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Conserved domains on  [gi|490522780|ref|WP_004388196|]
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MULTISPECIES: LysR substrate-binding domain-containing protein [Cronobacter]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK11482 super family cl32694
DNA-binding transcriptional regulator;
5-300 2.29e-48

DNA-binding transcriptional regulator;


The actual alignment was detected with superfamily member PRK11482:

Pssm-ID: 183159 [Multi-domain]  Cd Length: 317  Bit Score: 164.51  E-value: 2.29e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780   5 QDLKKFDLNLLVIFECIYLYRSVSKAAEALFLTPSAISQSLQRLRNQLNDPLFVRSGKGITPTTVGTNLHHYLEDNLNQL 84
Cdd:PRK11482  24 RTLRNIDLNLLTIFEAVYVHKGIVNAAKILNLTPSAISQSIQKLRVIFPDPLFIRKGQGVTPTAYATHLHEYISQGLESI 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780  85 EQTINIMQGAPLRKNFVLYCPPALAADHLPALVSAFREHYDFELEHydtTLASETVEDLLAYRKADLIIGMAPVASHSLI 164
Cdd:PRK11482 104 LGALDITGSYDKQRTITIATTPSVGALVMPVIYQAIKTHYPQLLLR---NIPISDAENQLSQFQTDLIIDTHSCSNRTIQ 180

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780 165 CKHCFSEETVLVCSENHPRLGEHADEAALAQEKFTLFngTAEGQKQFHVKS--AELFGERQIAFTSNSISSIMAVIGSTD 242
Cdd:PRK11482 181 HHVLFTDNVVLVCRQGHPLLSLEDDEETLDNAEHTLL--LPEGQNFSGLRQrlQEMFPDRQISFSSYNILTIAALIASSD 258

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 490522780 243 FVGILPAPVLRRYRQLFGLRPVKL-NFSLPQYDYYLIYNRSSLTNASFVSFVSLIEQHF 300
Cdd:PRK11482 259 MLGIMPSRFYNLFSRCWPLEKLPFpSLNEEQIDFSLHYNKLSLRDPVLENVIDVIRNAF 317
 
Name Accession Description Interval E-value
PRK11482 PRK11482
DNA-binding transcriptional regulator;
5-300 2.29e-48

DNA-binding transcriptional regulator;


Pssm-ID: 183159 [Multi-domain]  Cd Length: 317  Bit Score: 164.51  E-value: 2.29e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780   5 QDLKKFDLNLLVIFECIYLYRSVSKAAEALFLTPSAISQSLQRLRNQLNDPLFVRSGKGITPTTVGTNLHHYLEDNLNQL 84
Cdd:PRK11482  24 RTLRNIDLNLLTIFEAVYVHKGIVNAAKILNLTPSAISQSIQKLRVIFPDPLFIRKGQGVTPTAYATHLHEYISQGLESI 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780  85 EQTINIMQGAPLRKNFVLYCPPALAADHLPALVSAFREHYDFELEHydtTLASETVEDLLAYRKADLIIGMAPVASHSLI 164
Cdd:PRK11482 104 LGALDITGSYDKQRTITIATTPSVGALVMPVIYQAIKTHYPQLLLR---NIPISDAENQLSQFQTDLIIDTHSCSNRTIQ 180

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780 165 CKHCFSEETVLVCSENHPRLGEHADEAALAQEKFTLFngTAEGQKQFHVKS--AELFGERQIAFTSNSISSIMAVIGSTD 242
Cdd:PRK11482 181 HHVLFTDNVVLVCRQGHPLLSLEDDEETLDNAEHTLL--LPEGQNFSGLRQrlQEMFPDRQISFSSYNILTIAALIASSD 258

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 490522780 243 FVGILPAPVLRRYRQLFGLRPVKL-NFSLPQYDYYLIYNRSSLTNASFVSFVSLIEQHF 300
Cdd:PRK11482 259 MLGIMPSRFYNLFSRCWPLEKLPFpSLNEEQIDFSLHYNKLSLRDPVLENVIDVIRNAF 317
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
10-300 2.41e-45

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 154.64  E-value: 2.41e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780  10 FDLNLLVIFECIYLYRSVSKAAEALFLTPSAISQSLQRLRNQLNDPLFVRSGKGITPTTVGTNLHHYLEDNLNQLEQTIN 89
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780  90 IMQG--APLRKNFVLYCPPALAADHLPALVSAFREHY---DFELehydTTLASETVEDLLAYRKADLIIGMAPVASHSLI 164
Cdd:COG0583   81 ELRAlrGGPRGTLRIGAPPSLARYLLPPLLARFRARHpgvRLEL----REGNSDRLVDALLEGELDLAIRLGPPPDPGLV 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780 165 CKHCFSEETVLVCSENHPrlgehadeaaLAQEKftlfngtaegqkqfhvksaelfgerqiaFTSNSISSIMAVIGSTDFV 244
Cdd:COG0583  157 ARPLGEERLVLVASPDHP----------LARRA----------------------------PLVNSLEALLAAVAAGLGI 198

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 490522780 245 GILPAPVLRRYRQLFGLRPVKLNFSLPQYDYYLIYNRSSLTNASFVSFVSLIEQHF 300
Cdd:COG0583  199 ALLPRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREAL 254
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 104-300 5.84e-24

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: 96.97  E-value: 5.84e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780  104 CPPALAADHLPALVSAFREHY---DFELehydTTLASETVEDLLAYRKADLIIGMAPVASHSLICKHCFSEETVLVCSEN 180
Cdd:pfam03466   8 APPTLASYLLPPLLARFRERYpdvELEL----TEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVAPPD 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780  181 HPRL-GEHADEAALAQEKFTLFNGTAEGQKQFHVKSAELFGERQIAFTSNSISSIMAVIGSTDFVGILPAPVLRRYRQLF 259
Cdd:pfam03466  84 HPLArGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARELADG 163

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 490522780  260 GLRPVKLNFSLPQYDYYLIYNRSSLTNASFVSFVSLIEQHF 300
Cdd:pfam03466 164 RLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREAL 204
PBP2_LeuO cd08466
The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an ...
 99-288 8.22e-24

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


Pssm-ID: 176155 [Multi-domain]  Cd Length: 200  Bit Score: 96.55  E-value: 8.22e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780  99 NFVLYCPPALAADHLPALVSAFREH-YDFELEHydTTLASETVEDLLAYRKADLIIGMAPVASHSLICKHCFSEETVLVC 177
Cdd:cd08466    1 TFNIAANETLDLLLLPRLLARLKQLaPNISLRE--SPSSEEDLFEDLRLQEVDLVIDYVPFRDPSFKSELLFEDELVCVA 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780 178 SENHPRLGEHADEAALAQEKFTLFNGtaegqKQFHVKSAELFGE-----RQIAFTSNSISSIMAVIGSTDFVGILPAPVL 252
Cdd:cd08466   79 RKDHPRIQGSLSLEQYLAEKHVVLSL-----RRGNLSALDLLTEevlpqRNIAYEVSSLLSMLAVVSQTDLIAIAPRWLA 153

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 490522780 253 RRYRQLFGLRPVKLNFSLPQYDYYLIYNRSSLTNAS 288
Cdd:cd08466  154 DQYAEQLNLQILPLPFKTKPIPLYMVWHKSRERDPA 189
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 11-293 4.69e-16

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: 76.89  E-value: 4.69e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780  11 DLNLLVIFECIYLYRSVSKAAEALFLTPSAISQSLQRLRNQLNDPLFVRSGKGITPTTVGTNLHHY------LEDNL--- 81
Cdd:NF040786   2 NLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYakemldLWEKLeee 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780  82 -----NQLEQTINImqGAplrknfvlycpPALAADH-LPALVSAFREHY---DFELEHYDttlaSETVEDLLAYRKADL- 151
Cdd:NF040786  82 fdrygKESKGVLRI--GA-----------STIPGQYlLPELLKKFKEKYpnvRFKLMISD----SIKVIELLLEGEVDIg 144

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780 152 IIGMAPVASHsliCKHC--FSEETVLVC---SENHPRLGEHADEAALAQEKFTLF---NGT-AEGQKQFH---VKSAELf 219
Cdd:NF040786 145 FTGTKLEKKR---LVYTpfYKDRLVLITpngTEKYRMLKEEISISELQKEPFIMReegSGTrKEAEKALKslgISLEDL- 220

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780 220 gerQIAFTSNS----ISSIMAVIGSTdFVGILPAPVLRRYRQLFgLRPVKlnfSLPQY-DYYLIYNRS---SLTNASFVS 291
Cdd:NF040786 221 ---NVVASLGSteaiKQSVEAGLGIS-VISELAAEKEVERGRVL-IFPIP---GLPKNrDFYLVYNKNrqlSPTAEAFLQ 292


                 ..
gi 490522780 292 FV 293
Cdd:NF040786 293 FV 294
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 10-70 5.55e-06

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: 47.22  E-value: 5.55e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 490522780   10 FDLNLLVIFECIYLYRSVSKAAEALFLTPSAISQSLQRLRNQLNDPLFVRsGKGITPTTVG 70
Cdd:TIGR03298   1 LDYRQLAALAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVR-TQPCRATEAG 60
 
Name Accession Description Interval E-value
PRK11482 PRK11482
DNA-binding transcriptional regulator;
5-300 2.29e-48

DNA-binding transcriptional regulator;


Pssm-ID: 183159 [Multi-domain]  Cd Length: 317  Bit Score: 164.51  E-value: 2.29e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780   5 QDLKKFDLNLLVIFECIYLYRSVSKAAEALFLTPSAISQSLQRLRNQLNDPLFVRSGKGITPTTVGTNLHHYLEDNLNQL 84
Cdd:PRK11482  24 RTLRNIDLNLLTIFEAVYVHKGIVNAAKILNLTPSAISQSIQKLRVIFPDPLFIRKGQGVTPTAYATHLHEYISQGLESI 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780  85 EQTINIMQGAPLRKNFVLYCPPALAADHLPALVSAFREHYDFELEHydtTLASETVEDLLAYRKADLIIGMAPVASHSLI 164
Cdd:PRK11482 104 LGALDITGSYDKQRTITIATTPSVGALVMPVIYQAIKTHYPQLLLR---NIPISDAENQLSQFQTDLIIDTHSCSNRTIQ 180

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780 165 CKHCFSEETVLVCSENHPRLGEHADEAALAQEKFTLFngTAEGQKQFHVKS--AELFGERQIAFTSNSISSIMAVIGSTD 242
Cdd:PRK11482 181 HHVLFTDNVVLVCRQGHPLLSLEDDEETLDNAEHTLL--LPEGQNFSGLRQrlQEMFPDRQISFSSYNILTIAALIASSD 258

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 490522780 243 FVGILPAPVLRRYRQLFGLRPVKL-NFSLPQYDYYLIYNRSSLTNASFVSFVSLIEQHF 300
Cdd:PRK11482 259 MLGIMPSRFYNLFSRCWPLEKLPFpSLNEEQIDFSLHYNKLSLRDPVLENVIDVIRNAF 317
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
10-300 2.41e-45

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 154.64  E-value: 2.41e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780  10 FDLNLLVIFECIYLYRSVSKAAEALFLTPSAISQSLQRLRNQLNDPLFVRSGKGITPTTVGTNLHHYLEDNLNQLEQTIN 89
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780  90 IMQG--APLRKNFVLYCPPALAADHLPALVSAFREHY---DFELehydTTLASETVEDLLAYRKADLIIGMAPVASHSLI 164
Cdd:COG0583   81 ELRAlrGGPRGTLRIGAPPSLARYLLPPLLARFRARHpgvRLEL----REGNSDRLVDALLEGELDLAIRLGPPPDPGLV 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780 165 CKHCFSEETVLVCSENHPrlgehadeaaLAQEKftlfngtaegqkqfhvksaelfgerqiaFTSNSISSIMAVIGSTDFV 244
Cdd:COG0583  157 ARPLGEERLVLVASPDHP----------LARRA----------------------------PLVNSLEALLAAVAAGLGI 198

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 490522780 245 GILPAPVLRRYRQLFGLRPVKLNFSLPQYDYYLIYNRSSLTNASFVSFVSLIEQHF 300
Cdd:COG0583  199 ALLPRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREAL 254
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 104-300 5.84e-24

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: 96.97  E-value: 5.84e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780  104 CPPALAADHLPALVSAFREHY---DFELehydTTLASETVEDLLAYRKADLIIGMAPVASHSLICKHCFSEETVLVCSEN 180
Cdd:pfam03466   8 APPTLASYLLPPLLARFRERYpdvELEL----TEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVAPPD 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780  181 HPRL-GEHADEAALAQEKFTLFNGTAEGQKQFHVKSAELFGERQIAFTSNSISSIMAVIGSTDFVGILPAPVLRRYRQLF 259
Cdd:pfam03466  84 HPLArGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARELADG 163

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 490522780  260 GLRPVKLNFSLPQYDYYLIYNRSSLTNASFVSFVSLIEQHF 300
Cdd:pfam03466 164 RLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREAL 204
PBP2_LeuO cd08466
The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an ...
 99-288 8.22e-24

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


Pssm-ID: 176155 [Multi-domain]  Cd Length: 200  Bit Score: 96.55  E-value: 8.22e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780  99 NFVLYCPPALAADHLPALVSAFREH-YDFELEHydTTLASETVEDLLAYRKADLIIGMAPVASHSLICKHCFSEETVLVC 177
Cdd:cd08466    1 TFNIAANETLDLLLLPRLLARLKQLaPNISLRE--SPSSEEDLFEDLRLQEVDLVIDYVPFRDPSFKSELLFEDELVCVA 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780 178 SENHPRLGEHADEAALAQEKFTLFNGtaegqKQFHVKSAELFGE-----RQIAFTSNSISSIMAVIGSTDFVGILPAPVL 252
Cdd:cd08466   79 RKDHPRIQGSLSLEQYLAEKHVVLSL-----RRGNLSALDLLTEevlpqRNIAYEVSSLLSMLAVVSQTDLIAIAPRWLA 153

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 490522780 253 RRYRQLFGLRPVKLNFSLPQYDYYLIYNRSSLTNAS 288
Cdd:cd08466  154 DQYAEQLNLQILPLPFKTKPIPLYMVWHKSRERDPA 189
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 100-283 2.90e-21

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: 89.58  E-value: 2.90e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780 100 FVLYCPPALAADHLPALVSAFREHY---DFELEHYDttlaSETVEDLLAYRKADLIIGMAPVASHSLICKHCFSEETVLV 176
Cdd:cd08417    2 FRIAASDYLEALLLPPLLARLRQEApgvRLRFVPLD----RDDLEEALESGEIDLAIGVFPELPPGLRSQPLFEDRFVCV 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780 177 CSENHPRLGEHADEAALAQEKFTLFNGTAEGQKQFHVKSAELFGERQIAFTSNSISSIMAVIGSTDFVGILPAPVLRRYR 256
Cdd:cd08417   78 ARKDHPLAGGPLTLEDYLAAPHVLVSPRGRGHGLVDDALAELGLSRRVALTVPHFLAAPALVAGTDLIATVPRRLAEALA 157

                        170       180
                 ....*....|....*....|....*..
gi 490522780 257 QLFGLRPVKLNFSLPQYDYYLIYNRSS 283
Cdd:cd08417  158 ERLGLRVLPLPFELPPFTVSLYWHPRR 184
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 104-296 4.93e-20

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


Pssm-ID: 176102 [Multi-domain]  Cd Length: 197  Bit Score: 86.11  E-value: 4.93e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780 104 CPPALAADHLPALVSAFREHY---DFELehydTTLASETVEDLLAYRKADLIIGMAPVASHSLICKHCFSEETVLVCSEN 180
Cdd:cd05466    6 ASPSIAAYLLPPLLAAFRQRYpgvELSL----VEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPPD 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780 181 HPRLGEHA-DEAALAQEKFTLFNGTAEGQKQFHVKSAELFGERQIAFTSNSISSIMAVIGSTDFVGILPAPVLRRYRQlF 259
Cdd:cd05466   82 HPLAKRKSvTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEELAD-G 160

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 490522780 260 GLRPVKLNFSLPQYDYYLIYNRSSLTNASFVSFVSLI 296
Cdd:cd05466  161 GLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
leuO PRK09508
leucine transcriptional activator; Reviewed
 7-283 3.51e-19

leucine transcriptional activator; Reviewed


Pssm-ID: 181918 [Multi-domain]  Cd Length: 314  Bit Score: 86.23  E-value: 3.51e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780   7 LKKFDLNLLVIFECIYLYRSVSKAAEALFLTPSAISQSLQRLRNQLNDPLFVRSGKGITPTTVGTNLHHYLEDNLnQLEQ 86
Cdd:PRK09508  19 LRMVDLNLLTVFDAVMQEQNITRAAHNLGMSQPAVSNAVARLKVMFNDELFVRYGRGIQPTARARQLFGPVRQAL-QLVQ 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780  87 tiNIMQGA---PLRKNFVLY---CPPA---LAA-------DHLPALVSAFREHYDFELEHYdttlasetvedlLAYRKAD 150
Cdd:PRK09508  98 --NELPGSgfePESSERVFNlciCSPLdirLTSqiynrieQIAPNIHVVFKSSLNQNIEHQ------------LRYQETE 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780 151 LIIGMAPVASHSLICKHCFSEETVLVCSENHPRLGEHADEAALAQEKFTL--FNGTAEGQKQFHvKSAELfgERQIAFTS 228
Cdd:PRK09508 164 FVISYEEFDRPEFTSVPLFKDELVLVASKNHPRIKGPITEEQLYNEQHAVvsLDRFASFSQPWY-DTVDK--QASIAYQG 240

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 490522780 229 NSISSIMAVIGSTDFVGILPAPVLRRYRQLFGLRPVKLNFSLPQYDYYLIYNRSS 283
Cdd:PRK09508 241 TALSSVLNVVSQTHLVAIAPRWLAEEFAESLELQILPLPLKNNSRTCYLSWHESA 295
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
12-70 5.65e-18

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 76.27  E-value: 5.65e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 490522780   12 LNLLVIFECIYLYRSVSKAAEALFLTPSAISQSLQRLRNQLNDPLFVRSGKGITPTTVG 70
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 11-293 4.69e-16

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: 76.89  E-value: 4.69e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780  11 DLNLLVIFECIYLYRSVSKAAEALFLTPSAISQSLQRLRNQLNDPLFVRSGKGITPTTVGTNLHHY------LEDNL--- 81
Cdd:NF040786   2 NLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYakemldLWEKLeee 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780  82 -----NQLEQTINImqGAplrknfvlycpPALAADH-LPALVSAFREHY---DFELEHYDttlaSETVEDLLAYRKADL- 151
Cdd:NF040786  82 fdrygKESKGVLRI--GA-----------STIPGQYlLPELLKKFKEKYpnvRFKLMISD----SIKVIELLLEGEVDIg 144

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780 152 IIGMAPVASHsliCKHC--FSEETVLVC---SENHPRLGEHADEAALAQEKFTLF---NGT-AEGQKQFH---VKSAELf 219
Cdd:NF040786 145 FTGTKLEKKR---LVYTpfYKDRLVLITpngTEKYRMLKEEISISELQKEPFIMReegSGTrKEAEKALKslgISLEDL- 220

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780 220 gerQIAFTSNS----ISSIMAVIGSTdFVGILPAPVLRRYRQLFgLRPVKlnfSLPQY-DYYLIYNRS---SLTNASFVS 291
Cdd:NF040786 221 ---NVVASLGSteaiKQSVEAGLGIS-VISELAAEKEVERGRVL-IFPIP---GLPKNrDFYLVYNKNrqlSPTAEAFLQ 292


                 ..
gi 490522780 292 FV 293
Cdd:NF040786 293 FV 294
PRK10216 PRK10216
HTH-type transcriptional regulator YidZ;
7-84 1.52e-13

HTH-type transcriptional regulator YidZ;


Pssm-ID: 182312 [Multi-domain]  Cd Length: 319  Bit Score: 70.23  E-value: 1.52e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780   7 LKKFDLNLLVIFECIYLYRSVSKAAEALFLTPSAISQSLQRLRNQLNDPLFVRSGKGITPTTVGTNLHHYLEDNL---NQ 83
Cdd:PRK10216   5 LTTLDLNLLLCLQLLMQERSVTKAAKRMNVTPSAVSKSLAKLRAWFDDPLFVNTPLGLSPTPLMVSMEQNLAEWMqmgNQ 84


                 .
gi 490522780  84 L 84
Cdd:PRK10216  85 L 85
PBP2_DntR_NahR_LinR_like cd08459
The C-terminal substrate binding domain of LysR-type transcriptional regulators that are ...
 113-274 5.13e-13

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: 66.83  E-value: 5.13e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780 113 LPALVSAFRE---HYDFELEhydtTLASETVEDLLAYRKADLIIGMAPVASHSLICKHCFSEETVLVCSENHPRLGEHAD 189
Cdd:cd08459   15 LPRLLAALREvapGVRIETV----RLPVDELEEALESGEIDLAIGYLPDLGAGFFQQRLFRERYVCLVRKDHPRIGSTLT 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780 190 EAALAQEKFTLFNGTAEGQKQFHVKSAELFGERQIAFTSNSISSIMAVIGSTDFVGILPAPVLRRYRQLFGLRPVKLNFS 269
Cdd:cd08459   91 LEQFLAARHVVVSASGTGHGLVEQALREAGIRRRIALRVPHFLALPLIVAQTDLVATVPERLARLFARAGGLRIVPLPFP 170


                 ....*
gi 490522780 270 LPQYD 274
Cdd:cd08459  171 LPPFE 175
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 25-300 8.38e-13

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 67.67  E-value: 8.38e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780  25 RSVSKAAEALFLTPSAISQSLQRLRNQLNDPLFVRSGKGITPTTVGTNLHHYLEDNLNQLE---QTINIMQGAPlRKNFV 101
Cdd:PRK11242  16 GNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEagrRAIHDVADLS-RGSLR 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780 102 LYCPPALAADHLPALVSAFREHY-DFELEHYDTTLasETVEDLLAYRKADLIIGMAPVASHSLICKHCFSEETVLVCSEN 180
Cdd:PRK11242  95 LAMTPTFTAYLIGPLIDAFHARYpGITLTIREMSQ--ERIEALLADDELDVGIAFAPVHSPEIEAQPLFTETLALVVGRH 172

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780 181 HPRLGEHAD--EAALAQEKFTLFngTAEGQKQFHVksAELFGER----QIAFTSNSISSIMAVIGSTDFVGILPAPVLRR 254
Cdd:PRK11242 173 HPLAARRKAltLDELADEPLVLL--SAEFATREQI--DRYFRRHgvtpRVAIEANSISAVLEIVRRGRLATLLPAAIARE 248

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*.
gi 490522780 255 YRqlfGLRPVKLNFSLPQYDYYLIYNRSSLTNASFVSFVSLIEQHF 300
Cdd:PRK11242 249 HD---GLCAIPLDPPLPQRTAALLRRKGAYRSAAARAFIELALERR 291
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
7-178 2.60e-12

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 66.18  E-value: 2.60e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780   7 LKKFDLNLLVIFECIYLYRSVSKAAEALFLTPSAISQSLQRLRNQLNDPLFVRSGKGITPTTVGTNLHHYLEDNLNQLEQ 86
Cdd:PRK10086  11 LNGWQLSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLDTLNQ 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780  87 TINIMQGAPLRKNFVLYCPPALAADHL-PALVSAFREHYDFELehyDTTLASETVEdlLAYRKADLIIGMAPVASHSLIC 165
Cdd:PRK10086  91 EILDIKNQELSGTLTVYSRPSIAQCWLvPRLADFTRRYPSISL---TILTGNENVN--FQRAGIDLAIYFDDAPSAQLTH 165

                        170
                 ....*....|...
gi 490522780 166 KHCFSEETVLVCS 178
Cdd:PRK10086 166 HFLMDEEILPVCS 178
PBP2_TdcA cd08418
The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is ...
 113-299 9.75e-11

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: 60.06  E-value: 9.75e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780 113 LPALVSAFRE-HYDFELEHYDTTLASeTVEDLLAYRkADLIIGMAP--VASHSLICKHCFSEETVLVCSENHPRLGEHAD 189
Cdd:cd08418   15 MPAVINRFKEqFPDVQISIYEGQLSS-LLPELRDGR-LDFAIGTLPdeMYLKELISEPLFESDFVVVARKDHPLQGARSL 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780 190 EAaLAQEKFTLfNGTAEGQKQFHVKSAELFGER-QIAFTSNSISSIMAVIGSTDFVGILPAPVLRRYRQLFGLRPVKLNF 268
Cdd:cd08418   93 EE-LLDASWVL-PGTRMGYYNNLLEALRRLGYNpRVAVRTDSIVSIINLVEKADFLTILSRDMGRGPLDSFRLITIPVEE 170

                        170       180       190
                 ....*....|....*....|....*....|.
gi 490522780 269 SLPQYDYYLIYNRSSLTNASFVSFVSLIEQH 299
Cdd:cd08418  171 PLPSADYYLIYRKKSRLTPLAEQLVELFRRY 201
PRK10341 PRK10341
transcriptional regulator TdcA;
15-299 1.75e-09

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 57.95  E-value: 1.75e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780  15 LVIFECIYLYRSVSKAAEALFLTPSAISQSLQRLRNQLNDPLFVRSGKGITPTTVGTNLHHYLEDNLNQLEQTINIMQGA 94
Cdd:PRK10341  12 LVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEINGM 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780  95 PLR--KNFVLYCPPALAADHLPALVSAFREHY-DFELEHYDTTLASEtvedLLAYR--KADLIIG--MAPVASHSLICKH 167
Cdd:PRK10341  92 SSEavVDVSFGFPSLIGFTFMSDMINKFKEVFpKAQVSMYEAQLSSF----LPAIRdgRLDFAIGtlSNEMKLQDLHVEP 167

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780 168 CFSEETVLVCSENHP-----RLGEHADEA-ALAQEKFTLFNGTAEGQKQFHVKSAElfgerqiAFTSNSISSIMAVIGST 241
Cdd:PRK10341 168 LFESEFVLVASKSRTctgttTLESLKNEQwVLPQTNMGYYSELLTTLQRNGISIEN-------IVKTDSVVTIYNLVLNA 240

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 490522780 242 DFVGILPAPVLRRyrqlFG---LRPVKLNFSLPQYDYYLIYNRSSLTNASFVSFVSLIEQH 299
Cdd:PRK10341 241 DFLTVIPCDMTSP----FGsnqFITIPIEETLPVAQYAAVWSKNYRIKKAASVLVELAKEY 297
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 113-296 2.84e-09

C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which activates the transcription of the cysJI operon encoding sulfite reductase, contains the type 2 periplasmic binding fold; CysL, also known as YwfK, is a regular of sulfur metabolism in Bacillus subtilis. Sulfur is required for the synthesis of proteins and essential cofactors in all living organism. Sulfur can be assimilated either from inorganic sources (sulfate and thiosulfate), or from organic sources (sulfate esters, sulfamates, and sulfonates). CysL activates the transcription of the cysJI operon encoding sulfite reductase, which reduces sulfite to sulfide. Both cysL mutant and cysJI mutant are unable to grow using sulfate or sulfite as the sulfur source. Like other LysR-type regulators, CysL also negatively regulates its own transcription. In Escherichia coli, three LysR-type activators are involved in the regulation of sulfur metabolism: CysB, Cbl and MetR. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176112 [Multi-domain]  Cd Length: 201  Bit Score: 55.96  E-value: 2.84e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780 113 LPALVSAFREHY---DFELEHYDTtlasETVEDLLAYRKADL-IIGmAPVASHSLICKHCFSEETVLVCSENHP--RLGE 186
Cdd:cd08420   15 LPRLLARFRKRYpevRVSLTIGNT----EEIAERVLDGEIDLgLVE-GPVDHPDLIVEPFAEDELVLVVPPDHPlaGRKE 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780 187 hADEAALAQEKFTLF---NGTAEGQKQFhVKSAELFGER-QIAFTSNSISSIMAVIGSTDFVGILPAPVLRRYRQLFGLR 262
Cdd:cd08420   90 -VTAEELAAEPWILRepgSGTREVFERA-LAEAGLDGLDlNIVMELGSTEAIKEAVEAGLGISILSRLAVRKELELGRLV 167

                        170       180       190
                 ....*....|....*....|....*....|....
gi 490522780 263 PVKLNFSLPQYDYYLIYNRSSLTNASFVSFVSLI 296
Cdd:cd08420  168 ALPVEGLRLTRPFSLIYHKDKYLSPAAEAFLEFL 201
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 26-195 8.32e-09

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 55.84  E-value: 8.32e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780  26 SVSKAAEALFLTPSAISQSLQRLRNQLNDPLFVRSGKGITPTTVGTNLHHYLEDNLNQLEQTINIMQGA--PLRKNFVLY 103
Cdd:PRK11233  17 SLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQLAVHNVgqALSGQVSIG 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780 104 CPPALAADHL--PALVSAFREHYDFEL---EHYDTTLAsetveDLLAYRKADL--IIGMAPVasHSLICKHCFSEETVLV 176
Cdd:PRK11233  97 LAPGTAASSLtmPLLQAVRAEFPGIVLylhENSGATLN-----EKLMNGQLDMavIYEHSPV--AGLSSQPLLKEDLFLV 169

                        170
                 ....*....|....*....
gi 490522780 177 CSENHPrlGEHADEAALAQ 195
Cdd:PRK11233 170 GTQDCP--GQSVDLAAVAQ 186
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
35-157 1.38e-08

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 54.82  E-value: 1.38e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780  35 FLTPSAISQSLQRLRNQLNDPLFVRSGKGITPTTVGTNLHHYLEDNLN---QLEQTINiMQGAPLRKNFVLYCPPALAAD 111
Cdd:PRK11716   2 HVSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLqwqQLRHTLD-QQGPSLSGELSLFCSVTAAYS 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 490522780 112 HLPALVSAFREHY---DFELEHYDTTLASETVEDllayRKADLIIGMAP 157
Cdd:PRK11716  81 HLPPILDRFRAEHplvEIKLTTGDAADAVEKVQS----GEADLAIAAKP 125
PBP2_CynR cd08425
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, ...
 115-296 1.45e-08

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


Pssm-ID: 176116  Cd Length: 197  Bit Score: 53.87  E-value: 1.45e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780 115 ALVSAFREHY-DFELEHYDTTLasETVEDLLAYRKADLIIGMAPVASHSLICKHCFSEETVLVCSENHPRLGEHADEAA- 192
Cdd:cd08425   18 PLIDRFHARYpGIALSLREMPQ--ERIEAALADDRLDLGIAFAPVRSPDIDAQPLFDERLALVVGATHPLAQRRTALTLd 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780 193 -LAQEKFTLFngTAEGQKQFHVksAELFGER----QIAFTSNSISSIMAVIGSTDFVGILPAPVLRRYRqlfGLRPVKLN 267
Cdd:cd08425   96 dLAAEPLALL--SPDFATRQHI--DRYFQKQgikpRIAIEANSISAVLEVVRRGRLATILPDAIAREQP---GLCAVALE 168

                        170       180
                 ....*....|....*....|....*....
gi 490522780 268 FSLPQYDYYLIYNRSSLTNASFVSFVSLI 296
Cdd:cd08425  169 PPLPGRTAALLRRKGAYRSAAARAFAALA 197
PRK09791 PRK09791
LysR family transcriptional regulator;
12-283 5.87e-08

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 53.23  E-value: 5.87e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780  12 LNLLVIFECIYLYRSVSKAAEALFLTPSAISQSLQRLRNQLNDPLFVRSGKGITPTTVGTNLHHY--------------L 77
Cdd:PRK09791   7 IHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHaslileelraaqedI 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780  78 EDNLNQLEQTINIMQGAplrknfvlycppALAADHLPALVSAF-REHYDFELEHYDTTLASETVEdlLAYRKADLIIGMA 156
Cdd:PRK09791  87 RQRQGQLAGQINIGMGA------------SIARSLMPAVISRFhQQHPQVKVRIMEGQLVSMINE--LRQGELDFTINTY 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780 157 PVAS--HSLICKHCFSEETVLVCSENHPRLGEHADEAALAQEkFTLFNGTAEGQKQFHVKSAELFGERQIAFTSNSISSI 234
Cdd:PRK09791 153 YQGPydHEFTFEKLLEKQFAVFCRPGHPAIGARSLKQLLDYS-WTMPTPHGSYYKQLSELLDDQAQTPQVGVVCETFSAC 231

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*....
gi 490522780 235 MAVIGSTDFVGILPAPVLRRYRQLFGLRPVKLNFSLPQYDYYLIYNRSS 283
Cdd:PRK09791 232 ISLVAKSDFLSILPEEMGCDPLHGQGLVMLPVSEILPKATYYLIQRRDT 280
nhaR PRK11062
transcriptional activator NhaR; Provisional
 26-70 2.49e-07

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 51.16  E-value: 2.49e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 490522780  26 SVSKAAEALFLTPSAISQSLQRLRNQLNDPLFVRSGKGITPTTVG 70
Cdd:PRK11062  20 SVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELG 64
rbcR CHL00180
LysR transcriptional regulator; Provisional
 10-87 2.79e-07

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 51.17  E-value: 2.79e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 490522780  10 FDLNLLVIFECIYLYRSVSKAAEALFLTPSAISQSLQRLRNQLNDPLFVRSGKGITPTTVGTNLHHYLEDNLNQLEQT 87
Cdd:CHL00180   5 FTLDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEET 82
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 26-200 4.19e-06

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 47.38  E-value: 4.19e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780  26 SVSKAAEALFLTPSAISQSLQRLRNQLNDPLFVRSGKGITpttvgTNLHHYL--EDNLNQLEQTINIMQ------GApLR 97
Cdd:PRK10837  19 STTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLV-----VNEHGRLlyPRALALLEQAVEIEQlfrednGA-LR 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780  98 knfvLYCPPALAADHLPALVSAFREHY-DFELE-HYDTTLasETVEDLLAYRkADLIIGMAPVASHSLICKHCFSEETVL 175
Cdd:PRK10837  93 ----IYASSTIGNYILPAMIARYRRDYpQLPLElSVGNSQ--DVINAVLDFR-VDIGLIEGPCHSPELISEPWLEDELVV 165

                        170       180
                 ....*....|....*....|....*
gi 490522780 176 VCSENHPRLGEHADEAALAQEKFTL 200
Cdd:PRK10837 166 FAAPDSPLARGPVTLEQLAAAPWIL 190
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 108-202 4.92e-06

The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA expression of glutamate synthase operon, contains type 2 periplasmic binding fold; GltC, a member of the LysR family of bacterial transcriptional factors, activates the expression of gltA gene of glutamate synthase operon and is essential for cell growth in the absence of glutamate. Glutamate synthase is a heterodimeric protein that encoded by gltA and gltB, whose expression is subject to nutritional regulation. GltC also negatively auto-regulates its own expression. This substrate-binding domain has strong homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176125 [Multi-domain]  Cd Length: 195  Bit Score: 46.38  E-value: 4.92e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780 108 LAADHLPALVSAFREHY---DFELEHYdttlASETVEDLLAYRKADLIIGMAPVASHSLICKHCFSEETVLVCSENHPRL 184
Cdd:cd08434   10 LGTSLVPDLIRAFRKEYpnvTFELHQG----STDELLDDLKNGELDLALCSPVPDEPDIEWIPLFTEELVLVVPKDHPLA 85

                         90
                 ....*....|....*....
gi 490522780 185 GEHA-DEAALAQEKFTLFN 202
Cdd:cd08434   86 GRDSvDLAELADEPFVLLS 104
PBP2_SyrM cd08467
The C-terminal substrate binding of LysR-type symbiotic regulator SyrM, which activates ...
 113-279 5.18e-06

The C-terminal substrate binding of LysR-type symbiotic regulator SyrM, which activates expression of nodulation gene NodD3, contains the type 2 periplasmic binding fold; Rhizobium is a nitrogen fixing bacteria present in the roots of leguminous plants, which fixes atmospheric nitrogen to the soil. Most Rhizobium species possess multiple nodulation (nod) genes for the development of nodules. For example, Rhizobium meliloti possesses three copies of nodD genes. NodD1 and NodD2 activate nod operons when Rhizobium is exposed to inducers synthesized by the host plant, while NodD3 acts independent of plant inducers and requires the symbiotic regulator SyrM for nod gene expression. SyrM activates the expression of the regulatory nodulation gene nodD3. In turn, NodD3 activates expression of syrM. In addition, SyrM is involved in exopolysaccharide synthesis. 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: 176156 [Multi-domain]  Cd Length: 200  Bit Score: 46.28  E-value: 5.18e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780 113 LPALVSAFRE---HYDFELEHYDTTLAsetvEDLLAYRKADLIIGMAPVASHSLICKHCFSEETVLVCSENHPRLGEHAD 189
Cdd:cd08467   15 LPRLAPRLRErapGLDLRLCPIGDDLA----ERGLEQGTIDLAVGRFAVPPDGLVVRRLYDDGFACLVRHGHPALAQEWT 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780 190 EAALAQEKFTLFNGTAEGQKQFHVKSAELFGERQIAFTSNSISSIMAVIGSTDFVGILPAPVLRRYRQLFGLRPVKLNFS 269
Cdd:cd08467   91 LDDFATLRHVAIAPPGRLFGGIYKRLENLGLKRNVAIAVSSFLTAAATVAATDLIATVPRRVATQVAAMLPLRVVPPPVD 170

                        170
                 ....*....|
gi 490522780 270 LPQYDYYLIY 279
Cdd:cd08467  171 LGTFPVMLIW 180
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 10-70 5.55e-06

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: 47.22  E-value: 5.55e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 490522780   10 FDLNLLVIFECIYLYRSVSKAAEALFLTPSAISQSLQRLRNQLNDPLFVRsGKGITPTTVG 70
Cdd:TIGR03298   1 LDYRQLAALAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVR-TQPCRATEAG 60
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 28-303 6.99e-06

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 46.69  E-value: 6.99e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780  28 SKAAEALFLTPSAISQSLQRLRNQLNDPLFVRSGKGITPTTVGtnlHHYLEDNLNQLEQTINIMQGA--------PLRKN 99
Cdd:PRK09906  19 TKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAG---EVFLQDARAILEQAEKAKLRArkivqedrQLTIG 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780 100 FVlycpPALAADHLPALVSAFRehydfeLEHYDTT--LAS-ETVEDLLAYRKADLIIGMA--PVASHSLICKHCFSEETV 174
Cdd:PRK09906  96 FV----PSAEVNLLPKVLPMFR------LRHPDTLieLVSlITTQQEEKLRRGELDVGFMrhPVYSDEIDYLELLDEPLV 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780 175 LVCSENHP-RLGEHADEAALAQEKFTLFNGTAEGQKQFHVKsaELFGERQIAF----TSNSISSIMAVIGSTDFVGILPA 249
Cdd:PRK09906 166 VVLPVDHPlAHEKEITAAQLDGVNFISTDPAYSGSLAPIIK--AWFAQHNSQPnivqVATNILVTMNLVGMGLGCTIIPG 243

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....
gi 490522780 250 PVLRRYRQLFGLRPvkLNFSLPQYDYYLIYNRSSLTNAsFVSFVSLIEQHFLRD 303
Cdd:PRK09906 244 YMNNFNTGQVVFRP--LAGNVPSIALLMAWKKGEMKPA-LRDFIAIVQERLASV 294
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 27-187 7.29e-06

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 46.96  E-value: 7.29e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780  27 VSKAAEALFLTPSAISQSLQRLRNQLNDPLFVRSGKGITP-TTVGTNLHHYLE------DNLNQLEQTINIMQGAPLrkn 99
Cdd:PRK12683  19 LTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTGlTEPGKELLQIVErmlldaENLRRLAEQFADRDSGHL--- 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780 100 fvlycppALAADH------LPALVSAFREHYDfelehyDTTLA------SETVEDLLAyRKADLIIGMAPVASHS-LICK 166
Cdd:PRK12683  96 -------TVATTHtqaryaLPKVVRQFKEVFP------KVHLAlrqgspQEIAEMLLN-GEADIGIATEALDREPdLVSF 161

                        170       180
                 ....*....|....*....|.
gi 490522780 167 HCFSEETVLVCSENHPRLGEH 187
Cdd:PRK12683 162 PYYSWHHVVVVPKGHPLTGRE 182
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
24-99 8.39e-06

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 46.50  E-value: 8.39e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 490522780  24 YRSVSKAAEALFLTPSAISQSLQRLRNQLNDPLFVRsGKGITPTTVGTNLHHYLEdnlnqleqTINIMQGAPLRKN 99
Cdd:PRK13348  16 TGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQRLLRHLR--------QVALLEADLLSTL 82
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 106-281 1.10e-05

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: 45.58  E-value: 1.10e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780 106 PALAADHLPALVSAFREHY---DFELEHYDTtlaSETVEDLLAyRKADLIIGMAPVASHSLICKHCFSEETVLVCSENHP 182
Cdd:cd08414    8 GSALYGLLPRLLRRFRARYpdvELELREMTT---AEQLEALRA-GRLDVGFVRPPPDPPGLASRPLLREPLVVALPADHP 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780 183 RLG-EHADEAALAQEKFTLFngTAEGQKQFHVKSAELFGER----QIAFTSNSISSIMAVIGSTDFVGILPAPVLRRYRQ 257
Cdd:cd08414   84 LAArESVSLADLADEPFVLF--PREPGPGLYDQILALCRRAgftpRIVQEASDLQTLLALVAAGLGVALVPASVARLQRP 161

                        170       180
                 ....*....|....*....|....
gi 490522780 258 LFGLRPVKLnfSLPQYDYYLIYNR 281
Cdd:cd08414  162 GVVYRPLAD--PPPRSELALAWRR 183
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 104-182 1.10e-05

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


Pssm-ID: 176131 [Multi-domain]  Cd Length: 197  Bit Score: 45.21  E-value: 1.10e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780 104 CPPALAADHLPALVSAFREHY-DFELEHYDTTlaSETVEDLLAYRKADLIIGMAPVASHSLICKHCFSEETVLVCSENHP 182
Cdd:cd08440    6 ALPSLAATLLPPVLAAFRRRHpGIRVRLRDVS--AEQVIEAVRSGEVDFGIGSEPEADPDLEFEPLLRDPFVLVCPKDHP 83
PBP2_YofA_SoxR_like cd08442
The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, ...
 109-296 3.51e-05

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: 43.75  E-value: 3.51e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780 109 AADHLPALVSAFREHY---DFELEhydtTLASET-VEDLLAYR-KADLIIGmaPVASHSLICKHCFSEETVLVCSENHPR 183
Cdd:cd08442   11 AAVRLPPLLAAYHARYpkvDLSLS----TGTTGAlIQAVLEGRlDGAFVAG--PVEHPRLEQEPVFQEELVLVSPKGHPP 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780 184 LGEHADeaaLAQEKFTLF-NGTAEGQKQFHVKSAELFGERQIaFTSNSISSIMAVIGSTDFVGILPAPVLRRYRQLFGLR 262
Cdd:cd08442   85 VSRAED---LAGSTLLAFrAGCSYRRRLEDWLAEEGVSPGKI-MEFGSYHAILGCVAAGMGIALLPRSVLDSLQGRGSVS 160

                        170       180       190
                 ....*....|....*....|....*....|....
gi 490522780 263 PVKLNFSLPQYDYYLIYNRSSLTNAsFVSFVSLI 296
Cdd:cd08442  161 IHPLPEPFADVTTWLVWRKDSFTAA-LQAFLDLL 193
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
26-182 5.36e-05

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 44.03  E-value: 5.36e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780  26 SVSKAAEALFLTPSAISQSLQRLRNQLNDPLFVRSGKGITPTTVGTNLHHYLEDNLNQLE------QTINimQGAPLRKN 99
Cdd:PRK10094  18 SFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLEsmpselQQVN--DGVERQVN 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780 100 FV----LYCPPALAadhlpALVSAFREHYDFELEHYdTTLASETVEDLLAYRKADLIIGMA---PVASHSLICKhCFSEE 172
Cdd:PRK10094  96 IVinnlLYNPQAVA-----QLLAWLNERYPFTQFHI-SRQIYMGVWDSLLYEGFSLAIGVTgteALANTFSLDP-LGSVQ 168

                        170
                 ....*....|
gi 490522780 173 TVLVCSENHP 182
Cdd:PRK10094 169 WRFVMAADHP 178
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 12-70 7.68e-05

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 43.68  E-value: 7.68e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 490522780  12 LNLLVIFECIYLYRSVSKAAEALFLTPSAISQSLQRLRNQLNDPLFVRSGKGITPTTVG 70
Cdd:PRK11139   8 LNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEG 66
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 11-76 7.77e-05

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 43.86  E-value: 7.77e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 490522780  11 DLNLLVIFECIYLYRSVSKAAEALFLTPSAISQSLQRLRNQLNDPLFVRSGKGITPTTVGTNLHHY 76
Cdd:PRK15092  12 DLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGY 77
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
25-82 9.10e-05

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 43.47  E-value: 9.10e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 490522780  25 RSVSKAAEALFLTPSAISQSLQRLRNQLNDPLFVRSGKGITPTTVGTNLHHYLEDNLN 82
Cdd:PRK03601  16 RHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYAETLMN 73
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
29-86 1.00e-04

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 43.22  E-value: 1.00e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 490522780  29 KAAEALFLTPSAISQSLQRLRNQLNDPLFVRsGKGITPTTVGTNL-HHYleDNLNQLEQ 86
Cdd:PRK03635  21 RAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRLlRHA--RQVRLLEA 76
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 27-196 1.75e-04

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 42.67  E-value: 1.75e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780  27 VSKAAEALFLTPSAISQSLQRLRNQLNDPLFVRSGKGITP-TTVGTNLHHYLE------DNLNQLEQTINIMQGAPLrkn 99
Cdd:PRK12682  19 LTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKGlTEPGKAVLDVIErilrevGNIKRIGDDFSNQDSGTL--- 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780 100 fVLYCPPALAADHLPALVSAFREHYDfelehyDTTLA-----SETVEDLLAYRKADLIIGMAPVASH-SLICKHCFSEET 173
Cdd:PRK12682  96 -TIATTHTQARYVLPRVVAAFRKRYP------KVNLSlhqgsPDEIARMVISGEADIGIATESLADDpDLATLPCYDWQH 168

                        170       180
                 ....*....|....*....|....
gi 490522780 174 VLVCSENHP-RLGEHADEAALAQE 196
Cdd:PRK12682 169 AVIVPPDHPlAQEERITLEDLAEY 192
PBP2_DntR_like_2 cd08464
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 139-298 2.81e-04

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


Pssm-ID: 176153 [Multi-domain]  Cd Length: 200  Bit Score: 41.45  E-value: 2.81e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780 139 TVEDLLAYRKADLIIGMAPVASHSLICKHCFSEETVLVCSENHPRLGEHADEAALAQEKFTL--FNGTAEG--QKQFhvk 214
Cdd:cd08464   40 NVGDMLDRGEIDLAIGVFGELPAWLKREVLYTEGYACLFDPQQLSLSAPLTLEDYVARPHVLvsYRGGLRGfvDDAL--- 116

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780 215 sAELFGERQIAFTSNSISSIMAVIGSTDFVGILPAPVLRRYRQLFGLRPVKLNFSLPQYDYYLIYNRSSLTNASFVSFVS 294
Cdd:cd08464  117 -AELGRSRRVVASTPHFAALPALLRGTPLIATVPARLARAWAAALGLRASPPPLDLPEFPISLLWHARTDNDPALVWLRE 195


                 ....
gi 490522780 295 LIEQ 298
Cdd:cd08464  196 QIVQ 199
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
26-184 2.88e-04

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 41.89  E-value: 2.88e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780  26 SVSKAAEALFLTPSAISQSLQRLRNQLNDPLFVRSGKGITPTTV-GTNLHHYLE------DNLNQL-EQTINIMQGaplr 97
Cdd:PRK12684  18 NLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRGLTEpGRIILASVErilqevENLKRVgKEFAAQDQG---- 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780  98 kNFVlycppaLAADH------LPALVSAFREHY-DFELEHYDTTLASetVEDLLAYRKADLIIGMAPVASHS-LICKHCF 169
Cdd:PRK12684  94 -NLT------IATTHtqaryaLPAAIKEFKKRYpKVRLSILQGSPTQ--IAEMVLHGQADLAIATEAIADYKeLVSLPCY 164

                        170
                 ....*....|....*
gi 490522780 170 SEETVLVCSENHPRL 184
Cdd:PRK12684 165 QWNHCVVVPPDHPLL 179
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 113-197 1.63e-03

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: 39.05  E-value: 1.63e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780 113 LPALVSAFREHY-DFELE-HYDTTlasETVEDLLAYRKADLIIGMAPVASHSLICKHCFSEETVLVCSENHP-RLGEHAD 189
Cdd:cd08411   16 LPRLLPALRQAYpKLRLYlREDQT---ERLLEKLRSGELDAALLALPVDEPGLEEEPLFDEPFLLAVPKDHPlAKRKSVT 92


                 ....*...
gi 490522780 190 EAALAQEK 197
Cdd:cd08411   93 PEDLAGER 100
PBP2_DntR_like_3 cd08461
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 135-274 4.22e-03

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


Pssm-ID: 176150 [Multi-domain]  Cd Length: 198  Bit Score: 37.65  E-value: 4.22e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522780 135 LASETVEDLLAYRKADLIIGMAPVASHSLICKHCFSEETVLVCSENHPRLGEHADEAALAQEKFTL-------FNGTAEg 207
Cdd:cd08461   36 LESDNLEAQLERGEVDLALTTPEYAPDGLRSRPLFEERYVCVTRRGHPLLQGPLSLDQFCALDHIVvspsgggFAGSTD- 114

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 490522780 208 qKQFhvksAELFGERQIAFTSNSISSIMAVIGSTDFVGILPApvlRRYRQLFGLRPVKLNFSLPQYD 274
Cdd:cd08461  115 -EAL----AALGLTRNVVLSVPSFLVVPEILAATDMVAFVPS---RLVPNLEGLQEVELPLEPPGFD 173
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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