NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|489247162|ref|WP_003155320|]
View 

MULTISPECIES: LysR family transcriptional regulator [Bacillus]

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];
1-288 2.02e-55

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 179.68  E-value: 2.02e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162   1 MDFKWLHTFVTAAKYENFRKTAETLFLSQPTVTVHIKLLEKEISCKLFQRSGRKIQLTEEGKAYVPFAMRLLEDYENSMA 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162  81 ELHRVRQGYSHTLTLAVSPLIADTVLPSVMKRYTEDNKETEMTVTIFESEEIASQIRNGSADIGLSCLKVQSSSLTCLPL 160
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162 161 YNDPVVLVAPPGrkpgtgkadevkdlfgqylllthnHPdywddLLRQVRIqfpfvrtmkVTQTHITKRFIKEGLGVSFLP 240
Cdd:COG0583  161 GEERLVLVASPD------------------------HP-----LARRAPL---------VNSLEALLAAVAAGLGIALLP 202

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|..
gi 489247162 241 LSAVRSELAAGSMIEIPceFAQMPSAGAYAIALYENEKK----KTFLDFLSH 288
Cdd:COG0583  203 RFLAADELAAGRLVALP--LPDPPPPRPLYLVWRRRRHLspavRAFLDFLRE 252
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-288 2.02e-55

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 179.68  E-value: 2.02e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162   1 MDFKWLHTFVTAAKYENFRKTAETLFLSQPTVTVHIKLLEKEISCKLFQRSGRKIQLTEEGKAYVPFAMRLLEDYENSMA 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162  81 ELHRVRQGYSHTLTLAVSPLIADTVLPSVMKRYTEDNKETEMTVTIFESEEIASQIRNGSADIGLSCLKVQSSSLTCLPL 160
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162 161 YNDPVVLVAPPGrkpgtgkadevkdlfgqylllthnHPdywddLLRQVRIqfpfvrtmkVTQTHITKRFIKEGLGVSFLP 240
Cdd:COG0583  161 GEERLVLVASPD------------------------HP-----LARRAPL---------VNSLEALLAAVAAGLGIALLP 202

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|..
gi 489247162 241 LSAVRSELAAGSMIEIPceFAQMPSAGAYAIALYENEKK----KTFLDFLSH 288
Cdd:COG0583  203 RFLAADELAAGRLVALP--LPDPPPPRPLYLVWRRRRHLspavRAFLDFLRE 252
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-263 2.20e-47

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: 160.09  E-value: 2.20e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162   1 MDFKWLHTFVTAAKYENFRKTAETLFLSQPTVTVHIKLLEKEISCKLFQRSGRKIQLTEEGKAYVPFAMRLLEDYENSMA 80
Cdd:NF040786   1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162  81 ELHRVRQGYSHTLTLAVSPLIADTVLPSVMKRYTEDNKETEMTVTIFESEEIASQIRNGSADIGLSCLKVQSSSLTCLPL 160
Cdd:NF040786  81 EFDRYGKESKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKKRLVYTPF 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162 161 YNDPVVLVAPPG--RKPGTGKADEVKDLFGQYLLLTHNHPDYW---DDLLRQVRIQfpfVRTMKV----TQTHITKRFIK 231
Cdd:NF040786 161 YKDRLVLITPNGteKYRMLKEEISISELQKEPFIMREEGSGTRkeaEKALKSLGIS---LEDLNVvaslGSTEAIKQSVE 237

                        250       260       270
                 ....*....|....*....|....*....|..
gi 489247162 232 EGLGVSFLPLSAVRSELAAGSMIEIPCEFAQM 263
Cdd:NF040786 238 AGLGISVISELAAEKEVERGRVLIFPIPGLPK 269
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 90-286 1.48e-30

LysR substrate binding domain; The structure of this domain is known and is similar to the periplasmic binding proteins. This domain binds a variety of ligands that caries in size and structure, such as amino acids, sugar phosphates, organic acids, metal cations, flavonoids, C6-ring carboxylic acids, H2O2, HOCl, homocysteine, NADPH, ATP, sulphate, muropeptides, acetate, salicylate, citrate, phenol- and quinolone derivatives, acetylserines, fatty acid CoA, shikimate, chorismate, homocysteine, indole-3-acetic acid, Na(I), c-di-GMP, ppGpp and hydrogen peroxide (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 460931 [Multi-domain]  Cd Length: 205  Bit Score: 113.54  E-value: 1.48e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162   90 SHTLTLAVSPLIADTVLPSVMKRYTEDNKETEMTVTIFESEEIASQIRNGSADIGLSCLKVQSSSLTCLPLYNDPVVLVA 169
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162  170 PPGRKPGTGKADEVKDLFGQYLLL---THNHPDYWDDLLRQVRIQFPfvRTMKVTQTHITKRFIKEGLGVSFLPLSAVRS 246
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILlppGSGLRDLLDRALRAAGLRPR--VVLEVNSLEALLQLVAAGLGIALLPRSAVAR 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 489247162  247 ELAAGSMIEIPCEFAQMPSAgAYAIAL---YENEKKKTFLDFL 286
Cdd:pfam03466 159 ELADGRLVALPLPEPPLPRE-LYLVWRkgrPLSPAVRAFIEFL 200
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 92-286 2.40e-26

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: 102.29  E-value: 2.40e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162  92 TLTLAVSPLIADTVLPSVMKRYTEDNKETEMTVTIFESEEIASQIRNGSADIGLSCLKVQSSSLTCLPLYNDPVVLVAPP 171
Cdd:cd05466    1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162 172 GRKPGTGKADEVKDLFGQYLLLTHNHPDYW---DDLLRQVRIQFPFVrtMKVTQTHITKRFIKEGLGVSFLPLSAVRsEL 248
Cdd:cd05466   81 DHPLAKRKSVTLADLADEPLILFERGSGLRrllDRAFAEAGFTPNIA--LEVDSLEAIKALVAAGLGIALLPESAVE-EL 157

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 489247162 249 AAGSMIEIPCEFAQMPSagayAIAL------YENEKKKTFLDFL 286
Cdd:cd05466  158 ADGGLVVLPLEDPPLSR----TIGLvwrkgrYLSPAARAFLELL 197
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 1-172 3.53e-21

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 90.87  E-value: 3.53e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162   1 MDFKWLHTFVTAAKyENFRKT--AETLFLSQPTVTVHIKLLEKEISCKLFQRSG-RKIQLTEEGKAYVPFAMRLLEDYEN 77
Cdd:PRK12683   1 MNFQQLRIIREAVR-QNFNLTevANALYTSQSGVSKQIKDLEDELGVEIFIRRGkRLTGLTEPGKELLQIVERMLLDAEN 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162  78 smaeLHRVRQGYSH----TLTLAVSPLIADTVLPSVMKRYTEDNKETEMTVTIFESEEIASQIRNGSADIGLSCLKV-QS 152
Cdd:PRK12683  80 ----LRRLAEQFADrdsgHLTVATTHTQARYALPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGIATEALdRE 155

                        170       180
                 ....*....|....*....|
gi 489247162 153 SSLTCLPLYNDPVVLVAPPG 172
Cdd:PRK12683 156 PDLVSFPYYSWHHVVVVPKG 175
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-288 2.02e-55

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 179.68  E-value: 2.02e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162   1 MDFKWLHTFVTAAKYENFRKTAETLFLSQPTVTVHIKLLEKEISCKLFQRSGRKIQLTEEGKAYVPFAMRLLEDYENSMA 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162  81 ELHRVRQGYSHTLTLAVSPLIADTVLPSVMKRYTEDNKETEMTVTIFESEEIASQIRNGSADIGLSCLKVQSSSLTCLPL 160
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162 161 YNDPVVLVAPPGrkpgtgkadevkdlfgqylllthnHPdywddLLRQVRIqfpfvrtmkVTQTHITKRFIKEGLGVSFLP 240
Cdd:COG0583  161 GEERLVLVASPD------------------------HP-----LARRAPL---------VNSLEALLAAVAAGLGIALLP 202

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|..
gi 489247162 241 LSAVRSELAAGSMIEIPceFAQMPSAGAYAIALYENEKK----KTFLDFLSH 288
Cdd:COG0583  203 RFLAADELAAGRLVALP--LPDPPPPRPLYLVWRRRRHLspavRAFLDFLRE 252
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-263 2.20e-47

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: 160.09  E-value: 2.20e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162   1 MDFKWLHTFVTAAKYENFRKTAETLFLSQPTVTVHIKLLEKEISCKLFQRSGRKIQLTEEGKAYVPFAMRLLEDYENSMA 80
Cdd:NF040786   1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162  81 ELHRVRQGYSHTLTLAVSPLIADTVLPSVMKRYTEDNKETEMTVTIFESEEIASQIRNGSADIGLSCLKVQSSSLTCLPL 160
Cdd:NF040786  81 EFDRYGKESKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKKRLVYTPF 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162 161 YNDPVVLVAPPG--RKPGTGKADEVKDLFGQYLLLTHNHPDYW---DDLLRQVRIQfpfVRTMKV----TQTHITKRFIK 231
Cdd:NF040786 161 YKDRLVLITPNGteKYRMLKEEISISELQKEPFIMREEGSGTRkeaEKALKSLGIS---LEDLNVvaslGSTEAIKQSVE 237

                        250       260       270
                 ....*....|....*....|....*....|..
gi 489247162 232 EGLGVSFLPLSAVRSELAAGSMIEIPCEFAQM 263
Cdd:NF040786 238 AGLGISVISELAAEKEVERGRVLIFPIPGLPK 269
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 90-286 1.48e-30

LysR substrate binding domain; The structure of this domain is known and is similar to the periplasmic binding proteins. This domain binds a variety of ligands that caries in size and structure, such as amino acids, sugar phosphates, organic acids, metal cations, flavonoids, C6-ring carboxylic acids, H2O2, HOCl, homocysteine, NADPH, ATP, sulphate, muropeptides, acetate, salicylate, citrate, phenol- and quinolone derivatives, acetylserines, fatty acid CoA, shikimate, chorismate, homocysteine, indole-3-acetic acid, Na(I), c-di-GMP, ppGpp and hydrogen peroxide (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 460931 [Multi-domain]  Cd Length: 205  Bit Score: 113.54  E-value: 1.48e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162   90 SHTLTLAVSPLIADTVLPSVMKRYTEDNKETEMTVTIFESEEIASQIRNGSADIGLSCLKVQSSSLTCLPLYNDPVVLVA 169
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162  170 PPGRKPGTGKADEVKDLFGQYLLL---THNHPDYWDDLLRQVRIQFPfvRTMKVTQTHITKRFIKEGLGVSFLPLSAVRS 246
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILlppGSGLRDLLDRALRAAGLRPR--VVLEVNSLEALLQLVAAGLGIALLPRSAVAR 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 489247162  247 ELAAGSMIEIPCEFAQMPSAgAYAIAL---YENEKKKTFLDFL 286
Cdd:pfam03466 159 ELADGRLVALPLPEPPLPRE-LYLVWRkgrPLSPAVRAFIEFL 200
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 92-286 2.40e-26

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: 102.29  E-value: 2.40e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162  92 TLTLAVSPLIADTVLPSVMKRYTEDNKETEMTVTIFESEEIASQIRNGSADIGLSCLKVQSSSLTCLPLYNDPVVLVAPP 171
Cdd:cd05466    1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162 172 GRKPGTGKADEVKDLFGQYLLLTHNHPDYW---DDLLRQVRIQFPFVrtMKVTQTHITKRFIKEGLGVSFLPLSAVRsEL 248
Cdd:cd05466   81 DHPLAKRKSVTLADLADEPLILFERGSGLRrllDRAFAEAGFTPNIA--LEVDSLEAIKALVAAGLGIALLPESAVE-EL 157

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 489247162 249 AAGSMIEIPCEFAQMPSagayAIAL------YENEKKKTFLDFL 286
Cdd:cd05466  158 ADGGLVVLPLEDPPLSR----TIGLvwrkgrYLSPAARAFLELL 197
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 1-172 3.53e-21

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 90.87  E-value: 3.53e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162   1 MDFKWLHTFVTAAKyENFRKT--AETLFLSQPTVTVHIKLLEKEISCKLFQRSG-RKIQLTEEGKAYVPFAMRLLEDYEN 77
Cdd:PRK12683   1 MNFQQLRIIREAVR-QNFNLTevANALYTSQSGVSKQIKDLEDELGVEIFIRRGkRLTGLTEPGKELLQIVERMLLDAEN 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162  78 smaeLHRVRQGYSH----TLTLAVSPLIADTVLPSVMKRYTEDNKETEMTVTIFESEEIASQIRNGSADIGLSCLKV-QS 152
Cdd:PRK12683  80 ----LRRLAEQFADrdsgHLTVATTHTQARYALPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGIATEALdRE 155

                        170       180
                 ....*....|....*....|
gi 489247162 153 SSLTCLPLYNDPVVLVAPPG 172
Cdd:PRK12683 156 PDLVSFPYYSWHHVVVVPKG 175
rbcR CHL00180
LysR transcriptional regulator; Provisional
 6-248 1.74e-20

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 88.92  E-value: 1.74e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162   6 LHTFVTAAKYENFRKTAETLFLSQPTVTVHIKLLEKEISCKLFQRSGRKIQLTEEGKAYVPFAMRLLEDYENSMAELHRV 85
Cdd:CHL00180  10 LRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRALEDL 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162  86 RQGYSHTLTLAVSPLIADTVLPSVMKRYTEDNKETEMTVTIFESEEIASQIRNGSADIGLSCLKVQ---SSSLTCLPLYN 162
Cdd:CHL00180  90 KNLQRGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVGGEVPtelKKILEITPYVE 169

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162 163 DPVVLVAPPGRKPGTGKADEVKDLFGQYLLLTHNHP---DYWDDLLRQVRIQFPFVRT-MKVTQTHITKRFIKEGLGVSF 238
Cdd:CHL00180 170 DELALIIPKSHPFAKLKKIQKEDLYRLNFITLDSNStirKVIDNILIQNGIDSKRFKIeMELNSIEAIKNAVQSGLGAAF 249

                        250
                 ....*....|
gi 489247162 239 LPLSAVRSEL 248
Cdd:CHL00180 250 VSVSAIEKEL 259
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-62 5.37e-19

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 78.58  E-value: 5.37e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162    3 FKWLHTFVTAAKYENFRKTAETLFLSQPTVTVHIKLLEKEISCKLFQRSGRKIQLTEEGK 62
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 17-172 5.67e-19

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 85.04  E-value: 5.67e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162  17 NFRKTAETLFLSQPTVTVHIKLLEKEISCKLFQRSGRKIQ-LTEEGKAYVPFAMRLLEDYENsmaeLHRVRQGYSH---- 91
Cdd:PRK12682  18 NLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKgLTEPGKAVLDVIERILREVGN----IKRIGDDFSNqdsg 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162  92 TLTLAVSPLIADTVLPSVMKRYTEdnKETEMTVTIFES--EEIASQIRNGSADIGLSCLKV-QSSSLTCLPLYNDPVVLV 168
Cdd:PRK12682  94 TLTIATTHTQARYVLPRVVAAFRK--RYPKVNLSLHQGspDEIARMVISGEADIGIATESLaDDPDLATLPCYDWQHAVI 171


                 ....
gi 489247162 169 APPG 172
Cdd:PRK12682 172 VPPD 175
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
17-172 1.58e-17

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 80.79  E-value: 1.58e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162  17 NFRKTAETLFLSQPTVTVHIKLLEKEISCKLFQRSGRKIQ-LTEEGKAYVPFAMRLLEDYENsmaeLHRVRQGYSH---- 91
Cdd:PRK12684  18 NLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRgLTEPGRIILASVERILQEVEN----LKRVGKEFAAqdqg 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162  92 TLTLAVSPLIADTVLPSVMKRYTEDNKETEMTVTIFESEEIASQIRNGSADIGLSCLKVQS-SSLTCLPLYNDPVVLVAP 170
Cdd:PRK12684  94 NLTIATTHTQARYALPAAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAIATEAIADyKELVSLPCYQWNHCVVVP 173


                 ..
gi 489247162 171 PG 172
Cdd:PRK12684 174 PD 175
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 6-169 8.41e-17

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 78.46  E-value: 8.41e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162   6 LHTFVTAAKYENFRKTAETLFLSQPTVTVHIKLLEKEISCKLFQRSGRKIQLTEEGKAYVPFAMRLLEDYENSMAELHRV 85
Cdd:PRK11242   6 IRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRRAIHDV 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162  86 RQGYSHTLTLAVSPLIADTVLPSVMKRYTEDNKETEMTVTIFESEEIASQIRNGSADIGLSCLKVQSSSLTCLPLYNDPV 165
Cdd:PRK11242  86 ADLSRGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMSQERIEALLADDELDVGIAFAPVHSPEIEAQPLFTETL 165


                 ....
gi 489247162 166 VLVA 169
Cdd:PRK11242 166 ALVV 169
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 92-259 1.84e-16

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: 75.99  E-value: 1.84e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162  92 TLTLAVSPLIADTVLPSVMKRYTEDNKETEMTVTIFESEEIASQIRNGSADIGLSCLKVQSSSLTCLPLYNDPVVLVAPP 171
Cdd:cd08420    1 TLRIGASTTIGEYLLPRLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLVEGPVDHPDLIVEPFAEDELVLVVPP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162 172 GRKPGTGKADEVKDLFGQYLLL------THNhpdYWDDLLRQVRIQFPFVRT-MKVTQTHITKRFIKEGLGVSFLPLSAV 244
Cdd:cd08420   81 DHPLAGRKEVTAEELAAEPWILrepgsgTRE---VFERALAEAGLDGLDLNIvMELGSTEAIKEAVEAGLGISILSRLAV 157

                        170
                 ....*....|....*
gi 489247162 245 RSELAAGSMIEIPCE 259
Cdd:cd08420  158 RKELELGRLVALPVE 172
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
1-254 6.42e-16

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 76.25  E-value: 6.42e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162   1 MDFKWLHTFVTAAKYENFRKTAETLFLSQPTVTVHIKLLEKEISCKLFQRSGRKIQLTEEGKAYVPFAMRLLEDYENSMA 80
Cdd:PRK10082  11 IETKWLYDFLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESNLA 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162  81 EL--------HRVRQGYSHTLTLAVSPLIADTVLPsvmkRYTednketeMTVTIFESEEIASQIRNGSADiglsclkvqs 152
Cdd:PRK10082  91 ELrggsdyaqRKIKIAAAHSLSLGLLPSIISQMPP----LFT-------WAIEAIDVDEAVDKLREGQSD---------- 149

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162 153 ssltCLPLYNDPVVLVAPPGRK--------PGTGKADEVKDLFG----QYLLLTHNHPDYWDDLL-----RQVRIQFP-- 213
Cdd:PRK10082 150 ----CIFSFHDEDLLEAPFDHIrlfesqlfPVCASDEHGEALFNlaqpHFPLLNYSRNSYMGRLInrtltRHSELSFStf 225

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|.
gi 489247162 214 FVRTMkvtqTHITKRFIKEGLGVSFLPLSAVRSELAAGSMI 254
Cdd:PRK10082 226 FVSSM----SELLKQVALDGCGIAWLPEYAIQQEIRSGQLV 262
PRK09986 PRK09986
LysR family transcriptional regulator;
1-242 7.94e-16

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 75.91  E-value: 7.94e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162   1 MDFKWLHTFVTAAKYENFRKTAETLFLSQPTVTVHIKLLEKEISCKLFQRSGRKIQLTEEGKAYVPFAMRLLEDYENSMA 80
Cdd:PRK09986   7 IDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLA 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162  81 ELHRVRQGYSHTLTLAVSPLIADTVLPSVMKRYTEDNKETEMtvtIFESEEIASQI---RNGSADIGL-SCLKVQ-SSSL 155
Cdd:PRK09986  87 RVEQIGRGEAGRIEIGIVGTALWGRLRPAMRHFLKENPNVEW---LLRELSPSMQMaalERRELDAGIwRMADLEpNPGF 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162 156 TCLPLYNDPVVLVAPPGRKPGTGKADEVKDLFGQYLL-LTHNHPDyWDDLLRQVRIQFPF----VRTMKVTQTHITkrFI 230
Cdd:PRK09986 164 TSRRLHESAFAVAVPEEHPLASRSSVPLKALRNEYFItLPFVHSD-WGKFLQRVCQQAGFspqiIRQVNEPQTVLA--MV 240

                        250
                 ....*....|..
gi 489247162 231 KEGLGVSFLPLS 242
Cdd:PRK09986 241 SMGIGITLLPDS 252
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 1-170 1.20e-15

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 75.58  E-value: 1.20e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162   1 MDFKWLHTFVTAAKYENFRKTAETLFLSQPTVTVHIKLLEKEISCKLFQRSGRKIQLTEEGKAYVPFAMRLLEDYENSMA 80
Cdd:PRK09906   1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162  81 ELHRVRQGySHTLTLAVSPLIADTVLPSVMKRYTEDNKETEMTVTIFESEEIASQIRNGSADIGLSCLKVQSSSLTCLPL 160
Cdd:PRK09906  81 RARKIVQE-DRQLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPVYSDEIDYLEL 159

                        170
                 ....*....|
gi 489247162 161 YNDPVVLVAP 170
Cdd:PRK09906 160 LDEPLVVVLP 169
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 6-257 1.62e-15

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 75.11  E-value: 1.62e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162   6 LHTFVTAAKYENFRKTAETLFLSQPTVTVHIKLLEKEISCKLFQRSGRKIQLTEEGKAYVPFAMRLLEdyenSMAELHRV 85
Cdd:PRK10837   8 LEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLE----QAVEIEQL 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162  86 RQGYSHTLTLAVSPLIADTVLPSVMKRYTEDNKETEMTVTIFESEEIASQIRNGSADIGL---SClkvQSSSLTCLPLYN 162
Cdd:PRK10837  84 FREDNGALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNSQDVINAVLDFRVDIGLiegPC---HSPELISEPWLE 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162 163 DPVVLVAPPG--------------------RKPGTGKADEVkdlfgQYLLLTHnhpdywddlLRQVRIqfpfvrTMKVTQ 222
Cdd:PRK10837 161 DELVVFAAPDsplargpvtleqlaaapwilRERGSGTREIV-----DYLLLSH---------LPRFEL------AMELGN 220

                        250       260       270
                 ....*....|....*....|....*....|....*
gi 489247162 223 THITKRFIKEGLGVSFLPLSAVRSELAAGSMIEIP 257
Cdd:PRK10837 221 SEAIKHAVRHGLGISCLSRRVIADQLQAGTLVEVA 255
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
6-106 1.82e-15

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 75.04  E-value: 1.82e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162   6 LHTFVTAAKYENFRKTAETLFLSQPTVTVHIKLLEKEISCKLFQRSGRKIQLTEEGKayvpfamRLLEDYENSMAEL-HR 84
Cdd:PRK10086  19 LHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGK-------RVFWALKSSLDTLnQE 91

                         90       100
                 ....*....|....*....|....*.
gi 489247162  85 VR----QGYSHTLTLAVSPLIADTVL 106
Cdd:PRK10086  92 ILdiknQELSGTLTVYSRPSIAQCWL 117
cbl PRK12679
HTH-type transcriptional regulator Cbl;
1-172 1.24e-14

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 72.92  E-value: 1.24e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162   1 MDFKWLHTFVTAAKYE-NFRKTAETLFLSQPTVTVHIKLLEKEISCKLFQRSG-RKIQLTEEGKAYVPFAMRLLEDYEN- 77
Cdd:PRK12679   1 MNFQQLKIIREAARQDyNLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGkRLLGMTEPGKALLVIAERILNEASNv 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162  78 -SMAELhrVRQGYSHTLTLAVSPLIADTVLPSVMKRYTEDNKETEMTVTIFESEEIASQIRNGSADIGL-SCLKVQSSSL 155
Cdd:PRK12679  81 rRLADL--FTNDTSGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIaSERLSNDPQL 158

                        170
                 ....*....|....*..
gi 489247162 156 TCLPLYNDPVVLVAPPG 172
Cdd:PRK12679 159 VAFPWFRWHHSLLVPHD 175
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-245 2.80e-14

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: 69.86  E-value: 2.80e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162  92 TLTLAVSPLIADTVLPSVMKRYTEDNKEteMTVTIFE--SEEIASQIRNGSADIGLSCLKVQSSSLTCLPLYNDPVVLVA 169
Cdd:cd08440    1 RVRVAALPSLAATLLPPVLAAFRRRHPG--IRVRLRDvsAEQVIEAVRSGEVDFGIGSEPEADPDLEFEPLLRDPFVLVC 78

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489247162 170 PPGRKPGTGKADEVKDLFGQYLLLTHNHP---DYWDDLLRQVRIQFPFVrtMKVTQTHITKRFIKEGLGVSFLPLSAVR 245
Cdd:cd08440   79 PKDHPLARRRSVTWAELAGYPLIALGRGSgvrALIDRALAAAGLTLRPA--YEVSHMSTALGMVAAGLGVAVLPALALP 155
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 2-193 2.08e-12

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 66.21  E-value: 2.08e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162   2 DFKWLhtfVTAAKYENFRKTAETLFLSQPTVTVHIKLLEKEISCKLFQRSGRKIQLTEEGKAYVPFAMRLLEDYE--NSM 79
Cdd:PRK11151   5 DLEYL---VALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKvlKEM 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162  80 AELhrvrQGYSHT--LTLAVSPLIADTVLPSVMKRYTEDNKETEMTVTIFESEEIASQIRNGSADIGLSCLKVQSSSLTC 157
Cdd:PRK11151  82 ASQ----QGETMSgpLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCAILALVKESEAFIE 157

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 489247162 158 LPLYNDPVVLVAPPGRKPGTGKADEVKDLFGQYLLL 193
Cdd:PRK11151 158 VPLFDEPMLLAVYEDHPWANRDRVPMSDLAGEKLLM 193
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
26-170 2.27e-12

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 65.61  E-value: 2.27e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162  26 FLSQPTVTVHIKLLEKEISCKLFQRSGRKIQLTEEGKAYVPFAMRLLEDYENSMAELHRVRQGYSHTLTLAVSPLIADTV 105
Cdd:PRK11716   2 HVSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSLFCSVTAAYSH 81

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489247162 106 LPSVMKRYTEDNKETEMTVTIFESEEIASQIRNGSADIGLSCL-KVQSSSLTCLPLYNDPVVLVAP 170
Cdd:PRK11716  82 LPPILDRFRAEHPLVEIKLTTGDAADAVEKVQSGEADLAIAAKpETLPASVAFSPIDEIPLVLIAP 147
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 6-66 1.05e-11

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 64.09  E-value: 1.05e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 489247162   6 LHTFVTAAKYENFRKTAETLFLSQPTVTVHIKLLEKEISCKLFQRSGRKIQLTEEGKAYVP 66
Cdd:PRK11139  11 LRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFL 71
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 92-254 4.37e-10

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: 57.92  E-value: 4.37e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162  92 TLTLAVSPLIADTVLPSVMKRYTEdnKETEMTVTIFE--SEEIASQIRNGSADIGLSCLKVQSSSLTCLPLYNDPVVLVA 169
Cdd:cd08411    2 PLRLGVIPTIAPYLLPRLLPALRQ--AYPKLRLYLREdqTERLLEKLRSGELDAALLALPVDEPGLEEEPLFDEPFLLAV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162 170 PPGRKPGTGKADEVKDLFGQ-YLLLTHNHPdywddlLR-QVRIQFPFVRTMKVTQTHIT-----KRFIKEGLGVSFLPLS 242
Cdd:cd08411   80 PKDHPLAKRKSVTPEDLAGErLLLLEEGHC------LRdQALELCRLAGAREQTDFEATsletlRQMVAAGLGITLLPEL 153

                        170
                 ....*....|..
gi 489247162 243 AVRSELAAGSMI 254
Cdd:cd08411  154 AVPSEELRGDRL 165
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 92-245 5.75e-10

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: 57.57  E-value: 5.75e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162  92 TLTLAVSPLIADTVLPSVMKRYTEDNKETEMTVTIFESEEIASQIRNGSADIGLSCLKVQSSSLTCLPLYNDPVVLVAPP 171
Cdd:cd08438    1 HLRLGLPPLGGSLLFAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVLPVDEEEFDSQPLCNEPLVAVLPR 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489247162 172 GRKPGTGKADEVKDLFGQ-YLLLTHNHpdYWDDLLRQVRIQFPFVRTM--KVTQTHITKRFIKEGLGVSFLPLSAVR 245
Cdd:cd08438   81 GHPLAGRKTVSLADLADEpFILFNEDF--ALHDRIIDACQQAGFTPNIaaRSSQWDFIAELVAAGLGVALLPRSIAQ 155
PRK09791 PRK09791
LysR family transcriptional regulator;
6-142 7.04e-10

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 58.62  E-value: 7.04e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162   6 LHTFVTAAKYENFRKTAETLFLSQPTVTVHIKLLEKEISCKLFQRSGRKIQLTEEGKAYVPFAMRLLEDYENSMAELhRV 85
Cdd:PRK09791  10 IRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQEDI-RQ 88

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162  86 RQGY-SHTLTLAVSPLIADTVLPSVMKRYTEDNKETEmtVTIFESEEIA--SQIRNGSAD 142
Cdd:PRK09791  89 RQGQlAGQINIGMGASIARSLMPAVISRFHQQHPQVK--VRIMEGQLVSmiNELRQGELD 146
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 92-243 2.04e-09

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: 56.03  E-value: 2.04e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162  92 TLTLAVSPLIADTVLPSVMKRYTEDNKETEMTVTIFESEEIASQIRNGSADIGLSCLKVQSSSLTCLPLYNDPVVLVAPP 171
Cdd:cd08415    1 TLRIAALPALALSLLPRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPLDHPGLESEPLASGRAVCVLPP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162 172 GRkPGTGKaDEV--KDLFGQYLLLTHNhpdywDDLLRQvRIQFPFVR-------TMKVTQTHITKRFIKEGLGVSFL-PL 241
Cdd:cd08415   81 GH-PLARK-DVVtpADLAGEPLISLGR-----GDPLRQ-RVDAAFERagvepriVIETQLSHTACALVAAGLGVAIVdPL 152


                 ..
gi 489247162 242 SA 243
Cdd:cd08415  153 TA 154
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 7-244 6.19e-09

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 55.77  E-value: 6.19e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162   7 HTFVTAAkyeNFRKTAETLFLSQPTVTVHIKLLEKEISCKLFQRSGRKIQLTEEGkayvpfaMRLLEDYENSMAELHRV- 85
Cdd:PRK11013  13 HAVMTAG---SLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQG-------LRLFEEVQRSYYGLDRIv 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162  86 ---------RQGyshTLTLAVSPLIADTVLPSVMKRYTEDNKETEMTVTIFES---EEIASQIRNgsaDIGLSCLKVQSS 153
Cdd:PRK11013  83 saaeslrefRQG---QLSIACLPVFSQSLLPGLCQPFLARYPDVSLNIVPQESpllEEWLSAQRH---DLGLTETLHTPA 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162 154 SLTCLPLYNDPVVLVAPPGRkPGTGKAD-EVKDLFGQ-YLLLTHNHPdY---WDDLLRQVRIQfpfvRTMkVTQTHITKR 228
Cdd:PRK11013 157 GTERTELLTLDEVCVLPAGH-PLAAKKVlTPDDFAGEnFISLSRTDS-YrqlLDQLFAEHGVK----RRM-VVETHSAAS 229

                        250       260
                 ....*....|....*....|
gi 489247162 229 ---FIKEGLGVSFL-PLSAV 244
Cdd:PRK11013 230 vcaMVRAGVGVSIVnPLTAL 249
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 1-146 6.24e-09

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 55.80  E-value: 6.24e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162   1 MDFKWLHTFVTAAKYENFRKTAETLFLSQPTVTVHIKLLEKEISCKLFQRSGRKIQLTEEGKAYVPFAMRLLE-DYENSM 79
Cdd:PRK15092  11 LDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRfNDEACS 90

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489247162  80 AELHRVRQGyshTLTLAVSPLIADTVLPSVMKRYTEDNKETEMTVTIFESEEIASQIRNGSADIGLS 146
Cdd:PRK15092  91 SLMYSNLQG---VLTIGASDDTADTILPFLLNRVSSVYPKLALDVRVKRNAFMMEMLESQEVDLAVT 154
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 84-257 3.16e-08

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


Pssm-ID: 176124  Cd Length: 198  Bit Score: 52.60  E-value: 3.16e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162  84 RVRQGyshtLTLAVSPLIADTVLPSVMKRYTEdnketeMTVTIFE--SEEIASQIRNGSADIGLSCLKVQSSSLTCLPLY 161
Cdd:cd08433    1 RVSVG----LPPSAASVLAVPLLRAVRRRYPG------IRLRIVEglSGHLLEWLLNGRLDLALLYGPPPIPGLSTEPLL 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162 162 NDPVVLVAPPGRKPGTGKADEVKDLFGQYLLLthnhPDYWDDLLRQVRIQFPFVRT-----MKVTQTHITKRFIKEGLGV 236
Cdd:cd08433   71 EEDLFLVGPADAPLPRGAPVPLAELARLPLIL----PSRGHGLRRLVDEAAARAGLtlnvvVEIDSVATLKALVAAGLGY 146

                        170       180
                 ....*....|....*....|.
gi 489247162 237 SFLPLSAVRSELAAGSMIEIP 257
Cdd:cd08433  147 TILPASAVAAEVAAGRLVAAP 167
cysB PRK12681
HTH-type transcriptional regulator CysB;
17-115 5.77e-08

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 52.98  E-value: 5.77e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162  17 NFRKTAETLFLSQPTVTVHIKLLEKEISCKLFQRSGRKI-QLTEEGKAYVPFAMRLLEDYENsmaeLHRVRQGYSH---- 91
Cdd:PRK12681  18 NVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLtQVTPAGEEIIRIAREILSKVES----IKSVAGEHTWpdkg 93

                         90       100
                 ....*....|....*....|....
gi 489247162  92 TLTLAVSPLIADTVLPSVMKRYTE 115
Cdd:PRK12681  94 SLYIATTHTQARYALPPVIKGFIE 117
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
1-254 7.01e-08

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 52.89  E-value: 7.01e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162   1 MDFKWLHTFVTAAKYENFRKTAETLFLSQPTVTVHIKLLEKEISCKLFQRSGRKIQLTEEGKAYVPFAMRLLEDYENSMA 80
Cdd:PRK10094   2 FDPETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPS 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162  81 ELHRVRQGYSHTLTLAVSPLIAD-----TVLPSVMKRYTednketemtvtiFESEEIASQIRNGSAD----------IGL 145
Cdd:PRK10094  82 ELQQVNDGVERQVNIVINNLLYNpqavaQLLAWLNERYP------------FTQFHISRQIYMGVWDsllyegfslaIGV 149

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162 146 SCLKVQSSSLTCLPLYNDPVVLVAPPGRKPGTGKADEVKDLFGQYLLLthNHPDYWDDLLRQVRIQFPFVRTMKVTQTHI 225
Cdd:PRK10094 150 TGTEALANTFSLDPLGSVQWRFVMAADHPLANVEEPLTEAQLRRFPAV--NIEDSARTLTKRVAWRLPGQKEIIVPDMET 227

                        250       260
                 ....*....|....*....|....*....
gi 489247162 226 TKRFIKEGLGVSFLPLSAVRSELAAGSMI 254
Cdd:PRK10094 228 KIAAHLAGVGIGFLPKSLCQSMIDNQQLV 256
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 92-245 8.60e-08

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: 51.35  E-value: 8.60e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162  92 TLTLAVSPLIADTVLPSVMKRYTEDNKETEMTVTIFESEEIASQIRNGSADIGLSCLKVQSSSLTCLPLYNDPVVLVAPP 171
Cdd:cd08414    1 RLRIGFVGSALYGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPPPDPPGLASRPLLREPLVVALPA 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489247162 172 GRKPGTGKADEVKDLFGQYLLLTHNHP-----DYWDDLLRQVRIQFPFVRTMKVTQTHITkrFIKEGLGVSFLPLSAVR 245
Cdd:cd08414   81 DHPLAARESVSLADLADEPFVLFPREPgpglyDQILALCRRAGFTPRIVQEASDLQTLLA--LVAAGLGVALVPASVAR 157
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
1-119 2.58e-07

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 50.79  E-value: 2.58e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162   1 MDFKWLHTFVTAAKYENFRKTAETLFLSQPTVTVHIKLLEKEISCKLFQRSGRKIQLTEEGKAYVPFAMRLLEDYENSMA 80
Cdd:PRK03601   1 MDTELLKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYAETLMNTWQAAKK 80

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 489247162  81 ELHRVRQgySHTLTLAVSPLIADTVLPSVMKRYTEDNKE 119
Cdd:PRK03601  81 EVAHTSQ--HNELSIGASASLWECMLTPWLGRLYQNQEA 117
PRK10341 PRK10341
transcriptional regulator TdcA;
22-178 4.89e-07

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 50.25  E-value: 4.89e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162  22 AETLFLSQPTVTVHIKLLEKEISCKLFQRSGRKIQLTEEGKAYVPFAMRLLEDYENSMAELHRVRQGYSHTLTLAVSPLI 101
Cdd:PRK10341  28 AKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEINGMSSEAVVDVSFGFPSLI 107

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162 102 ADTVLPSVMKRYTEDNKETEmtVTIFESE--EIASQIRNGSADIGLSCL--KVQSSSLTCLPLYNDPVVLVAPPGRkPGT 177
Cdd:PRK10341 108 GFTFMSDMINKFKEVFPKAQ--VSMYEAQlsSFLPAIRDGRLDFAIGTLsnEMKLQDLHVEPLFESEFVLVASKSR-TCT 184


                 .
gi 489247162 178 G 178
Cdd:PRK10341 185 G 185
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-257 7.33e-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: 48.84  E-value: 7.33e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162  92 TLTLAVSPLIADTVLPSVMKRYTEDNKETEMTVTIFESEEIASQIRNGSADIGLSCLKVQSSSLTCLPLYNDPVVLVAPP 171
Cdd:cd08426    1 RVRVATGEGLAAELLPSLIARFRQRYPGVFFTVDVASTADVLEAVLSGEADIGLAFSPPPEPGIRVHSRQPAPIGAVVPP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162 172 GRKPGTGKADEVKDLFGQYLLLThnHPDY-----WDDLLRQVRIQF-PFVRTmkvTQTHITKRFIKEGLGVSFLPLSAVR 245
Cdd:cd08426   81 GHPLARQPSVTLAQLAGYPLALP--PPSFslrqiLDAAFARAGVQLePVLIS---NSIETLKQLVAAGGGISLLTELAVR 155

                        170
                 ....*....|..
gi 489247162 246 SELAAGSMIEIP 257
Cdd:cd08426  156 REIRRGQLVAVP 167
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 155-269 6.11e-06

The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate domain of LysR-type transcriptional regulators involved in controlling the expression of glutaryl-CoA dehydrogenase (GcdH), S-adenosyl-L-homocysteine hydrolase, cell division protein FtsW, tryptophan synthase, and beta-lactamase. 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: 176123 [Multi-domain]  Cd Length: 194  Bit Score: 46.03  E-value: 6.11e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162 155 LTCLPLYNDPVVLVAPPGRkPGTGKADEVKDLFGQYLLLTHNHPDYWDDLLRQVRIQ-FPFVRTMKVTQTHITKRFIKEG 233
Cdd:cd08432   61 LEAERLMDEELVPVCSPAL-LAGLPLLSPADLARHTLLHDATRPEAWQWWLWAAGVAdVDARRGPRFDDSSLALQAAVAG 139

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 489247162 234 LGVSFLPLSAVRSELAAGSMIeIPCEFAqMPSAGAY 269
Cdd:cd08432  140 LGVALAPRALVADDLAAGRLV-RPFDLP-LPSGGAY 173
nhaR PRK11062
transcriptional activator NhaR; Provisional
 20-61 9.72e-06

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 46.16  E-value: 9.72e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 489247162  20 KTAETLFLSQPTVTVHIKLLEKEISCKLFQRSGRKIQLTEEG 61
Cdd:PRK11062  23 GAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELG 64
PRK12680 PRK12680
LysR family transcriptional regulator;
1-246 1.30e-05

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 45.77  E-value: 1.30e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162   1 MDFKWLHTFVTAAKYE-NFRKTAETLFLSQPTVTVHIKLLEKEISCKLFQRSGRKIQ-LTEEGKAYVPFAMRLLEDYENS 78
Cdd:PRK12680   1 MTLTQLRYLVAIADAElNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLEsVTPAGVEVIERARAVLSEANNI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162  79 MAELHRVRQGYSHTLTLAVSPLIADTVLPSVMKRYTedNKETEMTVTIFESEEIAS--QIRNGSADIGL-SCLKVQSSSL 155
Cdd:PRK12680  81 RTYAANQRRESQGQLTLTTTHTQARFVLPPAVAQIK--QAYPQVSVHLQQAAESAAldLLGQGDADIAIvSTAGGEPSAG 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162 156 TCLPLYNDPVVLVAPPGRKPGT-GKADEVKDLfGQYLLLTHNHPDYWDDLLRQVRIQFPFVRTMKVT--QTHITKRFIKE 232
Cdd:PRK12680 159 IAVPLYRWRRLVVVPRGHALDTpRRAPDMAAL-AEHPLISYESSTRPGSSLQRAFAQLGLEPSIALTalDADLIKTYVRA 237

                        250
                 ....*....|....
gi 489247162 233 GLGVSFLPLSAVRS 246
Cdd:PRK12680 238 GLGVGLLAEMAVNA 251
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 2-256 1.49e-05

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 45.75  E-value: 1.49e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162   2 DFKWlhtFVTAAKYENFRKTAETLFLSQPTVTVHIKLLEKEISCKLFQRSGRKIQLTEEGKAYVPFAMRLL---EDYENS 78
Cdd:PRK14997   6 DFAW---FVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLveaQAAQDA 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162  79 MAELHRVRQGySHTLTLAVSPLIADT--VLPSVMKRYTEDNKETEMTV----TIFESEEIASQIRN---GSADIGLSCLK 149
Cdd:PRK14997  83 IAALQVEPRG-IVKLTCPVTLLHVHIgpMLAKFMARYPDVSLQLEATNrrvdVVGEGVDVAIRVRPrpfEDSDLVMRVLA 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162 150 VQSSSLTCLPLY-------NDPVVLVAPPGRKPGTGKADEVKDLFGQylllthnhpdywddllRQVRIQFPFVRTMKVTQ 222
Cdd:PRK14997 162 DRGHRLFASPDLiarmgipSAPAELSHWPGLSLASGKHIHRWELYGP----------------QGARAEVHFTPRMITTD 225

                        250       260       270
                 ....*....|....*....|....*....|....
gi 489247162 223 THITKRFIKEGLGVSFLPLSAVRSELAAGSMIEI 256
Cdd:PRK14997 226 MLALREAAMAGVGLVQLPVLMVKEQLAAGELVAV 259
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
4-279 2.32e-05

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 45.14  E-value: 2.32e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162   4 KWLHTFVTAAKYENFRKTAETLFLSQPTVTVHIKLLEKEISCKLFQRSGRKIQLTEEGKAYVPFAMRLLEDYENSMAELH 83
Cdd:PRK10632   5 KRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQLY 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162  84 RVRQGYSHTLTLAVSPLIADTVLPSVMKRYTEDnkETEMTVTIFESEEIASQIRNGsADIGLSCLKVQSSSLTCLPLYND 163
Cdd:PRK10632  85 AFNNTPIGTLRIGCSSTMAQNVLAGLTAKMLKE--YPGLSVNLVTGIPAPDLIADG-LDVVIRVGALQDSSLFSRRLGAM 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162 164 PVVLVAPPGRKPGTGKADEVKDLfGQYLLLTHN-HPDYWDDLLR------QVRIQFPFVrtMKVTQTHItkRFIKEGLGV 236
Cdd:PRK10632 162 PMVVCAAKSYLAQYGTPEKPADL-SSHSWLEYSvRPDNEFELIApegistRLIPQGRFV--TNDPQTLV--RWLTAGAGI 236

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|...
gi 489247162 237 SFLPLSAVRSELAAGsmiEIPCEFAQMPSAGAYAIALYENEKK 279
Cdd:PRK10632 237 AYVPLMWVIDEINRG---ELEILFPRYQSDPRPVYALYTEKDK 276
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
1-256 5.83e-05

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 43.61  E-value: 5.83e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162   1 MDFKWLHTFVTAAKYENFRKTAETLFLSQPTVTVHIKLLEKEISCKLFQRsGRKIQLTEEGKAYVPFA--MRLLE-DYEN 77
Cdd:PRK03635   2 LDYKQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRLLRHArqVRLLEaELLG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162  78 SMAELHRVRQgyshTLTLAVSpliAD---TVLPSVMKRYTEDNKeTEMTVTIFESEEIASQIRNGSAdigLSCLKVQSSS 154
Cdd:PRK03635  81 ELPALDGTPL----TLSIAVN---ADslaTWFLPALAPVLARSG-VLLDLVVEDQDHTAELLRRGEV---VGAVTTEPQP 149

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162 155 L---TCLPL----YndpvVLVAPPG----------RKPGTGKADEVkdLFGQYlllthnhpdywDDL----LRQV-RIQF 212
Cdd:PRK03635 150 VqgcRVDPLgamrY----LAVASPAfaaryfpdgvTAEALAKAPAV--VFNRK-----------DDLqdrfLRQAfGLPP 212

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....
gi 489247162 213 PFVRTMKVTQTHITKRFIKEGLGVSFLPLSAVRSELAAGSMIEI 256
Cdd:PRK03635 213 GSVPCHYVPSSEAFVRAALAGLGWGMIPELQIEPELASGELVDL 256
PBP2_TdcA cd08418
The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is ...
 94-271 7.22e-05

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: 42.73  E-value: 7.22e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162  94 TLAVSPLIADTVLPSVMKRYTEDNKETEmtVTIFESEEIA--SQIRNGSADIGLSCL--KVQSSSLTCLPLYNDPVVLVA 169
Cdd:cd08418    3 SIGVSSLIAHTLMPAVINRFKEQFPDVQ--ISIYEGQLSSllPELRDGRLDFAIGTLpdEMYLKELISEPLFESDFVVVA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162 170 PPGRkPGTGkADEVKDLFGQYLLLTHNHPDYWDDLLRQVRIQFPFVRTMKVTQT-HITKRFIKEGLGVSFLPLSAVRSEL 248
Cdd:cd08418   81 RKDH-PLQG-ARSLEELLDASWVLPGTRMGYYNNLLEALRRLGYNPRVAVRTDSiVSIINLVEKADFLTILSRDMGRGPL 158

                        170       180
                 ....*....|....*....|...
gi 489247162 249 AAGSMIEIPCEfAQMPSAGAYAI 271
Cdd:cd08418  159 DSFRLITIPVE-EPLPSADYYLI 180
PBP2_GcdR_like cd08481
The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, ...
 165-269 8.19e-05

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


Pssm-ID: 176170 [Multi-domain]  Cd Length: 194  Bit Score: 42.67  E-value: 8.19e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162 165 VVLVAPPGRKPGTGkADEVKDLfGQYLLLTHNH-PDYWDDLLRQVRIQFPF-VRTMKVTQTHITKRFIKEGLGVSFLPLS 242
Cdd:cd08481   71 VVPVCSPALLAGRA-LAAPADL-AHLPLLQQTTrPEAWRDWFEEVGLEVPTaYRGMRFEQFSMLAQAAVAGLGVALLPRF 148

                         90       100
                 ....*....|....*....|....*..
gi 489247162 243 AVRSELAAGSMIeIPCEFAqMPSAGAY 269
Cdd:cd08481  149 LIEEELARGRLV-VPFNLP-LTSDKAY 173
PBP2_LysR cd08456
The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine ...
 92-243 9.15e-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: 42.41  E-value: 9.15e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162  92 TLTLAVSPLIADTVLPSVMKRYTEDNKETEMTVTIFESEEIASQIRNGSADIGLSCLKVQSSSLTCLPLYNDPVVLVAPP 171
Cdd:cd08456    1 ELRIAVLPALSQSFLPRAIKAFLQRHPDVTISIHTRDSPTVEQWLSAQQCDLGLVSTLHEPPGIERERLLRIDGVCVLPP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162 172 GRKPGTGKADEVKDLFGQ-YLLLTHNhpdywdDLLRQvRIQFPF----VRTMKVTQTH---ITKRFIKEGLGVSFL-PLS 242
Cdd:cd08456   81 GHRLAVKKVLTPSDLEGEpFISLART------DGTRQ-RVDALFeqagVKRRIVVETSyaaTICALVAAGVGVSVVnPLT 153


                 .
gi 489247162 243 A 243
Cdd:cd08456  154 A 154
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
 155-259 1.78e-04

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: 41.72  E-value: 1.78e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162 155 LTCLPLYNDPVVLVAPPGRkPGTGKAD-EVKDLFGQYLLL------THNhpdYWDDLLRQVRIQFPFVRTMKVTQThitk 227
Cdd:cd08419   63 LVAEPFLDNPLVVIAPPDH-PLAGQKRiPLERLAREPFLLrepgsgTRL---AMERFFAEHGVTLRVRMELGSNEA---- 134

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 489247162 228 rfIKE----GLGVSFLPLSAVRSELAAGSMIEIPCE 259
Cdd:cd08419  135 --IKQavmaGLGLSVLSLHTLALELATGRLAVLDVE 168
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 92-255 1.92e-04

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: 41.38  E-value: 1.92e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162  92 TLTLAVSPLIADTVLPSVMKRYTEDNKETEmtVTIFE--SEEIASQIRNGSADIGLSCLKVQSSSLTCLPLYNDPVVLVA 169
Cdd:cd08412    1 TLRIGCFSTLAPYYLPGLLRRFREAYPGVE--VRVVEgnQEELEEGLRSGELDLALTYDLDLPEDIAFEPLARLPPYVWL 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162 170 PPGRKPGTGKADEVKDLFGQ-YLLLTHNHP-DYWDDLLRQVRIQfPFVRtMKVTQTHITKRFIKEGLGVSFLPLSAVRSE 247
Cdd:cd08412   79 PADHPLAGKDEVSLADLAAEpLILLDLPHSrEYFLSLFAAAGLT-PRIA-YRTSSFEAVRSLVANGLGYSLLNDRPYRPW 156


                 ....*...
gi 489247162 248 LAAGSMIE 255
Cdd:cd08412  157 SYDGKRLV 164
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 92-265 2.92e-04

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: 41.10  E-value: 2.92e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162  92 TLTLAVSPLIADTVLPSVMKRYTEDNKETEMTVTIFESEEIASQIRNGSADIGLSCLK--VQSSSLTCLPLYNDPVVLVA 169
Cdd:cd08435    1 TVRVGAVPAAAPVLLPPAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAIGRLAddEQPPDLASEELADEPLVVVA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162 170 PPGRKPGTGKADEVKDLFGQYLLLthnHP------DYWDDLLRQVRIQFPFVrTMKVTQTHITKRFIKEGLGVSFLPLSA 243
Cdd:cd08435   81 RPGHPLARRARLTLADLADYPWVL---PPpgtplrQRLEQLFAAAGLPLPRN-VVETASISALLALLARSDMLAVLPRSV 156

                        170       180
                 ....*....|....*....|..
gi 489247162 244 VRSELAAGSMIEIPCEFAQMPS 265
Cdd:cd08435  157 AEDELRAGVLRELPLPLPTSRR 178
PRK09801 PRK09801
LysR family transcriptional regulator;
4-289 2.92e-04

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 41.56  E-value: 2.92e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162   4 KWLHTFVTAAKYENFRKTAETLFLSQPTVTVHIKLLEKEISCKLFQRSGRKIQLTEEGKAYVPFAMRLLEDYENSMAELH 83
Cdd:PRK09801   9 KDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVT 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162  84 RVRQ--------------GYSHtltlaVSPLIADtvlpsVMKRYtednKETEMTVTIFESE--------EIASQIRNGSA 141
Cdd:PRK09801  89 QIKTrpegmirigcsfgfGRSH-----IAPAITE-----LMRNY----PELQVHFELFDRQidlvqdniDLDIRINDEIP 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162 142 DIGLSCLKVQSSSLTClplyndpvvlvAPPGRKPGTGKADEVKDLFGQYLLLTHNHP---DYWDDLLRQVRIQFPFVRTM 218
Cdd:PRK09801 155 DYYIAHLLTKNKRILC-----------AAPEYLQKYPQPQSLQELSRHDCLVTKERDmthGIWELGNGQEKKSVKVSGHL 223

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489247162 219 KVTQTHITKRFIKEGLGVSFLPLSAVRSELAAGSMIEIPCEFAQmpSAGAYAI---ALYENEKKKTFLDFLSHF 289
Cdd:PRK09801 224 SSNSGEIVLQWALEGKGIMLRSEWDVLPFLESGKLVQVLPEYAQ--SANIWAVyrePLYRSMKLRVCVEFLAAW 295
PBP2_NocR cd08458
The C-terminal substrate-domain of LysR-type transcriptional regulator, NocR, involved in the ...
 92-266 5.50e-04

The C-terminal substrate-domain of LysR-type transcriptional regulator, NocR, involved in the catabolism of nopaline, contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulator NocR, which is involved in the catabolism of nopaline. 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, NocR regulates expression of the divergently transcribed nocB and nocR genes of the nopaline catabolism (noc) region. 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: 176147  Cd Length: 196  Bit Score: 40.08  E-value: 5.50e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162  92 TLTLAVSPLIADTVLPSVMKRYTEDNKETEMTVTIFESEEIASQIRNGSADIGLSCLKVQSSSLTCLPLYNDPVVLVAPP 171
Cdd:cd08458    1 SLRVACYTAPALSFMSGVIQTFIADRPDVSVYLDTVPSQTVLELVSLQHYDLGISILAGDYPGLTTEPVPSFRAVCLLPP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162 172 GRKPGTGKADEVKDLFGQYLL-LTHNHPdywddllRQVRIQFPFV-------RTMKVTQTHITKRFIKEGLGVSFL-PLS 242
Cdd:cd08458   81 GHRLEDKETVHATDLEGESLIcLSPVSL-------LRMQTDAALDscgvhcnRRIESSLALNLCDLVSRGMGVGIVdPFT 153

                        170       180       190
                 ....*....|....*....|....*....|
gi 489247162 243 AVRseLAAGSMI------EIPCEFAQMPSA 266
Cdd:cd08458  154 ADY--YSANPVIqrsfdpVVPYHFAIVLPT 181
PBP2_Cbl cd08444
The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is ...
 93-161 5.98e-04

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: 40.18  E-value: 5.98e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162  93 LTLAVSPLIADTVLPSVMKRYTEDNKETEMTVTIFESEEIASQIRNGSADIGLSCLKVQSSS-LTCLPLY 161
Cdd:cd08444    2 LTIATTHTQARYALPWVVQAFKEQFPNVHLVLHQGSPEEIASMLANGQADIGIATEALENHPeLVSFPYY 71
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-172 6.90e-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: 176115 [Multi-domain]  Cd Length: 200  Bit Score: 39.89  E-value: 6.90e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162  92 TLTLAVSPLIADTVLPSVMKRYTEDNKETEMTVTIFESEEIASQIRNGSADIGL----SCLKVQSS-SLTCLPLYNDPVV 166
Cdd:cd08423    1 TLRVGAFPTAAAALLPPALAALRARHPGLEVRLREAEPPESLDALRAGELDLAVvfdyPVTPPPDDpGLTRVPLLDDPLD 80


                 ....*.
gi 489247162 167 LVAPPG 172
Cdd:cd08423   81 LVLPAD 86
PBP2_LTTR_like_1 cd08421
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 106-172 8.79e-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: 176113  Cd Length: 198  Bit Score: 39.43  E-value: 8.79e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489247162 106 LPSVMKRYTEDNKETEMTVTIFESEEIASQIRNGSADIGLSCLKVQSSSLTCLPLYNDPVVLVAPPG 172
Cdd:cd08421   15 LPEDLASFLAAHPDVRIDLEERLSADIVRAVAEGRADLGIVAGNVDAAGLETRPYRTDRLVVVVPRD 81
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 36-103 8.93e-04

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 40.31  E-value: 8.93e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489247162  36 IKLLEKEISCKLFQRSGRKIQLTEEGKAYVPFAMRLLEDYENSMAELHRVRQGYSHTLTLAV---------SPLIAD 103
Cdd:PRK11074  37 VRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRRQCQQVANGWRGQLSIAVdnivrpdrtRQLIVD 113
PBP2_HupR cd08431
The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which ...
 233-270 2.77e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which regulates expression of the heme uptake receptor HupA; contains the type 2 periplasmic binding fold; HupR, a member of the LysR family, activates hupA transcription under low-iron conditions in the presence of hemin. The expression of many iron-uptake genes, such as hupA, is regulated at the transcriptional level by iron and an iron-binding repressor protein called Fur (ferric uptake regulation). Under iron-abundant conditions with heme, the active Fur repressor protein represses transcription of the iron-uptake gene hupA, and prevents transcriptional activation via HupR. Under low-iron conditions with heme, the Fur repressor is inactive and transcription of the hupA is allowed. 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: 176122 [Multi-domain]  Cd Length: 195  Bit Score: 38.02  E-value: 2.77e-03
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 489247162 233 GLGVSFLPLSAVRSELAAGSMIEIPCEFAQMPSAGAYA 270
Cdd:cd08431  141 GLGVGYLPRHLAKPELASGELVEKALEDPRPPQELFLA 178
PBP2_LTTR_aromatics_like_1 cd08447
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 120-245 5.48e-03

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


Pssm-ID: 176138 [Multi-domain]  Cd Length: 198  Bit Score: 37.24  E-value: 5.48e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162 120 TEMtVTifeSEEIaSQIRNGSADIGLSCLKVQSSSLTCLPLYNDPVVLVAPPGRKPGTGKADEVKDLFGQYLLL-THNHP 198
Cdd:cd08447   34 REM-VT---TDQI-EALESGRIDLGLLRPPFARPGLETRPLVREPLVAAVPAGHPLAGAERLTLEDLDGQPFIMySPTEA 108

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 489247162 199 DYWDDLL----RQVRIQFPFVRTMkvTQTHITKRFIKEGLGVSFLPLSAVR 245
Cdd:cd08447  109 RYFHDLVvrlfASAGVQPRYVQYL--SQIHTMLALVRAGLGVALVPASASR 157
PBP2_OccR cd08457
The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the ...
 92-172 5.76e-03

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: 37.08  E-value: 5.76e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162  92 TLTLAVSPLIADTVLPSVMKRYTEDNKETEMTVTIFESEEIASQIRNGSADIGLSCLKVQSSSLTCLPLYNDPVVLVAPP 171
Cdd:cd08457    1 TLRIAAMPALANGFLPRFLAAFLRLRPNLHLSLMGLSSSQVLEAVASGRADLGIADGPLEERQGFLIETRSLPAVVAVPM 80


                 .
gi 489247162 172 G 172
Cdd:cd08457   81 G 81
PBP2_MleR cd08437
The substrate binding domain of LysR-type transcriptional regulator MleR which required for ...
 93-239 6.46e-03

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: 36.93  E-value: 6.46e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489247162  93 LTLAVSPLIADTVLPSVMKRYTEDNKETEMTVTIFESEEIASQIRNGSADIGL--SCLKVQSSSLTCLPLYNDPVVLVAP 170
Cdd:cd08437    2 LRFGLPPIIGNYYFPKLAKDLIKTGLMIQIDTYEGGSAELLEQLLQGDLDIALlgSLTPLENSALHSKIIKTQHFMIIVS 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489247162 171 PGRKPGTGKADEVKDLFG-QYLLLTHN--HPDYWDDLLRQVRIQFPFVrtMKVTQTHITKRFIKEGLGVSFL 239
Cdd:cd08437   82 KDHPLAKAKKVNFADLKKeNFILLNEHfvHPKAFDSLCQQANFQPNIV--YRTNDIHILKSMVRENVGIGFL 151
 
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