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Conserved domains on  [gi|15595331|ref|NP_248823|]
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HTH-type transcriptional activator BauR [Pseudomonas aeruginosa PAO1]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 11426483)

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

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
15-303 2.00e-48

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 161.96  E-value: 2.00e-48
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331  15 FDIRLLRIFKTIVECGSFSAAESTLGLSRSAISLHMGDLEKRLGMRLCQRGRAGFALTDEGREVYRATQTLLAALEGFRA 94
Cdd:COG0583   1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331  95 EVNDLHQHLRGELNIGIInnlVTLPQMRITHALSALKGQGPQVRINIGMTTPNEIELGVLDGHLHVGVVPLISPLSGLEY 174
Cdd:COG0583  81 ELRALRGGPRGTLRIGAP---PSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVA 157

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331 175 LPLYDEHAQLYCSRGHALferadgdiavdevlaadavapsyrlpaeaqARHQELnnsasASDREGMAFLILTGNFIGYLP 254
Cdd:COG0583 158 RPLGEERLVLVASPDHPL------------------------------ARRAPL-----VNSLEALLAAVAAGLGIALLP 202

                       250       260       270       280
                ....*....|....*....|....*....|....*....|....*....
gi 15595331 255 SHYAADWVAAGMLRPLLPERFHYAIALTIVTRKGRRPNLVLERFLEAVA 303
Cdd:COG0583 203 RFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLR 251
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
15-303 2.00e-48

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 161.96  E-value: 2.00e-48
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331  15 FDIRLLRIFKTIVECGSFSAAESTLGLSRSAISLHMGDLEKRLGMRLCQRGRAGFALTDEGREVYRATQTLLAALEGFRA 94
Cdd:COG0583   1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331  95 EVNDLHQHLRGELNIGIInnlVTLPQMRITHALSALKGQGPQVRINIGMTTPNEIELGVLDGHLHVGVVPLISPLSGLEY 174
Cdd:COG0583  81 ELRALRGGPRGTLRIGAP---PSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVA 157

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331 175 LPLYDEHAQLYCSRGHALferadgdiavdevlaadavapsyrlpaeaqARHQELnnsasASDREGMAFLILTGNFIGYLP 254
Cdd:COG0583 158 RPLGEERLVLVASPDHPL------------------------------ARRAPL-----VNSLEALLAAVAAGLGIALLP 202

                       250       260       270       280
                ....*....|....*....|....*....|....*....|....*....
gi 15595331 255 SHYAADWVAAGMLRPLLPERFHYAIALTIVTRKGRRPNLVLERFLEAVA 303
Cdd:COG0583 203 RFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLR 251
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 104-303 3.24e-22

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: 91.97  E-value: 3.24e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331   104 RGELNIGIINnlvTLPQMRITHALSALKGQGPQVRINIGMTTPNEIELGVLDGHLHVGVVPLISPLSGLEYLPLYDEHAQ 183
Cdd:pfam03466   1 SGRLRIGAPP---TLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLV 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331   184 LYCSRGHALFERADGDIA--VDEVLAADAVAPSYRLPAEA--QARHQELNNSASASDREGMAFLILTGNFIGYLPSHYAA 259
Cdd:pfam03466  78 LVAPPDHPLARGEPVSLEdlADEPLILLPPGSGLRDLLDRalRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVA 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 15595331   260 DWVAAGMLRPLLPERFHYAIALTIVTRKGRRPNLVLERFLEAVA 303
Cdd:pfam03466 158 RELADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLR 201
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 16-302 4.47e-22

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: 93.45  E-value: 4.47e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331   16 DIRLLRIFKTIVECGSFSAAESTLGLSRSAISLHMGDLEKRLGMRLCQRGRAGFALTDEGREVYRATQTLLAALEGFRAE 95
Cdd:NF040786   2 NLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEEE 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331   96 VNDLHQHLRGELNIGI--INNLVTLPQMrithaLSALKGQGPQVRINIGMTTPNEIELGVLDGHLHVGVVPLISPLSGLE 173
Cdd:NF040786  82 FDRYGKESKGVLRIGAstIPGQYLLPEL-----LKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKKRLV 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331  174 YLPLYDEHAQLYCSRGHALFERADGDIAVDEVL---------------AADAVAPSYRLPAEaqarhqELNNSASASDRE 238
Cdd:NF040786 157 YTPFYKDRLVLITPNGTEKYRMLKEEISISELQkepfimreegsgtrkEAEKALKSLGISLE------DLNVVASLGSTE 230

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15595331  239 GMAFLILTGNFIGYLPSHYAADWVAAGMLRPLLPERFHYAIALTIVTRKGRRPNLVLERFLEAV 302
Cdd:NF040786 231 AIKQSVEAGLGISVISELAAEKEVERGRVLIFPIPGLPKNRDFYLVYNKNRQLSPTAEAFLQFV 294
rbcR CHL00180
LysR transcriptional regulator; Provisional
 15-163 3.29e-11

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 62.73  E-value: 3.29e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331   15 FDIRLLRIFKTIVECGSFSAAESTLGLSRSAISLHMGDLEKRLGMRLCQRGRAGFALTDEGREVYRATQTLLAAL-EGFR 93
Cdd:CHL00180   5 FTLDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCeETCR 84

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331   94 AeVNDLHQHLRGELNIGIINNLVTLPQMRIthaLSALKGQGPQVRINIGMTTPNEIELGVLDGHLHVGVV 163
Cdd:CHL00180  85 A-LEDLKNLQRGTLIIGASQTTGTYLMPRL---IGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIV 150
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 106-302 9.16e-10

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: 57.22  E-value: 9.16e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331 106 ELNIGIINNLVTLpqmRITHALSALKGQGPQVRINIGMTTPNEIELGVLDGHLHVGVVPLISPLSGLEYLPLYDEHAQLY 185
Cdd:cd05466   1 TLRIGASPSIAAY---LLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLV 77

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331 186 CSRGHALFERADGDIA--VDE--VLAADAVAPSYRLPAEAQARHQELNNSASASDREGMAFLILTGNFIGYLPSHYAADW 261
Cdd:cd05466  78 VPPDHPLAKRKSVTLAdlADEplILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEEL 157

                       170       180       190       200
                ....*....|....*....|....*....|....*....|..
gi 15595331 262 VAAGM-LRPLLPERFHYAIALtiVTRKGRRPNLVLERFLEAV 302
Cdd:cd05466 158 ADGGLvVLPLEDPPLSRTIGL--VWRKGRYLSPAARAFLELL 197
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
15-303 2.00e-48

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 161.96  E-value: 2.00e-48
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331  15 FDIRLLRIFKTIVECGSFSAAESTLGLSRSAISLHMGDLEKRLGMRLCQRGRAGFALTDEGREVYRATQTLLAALEGFRA 94
Cdd:COG0583   1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331  95 EVNDLHQHLRGELNIGIInnlVTLPQMRITHALSALKGQGPQVRINIGMTTPNEIELGVLDGHLHVGVVPLISPLSGLEY 174
Cdd:COG0583  81 ELRALRGGPRGTLRIGAP---PSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVA 157

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331 175 LPLYDEHAQLYCSRGHALferadgdiavdevlaadavapsyrlpaeaqARHQELnnsasASDREGMAFLILTGNFIGYLP 254
Cdd:COG0583 158 RPLGEERLVLVASPDHPL------------------------------ARRAPL-----VNSLEALLAAVAAGLGIALLP 202

                       250       260       270       280
                ....*....|....*....|....*....|....*....|....*....
gi 15595331 255 SHYAADWVAAGMLRPLLPERFHYAIALTIVTRKGRRPNLVLERFLEAVA 303
Cdd:COG0583 203 RFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLR 251
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 104-303 3.24e-22

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: 91.97  E-value: 3.24e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331   104 RGELNIGIINnlvTLPQMRITHALSALKGQGPQVRINIGMTTPNEIELGVLDGHLHVGVVPLISPLSGLEYLPLYDEHAQ 183
Cdd:pfam03466   1 SGRLRIGAPP---TLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLV 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331   184 LYCSRGHALFERADGDIA--VDEVLAADAVAPSYRLPAEA--QARHQELNNSASASDREGMAFLILTGNFIGYLPSHYAA 259
Cdd:pfam03466  78 LVAPPDHPLARGEPVSLEdlADEPLILLPPGSGLRDLLDRalRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVA 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 15595331   260 DWVAAGMLRPLLPERFHYAIALTIVTRKGRRPNLVLERFLEAVA 303
Cdd:pfam03466 158 RELADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLR 201
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 16-302 4.47e-22

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: 93.45  E-value: 4.47e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331   16 DIRLLRIFKTIVECGSFSAAESTLGLSRSAISLHMGDLEKRLGMRLCQRGRAGFALTDEGREVYRATQTLLAALEGFRAE 95
Cdd:NF040786   2 NLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEEE 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331   96 VNDLHQHLRGELNIGI--INNLVTLPQMrithaLSALKGQGPQVRINIGMTTPNEIELGVLDGHLHVGVVPLISPLSGLE 173
Cdd:NF040786  82 FDRYGKESKGVLRIGAstIPGQYLLPEL-----LKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKKRLV 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331  174 YLPLYDEHAQLYCSRGHALFERADGDIAVDEVL---------------AADAVAPSYRLPAEaqarhqELNNSASASDRE 238
Cdd:NF040786 157 YTPFYKDRLVLITPNGTEKYRMLKEEISISELQkepfimreegsgtrkEAEKALKSLGISLE------DLNVVASLGSTE 230

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15595331  239 GMAFLILTGNFIGYLPSHYAADWVAAGMLRPLLPERFHYAIALTIVTRKGRRPNLVLERFLEAV 302
Cdd:NF040786 231 AIKQSVEAGLGISVISELAAEKEVERGRVLIFPIPGLPKNRDFYLVYNKNRQLSPTAEAFLQFV 294
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
17-76 1.49e-16

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 72.42  E-value: 1.49e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331    17 IRLLRIFKTIVECGSFSAAESTLGLSRSAISLHMGDLEKRLGMRLCQRGRAGFALTDEGR 76
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
rbcR CHL00180
LysR transcriptional regulator; Provisional
 15-163 3.29e-11

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 62.73  E-value: 3.29e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331   15 FDIRLLRIFKTIVECGSFSAAESTLGLSRSAISLHMGDLEKRLGMRLCQRGRAGFALTDEGREVYRATQTLLAAL-EGFR 93
Cdd:CHL00180   5 FTLDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCeETCR 84

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331   94 AeVNDLHQHLRGELNIGIINNLVTLPQMRIthaLSALKGQGPQVRINIGMTTPNEIELGVLDGHLHVGVV 163
Cdd:CHL00180  85 A-LEDLKNLQRGTLIIGASQTTGTYLMPRL---IGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIV 150
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
16-192 6.52e-11

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 61.96  E-value: 6.52e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331   16 DIRLLRIFKTIVECGSFSAAESTLGLSRSAISLHMGDLEKRLGMRLCQRGRAGFALTDEGREVYRATQTLLAALEGFRAE 95
Cdd:PRK15421   3 EVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQA 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331   96 VNDLHQhlrGELNIGIINNLVTlpqMRITHALSALKGQGPQVRINIGMTTPNEIELGVLDGHLHVGVVPLISPLSGLEYL 175
Cdd:PRK15421  83 CNEPQQ---TRLRIAIECHSCI---QWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLHYS 156

                        170
                 ....*....|....*..
gi 15595331  176 PLYDEHAQLYCSRGHAL 192
Cdd:PRK15421 157 PMFDYEVRLVLAPDHPL 173
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 106-302 9.16e-10

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: 57.22  E-value: 9.16e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331 106 ELNIGIINNLVTLpqmRITHALSALKGQGPQVRINIGMTTPNEIELGVLDGHLHVGVVPLISPLSGLEYLPLYDEHAQLY 185
Cdd:cd05466   1 TLRIGASPSIAAY---LLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLV 77

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331 186 CSRGHALFERADGDIA--VDE--VLAADAVAPSYRLPAEAQARHQELNNSASASDREGMAFLILTGNFIGYLPSHYAADW 261
Cdd:cd05466  78 VPPDHPLAKRKSVTLAdlADEplILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEEL 157

                       170       180       190       200
                ....*....|....*....|....*....|....*....|..
gi 15595331 262 VAAGM-LRPLLPERFHYAIALtiVTRKGRRPNLVLERFLEAV 302
Cdd:cd05466 158 ADGGLvVLPLEDPPLSRTIGL--VWRKGRYLSPAARAFLELL 197
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 16-188 1.98e-09

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 57.38  E-value: 1.98e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331   16 DIRLLRIFKTIVECGSFSAAESTLGLSRSAISLHMGDLEKRLGMRLCQRGRAGFALTDEGREVYRATQTLLAALEGFRAE 95
Cdd:PRK11233   2 NFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQLA 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331   96 VNDLHQHLRGELNIGI----INNLVTLPQMRithalsALKGQGPQVRI----NIGmTTPNEIelgVLDGHLHVGVVPLIS 167
Cdd:PRK11233  82 VHNVGQALSGQVSIGLapgtAASSLTMPLLQ------AVRAEFPGIVLylheNSG-ATLNEK---LMNGQLDMAVIYEHS 151

                        170       180
                 ....*....|....*....|.
gi 15595331  168 PLSGLEYLPLYDEHAQLYCSR 188
Cdd:PRK11233 152 PVAGLSSQPLLKEDLFLVGTQ 172
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
15-192 6.96e-09

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 55.97  E-value: 6.96e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331   15 FDIRLLRIFKTIVECGSFSAAESTLGLSRSAISLHMGDLEKRLGMRLCQRGRAGFALTDEGREVYRATQTLLAALEGFRA 94
Cdd:PRK10094   2 FDPETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPS 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331   95 EVNDLHQHLRGELNIgIINNLVTLPQMrITHALSALKGQGPQVRINIGmttpNEIELGVLD------GHLHVGvVPLISP 168
Cdd:PRK10094  82 ELQQVNDGVERQVNI-VINNLLYNPQA-VAQLLAWLNERYPFTQFHIS----RQIYMGVWDsllyegFSLAIG-VTGTEA 154

                        170       180
                 ....*....|....*....|....*
gi 15595331  169 LS-GLEYLPLYDEHAQLYCSRGHAL 192
Cdd:PRK10094 155 LAnTFSLDPLGSVQWRFVMAADHPL 179
PRK09986 PRK09986
LysR family transcriptional regulator;
12-195 1.32e-08

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 55.11  E-value: 1.32e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331   12 VSDFDIRLLRIFKTIVECGSFSAAESTLGLSRSAISLHMGDLEKRLGMRLCQRGRAGFALTDEGREVYRATQTLLAALEG 91
Cdd:PRK09986   4 LYRIDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQ 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331   92 FRAEVNDLHQHLRGELNIGIINNLV---TLPQMRithalsALKGQGPQVRINIGMTTPN-EIELgVLDGHLHVGV--VPL 165
Cdd:PRK09986  84 SLARVEQIGRGEAGRIEIGIVGTALwgrLRPAMR------HFLKENPNVEWLLRELSPSmQMAA-LERRELDAGIwrMAD 156

                        170       180       190
                 ....*....|....*....|....*....|
gi 15595331  166 ISPLSGLEYLPLYDEHAQLYCSRGHALFER 195
Cdd:PRK09986 157 LEPNPGFTSRRLHESAFAVAVPEEHPLASR 186
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
15-106 1.45e-08

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 54.98  E-value: 1.45e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331   15 FDIRLLRIFKTIVECGSFSAAESTLGLSRSAISLHMGDLEKRLGMRLCQRGRAgFALTDEGREVYRATQTlLAALEgfra 94
Cdd:PRK13348   2 LDYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRGRP-CRPTPAGQRLLRHLRQ-VALLE---- 75

                         90
                 ....*....|..
gi 15595331   95 evNDLHQHLRGE 106
Cdd:PRK13348  76 --ADLLSTLPAE 85
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
22-110 5.24e-08

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 53.23  E-value: 5.24e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331   22 IFKTIVECGSFSAAESTLGLSRSAISLHMGDLEKRLGMRLCQRGRAGFALTDEGREVYRATQTLLaalegfrAEVNDLHQ 101
Cdd:PRK10632   9 VFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRML-------HEVQDVHE 81

                         90
                 ....*....|....*.
gi 15595331  102 HLR-------GELNIG 110
Cdd:PRK10632  82 QLYafnntpiGTLRIG 97
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
31-191 7.07e-08

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 52.70  E-value: 7.07e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331   31 SFSAAESTLGLSRSAISLHMGDLEKRLGMRLCQRGRAGFALTDEGREVYRATQTLLAALEgfrAEVNDL-HQHLRGELNi 109
Cdd:PRK10086  30 SFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLDTLN---QEILDIkNQELSGTLT- 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331  110 giINNLVTLPQMRITHALSALKGQGPQVRINIgmTTPNE--------IELGVLDGHLhvgvvplisPLSGLEYLPLYDEH 181
Cdd:PRK10086 106 --VYSRPSIAQCWLVPRLADFTRRYPSISLTI--LTGNEnvnfqragIDLAIYFDDA---------PSAQLTHHFLMDEE 172

                        170
                 ....*....|
gi 15595331  182 AQLYCSRGHA 191
Cdd:PRK10086 173 ILPVCSPEYA 182
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 23-144 7.82e-08

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 52.69  E-value: 7.82e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331   23 FKTIVECGSFSAAESTLGLSRSAISLHMGDLEKRLGMRLCQRGRAGFALTDEGREVYRATQTLLAALEGFRAEVNDLHQH 102
Cdd:PRK14997  10 FVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDAIAALQVE 89

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 15595331  103 LRGELNigiINNLVTLPQMRITHALSALKGQGPQVRINIGMT 144
Cdd:PRK14997  90 PRGIVK---LTCPVTLLHVHIGPMLAKFMARYPDVSLQLEAT 128
PRK09791 PRK09791
LysR family transcriptional regulator;
15-155 9.04e-08

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 52.46  E-value: 9.04e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331   15 FDIRL--LRIFKTIVECGSFSAAESTLGLSRSAISLHMGDLEKRLGMRLCQRGRAGFALTDEGREVYRATQTLLaalEGF 92
Cdd:PRK09791   3 FQVKIhqIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLIL---EEL 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15595331   93 RAEVNDLHQ---HLRGELNIGIINNLV--TLPQMrithaLSALKGQGPQVRINIG----MTTPNEIELGVLD 155
Cdd:PRK09791  80 RAAQEDIRQrqgQLAGQINIGMGASIArsLMPAV-----ISRFHQQHPQVKVRIMegqlVSMINELRQGELD 146
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 18-195 2.90e-07

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 51.11  E-value: 2.90e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331   18 RLLRIFKTIVECGSFSAAESTLGLSRSAISLHMGDLEKRLGMRLCQRGRAGFALTDEGrEVYR--ATQTLLAALEGFRAe 95
Cdd:PRK11242   4 RHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAG-EVYLryARRALQDLEAGRRA- 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331   96 VNDLHQHLRGELNIGIINnlvTLPQMRITHALSALKGQGPQVRINIGMTTPNEIELGVLDGHLHVGV--VPLISPlsGLE 173
Cdd:PRK11242  82 IHDVADLSRGSLRLAMTP---TFTAYLIGPLIDAFHARYPGITLTIREMSQERIEALLADDELDVGIafAPVHSP--EIE 156

                        170       180
                 ....*....|....*....|..
gi 15595331  174 YLPLYDEHAQLYCSRGHALFER 195
Cdd:PRK11242 157 AQPLFTETLALVVGRHHPLAAR 178
PRK09801 PRK09801
LysR family transcriptional regulator;
20-110 2.03e-06

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 48.49  E-value: 2.03e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331   20 LRIFKTIVECGSFSAAESTLGLSRSAISLHMGDLEKRLGMRLCQRGRAGFALTDEGREVYRATQTLLAALEGFRAEVNDL 99
Cdd:PRK09801  11 LQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVTQI 90

                         90
                 ....*....|.
gi 15595331  100 HQHLRGELNIG 110
Cdd:PRK09801  91 KTRPEGMIRIG 101
PRK15243 PRK15243
virulence genes transcriptional activator SpvR;
14-96 3.42e-06

virulence genes transcriptional activator SpvR;


Pssm-ID: 185155 [Multi-domain]  Cd Length: 297  Bit Score: 47.74  E-value: 3.42e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331   14 DFDI-RLLRIFKTIVECGSFSAAESTLGLSRSAISLHMGDLEKRLGMRLCQRGRAGFALTDEGREVYRATQTLLAALEGF 92
Cdd:PRK15243   2 DFLInKKLKIFITLMETGSFSIATSVLYITRTPLSRVISDLERELKQRLFIRKNGTLIPTEFAQTIYRKVKSHYIFLHAL 81


                 ....
gi 15595331   93 RAEV 96
Cdd:PRK15243  82 EQEI 85
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 20-219 9.18e-06

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 46.52  E-value: 9.18e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331   20 LRIFKTIVECG-SFSAAESTLGLSRSAISLHMGDLEKRLGMRLCQR-GRAGFALTDEGREVYRATQTLLAALEGFRAEVN 97
Cdd:PRK12682   6 LRFVREAVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRhGKRLKGLTEPGKAVLDVIERILREVGNIKRIGD 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331   98 DLHQHLRGELNIGIINNLV--TLPQmrithALSALKGQGPQVRINIGMTTPNEIELGVLDGHLHVGVVP-LISPLSGLEY 174
Cdd:PRK12682  86 DFSNQDSGTLTIATTHTQAryVLPR-----VVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGIATeSLADDPDLAT 160

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15595331  175 LPLYDEHAQLYCSRGHALFERAD-------------------GDIAVDEVLAADAVAPSYRLPA 219
Cdd:PRK12682 161 LPCYDWQHAVIVPPDHPLAQEERitledlaeyplityhpgftGRSRIDRAFAAAGLQPDIVLEA 224
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 105-197 1.95e-05

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: 44.44  E-value: 1.95e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331 105 GELNIGIINNLVT--LPqmritHALSALKGQGPQVRINIGMTTPNEIELGVLDGHLHVGVVPLISPLSGLEYLPLYDEHA 182
Cdd:cd08411   1 GPLRLGVIPTIAPylLP-----RLLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAALLALPVDEPGLEEEPLFDEPF 75

                        90
                ....*....|....*
gi 15595331 183 QLYCSRGHALFERAD 197
Cdd:cd08411  76 LLAVPKDHPLAKRKS 90
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 17-121 3.05e-05

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 44.68  E-value: 3.05e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331   17 IRLLRIFKTIVECGSFSAAESTLGLSRSAISLHMGDLEKRLGMRLCQRGRAGFALTDEGREVY-RAtqtlLAALEGfRAE 95
Cdd:PRK10837   5 LRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYpRA----LALLEQ-AVE 79

                         90       100
                 ....*....|....*....|....*....
gi 15595331   96 VNDLHQHLRGELNIG---IINNLVtLPQM 121
Cdd:PRK10837  80 IEQLFREDNGALRIYassTIGNYI-LPAM 107
cbl PRK12679
HTH-type transcriptional regulator Cbl;
37-194 3.45e-05

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 44.80  E-value: 3.45e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331   37 STLGLSRSAISLHMGDLEKRLGMRL-CQRGRAGFALTDEGREVYRATQTLLAALEGFRAEVNDLHQHLRGELNIGiinnl 115
Cdd:PRK12679  24 NMLFTSQSGVSRHIRELEDELGIEIfIRRGKRLLGMTEPGKALLVIAERILNEASNVRRLADLFTNDTSGVLTIA----- 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331  116 VTLPQMR--ITHALSALKGQGPQVRINIGMTTPNEIELGVLDGHLHVGVVP-LISPLSGLEYLPLYDEHAQLYCSRGHAL 192
Cdd:PRK12679  99 TTHTQARysLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASeRLSNDPQLVAFPWFRWHHSLLVPHDHPL 178


                 ..
gi 15595331  193 FE 194
Cdd:PRK12679 179 TQ 180
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 118-300 9.15e-05

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: 42.48  E-value: 9.15e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331 118 LPQMrithaLSALKGQGPQVRINIGMTTPNEIELGVLDGHLHVGVVPLISPLSGLEYLPLYDEHAQLYCSRGHALFERAD 197
Cdd:cd08420  15 LPRL-----LARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLVEGPVDHPDLIVEPFAEDELVLVVPPDHPLAGRKE 89

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331 198 GDIA-------------------VDEVLAADAVAPSyRLPAEAqarhqELNNSasasdrEGMAFLILTGNFIGYLPSHYA 258
Cdd:cd08420  90 VTAEelaaepwilrepgsgtrevFERALAEAGLDGL-DLNIVM-----ELGST------EAIKEAVEAGLGISILSRLAV 157

                       170       180       190       200
                ....*....|....*....|....*....|....*....|..
gi 15595331 259 ADWVAAGMLRPLLPERFHYAIALTIVTRKGRRPNLVLERFLE 300
Cdd:cd08420 158 RKELELGRLVALPVEGLRLTRPFSLIYHKDKYLSPAAEAFLE 199
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 20-195 1.16e-04

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 43.11  E-value: 1.16e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331   20 LRIFKTIVECG-SFSAAESTLGLSRSAISLHMGDLEKRLGMRLCQR-GRAGFALTDEGREVYRATQTLLAALEGFRAEVN 97
Cdd:PRK12683   6 LRIIREAVRQNfNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRrGKRLTGLTEPGKELLQIVERMLLDAENLRRLAE 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331   98 DLHQHLRGELNIGiinnlVTLPQMRitHAL----SALKGQGPQVRINIGMTTPNEIELGVLDGHLHVGV-VPLISPLSGL 172
Cdd:PRK12683  86 QFADRDSGHLTVA-----TTHTQAR--YALpkvvRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGIaTEALDREPDL 158

                        170       180
                 ....*....|....*....|...
gi 15595331  173 EYLPLYDEHAQLYCSRGHALFER 195
Cdd:PRK12683 159 VSFPYYSWHHVVVVPKGHPLTGR 181
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 126-302 5.80e-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: 40.33  E-value: 5.80e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331 126 ALSALKGQGPQVRINIGMTTPNEIELGVLDGHLHVGVVPLISPL--SGLEYLPLYDEHAQLYCSRGHALFERAdgDIAVD 203
Cdd:cd08435  18 AIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAIGRLADDEqpPDLASEELADEPLVVVARPGHPLARRA--RLTLA 95

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331 204 EVLAADAVAPsyrlPAEAQARhQELNnsaSASDREGMAF---------------LILTGNFIGYLPSHYAADWVAAGMLR 268
Cdd:cd08435  96 DLADYPWVLP----PPGTPLR-QRLE---QLFAAAGLPLprnvvetasisallaLLARSDMLAVLPRSVAEDELRAGVLR 167

                       170       180       190
                ....*....|....*....|....*....|....
gi 15595331 269 PLLPERFHYAIALTIVTRKGRRPNLVLERFLEAV 302
Cdd:cd08435 168 ELPLPLPTSRRPIGITTRRGGPLSPAARALLDAL 201
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
14-66 7.70e-04

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 40.53  E-value: 7.70e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 15595331   14 DFDIRLLRIFKTIVECGSFSAAESTLGLSRSAISLHMGDLEKRLGMRLCQRGR 66
Cdd:PRK03635   1 MLDYKQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVRTQ 53
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 125-302 2.52e-03

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: 38.28  E-value: 2.52e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331 125 HALSALKGQGPQVRINIGMTTPNEIELGVLDGHLHVGVVPLISPLSGLEYLPLYDEHAQLYCSRGHALFERAdgDIAVDE 204
Cdd:cd08440  17 PVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEADPDLEFEPLLRDPFVLVCPKDHPLARRR--SVTWAE 94

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331 205 VLAADAVAPSY----RLPAEAQAR--------HQELNNSASASD--REGMAFLILTGNFigyLPSHYAADWVAagmlRPL 270
Cdd:cd08440  95 LAGYPLIALGRgsgvRALIDRALAaagltlrpAYEVSHMSTALGmvAAGLGVAVLPALA---LPLADHPGLVA----RPL 167

                       170       180       190
                ....*....|....*....|....*....|..
gi 15595331 271 LPERFHYAIALtiVTRKGRRPNLVLERFLEAV 302
Cdd:cd08440 168 TEPVVTRTVGL--IRRRGRSLSPAAQAFLDLL 197
PRK10341 PRK10341
transcriptional regulator TdcA;
20-106 3.61e-03

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 38.30  E-value: 3.61e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331   20 LRIFKTIVECGSFSAAESTLGLSRSAISLHMGDLEKRLGMRLCQRGRAGFALTDEGrevyratQTLLAALEGFRAEVNDL 99
Cdd:PRK10341  12 LVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAG-------QVLLSRSESITREMKNM 84


                 ....*..
gi 15595331  100 HQHLRGE 106
Cdd:PRK10341  85 VNEINGM 91
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 16-226 3.68e-03

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 38.21  E-value: 3.68e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331   16 DIRLLRIFKTIVECGSFSAAESTLGLSRSAISLHMGDLEKRLGMRLCQRGRAGFALTDEGREVYRATQTLLAALEGFRAE 95
Cdd:PRK09906   2 ELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKLR 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331   96 VNDLHQHLRgELNIGiinnLVTLPQMRI-THALSALKGQGPQVRIN-IGMTTPNEIElGVLDGHLHVGVV--PLISPlsG 171
Cdd:PRK09906  82 ARKIVQEDR-QLTIG----FVPSAEVNLlPKVLPMFRLRHPDTLIElVSLITTQQEE-KLRRGELDVGFMrhPVYSD--E 153

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 15595331  172 LEYLPLYDEHAQLYCSRGHALfeRADGDIAVDEVLAADAVAPSyrlPAEAQARHQ 226
Cdd:PRK09906 154 IDYLELLDEPLVVVLPVDHPL--AHEKEITAAQLDGVNFISTD---PAYSGSLAP 203
PBP2_LTTR_aromatics_like_2 cd08448
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 106-215 4.13e-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: 176139 [Multi-domain]  Cd Length: 197  Bit Score: 37.63  E-value: 4.13e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331 106 ELNIGIINNLVtlpQMRITHALSALKGQGPQVRINIG-MTTPNEIELgVLDGHLHVGVVPLISPLSGLEYLPLYDEHAQL 184
Cdd:cd08448   1 RLRIGFVGSML---YRGLPRILRAFRAEYPGIEVALHeMSSAEQIEA-LLRGELDLGFVHSRRLPAGLSARLLHREPFVC 76

                        90       100       110
                ....*....|....*....|....*....|....*
gi 15595331 185 YCSRGHALFERADGDIA----VDEVLAADAVAPSY 215
Cdd:cd08448  77 CLPAGHPLAARRRIDLRelagEPFVLFSREVSPDY 111
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 216-302 7.67e-03

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


Pssm-ID: 176114 [Multi-domain]  Cd Length: 197  Bit Score: 36.65  E-value: 7.67e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331 216 RLPAEAQARHQELNNSASASDREGMAFLILTGNFIGYLPSHYAADWVAAGMLRPLLPERFHYAIALTIVTRKGRRPNLVL 295
Cdd:cd08422 111 RFRRGGGEVEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAEDLASGRLVRVLPDWRPPPLPIYAVYPSRRHLPAKV 190


                ....*..
gi 15595331 296 ERFLEAV 302
Cdd:cd08422 191 RAFIDFL 197
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 135-301 8.58e-03

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: 36.77  E-value: 8.58e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331 135 PQVRINIGMTTPNEIELGVLDGHLHVGVVPLISPLSGLEYLPLYDEHAQLYCSRGHALFERAD---GDIA---------- 201
Cdd:cd08415  27 PDVRISLHTLSSSTVVEAVLSGQADLGLASLPLDHPGLESEPLASGRAVCVLPPGHPLARKDVvtpADLAgeplislgrg 106

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595331 202 ------VDEVLAADAVAPSYRLpaEAQarhqeLNNSASASDREGMAfliltgnfIGYLPSHYAADWVAAGM-LRPLLPE- 273
Cdd:cd08415 107 dplrqrVDAAFERAGVEPRIVI--ETQ-----LSHTACALVAAGLG--------VAIVDPLTAAGYAGAGLvVRPFRPAi 171

                       170       180
                ....*....|....*....|....*...
gi 15595331 274 RFHYAialtIVTRKGRRPNLVLERFLEA 301
Cdd:cd08415 172 PFEFA----LVRPAGRPLSRLAQAFIDL 195
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

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