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Conserved domains on  [gi|2068589442|ref|WP_218538571|]
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LysR family transcriptional regulator [Pseudomonas sp. PDM25]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 10444082)

LysR family transcriptional regulator with an N-terminal DNA binding motif and a C-terminal inducer binding domain

CATH:  3.40.190.10
Gene Ontology:  GO:0003700|GO:0003677|GO:0006355
PubMed:  19047729|8257110|11741199

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PBP2_YofA_SoxR_like cd08442
The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, ...
 90-282 1.13e-90

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


:

Pssm-ID: 176133  Cd Length: 193  Bit Score: 267.55  E-value: 1.13e-90
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442  90 SFPLGSLESTAAVRIPELLAAYNQKYAKVELDLSTGPSGTMIDGVLSGRLAAAFVDGPVLHPALEGVPAFEEEMVVIAPL 169
Cdd:cd08442     1 PLRLGSMETTAAVRLPPLLAAYHARYPKVDLSLSTGTTGALIQAVLEGRLDGAFVAGPVEHPRLEQEPVFQEELVLVSPK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442 170 NHSPIHRARDVNGENIYAFRSNCSYRHHFESWFAKDAAVPGKIFEMESYHGMLACVSAGAGLALMPRSMLDSMPGCTTVS 249
Cdd:cd08442    81 GHPPVSRAEDLAGSTLLAFRAGCSYRRRLEDWLAEEGVSPGKIMEFGSYHAILGCVAAGMGIALLPRSVLDSLQGRGSVS 160

                         170       180       190
                  ....*....|....*....|....*....|...
gi 2068589442 250 VWPLSESFRYLRTWLVWRRGTVSQSLTMFVRLL 282
Cdd:cd08442   161 IHPLPEPFADVTTWLVWRKDSFTAALQAFLDLL 193
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-61 1.06e-17

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


:

Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 75.11  E-value: 1.06e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2068589442   3 LVQLEIFKAVAEHGSISAAAQHIHRVPSNLTTRIKQLELDLGVDLFIREKSRLRLSPAG 61
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
 
Name Accession Description Interval E-value
PBP2_YofA_SoxR_like cd08442
The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, ...
 90-282 1.13e-90

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


Pssm-ID: 176133  Cd Length: 193  Bit Score: 267.55  E-value: 1.13e-90
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442  90 SFPLGSLESTAAVRIPELLAAYNQKYAKVELDLSTGPSGTMIDGVLSGRLAAAFVDGPVLHPALEGVPAFEEEMVVIAPL 169
Cdd:cd08442     1 PLRLGSMETTAAVRLPPLLAAYHARYPKVDLSLSTGTTGALIQAVLEGRLDGAFVAGPVEHPRLEQEPVFQEELVLVSPK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442 170 NHSPIHRARDVNGENIYAFRSNCSYRHHFESWFAKDAAVPGKIFEMESYHGMLACVSAGAGLALMPRSMLDSMPGCTTVS 249
Cdd:cd08442    81 GHPPVSRAEDLAGSTLLAFRAGCSYRRRLEDWLAEEGVSPGKIMEFGSYHAILGCVAAGMGIALLPRSVLDSLQGRGSVS 160

                         170       180       190
                  ....*....|....*....|....*....|...
gi 2068589442 250 VWPLSESFRYLRTWLVWRRGTVSQSLTMFVRLL 282
Cdd:cd08442   161 IHPLPEPFADVTTWLVWRKDSFTAALQAFLDLL 193
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-285 3.54e-56

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 181.60  E-value: 3.54e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442   1 MDLVQLEIFKAVAEHGSISAAAQHIHRVPSNLTTRIKQLELDLGVDLFIREKSRLRLSPAGWSFLDYARRILDLVQEARA 80
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442  81 TVAG--EEPQGSFPLGSLESTAAVRIPELLAAYNQKYAKVELDLSTGPSGTMIDGVLSGRLAAAFVDGPVLHPALEGVPA 158
Cdd:COG0583    81 ELRAlrGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442 159 FEEEMVVIAPLNHSPIHRARDVNgeniyafrsncsyrhhfeswfakdaavpgkifemeSYHGMLACVSAGAGLALMPRSM 238
Cdd:COG0583   161 GEERLVLVASPDHPLARRAPLVN-----------------------------------SLEALLAAVAAGLGIALLPRFL 205

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*...
gi 2068589442 239 LDSMPGCTTVSVWPLSESFRYLRTWLVWRRGT-VSQSLTMFVRLLEER 285
Cdd:COG0583   206 AADELAAGRLVALPLPDPPPPRPLYLVWRRRRhLSPAVRAFLDFLREA 253
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 88-285 1.01e-33

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


Pssm-ID: 460931 [Multi-domain]  Cd Length: 205  Bit Score: 122.01  E-value: 1.01e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442  88 QGSFPLGSLESTAAVRIPELLAAYNQKYAKVELDLSTGPSGTMIDGVLSGRLAAAFVDGPVLHPALEGVPAFEEEMVVIA 167
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442 168 PLNHS-----PIHRArDVNGENIYAFRSNCSYRHHFESWFAKDAAVPGKIFEMESYHGMLACVSAGAGLALMPRSMLDSM 242
Cdd:pfam03466  81 PPDHPlargePVSLE-DLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARE 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 2068589442 243 PGCTTVSVWPLSESFRYLRTWLVWRRGTV-SQSLTMFVRLLEER 285
Cdd:pfam03466 160 LADGRLVALPLPEPPLPRELYLVWRKGRPlSPAVRAFIEFLREA 203
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-285 1.16e-27

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: 108.47  E-value: 1.16e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442   1 MDLVQLEIFKAVAEHGSISAAAQHIHRVPSNLTTRIKQLELDLGVDLFIREKSRLRLSPAGWSFLDYARRILDLVQEARA 80
Cdd:NF040786    1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442  81 TVA--GEEPQGSFPLGSleST--AAVRIPELLAAYNQKYAKVELDLSTGPSGTMIDGVLSGRLAAAFVDGPVLHPALEGV 156
Cdd:NF040786   81 EFDryGKESKGVLRIGA--STipGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKKRLVYT 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442 157 PAFEEEMVVIAPlNHSPIHR--ARDVNGENI----YAFRSNCS-YRHHFESWFAK------DAAVpgkIFEMESYHGMLA 223
Cdd:NF040786  159 PFYKDRLVLITP-NGTEKYRmlKEEISISELqkepFIMREEGSgTRKEAEKALKSlgisleDLNV---VASLGSTEAIKQ 234

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2068589442 224 CVSAGAGLALMPRSMLDSMPGCTTVSVWPLSESFRYLRTWLVWRRG-TVSQSLTMFVRLLEER 285
Cdd:NF040786  235 SVEAGLGISVISELAAEKEVERGRVLIFPIPGLPKNRDFYLVYNKNrQLSPTAEAFLQFVKER 297
rbcR CHL00180
LysR transcriptional regulator; Provisional
 3-189 4.64e-24

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 98.94  E-value: 4.64e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442   3 LVQLEIFKAVAEHGSISAAAQHIHRVPSNLTTRIKQLELDLGVDLFIREKSRLRLSPAGWSFLDYARRILDLVQEA-RAT 81
Cdd:CHL00180    7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETcRAL 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442  82 VAGEEPQ-GSFPLGSLESTAAVRIPELLAAYNQKYAKVELDLSTGPSGTMIDGVLSGRLAAAFVDGPV---LHPALEGVP 157
Cdd:CHL00180   87 EDLKNLQrGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVGGEVpteLKKILEITP 166

                         170       180       190
                  ....*....|....*....|....*....|..
gi 2068589442 158 AFEEEMVVIAPLNHsPIHRARDVNGENIYAFR 189
Cdd:CHL00180  167 YVEDELALIIPKSH-PFAKLKKIQKEDLYRLN 197
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-61 1.06e-17

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 75.11  E-value: 1.06e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2068589442   3 LVQLEIFKAVAEHGSISAAAQHIHRVPSNLTTRIKQLELDLGVDLFIREKSRLRLSPAG 61
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 6-80 2.65e-15

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 74.59  E-value: 2.65e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2068589442   6 LEIFKAVAEHGSISAAAQHIHRVPSNLTTRIKQLELDLGVDLFIREKSRLRLSPAGWSFLDYARRILDLVQEARA 80
Cdd:PRK11074    7 LEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRR 81
 
Name Accession Description Interval E-value
PBP2_YofA_SoxR_like cd08442
The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, ...
 90-282 1.13e-90

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


Pssm-ID: 176133  Cd Length: 193  Bit Score: 267.55  E-value: 1.13e-90
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442  90 SFPLGSLESTAAVRIPELLAAYNQKYAKVELDLSTGPSGTMIDGVLSGRLAAAFVDGPVLHPALEGVPAFEEEMVVIAPL 169
Cdd:cd08442     1 PLRLGSMETTAAVRLPPLLAAYHARYPKVDLSLSTGTTGALIQAVLEGRLDGAFVAGPVEHPRLEQEPVFQEELVLVSPK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442 170 NHSPIHRARDVNGENIYAFRSNCSYRHHFESWFAKDAAVPGKIFEMESYHGMLACVSAGAGLALMPRSMLDSMPGCTTVS 249
Cdd:cd08442    81 GHPPVSRAEDLAGSTLLAFRAGCSYRRRLEDWLAEEGVSPGKIMEFGSYHAILGCVAAGMGIALLPRSVLDSLQGRGSVS 160

                         170       180       190
                  ....*....|....*....|....*....|...
gi 2068589442 250 VWPLSESFRYLRTWLVWRRGTVSQSLTMFVRLL 282
Cdd:cd08442   161 IHPLPEPFADVTTWLVWRKDSFTAALQAFLDLL 193
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-285 3.54e-56

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 181.60  E-value: 3.54e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442   1 MDLVQLEIFKAVAEHGSISAAAQHIHRVPSNLTTRIKQLELDLGVDLFIREKSRLRLSPAGWSFLDYARRILDLVQEARA 80
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442  81 TVAG--EEPQGSFPLGSLESTAAVRIPELLAAYNQKYAKVELDLSTGPSGTMIDGVLSGRLAAAFVDGPVLHPALEGVPA 158
Cdd:COG0583    81 ELRAlrGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442 159 FEEEMVVIAPLNHSPIHRARDVNgeniyafrsncsyrhhfeswfakdaavpgkifemeSYHGMLACVSAGAGLALMPRSM 238
Cdd:COG0583   161 GEERLVLVASPDHPLARRAPLVN-----------------------------------SLEALLAAVAAGLGIALLPRFL 205

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*...
gi 2068589442 239 LDSMPGCTTVSVWPLSESFRYLRTWLVWRRGT-VSQSLTMFVRLLEER 285
Cdd:COG0583   206 AADELAAGRLVALPLPDPPPPRPLYLVWRRRRhLSPAVRAFLDFLREA 253
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 88-285 1.01e-33

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


Pssm-ID: 460931 [Multi-domain]  Cd Length: 205  Bit Score: 122.01  E-value: 1.01e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442  88 QGSFPLGSLESTAAVRIPELLAAYNQKYAKVELDLSTGPSGTMIDGVLSGRLAAAFVDGPVLHPALEGVPAFEEEMVVIA 167
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442 168 PLNHS-----PIHRArDVNGENIYAFRSNCSYRHHFESWFAKDAAVPGKIFEMESYHGMLACVSAGAGLALMPRSMLDSM 242
Cdd:pfam03466  81 PPDHPlargePVSLE-DLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARE 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 2068589442 243 PGCTTVSVWPLSESFRYLRTWLVWRRGTV-SQSLTMFVRLLEER 285
Cdd:pfam03466 160 LADGRLVALPLPEPPLPRELYLVWRKGRPlSPAVRAFIEFLREA 203
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 93-282 4.51e-33

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: 120.01  E-value: 4.51e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442  93 LGSLESTAAVRIPELLAAYNQKYAKVELDLSTGPSGTMIDGVLSGRLAAAFVDGPVLHPALEGVPAFEEEMVVIAPLNH- 171
Cdd:cd05466     4 IGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPPDHp 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442 172 ---SPIHRARDVNGENIYAFRSNCSYRHHFESWFAKDAAVPGKIFEMESYHGMLACVSAGAGLALMPRSMLDSMPGCTTV 248
Cdd:cd05466    84 lakRKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEELADGGLV 163

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 2068589442 249 SVwPLSESFRYLRTWLVWRRG-TVSQSLTMFVRLL 282
Cdd:cd05466   164 VL-PLEDPPLSRTIGLVWRKGrYLSPAARAFLELL 197
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-285 1.16e-27

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: 108.47  E-value: 1.16e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442   1 MDLVQLEIFKAVAEHGSISAAAQHIHRVPSNLTTRIKQLELDLGVDLFIREKSRLRLSPAGWSFLDYARRILDLVQEARA 80
Cdd:NF040786    1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442  81 TVA--GEEPQGSFPLGSleST--AAVRIPELLAAYNQKYAKVELDLSTGPSGTMIDGVLSGRLAAAFVDGPVLHPALEGV 156
Cdd:NF040786   81 EFDryGKESKGVLRIGA--STipGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKKRLVYT 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442 157 PAFEEEMVVIAPlNHSPIHR--ARDVNGENI----YAFRSNCS-YRHHFESWFAK------DAAVpgkIFEMESYHGMLA 223
Cdd:NF040786  159 PFYKDRLVLITP-NGTEKYRmlKEEISISELqkepFIMREEGSgTRKEAEKALKSlgisleDLNV---VASLGSTEAIKQ 234

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2068589442 224 CVSAGAGLALMPRSMLDSMPGCTTVSVWPLSESFRYLRTWLVWRRG-TVSQSLTMFVRLLEER 285
Cdd:NF040786  235 SVEAGLGISVISELAAEKEVERGRVLIFPIPGLPKNRDFYLVYNKNrQLSPTAEAFLQFVKER 297
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 93-282 2.62e-24

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: 97.19  E-value: 2.62e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442  93 LGSLESTAAVRIPELLAAYNQKYAKVELDLSTGPSGTMIDGVLSGRLAAAFVDGPVLHPALEGVPAFEEEMVVIAPLNH- 171
Cdd:cd08414     4 IGFVGSALYGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPPPDPPGLASRPLLREPLVVALPADHp 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442 172 ----SPIhRARDVNGEN--IYAFRSNCSYRHHFESWFAKDAAVPGKIFEMESYHGMLACVSAGAGLALMPRSMLD-SMPG 244
Cdd:cd08414    84 laarESV-SLADLADEPfvLFPREPGPGLYDQILALCRRAGFTPRIVQEASDLQTLLALVAAGLGVALVPASVARlQRPG 162

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 2068589442 245 CTTVsvwPLSESFRYLRTWLVWRRGTVSQSLTMFVRLL 282
Cdd:cd08414   163 VVYR---PLADPPPRSELALAWRRDNASPALRAFLELA 197
rbcR CHL00180
LysR transcriptional regulator; Provisional
 3-189 4.64e-24

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 98.94  E-value: 4.64e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442   3 LVQLEIFKAVAEHGSISAAAQHIHRVPSNLTTRIKQLELDLGVDLFIREKSRLRLSPAGWSFLDYARRILDLVQEA-RAT 81
Cdd:CHL00180    7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETcRAL 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442  82 VAGEEPQ-GSFPLGSLESTAAVRIPELLAAYNQKYAKVELDLSTGPSGTMIDGVLSGRLAAAFVDGPV---LHPALEGVP 157
Cdd:CHL00180   87 EDLKNLQrGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVGGEVpteLKKILEITP 166

                         170       180       190
                  ....*....|....*....|....*....|..
gi 2068589442 158 AFEEEMVVIAPLNHsPIHRARDVNGENIYAFR 189
Cdd:CHL00180  167 YVEDELALIIPKSH-PFAKLKKIQKEDLYRLN 197
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 1-285 3.60e-23

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 96.38  E-value: 3.60e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442   1 MDLVQLEIFKAVAEHGSISAAAQHIHRVPSNLTTRIKQLELDLGVDLFIREKSRLRLSPAGWSFLDYARRILDLVQEA-- 78
Cdd:PRK09906    1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAkl 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442  79 RATVAGEEPQgSFPLGSLESTAAVRIPELLAAYNQKYAKVELDLSTGPSGTMIDGVLSGRLAAAFVDGPVLHPALEGVPA 158
Cdd:PRK09906   81 RARKIVQEDR-QLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPVYSDEIDYLEL 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442 159 FEEEMVVIAPLNHSPIHRAR----DVNGEN--IYAFRSNCSYRHHFESWFAKDAAVPGKIFEMESYHGMLACVSAGAGLA 232
Cdd:PRK09906  160 LDEPLVVVLPVDHPLAHEKEitaaQLDGVNfiSTDPAYSGSLAPIIKAWFAQHNSQPNIVQVATNILVTMNLVGMGLGCT 239

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2068589442 233 LMPRSMLDSMPGCTTVSvwPLSESFRYLRTWLVWRRGTVSQSLTMFVRLLEER 285
Cdd:PRK09906  240 IIPGYMNNFNTGQVVFR--PLAGNVPSIALLMAWKKGEMKPALRDFIAIVQER 290
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 93-269 4.30e-18

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


Pssm-ID: 176125 [Multi-domain]  Cd Length: 195  Bit Score: 80.27  E-value: 4.30e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442  93 LGSLESTAAVRIPELLAAYNQKYAKVELDLSTGPSGTMIDGVLSGRLAAAFVDGPVLHPALEGVPAFEEEMVVIAPLNH- 171
Cdd:cd08434     4 LGFLHSLGTSLVPDLIRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLALCSPVPDEPDIEWIPLFTEELVLVVPKDHp 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442 172 ----SPIHRArDVNGENIYAFRSNCSYRHHFESWFAKDAAVPGKIFEMESYHGMLACVSAGAGLALMPRSMLDSMPGctt 247
Cdd:cd08434    84 lagrDSVDLA-ELADEPFVLLSPGFGLRPIVDELCAAAGFTPKIAFEGEEDSTIAGLVAAGLGVAILPEMTLLNPPG--- 159

                         170       180
                  ....*....|....*....|....
gi 2068589442 248 VSVWPLSE--SFRYLrtWLVWRRG 269
Cdd:cd08434   160 VKKIPIKDpdAERTI--GLAWLKD 181
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-61 1.06e-17

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 75.11  E-value: 1.06e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2068589442   3 LVQLEIFKAVAEHGSISAAAQHIHRVPSNLTTRIKQLELDLGVDLFIREKSRLRLSPAG 61
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 1-235 3.89e-17

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 79.62  E-value: 3.89e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442   1 MDLVQLEIFKAVAEHGSISAAAQHIHRVPSNLTTRIKQLELDLGVDLFIREKSRLRLSPAGWSFLDYARRILDLVQEARA 80
Cdd:PRK11242    1 MLLRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442  81 TV--AGEEPQGSFPLGSLESTAAVRIPELLAAYNQKYAKVELDLSTGPSGTMIDGVLSGRLAAAFVDGPVLHPALEGVPA 158
Cdd:PRK11242   81 AIhdVADLSRGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMSQERIEALLADDELDVGIAFAPVHSPEIEAQPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442 159 FEEEMVVIAPLNHSPIHR-----ARDVNGENIYAFRSNCSYRHHFESWFAKDAAVPGKIFEMESYHGMLACVSAGAGLAL 233
Cdd:PRK11242  161 FTETLALVVGRHHPLAARrkaltLDELADEPLVLLSAEFATREQIDRYFRRHGVTPRVAIEANSISAVLEIVRRGRLATL 240


                  ..
gi 2068589442 234 MP 235
Cdd:PRK11242  241 LP 242
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 93-233 1.08e-16

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: 76.45  E-value: 1.08e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442  93 LGSLESTAAVRIPELLAAYNQKYAKVELDLSTGPSGTMIDGVLSGRLAAAFVDGPVLHPALEGVPAFEEEMVVIAPLNH- 171
Cdd:cd08415     4 IAALPALALSLLPRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPLDHPGLESEPLASGRAVCVLPPGHp 83

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2068589442 172 ----SPIHrARDVNGENIYAFRSNCSYRHHFESWFAKDAAVPGKIFEMESYHGMLACVSAGAGLAL 233
Cdd:cd08415    84 larkDVVT-PADLAGEPLISLGRGDPLRQRVDAAFERAGVEPRIVIETQLSHTACALVAAGLGVAI 148
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-282 2.58e-16

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


Pssm-ID: 176127 [Multi-domain]  Cd Length: 194  Bit Score: 75.33  E-value: 2.58e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442  93 LGSLESTAAVRIPELLAAYNQKYAKVELDLSTGPSGTMIDGVLSGRLAAAFVDGPVLHPA-LEGVPAFEEEMVVIAPLNH 171
Cdd:cd08436     4 IGTITSLAAVDLPELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAFVGLPERRPPgLASRELAREPLVAVVAPDH 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442 172 SPIHRAR----DVNGENIYAFRSNCSYRHHFESWFAKDAAVPGKIFEMESYHGMLACVSAGAGLALMPRSMLDSMPGCTT 247
Cdd:cd08436    84 PLAGRRRvalaDLADEPFVDFPPGTGARRQVDRAFAAAGVRRRVAFEVSDVDLLLDLVARGLGVALLPASVAARLPGLAA 163

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 2068589442 248 VsvwPLSESFRYlRTWLVWRRGTVSQSLTMFVRLL 282
Cdd:cd08436   164 L---PLEPAPRR-RLYLAWSAPPPSPAARAFLELL 194
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 6-80 2.65e-15

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 74.59  E-value: 2.65e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2068589442   6 LEIFKAVAEHGSISAAAQHIHRVPSNLTTRIKQLELDLGVDLFIREKSRLRLSPAGWSFLDYARRILDLVQEARA 80
Cdd:PRK11074    7 LEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRR 81
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 104-282 3.55e-15

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: 72.52  E-value: 3.55e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442 104 IPELLAAYNQKYAKVELDLSTGPSGTMIDGVLSGRLAAAFVDGPVLHPALEGVPAFEEEMVVIAPLNHsPIHRARDVNGE 183
Cdd:cd08420    15 LPRLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLVEGPVDHPDLIVEPFAEDELVLVVPPDH-PLAGRKEVTAE 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442 184 NIYAFR-------SncSYRHHFESWFAKDAAVPGKI---FEMESYHGMLACVSAGAGLALMPRSMLDSMPGCTTVSVWPL 253
Cdd:cd08420    94 ELAAEPwilrepgS--GTREVFERALAEAGLDGLDLnivMELGSTEAIKEAVEAGLGISILSRLAVRKELELGRLVALPV 171

                         170       180       190
                  ....*....|....*....|....*....|.
gi 2068589442 254 sESFRYLRT-WLVWRRG-TVSQSLTMFVRLL 282
Cdd:cd08420   172 -EGLRLTRPfSLIYHKDkYLSPAAEAFLEFL 201
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
1-280 2.01e-14

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 72.36  E-value: 2.01e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442   1 MDLVQLEIFKAVAEHGSISAAAQHIHRVPSNLTTRIKQLELDLGVDLFIREKSRLRLSPAGWSFLDYARRILDlvQEARA 80
Cdd:PRK15421    2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLP--QISQA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442  81 TVAGEEPQGSFPLGSLESTAAVR-IPELLAAYNQKYAKVELDLSTG----PSGTMIDGVLSGRLAAAFVDGPVLHPAleg 155
Cdd:PRK15421   80 LQACNEPQQTRLRIAIECHSCIQwLTPALENFHKNWPQVEMDFKSGvtfdPQPALQQGELDLVMTSDILPRSGLHYS--- 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442 156 vPAFEEEM-VVIAPlNHsPIHRARDVNGEN-------IYAFRsncsyRHHFESW--FAKDAAVPGKIFEMESYHGMLACV 225
Cdd:PRK15421  157 -PMFDYEVrLVLAP-DH-PLAAKTRITPEDlasetllIYPVQ-----RSRLDVWrhFLQPAGVSPSLKSVDNTLLLIQMV 228

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2068589442 226 SAGAGLALMPRSMLDSMPGCTTVSVWPLSESFrYLRTWLVWRRGTVSQSLT-MFVR 280
Cdd:PRK15421  229 AARMGIAALPHWVVESFERQGLVVTKTLGEGL-WSRLYAAVRDGEQRQPVTeAFIR 283
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
1-188 4.10e-14

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 71.16  E-value: 4.10e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442   1 MDLVQLEIFKAVAEHG-SISAAAQHIHRVPSNLTTRIKQLELDLGVDLFIREKSRLR-LSPAGWSFLDYARRILDLVQEA 78
Cdd:PRK12684    1 MNLHQLRFVREAVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRgLTEPGRIILASVERILQEVENL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442  79 RaTVAGE---EPQGSFPLGSLESTAAVRIPELLAAYNQKYAKVELDLSTGPSGTMIDGVLSGR--LAAAfVDGPVLHPAL 153
Cdd:PRK12684   81 K-RVGKEfaaQDQGNLTIATTHTQARYALPAAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQadLAIA-TEAIADYKEL 158

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 2068589442 154 EGVPAFEEEMVVIAPLNHsPIHRARDVNGENIYAF 188
Cdd:PRK12684  159 VSLPCYQWNHCVVVPPDH-PLLERKPLTLEDLAQY 192
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
26-243 7.25e-14

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 69.85  E-value: 7.25e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442  26 HRVPSNLTTRIKQLELDLGVDLFIREKSRLRLSPAGWSFLDYARRILDLVQEARATVAGEEPQGSfplGSLE---S-TAA 101
Cdd:PRK11716    2 HVSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLS---GELSlfcSvTAA 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442 102 VRI-PELLAAYNQKYAKVELDLSTGPSGTMIDGVLSGRLAAAFVDGPVLHPA-LEGVPAFEEEMVVIAPLNHSPIhrARD 179
Cdd:PRK11716   79 YSHlPPILDRFRAEHPLVEIKLTTGDAADAVEKVQSGEADLAIAAKPETLPAsVAFSPIDEIPLVLIAPALPCPV--RQQ 156

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2068589442 180 VNGENIYAfrSNCSY--------RHHFESWFAKDAAVPgKIFEMESYH-GMLACVSAGAGLALMPRSMLDSMP 243
Cdd:PRK11716  157 LSQEKPDW--SRIPFilpehgpaRRRIDLWFRRHKIKP-NIYATVSGHeAIVSMVALGCGVGLLPEVVLENSP 226
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 3-174 8.92e-14

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 70.10  E-value: 8.92e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442   3 LVQLEIFKAVAEHGSISAAAQHIHRVPSNLTTRIKQLELDLGVDLFIR--------EKSRLrLSPAGWSFLDYARRILDL 74
Cdd:PRK10837    5 LRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRvgkrlvvnEHGRL-LYPRALALLEQAVEIEQL 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442  75 VQEAratvageepqgsfpLGSLESTAAVRI-----PELLAAYNQKYAKVELDLSTGPSGTMIDGVLSGRLAAAFVDGPVL 149
Cdd:PRK10837   84 FRED--------------NGALRIYASSTIgnyilPAMIARYRRDYPQLPLELSVGNSQDVINAVLDFRVDIGLIEGPCH 149

                         170       180
                  ....*....|....*....|....*....
gi 2068589442 150 HPALEGVPAFEEEMVVIA----PLNHSPI 174
Cdd:PRK10837  150 SPELISEPWLEDELVVFAapdsPLARGPV 178
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 1-132 6.71e-13

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 67.75  E-value: 6.71e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442   1 MDLVQLEIFKAVAEHGSISAAAQHIHRVPSNLTTRIKQLELDLGVDLFIREKSRLRLSPAGWSFLDYARRILDLVQEARA 80
Cdd:PRK15092   11 LDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEACS 90

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2068589442  81 TVAGEEPQGSFPLGSLESTAAVRIPELLAAYNQKYAKVELDLSTGPSGTMID 132
Cdd:PRK15092   91 SLMYSNLQGVLTIGASDDTADTILPFLLNRVSSVYPKLALDVRVKRNAFMME 142
PRK12680 PRK12680
LysR family transcriptional regulator;
1-271 1.37e-12

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 66.95  E-value: 1.37e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442   1 MDLVQLEIFKAVAEHG-SISAAAQHIHRVPSNLTTRIKQLELDLGVDLFIREKSRLR-LSPAGWSFLDYARRILDLVQEA 78
Cdd:PRK12680    1 MTLTQLRYLVAIADAElNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLEsVTPAGVEVIERARAVLSEANNI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442  79 RATVAGE--EPQGSFPLGSLESTAAVRIPELLAAYNQKYAKVELDLSTGPSGTMIDGVLSGRLAAAFVDGPVLHP-ALEG 155
Cdd:PRK12680   81 RTYAANQrrESQGQLTLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVSTAGGEPsAGIA 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442 156 VPAFEEEMVVIAPLNHSPIH--RARDVNG---ENIYAFRSNCSYRHHFESWFAKDAAVPGKIFEMESYHGMLACVSAGAG 230
Cdd:PRK12680  161 VPLYRWRRLVVVPRGHALDTprRAPDMAAlaeHPLISYESSTRPGSSLQRAFAQLGLEPSIALTALDADLIKTYVRAGLG 240

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|.
gi 2068589442 231 LALMPRSMLDSMPgcTTVSVWPLSESFRYLRTWLVWRRGTV 271
Cdd:PRK12680  241 VGLLAEMAVNAND--EDLRAWPAPAPIAECIAWAVLPRDRV 279
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-269 7.67e-12

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: 62.93  E-value: 7.67e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442  93 LGSLESTAAVRIPELLAAYNQKYAKVELDLSTGPSGTMIDGVLSGRLAAAFVDGPVLHPALEGVPAFEEEMVVIAPLNHs 172
Cdd:cd08440     4 VAALPSLAATLLPPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEADPDLEFEPLLRDPFVLVCPKDH- 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442 173 PIHRAR-----DVNGENIYAFRSNCSYRHHFESWFAKDAAVPGKIFEMESYHGMLACVSAGAGLALMPRSMLDSMPGCTT 247
Cdd:cd08440    83 PLARRRsvtwaELAGYPLIALGRGSGVRALIDRALAAAGLTLRPAYEVSHMSTALGMVAAGLGVAVLPALALPLADHPGL 162

                         170       180
                  ....*....|....*....|..
gi 2068589442 248 VSVwPLSESFRYLRTWLVWRRG 269
Cdd:cd08440   163 VAR-PLTEPVVTRTVGLIRRRG 183
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 1-185 8.40e-12

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 64.63  E-value: 8.40e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442   1 MDLVQLEIFKAVAEHG-SISAAAQHIHRVPSNLTTRIKQLELDLGVDLFIREKSRL-RLSPAGWSFLDYARRILDLVQEA 78
Cdd:PRK12682    1 MNLQQLRFVREAVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLkGLTEPGKAVLDVIERILREVGNI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442  79 RATvaGEE----PQGSFPLGSLESTAAVRIPELLAAYNQKYAKVELDLSTGPSGTMIDGVLSGR----LAAAFVDgpvLH 150
Cdd:PRK12682   81 KRI--GDDfsnqDSGTLTIATTHTQARYVLPRVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEadigIATESLA---DD 155

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 2068589442 151 PALEGVPAFEEEMVVIAPLNHsPIHRARDVNGENI 185
Cdd:PRK12682  156 PDLATLPCYDWQHAVIVPPDH-PLAQEERITLEDL 189
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
3-164 1.30e-11

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 63.87  E-value: 1.30e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442   3 LVQLEIFKAVAEHGSISAAAQHIHRVPSNLTTRIKQLELDLGVDLFIREKSRLRLSPAGWSFLDYARRILDLVQEARATV 82
Cdd:PRK10086   16 LSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLDTLNQEILDI 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442  83 AGEEPQGSFPLGSLESTAAVRIPELLAAYNQKYAKVELDLSTGP-----SGTMIDgvlsgrLAAAFVDGPvlHPALEGVP 157
Cdd:PRK10086   96 KNQELSGTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTILTGNenvnfQRAGID------LAIYFDDAP--SAQLTHHF 167


                  ....*..
gi 2068589442 158 AFEEEMV 164
Cdd:PRK10086  168 LMDEEIL 174
PRK09791 PRK09791
LysR family transcriptional regulator;
3-139 1.73e-11

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 63.63  E-value: 1.73e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442   3 LVQLEIFKAVAEHGSISAAAQHIHRVPSNLTTRIKQLELDLGVDLFIREKSRLRLSPAGWSFLDYARRILdlvQEARatV 82
Cdd:PRK09791    7 IHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLIL---EELR--A 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2068589442  83 AGEEPQ-------GSFPLGSLESTAAVRIPELLAAYNQKYAKVELDLSTGPSGTMIDGVLSGRL 139
Cdd:PRK09791   82 AQEDIRqrqgqlaGQINIGMGASIARSLMPAVISRFHQQHPQVKVRIMEGQLVSMINELRQGEL 145
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
6-115 1.95e-11

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 63.29  E-value: 1.95e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442   6 LEIFKAVAEHGSISAAAQHIHRVPSNLTTRIKQLELDLGVDLFIREKSRLRLSPAGWSFLDYARRILDLVQ----EARAT 81
Cdd:PRK10094    7 LRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLEsmpsELQQV 86

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2068589442  82 VAGEEPQGSFPLGSL--ESTAAVRipeLLAAYNQKY 115
Cdd:PRK10094   87 NDGVERQVNIVINNLlyNPQAVAQ---LLAWLNERY 119
PBP2_LTTR_aromatics_like_1 cd08447
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 104-282 7.33e-11

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: 60.35  E-value: 7.33e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442 104 IPELLAAYNQKYAKVELDLSTGPSGTMIDGVLSGRLAAAFVDGPVLHPALEGVPAFEEEMVVIAPLNHsPIHRA-----R 178
Cdd:cd08447    15 LPRLLAAARAALPDVDLVLREMVTTDQIEALESGRIDLGLLRPPFARPGLETRPLVREPLVAAVPAGH-PLAGAerltlE 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442 179 DVNGENIYAFrSNCSYRHHFE---SWFAKDAAVPGKIFEMESYHGMLACVSAGAGLALMPRS-MLDSMPGCTTVSVWPLS 254
Cdd:cd08447    94 DLDGQPFIMY-SPTEARYFHDlvvRLFASAGVQPRYVQYLSQIHTMLALVRAGLGVALVPASaSRLRFEGVVFRPLDLPR 172

                         170       180
                  ....*....|....*....|....*...
gi 2068589442 255 ESFRYLrtWLVWRRGTVSQSLTMFVRLL 282
Cdd:cd08447   173 DVPVEL--HLAWRRDNDNPALRALLDLI 198
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 104-284 8.63e-11

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


Pssm-ID: 176103 [Multi-domain]  Cd Length: 200  Bit Score: 60.23  E-value: 8.63e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442 104 IPELLAAYNQKYAKVELDLSTGPSGTMIDGVLSGRLAAAFVDGPVLHPALEGVPAFEEEMVVIAPLNH-----SPIHrAR 178
Cdd:cd08411    16 LPRLLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAALLALPVDEPGLEEEPLFDEPFLLAVPKDHplakrKSVT-PE 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442 179 DVNGENI------YAFrsncsyRHHFESWFAKDAAVPGKIFEMESYHGMLACVSAGAGLALMPRSMLDSMPGcttvsvWP 252
Cdd:cd08411    95 DLAGERLllleegHCL------RDQALELCRLAGAREQTDFEATSLETLRQMVAAGLGITLLPELAVPSEEL------RG 162

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 2068589442 253 LSESFRYLRTW-------LVWRRGTVSQSLtmFVRLLEE 284
Cdd:cd08411   163 DRLVVRPFAEPapsrtigLVWRRSSPRAAA--FEALAEL 199
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 92-270 2.13e-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: 59.11  E-value: 2.13e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442  92 PLGSlestaAVRIPELLAAYNQKYAKVELDLSTGPSGTMIDGVLSGRLAAAFVDGPVLHPALEGVPAFEEEMVVIAPLNH 171
Cdd:cd08438     8 PLGG-----SLLFAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVLPVDEEEFDSQPLCNEPLVAVLPRGH 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442 172 SPIHRAR----DVNGENIYAFRSNCSYRHHFESWFAKDAAVPGKIFEMESYHGMLACVSAGAGLALMPRSMLDSMPGcTT 247
Cdd:cd08438    83 PLAGRKTvslaDLADEPFILFNEDFALHDRIIDACQQAGFTPNIAARSSQWDFIAELVAAGLGVALLPRSIAQRLDN-AG 161

                         170       180
                  ....*....|....*....|...
gi 2068589442 248 VSVWPLSESFRYLRTWLVWRRGT 270
Cdd:cd08438   162 VKVIPLTDPDLRWQLALIWRKGR 184
PBP2_LTTR_aromatics_like_2 cd08448
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 104-282 1.00e-09

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: 56.89  E-value: 1.00e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442 104 IPELLAAYNQKYAKVELDLSTGPSGTMIDGVLSGRLAAAFVDGPVLHPALEGVPAFEEEMVVIAPLNHSPIHRA----RD 179
Cdd:cd08448    15 LPRILRAFRAEYPGIEVALHEMSSAEQIEALLRGELDLGFVHSRRLPAGLSARLLHREPFVCCLPAGHPLAARRridlRE 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442 180 VNGENIYAFRSNCSyRHHFESWFA--KDAAVPGKIF-EMESYHGMLACVSAGAGLALMPRSMLDS-MPGcttVSVWPLSE 255
Cdd:cd08448    95 LAGEPFVLFSREVS-PDYYDQIIAlcMDAGFHPKIRhEVRHWLTVVALVAAGMGVALVPRSLARAgLAG---VRFLPLKG 170

                         170       180
                  ....*....|....*....|....*..
gi 2068589442 256 SFRYLRTWLVWRRGTVSQSLTMFVRLL 282
Cdd:cd08448   171 ATQRSELYAAWKASAPNPALQAFLAAL 197
PBP2_BudR cd08451
The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is ...
 104-282 1.12e-09

The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is responsible for activation of the expression of the butanediol operon genes; contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of BudR regulator, which is responsible for induction of the butanediol formation pathway under fermentative growth conditions. Three enzymes are involved in the production of 1 mol of 2,3 butanediol from the condensation of 2 mol of pyruvate with acetolactate and acetoin as intermediates: acetolactate synthetase, acetolactate decarboxylase, and acetoin reductase. In Klebsiella terrigena, BudR regulates the expression of the budABC operon genes, encoding these three enzymes of the butanediol pathway. In many bacterial species, the use of this pathway can prevent intracellular acidification by diverting metabolism from acid production to the formation of neutral compounds (acetoin and butanediol). This substrate-binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176142 [Multi-domain]  Cd Length: 199  Bit Score: 56.80  E-value: 1.12e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442 104 IPELLAAYNQKYAKVELDLSTGPSGTMIDGVLSGRLAAAFVDGPVLHP-ALEGVPAFEEEMVVIAPLNHsPIHRARDV-- 180
Cdd:cd08451    16 VPGLIRRFREAYPDVELTLEEANTAELLEALREGRLDAAFVRPPVARSdGLVLELLLEEPMLVALPAGH-PLARERSIpl 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442 181 --------------NGENIY-AFRSNCsYRHHFESWFAKDAAvpgkifEMESYHGMlacVSAGAGLALMPRSMLD-SMPG 244
Cdd:cd08451    95 aaladepfilfprpVGPGLYdAIIAAC-RRAGFTPRIGQEAP------QMASAINL---VAAGLGVSIVPASMRQlQAPG 164

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 2068589442 245 cttVSVWPLSESFRYLRTWLVWRRGTVSQSLTMFVRLL 282
Cdd:cd08451   165 ---VVYRPLAGAPLTAPLALAYRRGERSPAVRNFIALV 199
PBP2_LTTR_like_1 cd08421
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 98-282 1.17e-09

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: 56.76  E-value: 1.17e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442  98 STAAV--RIPELLAAYNQKYAKVELDLSTGPSGTMIDGVLSGRLAAAFVDGPVLHPALEGVPAFEEEMVVIAPLNHSPIH 175
Cdd:cd08421     7 NTSAIveFLPEDLASFLAAHPDVRIDLEERLSADIVRAVAEGRADLGIVAGNVDAAGLETRPYRTDRLVVVVPRDHPLAG 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442 176 RAR----DVNGENIYAFRSNCSYrHHFESWFAKDAAVPGKI-FEMESYHGMLACVSAGAGLALMPRSMLDSMPGCTTVSV 250
Cdd:cd08421    87 RASvafaDTLDHDFVGLPAGSAL-HTFLREAAARLGRRLRLrVQVSSFDAVCRMVAAGLGIGIVPESAARRYARALGLRV 165

                         170       180       190
                  ....*....|....*....|....*....|..
gi 2068589442 251 WPLSESFRYLRTWLVWRRGtvsQSLTMFVRLL 282
Cdd:cd08421   166 VPLDDAWARRRLLLCVRSF---DALPPAARAL 194
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 93-255 2.78e-09

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: 55.68  E-value: 2.78e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442  93 LGSLESTAAVRIPELLAAYNQKYAKVELDLSTGPSGTMIDGVLSGRLAAAFVDGPVLHPALEGVPAFEEEMVVIAPLNHS 172
Cdd:cd08433     4 VGLPPSAASVLAVPLLRAVRRRYPGIRLRIVEGLSGHLLEWLLNGRLDLALLYGPPPIPGLSTEPLLEEDLFLVGPADAP 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442 173 -----PIhRARDVNGENIYAFRSNCSYRHHFESWFAKDAAVPGKIFEMESYHGMLACVSAGAGLALMPRSMLDSMPGCTT 247
Cdd:cd08433    84 lprgaPV-PLAELARLPLILPSRGHGLRRLVDEAAARAGLTLNVVVEIDSVATLKALVAAGLGYTILPASAVAAEVAAGR 162


                  ....*...
gi 2068589442 248 VSVWPLSE 255
Cdd:cd08433   163 LVAAPIVD 170
PRK09986 PRK09986
LysR family transcriptional regulator;
1-255 3.30e-09

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 56.65  E-value: 3.30e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442   1 MDLVQLEIFKAVAEHGSISAAAQHIHRVPSNLTTRIKQLELDLGVDLFIREKSRLRLSPAGWSFLDYARRILDLVQEARA 80
Cdd:PRK09986    7 IDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLA 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442  81 TVA--GEEPQGSFPLGSLESTAAVRIPELLAAYNQKYAKVELDLSTGPSGTMIDGVLSGRLAAAFVDGPVLHPAlegvPA 158
Cdd:PRK09986   87 RVEqiGRGEAGRIEIGIVGTALWGRLRPAMRHFLKENPNVEWLLRELSPSMQMAALERRELDAGIWRMADLEPN----PG 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442 159 F-----EEEMVVIAPLNHSPIHRAR-----DVNGENIYAFRSNcsyrHHFESWFAKDAAV-----PGKIFEMESYHGMLA 223
Cdd:PRK09986  163 FtsrrlHESAFAVAVPEEHPLASRSsvplkALRNEYFITLPFV----HSDWGKFLQRVCQqagfsPQIIRQVNEPQTVLA 238

                         250       260       270
                  ....*....|....*....|....*....|...
gi 2068589442 224 CVSAGAGLALMPRSM-LDSMPGCTTVsvwPLSE 255
Cdd:PRK09986  239 MVSMGIGITLLPDSYaQIPWPGVVFR---PLKE 268
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
2-85 4.41e-09

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 56.13  E-value: 4.41e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442   2 DLVQLEIFKAVAEHGSISAAAQHIHRVPSNLTTRIKQLELDLGVDLFIREKSrLRLSPAGWSFLDYARRILDLVQEARAT 81
Cdd:PRK13348    3 DYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRGRP-CRPTPAGQRLLRHLRQVALLEADLLST 81


                  ....
gi 2068589442  82 VAGE 85
Cdd:PRK13348   82 LPAE 85
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 6-238 4.94e-09

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 56.00  E-value: 4.94e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442   6 LEIFKAVAEHGSISAAAQHIHRVPSNLTTRIKQLELDLGVDLFIREKSRLRLSPAGWSFLDYARRILDLVQEA-RATVAG 84
Cdd:PRK11139   11 LRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEAtRKLRAR 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442  85 EEpQGSFPLGSLESTAAVRIPELLAAYNQKYAKVELDLSTgpsGTMIDGVLSGRLAAAFVDGPVLHPALEGVPAFEEEMV 164
Cdd:PRK11139   91 SA-KGALTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLKA---VDRLEDFLRDDVDVAIRYGRGNWPGLRVEKLLDEYLL 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442 165 -VIAPL---NHSPIHRARDVNGENIyaFRSncSYRHHFESWFA----KDAAVP-GKIFEMeSYHGMLACVsAGAGLALMP 235
Cdd:PRK11139  167 pVCSPAllnGGKPLKTPEDLARHTL--LHD--DSREDWRAWFRaaglDDLNVQqGPIFSH-SSMALQAAI-HGQGVALGN 240


                  ...
gi 2068589442 236 RSM 238
Cdd:PRK11139  241 RVL 243
PBP2_IlvR cd08453
The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved ...
 98-282 6.27e-09

The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved in the biosynthesis of isoleucine, leucine and valine; contains type 2 periplasmic binding fold; The IlvR is an activator of the upstream and divergently transcribed ilvD gene, which encodes dihydroxy acid dehydratase that participates in isoleucine, leucine, and valine biosynthesis. As in the case of other members of the LysR family, the expression of ilvR gene is repressed in the presence of its own gene product. 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: 176144 [Multi-domain]  Cd Length: 200  Bit Score: 54.67  E-value: 6.27e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442  98 STAAVRI-PELLAAYNQKYAKVELDLSTGPSGTMIDGVLSGRLAAAFV---DGPVLHPALEGVPAFEEEMVVIAPLNHSP 173
Cdd:cd08453     8 STADYSVlPELVRRFREAYPDVELQLREATSDVQLEALLAGEIDAGIVippPGASAPPALAYRPLLSEPLVLAVPAAWAA 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442 174 IHRAR----DVNGENIYAF-RSNCSYRHHFESWFAKDAAVPGKI----FEMESyhgMLACVSAGAGLALMPRSMLD-SMP 243
Cdd:cd08453    88 EGGAPlalaAVAAEPLVIFpRRIAPAFHDAVTGYYRAAGQTPRIaqeaIQMQT---IISLVSAGMGVALVPASLRNlARP 164

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 2068589442 244 GcttVSVWPLSESFRYLRTWLVWRRGTVSQSLTMFVRLL 282
Cdd:cd08453   165 G---VVYRELADPAPVLETGLVWRRDDASPVLARFLDLV 200
cbl PRK12679
HTH-type transcriptional regulator Cbl;
1-209 7.05e-09

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 55.97  E-value: 7.05e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442   1 MDLVQLEIFKAVA-EHGSISAAAQHIHRVPSNLTTRIKQLELDLGVDLFIREKSRLR-LSPAGWSFLDYARRILDLVQEA 78
Cdd:PRK12679    1 MNFQQLKIIREAArQDYNLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRLLgMTEPGKALLVIAERILNEASNV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442  79 R--ATVAGEEPQGSFPLGSLESTAAVRIPELLAAYNQKYAKVELDLSTGP---------SGTMIDGVLSGRLAAafvdgp 147
Cdd:PRK12679   81 RrlADLFTNDTSGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTpqeiatllqNGEADIGIASERLSN------ 154

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2068589442 148 vlHPALEGVPAFEEEMVVIAPLNHsPIHRARDVNGENIYA-----FRSNCSYRHHFESWFAKDAAVP 209
Cdd:PRK12679  155 --DPQLVAFPWFRWHHSLLVPHDH-PLTQITPLTLESIAKwplitYRQGITGRSRIDDAFARKGLLA 218
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 1-122 1.68e-08

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 54.61  E-value: 1.68e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442   1 MDLVQLEIFKAVAEHGSISAAAQHIHRVPSNLTTRIKQLELDLGVDLFIREKSRLRLSPAGWSFLDYARRILDLVQEARA 80
Cdd:PRK14997    2 TDLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQD 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 2068589442  81 TVAG--EEPQGSFPLGSLESTAAVRIPELLAAYNQKYAKVELDL 122
Cdd:PRK14997   82 AIAAlqVEPRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQL 125
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 1-235 1.69e-08

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 54.65  E-value: 1.69e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442   1 MDLVQLEIFKAVAEHGSISAAAQHIHRVPSNLTTRIKQLELDLGVDLFIREKSRLRLSPAGWSFLDYARRILDLVQEAR- 79
Cdd:PRK11151    1 MNIRDLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVLKe 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442  80 -ATVAGEEPQGSFPLGSLESTAAVRIPELLAAYNQKYAKVELDLSTGPSGTMIDGVLSGRL----------AAAFVDgpv 148
Cdd:PRK11151   81 mASQQGETMSGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLdcailalvkeSEAFIE--- 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442 149 lhpalegVPAFEEEMVVIAPLNHSPIHRAR----DVNGENI---------------YAFRSNCSYRHHFeswfakdaavp 209
Cdd:PRK11151  158 -------VPLFDEPMLLAVYEDHPWANRDRvpmsDLAGEKLlmledghclrdqamgFCFEAGADEDTHF----------- 219

                         250       260
                  ....*....|....*....|....*.
gi 2068589442 210 gKIFEMESYHGMlacVSAGAGLALMP 235
Cdd:PRK11151  220 -RATSLETLRNM---VAAGSGITLLP 241
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 1-251 1.91e-08

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 54.30  E-value: 1.91e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442   1 MDLVQLEIFKAVAEHGSISAAAQHIHRVPSNLTTRIKQLELDLGVDLFIREKSRLRLSPAGWSFLDYARRILDLVQEARA 80
Cdd:PRK11233    1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442  81 TV--AGEEPQGSFPLGSLESTAA--VRIPeLLAAYNQKYAKVELDLSTGPSGTMIDGVLSGRLAAAFV-DGPVLHpALEG 155
Cdd:PRK11233   81 AVhnVGQALSGQVSIGLAPGTAAssLTMP-LLQAVRAEFPGIVLYLHENSGATLNEKLMNGQLDMAVIyEHSPVA-GLSS 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442 156 VPAFEEEMVVIAPlNHSP---IHRArDVNGENIYAFRSNCSYRHHFESWFAKDAAVPGKIFEMESYHGMLACVSAGAGLA 232
Cdd:PRK11233  159 QPLLKEDLFLVGT-QDCPgqsVDLA-AVAQMNLFLPRDYSAVRLRVDEAFSLRRLTAKVIGEIESIATLTAAIASGMGVT 236

                         250
                  ....*....|....*....
gi 2068589442 233 LMPRSMLDSMpgCTTVSVW 251
Cdd:PRK11233  237 VLPESAARSL--CGAVNGW 253
PBP2_HcaR cd08450
The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in ...
 90-279 1.95e-08

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


Pssm-ID: 176141 [Multi-domain]  Cd Length: 196  Bit Score: 53.15  E-value: 1.95e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442  90 SFPLGSLESTAAVRIPELLAAYNQKYAKVELDLSTGPSGTMIDGVLSGRLAAAFVDGPVLHPALEGVPAFEEEMVVIAPL 169
Cdd:cd08450     1 VLTIGFLPGAEVQWLPEVLPILREEHPDLDVELSSLFSPQLAEALMRGKLDVAFMRPEIQSDGIDYQLLLKEPLIVVLPA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442 170 NHSPIHRAR----DVNGEN-IYAFRSNCSYRHHFESWFAKDAAVPGKIFEMESYHGMLACVSAGAGLALMPRSMLDSMPG 244
Cdd:cd08450    81 DHRLAGREKippqDLAGENfISPAPTAPVLQQVIENYAAQHNIQPNIIQEADNLLSAMSLVASTLGCALLPLYANNLLPP 160

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 2068589442 245 ctTVSVWPLSESFRYLRTWLVWRRGTVSQSLTMFV 279
Cdd:cd08450   161 --SVVARPLSGETPTIDLVMGYNKANTSPLLKRFL 193
PBP2_OccR cd08457
The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the ...
 104-244 4.30e-08

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: 52.49  E-value: 4.30e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442 104 IPELLAAYNQKYAKVELDLSTGPSGTMIDGVLSGRLAAAFVDGPVLHPALEGVPAFEEEMVVIAPLNH----SPIHRARD 179
Cdd:cd08457    15 LPRFLAAFLRLRPNLHLSLMGLSSSQVLEAVASGRADLGIADGPLEERQGFLIETRSLPAVVAVPMGHplaqLDVVSPQD 94

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2068589442 180 VNGENIYAFRSNCSYRHHFESWFAKDAAVPGKIFEMESYHGMLACVSAGAGLALMPRSMLDSMPG 244
Cdd:cd08457    95 LAGERIITLENGYLFRMRVEVALGKIGVKRRPIIEVNLSHTALSLVREGLGIAIIDPATAIGLPL 159
PBP2_MdcR cd08416
The C-terminal substrate-binding domian of LysR-type transcriptional regulator MdcR, which ...
 91-258 6.25e-08

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


Pssm-ID: 176108  Cd Length: 199  Bit Score: 51.96  E-value: 6.25e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442  91 FPLGSLESTAAVRIPELLAAYNQKYAKVELDLSTGPSGTMIDGVLSGRLAAAFV--DGPVLHPALEGVPAFEEEMVVIAP 168
Cdd:cd08416     2 LRLGSLYSLTVNTVPRIIMGLKLRRPELDIELTLGSNKDLLKKLKDGELDAILVatPEGLNDPDFEVVPLFEDDIFLAVP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442 169 LN-----HSPIHrARDVNGENIYAFRSNCSYRHHFESWFAKDAAVPGKIFEMESYHGMLACVSAGAGLALMPRSMLDSMP 243
Cdd:cd08416    82 ATsplaaSSEID-LRDLKDEKFVTLSEGFATYRGFDEAFEIAGFEPNVVMRVNDIFSLMSMVSGGVGYALLPGRIADVYE 160

                         170
                  ....*....|....*
gi 2068589442 244 gcTTVSVWPLSESFR 258
Cdd:cd08416   161 --DKVQLIPLAEPYQ 173
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 1-185 3.82e-07

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 50.43  E-value: 3.82e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442   1 MDLVQLEIFKAVAEHG-SISAAAQHIHRVPSNLTTRIKQLELDLGVDLFIREKSRLR-LSPAGWSFLDYARRILDLVQEA 78
Cdd:PRK12683    1 MNFQQLRIIREAVRQNfNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTgLTEPGKELLQIVERMLLDAENL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442  79 RAtvAGEE----PQGSFPLGSLESTAAVRIPELLAAYNQKYAKVELDLSTGPSGTMIDGVLSGR----LAAAFVDGpvlH 150
Cdd:PRK12683   81 RR--LAEQfadrDSGHLTVATTHTQARYALPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEadigIATEALDR---E 155

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 2068589442 151 PALEGVPAFEEEMVVIAPLNHsPIHRARDVNGENI 185
Cdd:PRK12683  156 PDLVSFPYYSWHHVVVVPKGH-PLTGRENLTLEAI 189
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-270 4.09e-07

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


Pssm-ID: 176115 [Multi-domain]  Cd Length: 200  Bit Score: 49.52  E-value: 4.09e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442  93 LGSLESTAAVRIPELLAAYNQKYAKVELDLSTGPSGTMIDGVLSGRLAAAFVD-----GPVLHPALEGVPAFEEEMVVIA 167
Cdd:cd08423     4 VGAFPTAAAALLPPALAALRARHPGLEVRLREAEPPESLDALRAGELDLAVVFdypvtPPPDDPGLTRVPLLDDPLDLVL 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442 168 PLNHSPIHRAR----DVNGENIYAFRSNCSYRHHFESWFAKDAAVPGKIFEMESYHGMLACVSAGAGLALMPRSMLDSMP 243
Cdd:cd08423    84 PADHPLAGREEvalaDLADEPWIAGCPGSPCHRWLVRACRAAGFTPRIAHEADDYATVLALVAAGLGVALVPRLALGARP 163

                         170       180
                  ....*....|....*....|....*...
gi 2068589442 244 GctTVSVWPLSES-FRylRTWLVWRRGT 270
Cdd:cd08423   164 P--GVVVRPLRPPpTR--RIYAAVRAGA 187
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 3-259 4.98e-07

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 50.38  E-value: 4.98e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442   3 LVQLEIFKAVAEHGSISAAAQHIHRVPSNLTTRIKQLELDLGVDLFIREKSRLRLSPAGWSFLDYARRI---LDLVQEAR 79
Cdd:PRK11013    6 LRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLFEEVQRSyygLDRIVSAA 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442  80 ATVAgEEPQGSFPLGSLESTAAVRIPELLAAYNQKYAKVELDLSTGPSGtmidgVLSGRLAAAFVD-GPVLH----PALE 154
Cdd:PRK11013   86 ESLR-EFRQGQLSIACLPVFSQSLLPGLCQPFLARYPDVSLNIVPQESP-----LLEEWLSAQRHDlGLTETlhtpAGTE 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442 155 GVPAFEEEMVVIAPLNHSPIHRAR----DVNGENIYAFRSNCSYRHHFESWFAKDAAVPGKIFEMESYHGMLACVSAGAG 230
Cdd:PRK11013  160 RTELLTLDEVCVLPAGHPLAAKKVltpdDFAGENFISLSRTDSYRQLLDQLFAEHGVKRRMVVETHSAASVCAMVRAGVG 239

                         250       260       270
                  ....*....|....*....|....*....|
gi 2068589442 231 LALM-PRSMLDSmpGCTTVSVWPLSESFRY 259
Cdd:PRK11013  240 VSIVnPLTALDY--AGSGLVVRRFSISVPF 267
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 97-235 6.13e-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: 6.13e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442  97 ESTAAVRIPELLAAYNQKYAKVELDLSTGPSGTMIDGVLSGRLAAAFVDGPVLHPALEGVPAFEEEMVVIAPLNHsPIHR 176
Cdd:cd08426     8 EGLAAELLPSLIARFRQRYPGVFFTVDVASTADVLEAVLSGEADIGLAFSPPPEPGIRVHSRQPAPIGAVVPPGH-PLAR 86

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2068589442 177 ARDVNGENIYAFR-----SNCSYRHHFESWFAKDAAVPGKIFEMESYHGMLACVSAGAGLALMP 235
Cdd:cd08426    87 QPSVTLAQLAGYPlalppPSFSLRQILDAAFARAGVQLEPVLISNSIETLKQLVAAGGGISLLT 150
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
1-83 6.80e-07

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 49.63  E-value: 6.80e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442   1 MDLVQLEIFKAVAEHGSISAAAQHIHRVPSNLTTRIKQLELDLGVDLFIREKSRLRLSPAGWSFLDYARRILDLVQEARA 80
Cdd:PRK03601    1 MDTELLKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYAETLMNTWQAAKK 80


                  ...
gi 2068589442  81 TVA 83
Cdd:PRK03601   81 EVA 83
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
1-88 1.10e-06

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 49.00  E-value: 1.10e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442   1 MDLVQLEIFKAVAEHGSISAAAQHIHRVPSNLTTRIKQLELDLGVDLFIREKSrLRLSPAGWSFLDYARRILDLVQEARA 80
Cdd:PRK03635    2 LDYKQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVRTQP-CRPTEAGQRLLRHARQVRLLEAELLG 80


                  ....*...
gi 2068589442  81 TVAGEEPQ 88
Cdd:PRK03635   81 ELPALDGT 88
PBP2_BenM_CatM_CatR cd08445
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 103-238 3.52e-06

The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in benzoate catabolism; contains the type 2 periplasmic binding fold; This CD includes the C-terminal of LysR-type transcription regulators, BenM, CatM, and CatR, which are involved in the benzoate catabolism. The BenM and CatM are paralogs with overlapping functions. BenM responds synergistically to two effectors, benzoate and cis,cis-muconate, to activate expression of the benABCDE operon which is involved in benzoate catabolism, while CatM responses only to muconate. BenM and CatM share high protein sequence identity and bind to the operator-promoter regions that have similar DNA sequences. In Pseudomonas species, phenolic compounds are converted by different enzymes to central intermediates, such as protocatechuate and catechols. Generally, unsubstituted compounds, such as benzoate, are metabolized by an ortho-cleavage pathway. The catBCA operon encodes three enzymes of the ortho-pathway required for benzoate catabolism: muconate lactonizing enzyme I, muconolactone isomerase, and catechol 1,2-dioxygenase. CatR normally responds to benzoate and cis,cis-muconate, an inducer molecule, to activate transcription of the catBCA operon, whose gene products convert benzoate to catechol. 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: 176136  Cd Length: 203  Bit Score: 46.84  E-value: 3.52e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442 103 RIPELLAAYNQKYAKVELDLSTGPSGTMIDGVLSGRLAAAFvdGPVLH--PALEGVPAFEEEMVVIAPLNH------SPI 174
Cdd:cd08445    15 LLPELIRRFRQAAPDVEIELIEMTTVQQIEALKEGRIDVGF--GRLRIedPAIRRIVLREEPLVVALPAGHplaqekAPL 92

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2068589442 175 HRArDVNGEN--IYAFRSNCSYRHHFESWFAKDAAVPGKIFEMESYHGMLACVSAGAGLALMPRSM 238
Cdd:cd08445    93 TLA-QLADEPliLYPASPRPSFADQVLSLFRDHGLRPRVIQEVRELQTALGLVAAGEGVTLVPASV 157
PRK10341 PRK10341
transcriptional regulator TdcA;
5-284 5.33e-06

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 47.16  E-value: 5.33e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442   5 QLEIFKAVAEHGSISAAAQHIHRVPSNLTTRIKQLELDLGVDLFIREKSRLRLSPAGWSFLDYA----RRILDLVQEARA 80
Cdd:PRK10341   11 HLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSesitREMKNMVNEING 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442  81 TVAGEEPQGSFPLGSLesTAAVRIPELLAAYNQKYAKVELDLSTGPSGTMIDGVLSGRL--AAAFVDGPVLHPALEGVPA 158
Cdd:PRK10341   91 MSSEAVVDVSFGFPSL--IGFTFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLdfAIGTLSNEMKLQDLHVEPL 168

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442 159 FEEEMVVIAPLNhSPIHRARDVNG---ENIYAFRSNCSYRHHFESWFAKDAAVPGKIFEMESYHGMLACVSAGAGLALMP 235
Cdd:PRK10341  169 FESEFVLVASKS-RTCTGTTTLESlknEQWVLPQTNMGYYSELLTTLQRNGISIENIVKTDSVVTIYNLVLNADFLTVIP 247

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|
gi 2068589442 236 RSMLDSMpGCTTVSVWPLSESFRYLRTWLVWRRG-TVSQSLTMFVRLLEE 284
Cdd:PRK10341  248 CDMTSPF-GSNQFITIPIEETLPVAQYAAVWSKNyRIKKAASVLVELAKE 296
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 93-270 1.37e-05

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: 44.84  E-value: 1.37e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442  93 LGSLESTAAVRIPELLAAYNQKYAKVELDLSTGPSGTMIDGVLSGRLAAAFVDGPVLHPALEGVPAFEEEMVVIAPLNHS 172
Cdd:cd08412     4 IGCFSTLAPYYLPGLLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALTYDLDLPEDIAFEPLARLPPYVWLPADHP 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442 173 PIHRA----RDVNGENIYAFRSNCSyRHHFESWFAKDAAVPGKIFEMESYHGMLACVSAGAGLAL---MPRSMLdSMPGC 245
Cdd:cd08412    84 LAGKDevslADLAAEPLILLDLPHS-REYFLSLFAAAGLTPRIAYRTSSFEAVRSLVANGLGYSLlndRPYRPW-SYDGK 161

                         170       180
                  ....*....|....*....|....*
gi 2068589442 246 TTVSVwPLSESFRYLRTWLVWRRGT 270
Cdd:cd08412   162 RLVRR-PLADPVPPLRLGLAWRRGA 185
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 94-240 2.26e-05

The C-terminal substrate binding domain of galactose-binding protein regulator contains the type 2 periplasmic binding fold; Galactose-binding protein regulator (GbpR), a member of the LysR family of bacterial transcriptional regulators, regulates the expression of chromosomal virulence gene chvE. The chvE gene is involved in the uptake of specific sugars, in chemotaxis to these sugars, and in the VirA-VirG two-component signal transduction system. In the presence of an inducing sugar such as L-arabinose, D-fucose, or D-galactose, GbpR activates chvE expression, while in the absence of an inducing sugar, GbpR represses expression. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176126 [Multi-domain]  Cd Length: 201  Bit Score: 44.19  E-value: 2.26e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442  94 GSLESTAAVRIPELLAAYNQKYAKVELDLSTGPSGTMIDGVLSGR--LAAAFVDGPVLHPALEGVPAFEEEMVVIAPLNH 171
Cdd:cd08435     5 GAVPAAAPVLLPPAIARLLARHPRLTVRVVEGTSDELLEGLRAGEldLAIGRLADDEQPPDLASEELADEPLVVVARPGH 84

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2068589442 172 sPIHRARDVNGENIYAFR-----SNCSYRHHFESWFAKDA-AVPGKIFEMESYHGMLACVSAGAGLALMPRSMLD 240
Cdd:cd08435    85 -PLARRARLTLADLADYPwvlppPGTPLRQRLEQLFAAAGlPLPRNVVETASISALLALLARSDMLAVLPRSVAE 158
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
 98-269 3.55e-05

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: 43.65  E-value: 3.55e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442  98 STAAVRIPELLAAYNQKYAKVELDLSTGPSGTMIDGVLSGRLAAAFVDGPVLHPALEGVPAFEEEMVVIAPLNHsPIHRA 177
Cdd:cd08419     8 STAKYFAPRLLGAFCRRHPGVEVSLRVGNREQVLERLADNEDDLAIMGRPPEDLDLVAEPFLDNPLVVIAPPDH-PLAGQ 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442 178 RDVNGENI----YAFRSNCS-YRHHFESWFAKDAAVPGKIFEMESYHGMLACVSAGAGLALMPRS--MLDSMPGCTTV-S 249
Cdd:cd08419    87 KRIPLERLarepFLLREPGSgTRLAMERFFAEHGVTLRVRMELGSNEAIKQAVMAGLGLSVLSLHtlALELATGRLAVlD 166

                         170       180
                  ....*....|....*....|.
gi 2068589442 250 VwplsESFRYLRTW-LVWRRG 269
Cdd:cd08419   167 V----EGFPIRRQWyVVHRKG 183
PBP2_IlvY cd08430
The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates ...
 99-243 6.03e-05

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


Pssm-ID: 176121  Cd Length: 199  Bit Score: 42.95  E-value: 6.03e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442  99 TAAVRI-PELLAAYNQKYAKVELDLSTGPSGTMIDGVLSGRLAAAFVDGPVLHPA-LEGVPAFEEEMVVIAPLNHSPIHR 176
Cdd:cd08430     9 TASYSFlPPILERFRAQHPQVEIKLHTGDPADAIDKVLNGEADIAIAARPDKLPArLAFLPLATSPLVFIAPNIACAVTQ 88

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2068589442 177 ArdVNGENIYAfrSNCSY--------RHHFESWFAKDAAVPgKIFEMESYH-GMLACVSAGAGLALMPRSMLDSMP 243
Cdd:cd08430    89 Q--LSQGEIDW--SRLPFilperglaRERLDQWFRRRGIKP-NIYAQVAGHeAIVSMVALGCGVGIVPELVLDNSP 159
PBP2_AlsR cd08452
The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which ...
 104-237 2.43e-04

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


Pssm-ID: 176143 [Multi-domain]  Cd Length: 197  Bit Score: 41.33  E-value: 2.43e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442 104 IPELLAAYNQKYAKVELDLSTGPSGTMIDGVLSGRLAAAFVDGPVLHPALEGVPAFEEEMVVIAPLNHSPIHRA----RD 179
Cdd:cd08452    15 LPPIVREYRKKFPSVKVELRELSSPDQVEELLKGRIDIGFLHPPIQHTALHIETVQSSPCVLALPKQHPLASKEeitiED 94

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2068589442 180 VNGENIYAFRSncsyrhhfESW---------FAKDAAVPGKIF-EMESYHGMLACVSAGAGLALMPRS 237
Cdd:cd08452    95 LRDEPIITVAR--------EAWptlydeiiqLCEQAGFRPKIVqEATEYQTVIGLVSAGIGVTFVPSS 154
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
3-134 2.44e-04

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 42.05  E-value: 2.44e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442   3 LVQLEIFKAVAEHGSISAAAQHIHRVPSNLTTRIKQLELDLGVDLFIREKSRLRLSPAGWSFLDYARRILDLVQEARATV 82
Cdd:PRK10632    4 LKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQL 83

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2068589442  83 AG--EEPQGSFPLGSLESTAAVRIPELLAAYNQKYAKVELDLSTG-PSGTMI-DGV 134
Cdd:PRK10632   84 YAfnNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTGiPAPDLIaDGL 139
PBP2_LysR cd08456
The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine ...
 93-231 6.58e-04

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: 40.09  E-value: 6.58e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442  93 LGSLESTAAVRIPELLAAYNQKYAKVELDLSTGPSGTMIDGVLSGRLAAAFVDGPVLHPALEGVPAFEEEMVVIAPLNH- 171
Cdd:cd08456     4 IAVLPALSQSFLPRAIKAFLQRHPDVTISIHTRDSPTVEQWLSAQQCDLGLVSTLHEPPGIERERLLRIDGVCVLPPGHr 83

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2068589442 172 ---SPIHRARDVNGENIYAFRSNCSYRHHFESWFaKDAAVPGKIfEMESYHGMLACVSAGAGL 231
Cdd:cd08456    84 lavKKVLTPSDLEGEPFISLARTDGTRQRVDALF-EQAGVKRRI-VVETSYAATICALVAAGV 144
PRK09801 PRK09801
LysR family transcriptional regulator;
6-120 1.36e-03

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 39.63  E-value: 1.36e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442   6 LEIFKAVAEHGSISAAAQHIHRVPSNLTTRIKQLELDLGVDLFIREKSRLRLSPAGWSFLDYARRILDLVQEA--RATVA 83
Cdd:PRK09801   11 LQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLvdDVTQI 90

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 2068589442  84 GEEPQG------SFPLGslESTAAVRIPELLAAYNQKYAKVEL 120
Cdd:PRK09801   91 KTRPEGmirigcSFGFG--RSHIAPAITELMRNYPELQVHFEL 131
PBP2_LTTR_beta_lactamase cd08484
The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase ...
 108-266 2.57e-03

The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase genes, contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators, BlaA and AmpR, that are involved in control of the expression of beta-lactamase genes. Beta-lactamases are responsible for bacterial resistance to beta-lactam antibiotics such as penicillins. BlaA (a constitutive class A penicillinase) belongs to the LysR family of transcriptional regulators, while BlaB (an inducible class C cephalosporinase or AmpC) can be referred to as a penicillin-binding protein, but it does not act as a beta-lactamase. AmpR regulates the expression of beta-lactamases in many enterobacterial strains and many other gram-negative bacilli. In contrast to BlaA, AmpR acts an activator only in the presence of the beta-lactam inducer. In the absence of the inducer, AmpR acts as a repressor. 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: 176173 [Multi-domain]  Cd Length: 189  Bit Score: 38.12  E-value: 2.57e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442 108 LAAYNQKYAKVELDLSTgpSGTMIDGVLSG-RLAAAFVDGpvLHPALEGVPAFEEEMVVI-APLNHSPIHRARDVNGENI 185
Cdd:cd08484    19 LAEFRQLHPFIDLRLST--NNNRVDIAAEGlDFAIRFGEG--AWPGTDATRLFEAPLSPLcTPELARRLSEPADLANETL 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442 186 YAfrsncSYR-HHFESWFAKDAAVP----GKIFEmeSYHGMLACVSAGAGLALMPRSMLDSMPGCTTVsVWPLSESFRYL 260
Cdd:cd08484    95 LR-----SYRaDEWPQWFEAAGVPPppinGPVFD--SSLLMVEAALQGAGVALAPPSMFSRELASGAL-VQPFKITVSTG 166


                  ....*.
gi 2068589442 261 RTWLVW 266
Cdd:cd08484   167 SYWLTR 172
PBP2_XapR cd08449
The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved ...
 105-238 9.21e-03

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


Pssm-ID: 176140 [Multi-domain]  Cd Length: 197  Bit Score: 36.48  E-value: 9.21e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2068589442 105 PELLAAYNQKYAKVELDLSTGPSGTMIDGVLSGRLAAAFV---DGPVLHPaLEGVPAFEEEMVVIAPlNHSPIHRAR--- 178
Cdd:cd08449    16 GPALRRFKRQYPNVTVRFHELSPEAQKAALLSKRIDLGFVrfaDTLNDPP-LASELLWREPMVVALP-EEHPLAGRKslt 93

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2068589442 179 --DVNGENIYAFRSNCS------YRHHFESWFAkdaavPGKIFEMESYHGMLACVSAGAGLALMPRSM 238
Cdd:cd08449    94 laDLRDEPFVFLRLANSrfadflINCCLQAGFT-----PQITQEVVEPQTLMALVAAGFGVALVPESY 156
Imp COG2358
TRAP-type uncharacterized transport system, periplasmic component [General function prediction ...
 109-175 9.95e-03

TRAP-type uncharacterized transport system, periplasmic component [General function prediction only];


Pssm-ID: 441925 [Multi-domain]  Cd Length: 303  Bit Score: 37.13  E-value: 9.95e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2068589442 109 AAYNQKYAKVELD-LSTGPSGTMIDGVLSGRLAAAFVDGPVLHPALEGVPAFE----EEMVVIAPLNHSPIH 175
Cdd:COG2358    34 KVVNKELPGIRVTvQSTGGSVENLRLLRAGEADLAIVQSDVAYDAYNGTGPFEggplDNLRALASLYPEPVH 105
 
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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