAKALYTSQPGVSKAIIELEDELGVEIFTRhGKRLRgLTEPGRIILASVERILQEVENLKRVGKEFAAQDQGNLTIATTH 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007  99 PSASLILPKILKAFLADFPKlmVNVSVDDAN--TCSQKLIDGEIDFAICGE-----PELILenfyFPFFHDTLDLIVSES 171
Cdd:PRK12684 102 TQARYALPAAIKEFKKRYPK--VRLSILQGSptQIAEMVLHGQADLAIATEaiadyKELVS----LPCYQWNHCVVVPPD 175

                        170
                 ....*....|....
gi 345535007 172 HPLASRTSVELRDL 185
Cdd:PRK12684 176 HPLLERKPLTLEDL 189
PRK09791 PRK09791
LysR family transcriptional regulator;
1-187 1.72e-14

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 72.49  E-value: 1.72e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007   1 MEFRTIKTFYTVVNTGSFQRAAEVLNYSQPTISMRIKQLEQDLDVQLF-ERGKTLKLTHAGRLFYERAGQLIAQYEVLDH 79
Cdd:PRK09791   5 VKIHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFfRRSKGVTLTDAGESFYQHASLILEELRAAQE 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007  80 TIFDLKNGNAGLIKVGISEPSASLILPKILKAFLADFPKLMVNVSVDDANTCSQKLIDGEIDFAIcgepelileNFYFPF 159
Cdd:PRK09791  85 DIRQRQGQLAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDFTI---------NTYYQG 155

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 345535007 160 FHDT-----------LDLIVSESHPLASRTSveLRDLRD 187
Cdd:PRK09791 156 PYDHeftfekllekqFAVFCRPGHPAIGARS--LKQLLD 192
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 92-210 1.30e-13

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: 68.07  E-value: 1.30e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007  92 IKVGISEPSASLILPKILKAFLADFPKLMVNVSVDDANTCSQKLIDGEIDFAICGEPELILEN--FYFPFFHDTLDLIVS 169
Cdd:cd08435    2 VRVGAVPAAAPVLLPPAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAIGRLADDEQPPdlASEELADEPLVVVAR 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 345535007 170 ESHPLASRTSVELRDLRDECFIFTPANCPIRIQIEQHLKRA 210
Cdd:cd08435   82 PGHPLARRARLTLADLADYPWVLPPPGTPLRQRLEQLFAAA 122
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 92-269 1.88e-13

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


Pssm-ID: 176104 [Multi-domain]  Cd Length: 198  Bit Score: 67.57  E-value: 1.88e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007  92 IKVGISEPSASLILPKILKAFLADFPKLMVNVSVDDANTCSQKLIDGEIDFAICGEPELILENFYFPFFHDTLDLIVSES 171
Cdd:cd08412    2 LRIGCFSTLAPYYLPGLLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALTYDLDLPEDIAFEPLARLPPYVWLPAD 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007 172 HPLASRTSVELRDLRDECFIFTPANcPIR-----IQIEQHLKRAIGSDYKKMELTSSMshkyfVRENVGVSIF-TSTAHS 245
Cdd:cd08412   82 HPLAGKDEVSLADLAAEPLILLDLP-HSReyflsLFAAAGLTPRIAYRTSSFEAVRSL-----VANGLGYSLLnDRPYRP 155

                        170       180
                 ....*....|....*....|....*.
gi 345535007 246 ELLDG--TVRILIENLPISPPIGLLT 269
Cdd:cd08412  156 WSYDGkrLVRRPLADPVPPLRLGLAW 181
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
28-149 3.02e-13

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 68.31  E-value: 3.02e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007  28 SQPTISMRIKQLEQDLDVQLFER-GKTLKLTHAGRLFYERAGQLIAQYEVLDHTIFDLKNGNAGLIKVGISEPSASLILP 106
Cdd:PRK11716   4 SPSTLSRQIQRLEEELGQPLFVRdNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSLFCSVTAAYSHLP 83

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 345535007 107 KILKAFLADFPKLMVNVSVDDANTCSQKLIDGEIDFAICGEPE 149
Cdd:PRK11716  84 PILDRFRAEHPLVEIKLTTGDAADAVEKVQSGEADLAIAAKPE 126
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 1-208 3.41e-13

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: 68.61  E-value: 3.41e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007   1 MEFRTIKTFYTVVNTGSFQRAAEVLNYSQPTISMRIKQLEQDLDVQLFER-GKTLKLTHAGRLFYERAGQLIAQYEVLDH 79
Cdd:NF041036   1 METRYLKTLVIVAEEGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRsGPSLEPTAAGEMVLEKARRILDIEDSLMD 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007  80 TIFDLKngnaGLIKVGI-SEPSASLI-LPKILKAFladfpkLMVNVSVDDA----NTCSQKLI---DGEIDFAICGEPE- 149
Cdd:NF041036  81 ELKSFK----GRQRLSIcCTPTFGMAhLPGVLNRF------MLRNADVVDLkflfHSPAQALEgiqNKEFDLAIIEHCAd 150

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007 150 LILENFY-FPFFHDTLDLIVSESHPLASrTSVELRDLRDECFIFTPANCPIRIQIEQHLK 208
Cdd:NF041036 151 LDLGRFHtYPLPQDELVFVSAPSLGLPT-PNVTLERLLELCLITRRDGCSSRDLLRRNLA 209
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
1-212 6.59e-13

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 67.74  E-value: 6.59e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007   1 MEFRTIKTFYTVVNTGSFQRAAEVLNYSQPTISMRIKQLEQDLDVQLFER-GKTLKLTHAGRLFYERAGQLIAQyevLDH 79
Cdd:PRK15421   2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRkSQPLRFTPQGEILLQLANQVLPQ---ISQ 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007  80 TIFDLKNGNAGLIKVGISEPSASLILPKILKAFLADFPKLMVN----VSVDDANTCSQklidGEIDFAICGE--PELILE 153
Cdd:PRK15421  79 ALQACNEPQQTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDfksgVTFDPQPALQQ----GELDLVMTSDilPRSGLH 154

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 345535007 154 nfYFPFFHDTLDLIVSESHPLASRTSVELRDLRDECFIFTPANCPiRIQIEQHLKRAIG 212
Cdd:PRK15421 155 --YSPMFDYEVRLVLAPDHPLAAKTRITPEDLASETLLIYPVQRS-RLDVWRHFLQPAG 210
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 99-265 2.65e-12

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: 64.51  E-value: 2.65e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007  99 PSASL-ILPKILKAFLADFPKLMVNVSVDDANTCSQKLIDGEIDFAIC----GEPELILEnfyfPFFHDTLDLIVSESHP 173
Cdd:cd08415    8 PALALsLLPRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLAslplDHPGLESE----PLASGRAVCVLPPGHP 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007 174 LASRTSVELRDLRDECFIFTPANCPIRIQIEQHLKRAiGSDYK-KMELTSSMSHKYFVRENVGVSI---FtsTAHSELLD 249
Cdd:cd08415   84 LARKDVVTPADLAGEPLISLGRGDPLRQRVDAAFERA-GVEPRiVIETQLSHTACALVAAGLGVAIvdpL--TAAGYAGA 160

                        170
                 ....*....|....*.
gi 345535007 250 GtvrilIENLPISPPI 265
Cdd:cd08415  161 G-----LVVRPFRPAI 171
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 101-210 6.28e-12

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


Pssm-ID: 176127 [Multi-domain]  Cd Length: 194  Bit Score: 63.39  E-value: 6.28e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007 101 ASLILPKILKAFLADFPKLMVNVSVDDANTCSQKLIDGEIDFAICGEPELILENF-YFPFFHDTLDLIVSESHPLASRTS 179
Cdd:cd08436   11 AAVDLPELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAFVGLPERRPPGLaSRELAREPLVAVVAPDHPLAGRRR 90

                         90       100       110
                 ....*....|....*....|....*....|.
gi 345535007 180 VELRDLRDECFIFTPANCPIRIQIEQHLKRA 210
Cdd:cd08436   91 VALADLADEPFVDFPPGTGARRQVDRAFAAA 121
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
1-176 8.93e-12

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 64.31  E-value: 8.93e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007   1 MEFRTIKTFYTVVNTGSFQRAAEVLNYSQPTISMRIKQLEQDLDVQLFERGKT-LKLTHAGRLFYERAGQLIAQyevLDH 79
Cdd:PRK10082  11 IETKWLYDFLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTpLQLSEQGKIFHSQIRHLLQQ---LES 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007  80 TIFDLKNG-NAGLIKVGISEP-SASL-ILPKILKAFLADFPKLMVNVSVDDAntcSQKLIDGEIDFAICGEPELILENfy 156
Cdd:PRK10082  88 NLAELRGGsDYAQRKIKIAAAhSLSLgLLPSIISQMPPLFTWAIEAIDVDEA---VDKLREGQSDCIFSFHDEDLLEA-- 162

                        170       180
                 ....*....|....*....|
gi 345535007 157 fPFfhDTLDLIVSESHPLAS 176
Cdd:PRK10082 163 -PF--DHIRLFESQLFPVCA 179
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 1-149 1.63e-11

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


Pssm-ID: 274509 [Multi-domain]  Cd Length: 292  Bit Score: 63.40  E-value: 1.63e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007    1 MEFRTIKTFYTVVNTGSFQRAAEVLNYSQPTISMRIKQLEQDLDVQLFERGKTLKLTHAGRL---FYERAGQLIAQyevL 77
Cdd:TIGR03298   1 LDYRQLAALAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVRTQPCRATEAGQRllrHARQVRLLEAE---L 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 345535007   78 DHTIFDLKNGNAGLIKVGISEPS-ASLILPkILKAFLADfPKLMVNVSVDDANTCSQKLIDGEIDFAICGEPE 149
Cdd:TIGR03298  78 LAELPGLAPGAPTRLTIAVNADSlATWFLP-ALAPVLAR-EGVLLDLVVEDQDHTAELLRSGEVLGAVTTEAK 148
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
8-145 2.18e-11

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 63.48  E-value: 2.18e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007   8 TFYTVVNTGSFQRAAEVLNYSQPTISMRIKQLEQDLDVQLFERG-KTLKLTHAG-RLFYeragQLIAQYEVLDHTIFDLK 85
Cdd:PRK10086  21 TFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRShRKVELTEEGkRVFW----ALKSSLDTLNQEILDIK 96

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 345535007  86 NGN-AGLIKVgISEPS--ASLILPKIlKAFLADFPKLMVNVSV--DDANtcsqkLIDGEIDFAIC 145
Cdd:PRK10086  97 NQElSGTLTV-YSRPSiaQCWLVPRL-ADFTRRYPSISLTILTgnENVN-----FQRAGIDLAIY 154
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 11-188 2.52e-11

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 63.04  E-value: 2.52e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007  11 TVVNTGSFQRAAEVLNYSQPTISMRIKQLEQDLDVQLFER-GKTLKLTHAGRLFYERAGQLIAQYEVLDHTIFDLKNGNA 89
Cdd:PRK11074  12 AVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERrHRDVELTPAGEWFVKEARSVIKKMQETRRQCQQVANGWR 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007  90 GLIKVGISepsaSLILPKILKAFLADFPK------LMVNVSVddANTCSQKLIDGEIDFAIcGEPELIlenfyfPF---- 159
Cdd:PRK11074  92 GQLSIAVD----NIVRPDRTRQLIVDFYRhfddveLIIRQEV--FNGVWDALADGRVDIAI-GATRAI------PVggrf 158

                        170       180       190
                 ....*....|....*....|....*....|....
gi 345535007 160 -FHDTLDL----IVSESHPLASRTsvelRDLRDE 188
Cdd:PRK11074 159 aFRDMGMLswacVVSSDHPLASMD----GPLSDD 188
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
1-149 3.85e-11

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 62.48  E-value: 3.85e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007   1 MEFRTIKTFYTVVNTGSFQRAAEVLNYSQPTISMRIKQLEQDLDVQLFERGKTLKLTHAGRL---FYERAGQLiaQYEVL 77
Cdd:PRK03635   2 LDYKQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVRTQPCRPTEAGQRllrHARQVRLL--EAELL 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 345535007  78 DhtifDLKNGNAGLIKVGISEPSASL---ILPkILKAFLADfPKLMVNVSVDDANTCSQKLIDGEIDFAICGEPE 149
Cdd:PRK03635  80 G----ELPALDGTPLTLSIAVNADSLatwFLP-ALAPVLAR-SGVLLDLVVEDQDHTAELLRRGEVVGAVTTEPQ 148
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
1-123 7.85e-11

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 61.70  E-value: 7.85e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007   1 ME-FRTIKTFYTVVNTGSFQRAAEVLNYSQPTISMRIKQLEQDLDVQLFERG-KTLKLTHAGRLFYERAGQLIAQYEVLD 78
Cdd:PRK10632   1 MErLKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRStRSIGLTEAGRIYYQGCRRMLHEVQDVH 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 345535007  79 HTIFDLKNGNAGLIKVGISEPSASLILPKILKAFLADFPKLMVNV 123
Cdd:PRK10632  81 EQLYAFNNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNL 125
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 90-188 8.34e-11

The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a member of the type 2 periplasmic binding fold protein superfamily; OxyR senses hydrogen peroxide and is activated through the formation of an intramolecular disulfide bond. The OxyR activation induces the transcription of genes necessary for the bacterial defense against oxidative stress. The OxyR of LysR-type transcriptional regulator family is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The C-terminal domain also contains the redox-active cysteines that mediate the redox-dependent conformational switch. Thus, the interaction between the OxyR-tetramer and DNA is notably different between the oxidized and reduced forms. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176103 [Multi-domain]  Cd Length: 200  Bit Score: 60.23  E-value: 8.34e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007  90 GLIKVGISePS-ASLILPKILKAFLADFPKLMVNVSVDDANTCSQKLIDGEIDFAI----CGEPELILEnfyfPFFHDTL 164
Cdd:cd08411    1 GPLRLGVI-PTiAPYLLPRLLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAALlalpVDEPGLEEE----PLFDEPF 75

                         90       100
                 ....*....|....*....|....
gi 345535007 165 DLIVSESHPLASRTSVELRDLRDE 188
Cdd:cd08411   76 LLAVPKDHPLAKRKSVTPEDLAGE 99
PBP2_OccR cd08457
The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the ...
 104-252 7.07e-10

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


Pssm-ID: 176146 [Multi-domain]  Cd Length: 196  Bit Score: 57.50  E-value: 7.07e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007 104 ILPKILKAFLADFPKLMVNVSVDDANTCSQKLIDGEIDFAICGEPELilenfyfpffHDTLDLI----------VSESHP 173
Cdd:cd08457   14 FLPRFLAAFLRLRPNLHLSLMGLSSSQVLEAVASGRADLGIADGPLE----------ERQGFLIetrslpavvaVPMGHP 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007 174 LASRTSVELRDLRDECFIFTPANCPIRIQIEQHLKRAIGSDYKKMELTSSMSHKYFVRENVGVSIFT-STAHSELLDGTV 252
Cdd:cd08457   84 LAQLDVVSPQDLAGERIITLENGYLFRMRVEVALGKIGVKRRPIIEVNLSHTALSLVREGLGIAIIDpATAIGLPLDGIV 163
PBP2_LTTR_like_1 cd08421
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 105-210 8.27e-10

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


Pssm-ID: 176113  Cd Length: 198  Bit Score: 57.15  E-value: 8.27e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007 105 LPKILKAFLADFPKlmVNVSVDDANtcSQK----LIDGEIDFAIC--GEPELILEnfYFPFFHDTLDLIVSESHPLASRT 178
Cdd:cd08421   15 LPEDLASFLAAHPD--VRIDLEERL--SADivraVAEGRADLGIVagNVDAAGLE--TRPYRTDRLVVVVPRDHPLAGRA 88

                         90       100       110
                 ....*....|....*....|....*....|..
gi 345535007 179 SVELRDLRDECFIFTPANCPIRIQIEQHLKRA 210
Cdd:cd08421   89 SVAFADTLDHDFVGLPAGSALHTFLREAAARL 120
PBP2_YofA_SoxR_like cd08442
The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, ...
 91-222 1.92e-09

The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, contains the type 2 periplasmic binding fold; YofA is a LysR-like transcriptional regulator of cell growth in Bacillus subtillis. YofA controls cell viability and the formation of constrictions during cell division. YofaA positively regulates expression of the cell division gene ftsW, and thus is essential for cell viability during stationary-phase growth of Bacillus substilis. YofA shows significant homology to SoxR from Arthrobacter sp. TE1826. SoxR is a negative regulator for the sarcosine oxidase gene soxA. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine, which is involved in the metabolism of creatine and choline. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176133  Cd Length: 193  Bit Score: 56.08  E-value: 1.92e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007  91 LIKVGISEPSASLILPKILKAFLADFPKLMVNVSVDDANTCSQKLIDGEIDFA-ICG---EPELILEnfyfPFFHDTLDL 166
Cdd:cd08442    1 PLRLGSMETTAAVRLPPLLAAYHARYPKVDLSLSTGTTGALIQAVLEGRLDGAfVAGpveHPRLEQE----PVFQEELVL 76

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 345535007 167 IVSESHPLASRTSvelrDLRDECFIFTPANCPIRIQIEQHLKRAIGSDYKKMELTS 222
Cdd:cd08442   77 VSPKGHPPVSRAE----DLAGSTLLAFRAGCSYRRRLEDWLAEEGVSPGKIMEFGS 128
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 6-144 2.06e-09

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 57.35  E-value: 2.06e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007   6 IKTFYTVVNTGSFQRAAEVLNYSQPTISMRIKQLEQDLDVQLFER-GKTLKLTHAG--RLFYERAgqlIAQYEvlDHTIF 82
Cdd:PRK15092  16 LRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARhGRNKLLTEHGiqLLGYARK---ILRFN--DEACS 90

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 345535007  83 DLKNGNA-GLIKVGISEPSASLILPKILKAFLADFPKLMVNVSVDDANTCSQKLIDGEIDFAI 144
Cdd:PRK15092  91 SLMYSNLqGVLTIGASDDTADTILPFLLNRVSSVYPKLALDVRVKRNAFMMEMLESQEVDLAV 153
PRK09801 PRK09801
LysR family transcriptional regulator;
4-144 2.73e-09

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 56.97  E-value: 2.73e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007   4 RTIKTFYTVVNTGSFQRAAEVLNYSQPTISMRIKQLEQDLDVQLFER-GKTLKLTHAGRLFYERAGQLIAQYEVLDHTIF 82
Cdd:PRK09801   9 KDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRsARGVALTESGQRCYEHALEILTQYQRLVDDVT 88

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 345535007  83 DLKNGNAGLIKVGISEP-SASLILPKILKaFLADFPKLMVNVSVDDANTcsqKLIDGEIDFAI 144
Cdd:PRK09801  89 QIKTRPEGMIRIGCSFGfGRSHIAPAITE-LMRNYPELQVHFELFDRQI---DLVQDNIDLDI 147
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 17-67 4.80e-09

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 56.39  E-value: 4.80e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 345535007  17 SFQRAAEVLNYSQPTISMRIKQLEQDLDVQLFER-GKTLKLTHAGRLFYERA 67
Cdd:PRK11139  22 SFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRrNRSLLLTEEGQRYFLDI 73
cbl PRK12679
HTH-type transcriptional regulator Cbl;
22-185 5.85e-09

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 55.97  E-value: 5.85e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007  22 AEVLNYSQPTISMRIKQLEQDLDVQLF-ERGKT-LKLTHAGRLFYERAGQLIAQYEVLDHTIFDLKNGNAGLIKVGISEP 99
Cdd:PRK12679  23 ANMLFTSQSGVSRHIRELEDELGIEIFiRRGKRlLGMTEPGKALLVIAERILNEASNVRRLADLFTNDTSGVLTIATTHT 102

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007 100 SASLILPKILKAFLADFPKLMVNVSVDDANTCSQKLIDGEIDFAICGE-----PELILenfyFPFFHDTLDLIVSESHPL 174
Cdd:PRK12679 103 QARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASErlsndPQLVA----FPWFRWHHSLLVPHDHPL 178

                        170
                 ....*....|.
gi 345535007 175 ASRTSVELRDL 185
Cdd:PRK12679 179 TQITPLTLESI 189
PRK10341 PRK10341
transcriptional regulator TdcA;
9-188 9.81e-09

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 55.25  E-value: 9.81e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007   9 FYTVVNTGSFQRAAEVLNYSQPTISMRIKQLEQDLDVQLFERGKT-LKLTHAGRLFYERAGQLIAQYEVLDHTIFDLKNG 87
Cdd:PRK10341  15 FQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTgVTLTPAGQVLLSRSESITREMKNMVNEINGMSSE 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007  88 NAGLIKVGISEPSASLILPKILKAFLADFPKlmVNVSVDDANTCS--QKLIDGEIDFAICG-EPELILENFYF-PFFHDT 163
Cdd:PRK10341  95 AVVDVSFGFPSLIGFTFMSDMINKFKEVFPK--AQVSMYEAQLSSflPAIRDGRLDFAIGTlSNEMKLQDLHVePLFESE 172

                        170       180
                 ....*....|....*....|....*
gi 345535007 164 LDLIVSESHPLASRTSveLRDLRDE 188
Cdd:PRK10341 173 FVLVASKSRTCTGTTT--LESLKNE 195
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 99-198 1.42e-08

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


Pssm-ID: 176115 [Multi-domain]  Cd Length: 200  Bit Score: 53.76  E-value: 1.42e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007  99 PSASL-ILPKILKAFLADFPKLMVNVSVDDANTCSQKLIDGEIDFAIC----GEPELILENFYF-PFFHDTLDLIVSESH 172
Cdd:cd08423    8 PTAAAaLLPPALAALRARHPGLEVRLREAEPPESLDALRAGELDLAVVfdypVTPPPDDPGLTRvPLLDDPLDLVLPADH 87

                         90       100
                 ....*....|....*....|....*.
gi 345535007 173 PLASRTSVELRDLRDECFIFTPANCP 198
Cdd:cd08423   88 PLAGREEVALADLADEPWIAGCPGSP 113
PBP2_XapR cd08449
The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved ...
 105-196 3.71e-08

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: 52.66  E-value: 3.71e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007 105 LPKILKAFLADFPKlmVNVSVDDANTCSQK--LIDGEIDFAI------CGEPELILENFYfpffHDTLDLIVSESHPLAS 176
Cdd:cd08449   15 LGPALRRFKRQYPN--VTVRFHELSPEAQKaaLLSKRIDLGFvrfadtLNDPPLASELLW----REPMVVALPEEHPLAG 88

                         90       100
                 ....*....|....*....|.
gi 345535007 177 RTSVELRDLRDECFIF-TPAN 196
Cdd:cd08449   89 RKSLTLADLRDEPFVFlRLAN 109
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
1-62 3.72e-08

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 53.48  E-value: 3.72e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 345535007   1 MEFRTIKTFYTVVNTGSFQRAAEVLNYSQPTISMRIKQLEQDLDVQLFERGK-TLKLTHAG-RL 62
Cdd:PRK03601   1 MDTELLKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRnNIRLTAAGeRL 64
PBP2_LTTR_aromatics_like_2 cd08448
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 104-194 4.46e-08

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


Pssm-ID: 176139 [Multi-domain]  Cd Length: 197  Bit Score: 52.27  E-value: 4.46e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007 104 ILPKILKAFLADFPKLMVnvSVDDANTCSQ--KLIDGEIDFAICGEPELILENFYFPFFHDTLDLIVSESHPLASRTSVE 181
Cdd:cd08448   14 GLPRILRAFRAEYPGIEV--ALHEMSSAEQieALLRGELDLGFVHSRRLPAGLSARLLHREPFVCCLPAGHPLAARRRID 91

                         90
                 ....*....|...
gi 345535007 182 LRDLRDECFIFTP 194
Cdd:cd08448   92 LRELAGEPFVLFS 104
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-266 3.14e-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: 176117 [Multi-domain]  Cd Length: 199  Bit Score: 50.00  E-value: 3.14e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007  92 IKVGISEPSASLILPKILKAFLADFPKLMVNVSVDDANTCSQKLIDGEIDFAIC----GEPEL-ILENFYFPffhdtLDL 166
Cdd:cd08426    2 VRVATGEGLAAELLPSLIARFRQRYPGVFFTVDVASTADVLEAVLSGEADIGLAfsppPEPGIrVHSRQPAP-----IGA 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007 167 IVSESHPLASRTSVELRDLRDECFIFTPANCPIRiqieQHLKRAIGSDYKKMELTSSMSH----KYFVRENVGVSIFTS- 241
Cdd:cd08426   77 VVPPGHPLARQPSVTLAQLAGYPLALPPPSFSLR----QILDAAFARAGVQLEPVLISNSietlKQLVAAGGGISLLTEl 152

                        170       180
                 ....*....|....*....|....*
gi 345535007 242 TAHSELLDGTvrilIENLPISPPIG 266
Cdd:cd08426  153 AVRREIRRGQ----LVAVPLADPHM 173
PBP2_MleR cd08437
The substrate binding domain of LysR-type transcriptional regulator MleR which required for ...
 92-243 4.46e-07

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: 49.25  E-value: 4.46e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007  92 IKVGISEPSASLILPKILKAFLADfpKLMVNVSVDDANT--CSQKLIDGEIDFAICGEPELIlENFYFP---FFHDTLDL 166
Cdd:cd08437    2 LRFGLPPIIGNYYFPKLAKDLIKT--GLMIQIDTYEGGSaeLLEQLLQGDLDIALLGSLTPL-ENSALHskiIKTQHFMI 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007 167 IVSESHPLASRTSVELRDLRDECFIFTPANCPIR---IQIEQHLKRAIGSDYKKMELTSSmshKYFVRENVGVSIFTSTA 243
Cdd:cd08437   79 IVSKDHPLAKAKKVNFADLKKENFILLNEHFVHPkafDSLCQQANFQPNIVYRTNDIHIL---KSMVRENVGIGFLTDIA 155
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 9-148 6.59e-07

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 49.99  E-value: 6.59e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007   9 FYTVVNTGSFQRAAEVLNYSQPTISMRIKQLEQDLDVQLFER-GKTLKLTHAGRLFYERAGQLIAQYEVLDHTIFDLKNG 87
Cdd:PRK14997  10 FVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRtTRQFNVTEVGQTFYEHCKAMLVEAQAAQDAIAALQVE 89

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 345535007  88 NAGLIKVGISEPSASLILPKILKAFLADFPKlmVNVSVDDANtcsqKLID--GE-IDFAICGEP 148
Cdd:PRK14997  90 PRGIVKLTCPVTLLHVHIGPMLAKFMARYPD--VSLQLEATN----RRVDvvGEgVDVAIRVRP 147
PBP2_CysB_like cd08413
The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains ...
 105-185 1.61e-06

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: 47.62  E-value: 1.61e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007 105 LPKILKAFLADFPKlmVNVSVDDANTCS--QKLIDGEIDFAICGE-----PELILenfyFPFFHDTLDLIVSESHPLASR 177
Cdd:cd08413   15 LPPVIAAFRKRYPK--VKLSLHQGTPSQiaEMVLKGEADIAIATEalddhPDLVT----LPCYRWNHCVIVPPGHPLADL 88


                 ....*...
gi 345535007 178 TSVELRDL 185
Cdd:cd08413   89 GPLTLEDL 96
PBP2_TdcA cd08418
The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is ...
 92-188 1.65e-06

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: 47.73  E-value: 1.65e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007  92 IKVGISEPSASLILPKILKAFLADFPKLMVNVSVDDANTCSQKLIDGEIDFAICGEP-ELILENFYF-PFFHDTLDLIVS 169
Cdd:cd08418    2 VSIGVSSLIAHTLMPAVINRFKEQFPDVQISIYEGQLSSLLPELRDGRLDFAIGTLPdEMYLKELISePLFESDFVVVAR 81

                         90
                 ....*....|....*....
gi 345535007 170 ESHPLASRTSveLRDLRDE 188
Cdd:cd08418   82 KDHPLQGARS--LEELLDA 98
PRK12680 PRK12680
LysR family transcriptional regulator;
21-243 3.26e-06

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 47.69  E-value: 3.26e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007  21 AAEVLNYSQPTISMRIKQLEQDLDVQLFER-GKTLK-LTHAGRLFYERAGQLIAQYEVLDHTIFDLKNGNAGLIKVGISE 98
Cdd:PRK12680  22 AAARVHATQPGLSKQLKQLEDELGFLLFVRkGRSLEsVTPAGVEVIERARAVLSEANNIRTYAANQRRESQGQLTLTTTH 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007  99 PSASLILPKILKAFLADFPKLMVNVSVDDANTCSQKLIDGEIDFAIC----GEPElilENFYFPFFHDTLDLIVSESHPL 174
Cdd:PRK12680 102 TQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVstagGEPS---AGIAVPLYRWRRLVVVPRGHAL 178

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 345535007 175 -ASRTSVELRDLRDECFIFTPANcpirIQIEQHLKRAigsdYKKMELTSSMSH--------KYFVRENVGVSIFTSTA 243
Cdd:PRK12680 179 dTPRRAPDMAALAEHPLISYESS----TRPGSSLQRA----FAQLGLEPSIALtaldadliKTYVRAGLGVGLLAEMA 248
nhaR PRK11062
transcriptional activator NhaR; Provisional
 9-115 3.85e-06

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 47.31  E-value: 3.85e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007   9 FYTVVNTGSFQRAAEVLNYSQPTISMRIKQLEQDLDVQLFER-GKTLKLTHAGRLFYERAGQLIA-QYEVLDhtIFDLKN 86
Cdd:PRK11062  12 FWMVCKEGSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRkGRGLEPTELGELVFRYADKMFTlSQEMLD--IVNYRK 89

                         90       100
                 ....*....|....*....|....*....
gi 345535007  87 GNAGLIKVGISEPSASLILPKILKAFLAD 115
Cdd:PRK11062  90 ESNLLFDVGVADALSKRLVSRVLLTAVPE 118
PBP2_MetR cd08441
The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which ...
 133-194 1.10e-05

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


Pssm-ID: 176132  Cd Length: 198  Bit Score: 45.25  E-value: 1.10e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 345535007 133 QKLIDGEIDFAICGEPELILENFYFPFFHDTLDLIVSESHPLASRTSVELRDLRDECFIFTP 194
Cdd:cd08441   43 PALLRGELDLVITSDPLPLPGIAYEPLFDYEVVLVVAPDHPLAAKEFITPEDLADETLITYP 104
PBP2_LysR cd08456
The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine ...
 105-238 1.29e-05

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


Pssm-ID: 176145 [Multi-domain]  Cd Length: 196  Bit Score: 45.10  E-value: 1.29e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007 105 LPKILKAFLADFPKLMVNVSVDDANTCSQKLIDGEIDFAICG--------EPELILEnfyfpffHDTLdLIVSESHPLAS 176
Cdd:cd08456   15 LPRAIKAFLQRHPDVTISIHTRDSPTVEQWLSAQQCDLGLVStlheppgiERERLLR-------IDGV-CVLPPGHRLAV 86

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 345535007 177 RTSVELRDLRDECFIFTPANCPIRIQI----EQH-LKRAIgsdykKMELTSSMSHKYFVRENVGVSI 238
Cdd:cd08456   87 KKVLTPSDLEGEPFISLARTDGTRQRVdalfEQAgVKRRI-----VVETSYAATICALVAAGVGVSV 148
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 94-178 1.33e-05

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


Pssm-ID: 176109 [Multi-domain]  Cd Length: 200  Bit Score: 44.90  E-value: 1.33e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007  94 VGISEPSASLILPKILKAFLADFPKLMVNVSVDDANTCSQKLIDGEIDFAICGEPELILENFYFPFFHDTLDLIVSESHP 173
Cdd:cd08417    4 IAASDYLEALLLPPLLARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELPPGLRSQPLFEDRFVCVARKDHP 83


                 ....*
gi 345535007 174 LASRT 178
Cdd:cd08417   84 LAGGP 88
PBP2_CysB cd08443
The C-terminal substrate domain of LysR-type transcriptional regulator CysB contains type 2 ...
 92-243 1.33e-05

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: 45.25  E-value: 1.33e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007  92 IKVGISEPSASLILPKILKAFLADFPKLMVNVSVDDANTCSQKLIDGEIDFAICGEPELILENFY-FPFFHDTLDLIVSE 170
Cdd:cd08443    2 LYVATTHTQARYVLPPVIKGFIERYPRVSLQMHQGSPTQIAEMVSKGLVDFAIATEALHDYDDLItLPCYHWNRCVVVKR 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 345535007 171 SHPLASRTSVELRDLRDECFIFTPANCPIRIQIEQHLKRAigSDYKKMELTSSMSH--KYFVRENVGVSIFTSTA 243
Cdd:cd08443   82 DHPLADKQSISIEELATYPIVTYTFGFTGRSELDTAFNRA--GLTPNIVLTATDADviKTYVRLGLGVGVIASMA 154
PBP2_BudR cd08451
The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is ...
 100-194 1.76e-05

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: 44.86  E-value: 1.76e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007 100 SASL--ILPKILKAFLADFPKlmVNVSVDDANTCS--QKLIDGEIDFAI----CGEPE-LILEnfyfPFFHDTLDLIVSE 170
Cdd:cd08451    9 SAAFhpLVPGLIRRFREAYPD--VELTLEEANTAEllEALREGRLDAAFvrppVARSDgLVLE----LLLEEPMLVALPA 82

                         90       100
                 ....*....|....*....|....
gi 345535007 171 SHPLASRTSVELRDLRDECFIFTP 194
Cdd:cd08451   83 GHPLARERSIPLAALADEPFILFP 106
PBP2_AlsR cd08452
The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which ...
 104-194 2.16e-05

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


Pssm-ID: 176143 [Multi-domain]  Cd Length: 197  Bit Score: 44.41  E-value: 2.16e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007 104 ILPKILKAFLADFPKlmVNVSVDDANTCSQ--KLIDGEIDFAICGEP----ELILEnfyfPFFHDTLDLIVSESHPLASR 177
Cdd:cd08452   14 FLPPIVREYRKKFPS--VKVELRELSSPDQveELLKGRIDIGFLHPPiqhtALHIE----TVQSSPCVLALPKQHPLASK 87

                         90
                 ....*....|....*..
gi 345535007 178 TSVELRDLRDECFIFTP 194
Cdd:cd08452   88 EEITIEDLRDEPIITVA 104
PBP2_HcaR cd08450
The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in ...
 99-287 1.29e-04

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


Pssm-ID: 176141 [Multi-domain]  Cd Length: 196  Bit Score: 41.98  E-value: 1.29e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007  99 PSASLI-LPKILKAFLADFPKLMVNVSVDDANTCSQKLIDGEIDFAICgEPELILENFYFPF-FHDTLDLIVSESHPLAS 176
Cdd:cd08450    8 PGAEVQwLPEVLPILREEHPDLDVELSSLFSPQLAEALMRGKLDVAFM-RPEIQSDGIDYQLlLKEPLIVVLPADHRLAG 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007 177 RTSVELRDLRDECFIFTPANCPIRIQ-IEQHLKR---AIGSDYKKMELTSSMShkyFVRENVGVSIFTSTAHSELLDGTV 252
Cdd:cd08450   87 REKIPPQDLAGENFISPAPTAPVLQQvIENYAAQhniQPNIIQEADNLLSAMS---LVASTLGCALLPLYANNLLPPSVV 163

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 345535007 253 -RILIENlpiSPPIGLLTNQKEKDFDSTTKELIDRI 287
Cdd:cd08450  164 aRPLSGE---TPTIDLVMGYNKANTSPLLKRFLSRA 196
PBP2_Chlorocatechol cd08446
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 105-195 2.32e-04

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


Pssm-ID: 176137 [Multi-domain]  Cd Length: 198  Bit Score: 41.50  E-value: 2.32e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007 105 LPKILKAFLADFPKlmVNVSVDDANTCSQ--KLIDGEIDFAIC----GEPELILENFYfpffHDTLDLIVSESHPLASRT 178
Cdd:cd08446   16 VPRLLRAFLTARPD--VTVSLHNMTKDEQieALRAGRIHIGFGrfypVEPDIAVENVA----QERLYLAVPKSHPLAARP 89

                         90
                 ....*....|....*..
gi 345535007 179 SVELRDLRDECFIFTPA 195
Cdd:cd08446   90 AVSLADLRNEPLILFPR 106
PBP2_MdcR cd08416
The C-terminal substrate-binding domian of LysR-type transcriptional regulator MdcR, which ...
 133-191 2.62e-04

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


Pssm-ID: 176108  Cd Length: 199  Bit Score: 41.18  E-value: 2.62e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 345535007 133 QKLIDGEIDFAICGEPELIL-ENF-YFPFFHDTLDLIVSESHPLASRTSVELRDLRDECFI 191
Cdd:cd08416   43 KKLKDGELDAILVATPEGLNdPDFeVVPLFEDDIFLAVPATSPLAASSEIDLRDLKDEKFV 103
PBP2_LTTR_like_2 cd08427
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 104-272 2.74e-04

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: 41.02  E-value: 2.74e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007 104 ILPKILKAFLADFPKLMVNVSVDDANTCSQKLIDGEIDFAICGEPELILE-NFYF-PFFHDTLDLIVSESHPlaSRTSVE 181
Cdd:cd08427   14 LLPRALARLRRRHPDLEVHIVPGLSAELLARVDAGELDAAIVVEPPFPLPkDLVWtPLVREPLVLIAPAELA--GDDPRE 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007 182 LrdLRDECFIFTPANCPIRIQIEQHLKRAIGSDYKKMELTS-----SMshkyfVRENVGVSIFTSTAHSELLDGTVRIL- 255
Cdd:cd08427   92 L--LATQPFIRYDRSAWGGRLVDRFLRRQGIRVREVMELDSleaiaAM-----VAQGLGVAIVPDIAVPLPAGPRVRVLp 164

                        170
                 ....*....|....*..
gi 345535007 256 IENLPISPPIGLLTNQK 272
Cdd:cd08427  165 LGDPAFSRRVGLLWRRS 181
PBP2_DntR_NahR_LinR_like cd08459
The C-terminal substrate binding domain of LysR-type transcriptional regulators that are ...
 103-188 7.86e-04

The C-terminal substrate binding domain of LysR-type transcriptional regulators that are involved in the catabolism of dinitrotoluene, naphthalene and gamma-hexachlorohexane; contains the type 2 periplasmic binding fold; This CD includes LysR-like bacterial transcriptional regulators, DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. DntR from Burkholderia species controls genes encoding enzymes for oxidative degradation of the nitro-aromatic compound 2,4-dinitrotoluene. The active form of DntR is homotetrameric, consisting of a dimer of dimers. NahR is a salicylate-dependent transcription activator of the nah and sal operons for naphthalene degradation. Salicylic acid is an intermediate of the oxidative degradation of the aromatic ring in soil bacteria. LinR positively regulates expression of the genes (linD and linE) encoding enzymes for gamma-hexachlorocyclohexane (a haloorganic insecticide) degradation. Expression of linD and linE are induced by their substrates, 2,5-dichlorohydroquinone (2,5-DCHQ) and chlorohydroquinone (CHQ). The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176148 [Multi-domain]  Cd Length: 201  Bit Score: 39.87  E-value: 7.86e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007 103 LILPKILKAFLADFPKLMVNVSVDDANTCSQKLIDGEIDFAICGEPELILENFYFPFFHDTLDLIVSESHPLAsRTSVEL 182
Cdd:cd08459   13 YFLPRLLAALREVAPGVRIETVRLPVDELEEALESGEIDLAIGYLPDLGAGFFQQRLFRERYVCLVRKDHPRI-GSTLTL 91


                 ....*.
gi 345535007 183 RDLRDE 188
Cdd:cd08459   92 EQFLAA 97
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 90-144 4.78e-03

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


Pssm-ID: 176114 [Multi-domain]  Cd Length: 197  Bit Score: 37.42  E-value: 4.78e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 345535007  90 GLIKVGISEPSASLILPKILKAFLADFPKLMVNVSVDDANTCsqkLIDGEIDFAI 144
Cdd:cd08422    1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVD---LVEEGFDLAI 52
PBP2_Cbl cd08444
The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is ...
 92-185 4.96e-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: 4.96e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007  92 IKVGISEPSASLILPKILKAFLADFPKLMVNVSVDDANTCSQKLIDGEIDFAICGE-----PELILenfyFPFFHDTLDL 166
Cdd:cd08444    2 LTIATTHTQARYALPWVVQAFKEQFPNVHLVLHQGSPEEIASMLANGQADIGIATEalenhPELVS----FPYYDWHHHI 77

                         90
                 ....*....|....*....
gi 345535007 167 IVSESHPLASRTSVELRDL 185
Cdd:cd08444   78 IVPVGHPLESITPLTIETI 96
leuO PRK09508
leucine transcriptional activator; Reviewed
 20-173 5.61e-03

leucine transcriptional activator; Reviewed


Pssm-ID: 181918 [Multi-domain]  Cd Length: 314  Bit Score: 37.69  E-value: 5.61e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007  20 RAAEVLNYSQPTISMRIKQLEQDLDVQLFER-GKTLKLT-HAGRLF--YERAGQLIaQYEvLDHTIFDLKNgNAGLIKVG 95
Cdd:PRK09508  41 RAAHNLGMSQPAVSNAVARLKVMFNDELFVRyGRGIQPTaRARQLFgpVRQALQLV-QNE-LPGSGFEPES-SERVFNLC 117

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007  96 ISEPSASLILPKILKAFLADFPKLMVNV-SVDDANTcSQKLIDGEIDFAIcGEPELILENFY-FPFFHDTLDLIVSESHP 173
Cdd:PRK09508 118 ICSPLDIRLTSQIYNRIEQIAPNIHVVFkSSLNQNI-EHQLRYQETEFVI-SYEEFDRPEFTsVPLFKDELVLVASKNHP 195
PBP2_IlvY cd08430
The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates ...
 104-206 8.64e-03

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


Pssm-ID: 176121  Cd Length: 199  Bit Score: 36.79  E-value: 8.64e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345535007 104 ILPKILKAFLADFPKLMVNVSVDDANTCSQKLIDGEIDFAICGEPELILENFYFpffhdtldlivsesHPLAsrtSVELr 183
Cdd:cd08430   14 FLPPILERFRAQHPQVEIKLHTGDPADAIDKVLNGEADIAIAARPDKLPARLAF--------------LPLA---TSPL- 75

                         90       100
                 ....*....|....*....|....
gi 345535007 184 dlrdeCFIfTPAN-CPIRIQIEQH 206
Cdd:cd08430   76 -----VFI-APNIaCAVTQQLSQG 93
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 89-130 9.74e-03

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 5. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176163 [Multi-domain]  Cd Length: 202  Bit Score: 36.67  E-value: 9.74e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 345535007  89 AGLIKVGISEPSASLILPKILKAFLADFPKLMVNVSVDDANT 130
Cdd:cd08474    2 AGTLRINAPRVAARLLLAPLLARFLARYPDIRLELVVDDGLV 43
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH