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Conserved domains on  [gi|1713952743|gb|TVX87901|]
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LysR family transcriptional regulator [Bacillus subtilis]

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, ...
 91-284 8.71e-102

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: 295.67  E-value: 8.71e-102
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  91 PLRIGSMETTAAVWLPQLLAHYNSLYPNVDLNLVTGPTEQQIQAVLHYELNGAFVSGPIEHPDLVQEKVLEEEMVLVTSA 170
Cdd:cd08442     1 PLRLGSMETTAAVRLPPLLAAYHARYPKVDLSLSTGTTGALIQAVLEGRLDGAFVAGPVEHPRLEQEPVFQEELVLVSPK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 171 SHPDISTIHDVQTQTMLVFREGCSYRAKLNHILQEEGLSPVKLMEFGILEAIIGCVSAGLGISLLPRSIIASHEKEGRIR 250
Cdd:cd08442    81 GHPPVSRAEDLAGSTLLAFRAGCSYRRRLEDWLAEEGVSPGKIMEFGSYHAILGCVAAGMGIALLPRSVLDSLQGRGSVS 160

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1713952743 251 SHTISDKYSFVSTMFIRRKDTlITPALSAFLTHM 284
Cdd:cd08442   161 IHPLPEPFADVTTWLVWRKDS-FTAALQAFLDLL 193
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-62 3.34e-19

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


:

Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 79.35  E-value: 3.34e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743   3 IQLLQVFLTTAREGSISKAAQTLNYAQSNVTNKIQQLENDLQTKLFYRHSRGITLTPPGQ 62
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
 
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, ...
 91-284 8.71e-102

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: 295.67  E-value: 8.71e-102
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  91 PLRIGSMETTAAVWLPQLLAHYNSLYPNVDLNLVTGPTEQQIQAVLHYELNGAFVSGPIEHPDLVQEKVLEEEMVLVTSA 170
Cdd:cd08442     1 PLRLGSMETTAAVRLPPLLAAYHARYPKVDLSLSTGTTGALIQAVLEGRLDGAFVAGPVEHPRLEQEPVFQEELVLVSPK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 171 SHPDISTIHDVQTQTMLVFREGCSYRAKLNHILQEEGLSPVKLMEFGILEAIIGCVSAGLGISLLPRSIIASHEKEGRIR 250
Cdd:cd08442    81 GHPPVSRAEDLAGSTLLAFRAGCSYRRRLEDWLAEEGVSPGKIMEFGSYHAILGCVAAGMGIALLPRSVLDSLQGRGSVS 160

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1713952743 251 SHTISDKYSFVSTMFIRRKDTlITPALSAFLTHM 284
Cdd:cd08442   161 IHPLPEPFADVTTWLVWRKDS-FTAALQAFLDLL 193
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-289 6.12e-67

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 209.34  E-value: 6.12e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743   1 MNIQLLQVFLTTAREGSISKAAQTLNYAQSNVTNKIQQLENDLQTKLFYRHSRGITLTPPGQILVSYSEKILNTIEEARA 80
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  81 AMGESSA-PSGPLRIGSMETTAAVWLPQLLAHYNSLYPNVDLNLVTGPTEQQIQAVLHYELNGAFVSGPIEHPDLVQEKV 159
Cdd:COG0583    81 ELRALRGgPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 160 LEEEMVLVTSASHPdistihdvqtqtmlvfregcsyRAKLNHILQEeglspvklmefgiLEAIIGCVSAGLGISLLPRSI 239
Cdd:COG0583   161 GEERLVLVASPDHP----------------------LARRAPLVNS-------------LEALLAAVAAGLGIALLPRFL 205

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|
gi 1713952743 240 IASHEKEGRIRSHTISDKYSFVSTMFIRRKDTLITPALSAFLTHMRDHFQ 289
Cdd:COG0583   206 AADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALA 255
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 89-289 6.18e-50

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: 164.00  E-value: 6.18e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  89 SGPLRIGSMETTAAVWLPQLLAHYNSLYPNVDLNLVTGPTEQQIQAVLHYELNGAFVSGPIEHPDLVQEKVLEEEMVLVT 168
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 169 SASHP----DISTIHDVQTQTMLVFREGCSYRAKLNHILQEEGLSPVKLMEFGILEAIIGCVSAGLGISLLPRSIIASHE 244
Cdd:pfam03466  81 PPDHPlargEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAREL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 1713952743 245 KEGRIRSHTISDKYSFVSTMFIRRKDTLITPALSAFLTHMRDHFQ 289
Cdd:pfam03466 161 ADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREALA 205
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-286 1.12e-44

selenium metabolism-associated LysR family transcriptional regulator; LysR family transcriptional regulators regularly appear encoded adjacent to selenecysteine incorporation proteins such as SelB. This model represents one especially well-conserved subgroup of such transcription factors from species such as Merdimonas faecis, Sellimonas intestinalis, Syntrophotalea acetylenica, and Hydrogenivirga caldilitoris. Seed alignment members were selected by proximity to selB, but not all family members are expected to have similar genomic locations.


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 153.16  E-value: 1.12e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743   1 MNIQLLQVFLTTAREGSISKAAQTLNYAQSNVTNKIQQLENDLQTKLFYRHSRGITLTPPGQILVSYSEKILNTIEEARA 80
Cdd:NF040786    1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  81 AMGESSA-PSGPLRIGSMETTAAVWLPQLLAHYNSLYPNVDLNLVTGPTEQQIQAVLHYELNGAFVSGPIEHPDLVQEKV 159
Cdd:NF040786   81 EFDRYGKeSKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKKRLVYTPF 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 160 LEEEMVLVTSASHPDISTIH------DVQTQTMLVFREGCSYRAKLNHILQEEGLSPVKL---MEFGILEAIIGCVSAGL 230
Cdd:NF040786  161 YKDRLVLITPNGTEKYRMLKeeisisELQKEPFIMREEGSGTRKEAEKALKSLGISLEDLnvvASLGSTEAIKQSVEAGL 240

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1713952743 231 GISLLPRSIIASHEKEGRIRshTISDKYSFVSTMF--IRRKDTLITPALSAFLTHMRD 286
Cdd:NF040786  241 GISVISELAAEKEVERGRVL--IFPIPGLPKNRDFylVYNKNRQLSPTAEAFLQFVKE 296
rbcR CHL00180
LysR transcriptional regulator; Provisional
 3-274 1.14e-30

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 116.66  E-value: 1.14e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743   3 IQLLQVFLTTAREGSISKAAQTLNYAQSNVTNKIQQLENDLQTKLFYRHSRGITLTPPGQILVSYSEKILNTIEEA-RAA 81
Cdd:CHL00180    7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETcRAL 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  82 MGESSAPSGPLRIGSMETTAAVWLPQLLAHYNSLYPNVDLNLVTGPTEQQIQAVLHYELNGAFVSG--PIEHPDLVQ-EK 158
Cdd:CHL00180   87 EDLKNLQRGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVGGevPTELKKILEiTP 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 159 VLEEEMVLVTSASHPdISTIHDVQTQTM-----LVFREGCSYRAKLNHILQEEGLSPVKL---MEFGILEAIIGCVSAGL 230
Cdd:CHL00180  167 YVEDELALIIPKSHP-FAKLKKIQKEDLyrlnfITLDSNSTIRKVIDNILIQNGIDSKRFkieMELNSIEAIKNAVQSGL 245

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....
gi 1713952743 231 GISLLPRSIIASHEKEGRIRSHTISDKYsfvstmfIRRKDTLIT 274
Cdd:CHL00180  246 GAAFVSVSAIEKELELGLLHWIKIENIT-------IKRMLSIIT 282
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-62 3.34e-19

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 79.35  E-value: 3.34e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743   3 IQLLQVFLTTAREGSISKAAQTLNYAQSNVTNKIQQLENDLQTKLFYRHSRGITLTPPGQ 62
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
1-118 3.17e-15

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 73.90  E-value: 3.17e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743   1 MNIQLLQVFLTTAREGSISKAAQTLNYAQSNVTNKIQQLENDLQTKLFYRHSRGITLTPPGQILVSYSEKILNTIEEARA 80
Cdd:PRK03601    1 MDTELLKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYAETLMNTWQAAKK 80

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1713952743  81 AMGESSAPSgPLRIGSmetTAAVWLPQLLAHYNSLYPN 118
Cdd:PRK03601   81 EVAHTSQHN-ELSIGA---SASLWECMLTPWLGRLYQN 114
 
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, ...
 91-284 8.71e-102

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: 295.67  E-value: 8.71e-102
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  91 PLRIGSMETTAAVWLPQLLAHYNSLYPNVDLNLVTGPTEQQIQAVLHYELNGAFVSGPIEHPDLVQEKVLEEEMVLVTSA 170
Cdd:cd08442     1 PLRLGSMETTAAVRLPPLLAAYHARYPKVDLSLSTGTTGALIQAVLEGRLDGAFVAGPVEHPRLEQEPVFQEELVLVSPK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 171 SHPDISTIHDVQTQTMLVFREGCSYRAKLNHILQEEGLSPVKLMEFGILEAIIGCVSAGLGISLLPRSIIASHEKEGRIR 250
Cdd:cd08442    81 GHPPVSRAEDLAGSTLLAFRAGCSYRRRLEDWLAEEGVSPGKIMEFGSYHAILGCVAAGMGIALLPRSVLDSLQGRGSVS 160

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1713952743 251 SHTISDKYSFVSTMFIRRKDTlITPALSAFLTHM 284
Cdd:cd08442   161 IHPLPEPFADVTTWLVWRKDS-FTAALQAFLDLL 193
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-289 6.12e-67

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 209.34  E-value: 6.12e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743   1 MNIQLLQVFLTTAREGSISKAAQTLNYAQSNVTNKIQQLENDLQTKLFYRHSRGITLTPPGQILVSYSEKILNTIEEARA 80
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  81 AMGESSA-PSGPLRIGSMETTAAVWLPQLLAHYNSLYPNVDLNLVTGPTEQQIQAVLHYELNGAFVSGPIEHPDLVQEKV 159
Cdd:COG0583    81 ELRALRGgPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 160 LEEEMVLVTSASHPdistihdvqtqtmlvfregcsyRAKLNHILQEeglspvklmefgiLEAIIGCVSAGLGISLLPRSI 239
Cdd:COG0583   161 GEERLVLVASPDHP----------------------LARRAPLVNS-------------LEALLAAVAAGLGIALLPRFL 205

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|
gi 1713952743 240 IASHEKEGRIRSHTISDKYSFVSTMFIRRKDTLITPALSAFLTHMRDHFQ 289
Cdd:COG0583   206 AADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALA 255
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 89-289 6.18e-50

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: 164.00  E-value: 6.18e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  89 SGPLRIGSMETTAAVWLPQLLAHYNSLYPNVDLNLVTGPTEQQIQAVLHYELNGAFVSGPIEHPDLVQEKVLEEEMVLVT 168
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 169 SASHP----DISTIHDVQTQTMLVFREGCSYRAKLNHILQEEGLSPVKLMEFGILEAIIGCVSAGLGISLLPRSIIASHE 244
Cdd:pfam03466  81 PPDHPlargEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAREL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 1713952743 245 KEGRIRSHTISDKYSFVSTMFIRRKDTLITPALSAFLTHMRDHFQ 289
Cdd:pfam03466 161 ADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREALA 205
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 92-284 2.82e-48

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: 159.30  E-value: 2.82e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  92 LRIGSMETTAAVWLPQLLAHYNSLYPNVDLNLVTGPTEQQIQAVLHYELNGAFVSGPIEHPDLVQEKVLEEEMVLVTSAS 171
Cdd:cd05466     2 LRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPPD 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 172 HP----DISTIHDVQTQTMLVFREGCSYRAKLNHILQEEGLSPVKLMEFGILEAIIGCVSAGLGISLLPRSIIASHEkEG 247
Cdd:cd05466    82 HPlakrKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEELA-DG 160

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1713952743 248 RIRSHTISDKYSFVSTMFIRRKDTLITPALSAFLTHM 284
Cdd:cd05466   161 GLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-286 1.12e-44

selenium metabolism-associated LysR family transcriptional regulator; LysR family transcriptional regulators regularly appear encoded adjacent to selenecysteine incorporation proteins such as SelB. This model represents one especially well-conserved subgroup of such transcription factors from species such as Merdimonas faecis, Sellimonas intestinalis, Syntrophotalea acetylenica, and Hydrogenivirga caldilitoris. Seed alignment members were selected by proximity to selB, but not all family members are expected to have similar genomic locations.


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 153.16  E-value: 1.12e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743   1 MNIQLLQVFLTTAREGSISKAAQTLNYAQSNVTNKIQQLENDLQTKLFYRHSRGITLTPPGQILVSYSEKILNTIEEARA 80
Cdd:NF040786    1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  81 AMGESSA-PSGPLRIGSMETTAAVWLPQLLAHYNSLYPNVDLNLVTGPTEQQIQAVLHYELNGAFVSGPIEHPDLVQEKV 159
Cdd:NF040786   81 EFDRYGKeSKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKKRLVYTPF 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 160 LEEEMVLVTSASHPDISTIH------DVQTQTMLVFREGCSYRAKLNHILQEEGLSPVKL---MEFGILEAIIGCVSAGL 230
Cdd:NF040786  161 YKDRLVLITPNGTEKYRMLKeeisisELQKEPFIMREEGSGTRKEAEKALKSLGISLEDLnvvASLGSTEAIKQSVEAGL 240

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1713952743 231 GISLLPRSIIASHEKEGRIRshTISDKYSFVSTMF--IRRKDTLITPALSAFLTHMRD 286
Cdd:NF040786  241 GISVISELAAEKEVERGRVL--IFPIPGLPKNRDFylVYNKNRQLSPTAEAFLQFVKE 296
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 92-283 8.02e-42

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: 143.02  E-value: 8.02e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  92 LRIGSMETTAAVWLPQLLAHYNSLYPNVDLNLVTGPTEQQIQAVLHYELNGAFVSGPIEHPDLVQEKVLEEEMVLVTSAS 171
Cdd:cd08420     2 LRIGASTTIGEYLLPRLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLVEGPVDHPDLIVEPFAEDELVLVVPPD 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 172 HP----DISTIHDVQTQTmLVFRE-GCSYRAKLNHILQEEGLSPVKL---MEFGILEAIIGCVSAGLGISLLPRSIIASH 243
Cdd:cd08420    82 HPlagrKEVTAEELAAEP-WILREpGSGTREVFERALAEAGLDGLDLnivMELGSTEAIKEAVEAGLGISILSRLAVRKE 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1713952743 244 EKEGRIRSHTISD---KYSFVstmFIRRKDTLITPALSAFLTH 283
Cdd:cd08420   161 LELGRLVALPVEGlrlTRPFS---LIYHKDKYLSPAAEAFLEF 200
rbcR CHL00180
LysR transcriptional regulator; Provisional
 3-274 1.14e-30

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 116.66  E-value: 1.14e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743   3 IQLLQVFLTTAREGSISKAAQTLNYAQSNVTNKIQQLENDLQTKLFYRHSRGITLTPPGQILVSYSEKILNTIEEA-RAA 81
Cdd:CHL00180    7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETcRAL 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  82 MGESSAPSGPLRIGSMETTAAVWLPQLLAHYNSLYPNVDLNLVTGPTEQQIQAVLHYELNGAFVSG--PIEHPDLVQ-EK 158
Cdd:CHL00180   87 EDLKNLQRGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVGGevPTELKKILEiTP 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 159 VLEEEMVLVTSASHPdISTIHDVQTQTM-----LVFREGCSYRAKLNHILQEEGLSPVKL---MEFGILEAIIGCVSAGL 230
Cdd:CHL00180  167 YVEDELALIIPKSHP-FAKLKKIQKEDLyrlnfITLDSNSTIRKVIDNILIQNGIDSKRFkieMELNSIEAIKNAVQSGL 245

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....
gi 1713952743 231 GISLLPRSIIASHEKEGRIRSHTISDKYsfvstmfIRRKDTLIT 274
Cdd:CHL00180  246 GAAFVSVSAIEKELELGLLHWIKIENIT-------IKRMLSIIT 282
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 92-284 2.02e-28

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: 107.98  E-value: 2.02e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  92 LRIGSMETTAAVWLPQLLAHYNSLYPNVDLNLVTGPTEQQIQAVLHYELNGAFVSGPIEHPDLVQEKVLEEEMVLVTSAS 171
Cdd:cd08414     2 LRIGFVGSALYGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPPPDPPGLASRPLLREPLVVALPAD 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 172 HP----DISTIHDVQTQTMLVFR--EGCSYRAKLNHILQEEGLSPVKLMEFGILEAIIGCVSAGLGISLLPRSIIASHEK 245
Cdd:cd08414    82 HPlaarESVSLADLADEPFVLFPrePGPGLYDQILALCRRAGFTPRIVQEASDLQTLLALVAAGLGVALVPASVARLQRP 161

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 1713952743 246 EgrIRSHTISDKYSFVSTMFIRRKDTLiTPALSAFLTHM 284
Cdd:cd08414   162 G--VVYRPLADPPPRSELALAWRRDNA-SPALRAFLELA 197
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 1-285 2.35e-26

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 104.77  E-value: 2.35e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743   1 MNIQL--LQVFLTTAREGSISKAAQTLNYAQSNVTNKIQQLENDLQTKLFYRHSRGITLTPPGQILVSyseKILNTIEEA 78
Cdd:PRK10837    1 MHITLrqLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYP---RALALLEQA 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  79 RAAMGESSAPSGPLRIGSMETTAAVWLPQLLAHYNSLYPNVDLNLVTGPTEQQIQAVLHYELNGAFVSGPIEHPDLVQEK 158
Cdd:PRK10837   78 VEIEQLFREDNGALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNSQDVINAVLDFRVDIGLIEGPCHSPELISEP 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 159 VLEEEMVLVTSASHPDIS---TIHDVQTQTMLVFREGCSYRAKLNHILQEEgLSPVKL-MEFGILEAIIGCVSAGLGISL 234
Cdd:PRK10837  158 WLEDELVVFAAPDSPLARgpvTLEQLAAAPWILRERGSGTREIVDYLLLSH-LPRFELaMELGNSEAIKHAVRHGLGISC 236

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1713952743 235 LPRSIIASHEKEGRIRSHTISDKYSFVSTMFIRRKDTLITPALSAFLTHMR 285
Cdd:PRK10837  237 LSRRVIADQLQAGTLVEVAVPLPRLMRTLYRIHHRQKHLSNALQRFLSYCQ 287
PRK09791 PRK09791
LysR family transcriptional regulator;
2-289 1.90e-23

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 97.14  E-value: 1.90e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743   2 NIQL--LQVFLTTAREGSISKAAQTLNYAQSNVTNKIQQLENDLQTKLFYRHSRGITLTPPGQILVSYSEKILntiEEAR 79
Cdd:PRK09791    4 QVKIhqIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLIL---EELR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  80 AA-------MGESsapSGPLRIGSMETTAAVWLPQLLAHYNSLYPNVDLNLVTGPTEQQIQAVLHYELN---GAFVSGPI 149
Cdd:PRK09791   81 AAqedirqrQGQL---AGQINIGMGASIARSLMPAVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDftiNTYYQGPY 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 150 EHpDLVQEKVLEEEMVLVTSASHPDI--STIHDVQ--TQTMLVFREgcSYRAKLNHILQEEGLSPVKLMEFGILEAIIGC 225
Cdd:PRK09791  158 DH-EFTFEKLLEKQFAVFCRPGHPAIgaRSLKQLLdySWTMPTPHG--SYYKQLSELLDDQAQTPQVGVVCETFSACISL 234

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1713952743 226 VSAGLGISLLPRSIIASHEKEGRIRSHTISDKYSFVSTMFIRRKDTLITPALSAFLTHMRDHFQ 289
Cdd:PRK09791  235 VAKSDFLSILPEEMGCDPLHGQGLVMLPVSEILPKATYYLIQRRDTRQTPLTASLITLFRRECG 298
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 6-288 2.73e-23

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 96.56  E-value: 2.73e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743   6 LQVFLTTAREGSISKAAQTLNYAQSNVTNKIQQLENDLQTKLFYRHSRGITLTPPGQILVSYSEKILNTIEEARAAMGES 85
Cdd:PRK11242    6 IRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRRAIHDV 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  86 SAPS-GPLRIGSMETTAAVWLPQLLAHYNSLYPNVDLNLVTGPTEQQIQAVLHYELNGAFVSGPIEHPDLVQEKVLEEEM 164
Cdd:PRK11242   86 ADLSrGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMSQERIEALLADDELDVGIAFAPVHSPEIEAQPLFTETL 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 165 VLVTSASHPDIS-----TIHDVQTQTMLVFREGCSYRAKLNHILQEEGLSPVKLMEFGILEAIIGCVSAGLGISLLPRSI 239
Cdd:PRK11242  166 ALVVGRHHPLAArrkalTLDELADEPLVLLSAEFATREQIDRYFRRHGVTPRVAIEANSISAVLEIVRRGRLATLLPAAI 245

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*....
gi 1713952743 240 IASHEKegrIRSHTISDKYSFVSTMFIRRKDTLITPALSAFLTHMRDHF 288
Cdd:PRK11242  246 AREHDG---LCAIPLDPPLPQRTAALLRRKGAYRSAAARAFIELALERR 291
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
1-287 2.78e-23

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 97.01  E-value: 2.78e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743   1 MNIQLLQVFLTTAREGSISKAAQTLNYAQSNVTNKIQQLENDLQTKLFYRHSRGITLTPPGQILVSYSEKILNTIEEARA 80
Cdd:PRK15421    2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQ 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  81 AMGESSAPSgpLRIGSMETTAAVWLPQLLAHYNSLYPNVDLNLVTGPTEQQIQAVLHYELNGAFVSGPIEHPDLVQEKVL 160
Cdd:PRK15421   82 ACNEPQQTR--LRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLHYSPMF 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 161 EEEMVLVTSASHPDIS----TIHDVQTQTMLVFRegcSYRAKLN---HILQEEGLSP-VKLMEFGILeaIIGCVSAGLGI 232
Cdd:PRK15421  160 DYEVRLVLAPDHPLAAktriTPEDLASETLLIYP---VQRSRLDvwrHFLQPAGVSPsLKSVDNTLL--LIQMVAARMGI 234

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1713952743 233 SLLPRSIIASHEKEGRIRSHTISDkySFVSTMFIRRKD-TLITPALSAFLTHMRDH 287
Cdd:PRK15421  235 AALPHWVVESFERQGLVVTKTLGE--GLWSRLYAAVRDgEQRQPVTEAFIRSARNH 288
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 92-284 5.68e-23

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: 93.37  E-value: 5.68e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  92 LRIGSMETTAAVWLPQLLAHYNSLYPNVDLNLVTGPTEQQIQAVLHYELNGAFVSGPIEHPDLVQEKVLEEEMVLVTSAS 171
Cdd:cd08434     2 VRLGFLHSLGTSLVPDLIRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLALCSPVPDEPDIEWIPLFTEELVLVVPKD 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 172 HP--DISTIH--DVQTQTMLVFREGCSYRAKLNHILQEEGLSPVKLMEFGILEAIIGCVSAGLGISLLPRSIIASHEKEG 247
Cdd:cd08434    82 HPlaGRDSVDlaELADEPFVLLSPGFGLRPIVDELCAAAGFTPKIAFEGEEDSTIAGLVAAGLGVAILPEMTLLNPPGVK 161

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1713952743 248 RIRshtISDKYSFVSTMFIRRKDTLITPALSAFLTHM 284
Cdd:cd08434   162 KIP---IKDPDAERTIGLAWLKDRYLSPAARRFKDFV 195
PRK09986 PRK09986
LysR family transcriptional regulator;
1-238 3.65e-22

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 93.63  E-value: 3.65e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743   1 MNIQLLQVFLTTAREGSISKAAQTLNYAQSNVTNKIQQLENDLQTKLFYRHSRGITLTPPGQILVSYSEKILNTIEEARA 80
Cdd:PRK09986    7 IDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLA 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  81 -----AMGEssapSGPLRIGSMETtaAVW--LPQLLAHYNSLYPNVDLNLVTGPTEQQIQAVLHYELNGAFVSGPIEHP- 152
Cdd:PRK09986   87 rveqiGRGE----AGRIEIGIVGT--ALWgrLRPAMRHFLKENPNVEWLLRELSPSMQMAALERRELDAGIWRMADLEPn 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 153 -DLVQEKVLEEEMVLVTSASHP----DISTIHDVQTQTM--LVFREGcSYRAKLNHILQEEGLSPVKLMEFGILEAIIGC 225
Cdd:PRK09986  161 pGFTSRRLHESAFAVAVPEEHPlasrSSVPLKALRNEYFitLPFVHS-DWGKFLQRVCQQAGFSPQIIRQVNEPQTVLAM 239

                         250
                  ....*....|...
gi 1713952743 226 VSAGLGISLLPRS 238
Cdd:PRK09986  240 VSMGIGITLLPDS 252
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 1-235 5.44e-22

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 93.52  E-value: 5.44e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743   1 MNIQLLQVFLTTAREG-SISKAAQTLNYAQSNVTNKIQQLENDLQTKLFYRHSRGIT-LTPPGQILVSYSEKILNTIEEA 78
Cdd:PRK12682    1 MNLQQLRFVREAVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKgLTEPGKAVLDVIERILREVGNI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  79 RAAMGESSAP-SGPLRIGSMETTAAVWLPQLLAHYNSLYPNVDLNLVTGPTEQQIQAVLHYELNGAFVSGPIE-HPDLVQ 156
Cdd:PRK12682   81 KRIGDDFSNQdSGTLTIATTHTQARYVLPRVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGIATESLAdDPDLAT 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 157 EKVLEEEMVLVTSASHP----DISTIHDVQTQTMLVFREGCSYRAKLNHILQEEGLSPVKLMEFGILEAIIGCVSAGLGI 232
Cdd:PRK12682  161 LPCYDWQHAVIVPPDHPlaqeERITLEDLAEYPLITYHPGFTGRSRIDRAFAAAGLQPDIVLEAIDSDVIKTYVRLGLGV 240


                  ...
gi 1713952743 233 SLL 235
Cdd:PRK12682  241 GIV 243
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
1-235 2.74e-21

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 91.58  E-value: 2.74e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743   1 MNIQLLQVFLTTAREG-SISKAAQTLNYAQSNVTNKIQQLENDLQTKLFYRHSRGIT-LTPPGQILVSYSEKILNTIEE- 77
Cdd:PRK12684    1 MNLHQLRFVREAVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRgLTEPGRIILASVERILQEVENl 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  78 ARAAMGESSAPSGPLRIGSMETTAAVWLPQLLAHYNSLYPNVDLNLVTGPTEQQIQAVLHYELNGAFVSGPIEH-PDLVQ 156
Cdd:PRK12684   81 KRVGKEFAAQDQGNLTIATTHTQARYALPAAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAIATEAIADyKELVS 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 157 EKVLEEEMVLVTSASHPDIS----TIHDVQTQTMLVFREGCSYRAKLNHILQEEGLSP-VklmefgILEAI----IGC-V 226
Cdd:PRK12684  161 LPCYQWNHCVVVPPDHPLLErkplTLEDLAQYPLITYDFAFAGRSKINKAFALRGLKPdI------VLEAIdadvIKTyV 234


                  ....*....
gi 1713952743 227 SAGLGISLL 235
Cdd:PRK12684  235 ELGLGVGIV 243
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 91-284 5.03e-21

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: 88.04  E-value: 5.03e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  91 PLRIGSMETTAAVWLPQLLAHYNSLYPNVDLNLVTGPTEQQIQAVLHYELNGAFVSGPIEHPDLVQEKVL-EEEMVLVTS 169
Cdd:cd08436     1 RLAIGTITSLAAVDLPELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAFVGLPERRPPGLASRELaREPLVAVVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 170 ASHPDIS----TIHDVQTQTMLVFREGCSYRAKLNHILQEEGLSPVKLMEFGILEAIIGCVSAGLGISLLPRSIIASHek 245
Cdd:cd08436    81 PDHPLAGrrrvALADLADEPFVDFPPGTGARRQVDRAFAAAGVRRRVAFEVSDVDLLLDLVARGLGVALLPASVAARL-- 158

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 1713952743 246 eGRIRSHTISDkySFVSTMFIRRKDTLITPALSAFLTHM 284
Cdd:cd08436   159 -PGLAALPLEP--APRRRLYLAWSAPPPSPAARAFLELL 194
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 90-248 4.32e-20

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: 85.65  E-value: 4.32e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  90 GPLRIGSMETTAAVWLPQLLAHYNSLYPNVDLNLVTGPTEQQIQAVLHYELNGAFVSGPIEHPDLVQEKVLEEEMVLVTS 169
Cdd:cd08411     1 GPLRLGVIPTIAPYLLPRLLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAALLALPVDEPGLEEEPLFDEPFLLAVP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 170 ASHP----DISTIHDVQTQTMLVFREGCSYRAklnHIL---QEEGLSPVKLMEFGILEAIIGCVSAGLGISLLPRSIIAS 242
Cdd:cd08411    81 KDHPlakrKSVTPEDLAGERLLLLEEGHCLRD---QALelcRLAGAREQTDFEATSLETLRQMVAAGLGITLLPELAVPS 157


                  ....*.
gi 1713952743 243 HEKEGR 248
Cdd:cd08411   158 EELRGD 163
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
 92-284 9.91e-20

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: 84.87  E-value: 9.91e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  92 LRIGsMETTAAVWLPQLLAHYNSLYPNVDLNLVTGPTEQQIQAVLHYELNGAFVSGPIEHPDLVQEKVLEEEMVLVTSAS 171
Cdd:cd08419     2 LRLA-VVSTAKYFAPRLLGAFCRRHPGVEVSLRVGNREQVLERLADNEDDLAIMGRPPEDLDLVAEPFLDNPLVVIAPPD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 172 HP----DISTIHDVQTQTMLVfRE-GCSYRAKLNHILQEEGLSPVKLMEFGILEAIIGCVSAGLGISLLPRSIIASHEKE 246
Cdd:cd08419    81 HPlagqKRIPLERLAREPFLL-REpGSGTRLAMERFFAEHGVTLRVRMELGSNEAIKQAVMAGLGLSVLSLHTLALELAT 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1713952743 247 GRIRshtISDKYSF--VSTMFI-RRKDTLITPALSAFLTHM 284
Cdd:cd08419   160 GRLA---VLDVEGFpiRRQWYVvHRKGKRLSPAAQAFLDFL 197
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-62 3.34e-19

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 79.35  E-value: 3.34e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743   3 IQLLQVFLTTAREGSISKAAQTLNYAQSNVTNKIQQLENDLQTKLFYRHSRGITLTPPGQ 62
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-283 2.43e-18

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


Pssm-ID: 176131 [Multi-domain]  Cd Length: 197  Bit Score: 81.03  E-value: 2.43e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  92 LRIGSMETTAAVWLPQLLAHYNSLYPNVDLNLVTGPTEQQIQAVLHYELNGAFVSGPIEHPDLVQEKVLEEEMVLVTSAS 171
Cdd:cd08440     2 VRVAALPSLAATLLPPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEADPDLEFEPLLRDPFVLVCPKD 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 172 HP----DISTIHDVQTQTMLVFREGCSYRAKLNHILQEEGLSPVKLMEFGILEAIIGCVSAGLGISLLPRSIIASHEKEG 247
Cdd:cd08440    82 HPlarrRSVTWAELAGYPLIALGRGSGVRALIDRALAAAGLTLRPAYEVSHMSTALGMVAAGLGVAVLPALALPLADHPG 161

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1713952743 248 rIRSHTISDKYSFVSTMFIRRKDTLITPALSAFLTH 283
Cdd:cd08440   162 -LVARPLTEPVVTRTVGLIRRRGRSLSPAAQAFLDL 196
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 1-236 5.79e-18

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 82.12  E-value: 5.79e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743   1 MNIQLLQVFLTTAREGSISKAAQTLNYAQSNVTNKIQQLENDLQTKLFYRHSRGITLTPPGQILVSYSEKILNTIEEARA 80
Cdd:PRK09906    1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  81 AMGESSAPSGPLRIGSMETTAAVWLPQLLAHYNSLYPNVDLNLVTGPTEQQIQAVLHYELNGAFVSGPIEHPDLVQEKVL 160
Cdd:PRK09906   81 RARKIVQEDRQLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPVYSDEIDYLELL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 161 EEEMVLVTSASHP----DISTIHDVQTQTMLVFREGCSyRAKLNHILQ---EEGLSPVKLMEFGILEAIIGCVSAGLGIS 233
Cdd:PRK09906  161 DEPLVVVLPVDHPlaheKEITAAQLDGVNFISTDPAYS-GSLAPIIKAwfaQHNSQPNIVQVATNILVTMNLVGMGLGCT 239


                  ...
gi 1713952743 234 LLP 236
Cdd:PRK09906  240 IIP 242
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 91-235 8.36e-18

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: 79.53  E-value: 8.36e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  91 PLRIGSMETTAAVWLPQLLAHYNSLYPNVDLNLVTGPTEQQIQAVLHYELNGAFVSGPIEHPDLVQEKVLEEEMVLVTSA 170
Cdd:cd08415     1 TLRIAALPALALSLLPRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPLDHPGLESEPLASGRAVCVLPP 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1713952743 171 SHP----DISTIHDVQTQTMLVFREGCSYRAKLNHILQEEGLSPVKLMEFGILEAIIGCVSAGLGISLL 235
Cdd:cd08415    81 GHPlarkDVVTPADLAGEPLISLGRGDPLRQRVDAAFERAGVEPRIVIETQLSHTACALVAAGLGVAIV 149
cbl PRK12679
HTH-type transcriptional regulator Cbl;
1-250 4.20e-17

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 79.85  E-value: 4.20e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743   1 MNIQLLQVFLTTAR-EGSISKAAQTLNYAQSNVTNKIQQLENDLQTKLFYRH-SRGITLTPPGQILVSYSEKILNtieEA 78
Cdd:PRK12679    1 MNFQQLKIIREAARqDYNLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRgKRLLGMTEPGKALLVIAERILN---EA 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  79 ----RAAMGESSAPSGPLRIGSMETTAAVWLPQLLAHYNSLYPNVDLNLVTGpTEQQIQAVLHyelNGAFVSG-----PI 149
Cdd:PRK12679   78 snvrRLADLFTNDTSGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQG-TPQEIATLLQ---NGEADIGiaserLS 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 150 EHPDLVQEKVLEEEMVLVTSASHPDIS----TIHDVQTQTMLVFREGCSYRAKLNHILQEEGLSPVKLMEFGILEAIIGC 225
Cdd:PRK12679  154 NDPQLVAFPWFRWHHSLLVPHDHPLTQitplTLESIAKWPLITYRQGITGRSRIDDAFARKGLLADIVLSAQDSDVIKTY 233

                         250       260
                  ....*....|....*....|....*
gi 1713952743 226 VSAGLGISLLPRSIIASHEKEGRIR 250
Cdd:PRK12679  234 VALGLGIGLVAEQSSGEQEESNLIR 258
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 1-242 6.48e-17

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 79.32  E-value: 6.48e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743   1 MNIQLLQVFLTTAREG-SISKAAQTLNYAQSNVTNKIQQLENDLQTKLFYRHSRGIT-LTPPGQILVSYSEKILNTIEEA 78
Cdd:PRK12683    1 MNFQQLRIIREAVRQNfNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTgLTEPGKELLQIVERMLLDAENL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  79 RAAMGE-SSAPSGPLRIGSMETTAAVWLPQLLAHYNSLYPNVDLNLVTGPTEQQIQAVLHYELN-GAFVSGPIEHPDLVQ 156
Cdd:PRK12683   81 RRLAEQfADRDSGHLTVATTHTQARYALPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADiGIATEALDREPDLVS 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 157 EKVLEEEMVLVTSASHPDIS----TIHDVQTQTMLVFREGCSYRAKLNHILQEEGLSPVKLMEFGILEAIIGCVSAGLGI 232
Cdd:PRK12683  161 FPYYSWHHVVVVPKGHPLTGrenlTLEAIAEYPIITYDQGFTGRSRIDQAFAEAGLVPDIVLTALDADVIKTYVELGMGV 240

                         250
                  ....*....|
gi 1713952743 233 sllprSIIAS 242
Cdd:PRK12683  241 -----GIVAA 245
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 91-237 1.17e-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: 176115 [Multi-domain]  Cd Length: 200  Bit Score: 76.48  E-value: 1.17e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  91 PLRIGSMETTAAVWLPQLLAHYNSLYPNVDLNLVTGPTEQQIQAVLHYELNGAFV-----SGPIEHPDLVQEKVLEEEMV 165
Cdd:cd08423     1 TLRVGAFPTAAAALLPPALAALRARHPGLEVRLREAEPPESLDALRAGELDLAVVfdypvTPPPDDPGLTRVPLLDDPLD 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1713952743 166 LVTSASHP----DISTIHDVQTQTMLVFREGCSYRAKLNHILQEEGLSPVKLMEFGILEAIIGCVSAGLGISLLPR 237
Cdd:cd08423    81 LVLPADHPlagrEEVALADLADEPWIAGCPGSPCHRWLVRACRAAGFTPRIAHEADDYATVLALVAAGLGVALVPR 156
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 92-284 1.01e-15

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: 73.75  E-value: 1.01e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  92 LRIGSMETTAAVWLPQLLAHYNSLYPNVDLNLVTGPTEQQIQAVLHYELNGAFVSGPIEHPDLVQEKVLEEEMVLVTSAS 171
Cdd:cd08438     2 LRLGLPPLGGSLLFAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVLPVDEEEFDSQPLCNEPLVAVLPRG 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 172 HP----DISTIHDVQTQTMLVFREGCSyrakLNHIL----QEEGLSPVKLMEFGILEAIIGCVSAGLGISLLPRSIIASH 243
Cdd:cd08438    82 HPlagrKTVSLADLADEPFILFNEDFA----LHDRIidacQQAGFTPNIAARSSQWDFIAELVAAGLGVALLPRSIAQRL 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 1713952743 244 EKEG----RIRSHTISDKYSfvstmFIRRKDTLITPALSAFLTHM 284
Cdd:cd08438   158 DNAGvkviPLTDPDLRWQLA-----LIWRKGRYLSHAARAWLALL 197
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
6-126 1.88e-15

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 75.04  E-value: 1.88e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743   6 LQVFLTTAREGSISKAAQTLNYAQSNVTNKIQQLENDLQTKLFYRHSRGITLTPPGQILVSYSEKILNTIEEARAAMgES 85
Cdd:PRK10086   19 LHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLDTLNQEILDI-KN 97

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1713952743  86 SAPSGPLRIGSMETTAAVWLPQLLAHYNSLYPNVDLNLVTG 126
Cdd:PRK10086   98 QELSGTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTILTG 138
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
1-118 3.17e-15

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 73.90  E-value: 3.17e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743   1 MNIQLLQVFLTTAREGSISKAAQTLNYAQSNVTNKIQQLENDLQTKLFYRHSRGITLTPPGQILVSYSEKILNTIEEARA 80
Cdd:PRK03601    1 MDTELLKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYAETLMNTWQAAKK 80

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1713952743  81 AMGESSAPSgPLRIGSmetTAAVWLPQLLAHYNSLYPN 118
Cdd:PRK03601   81 EVAHTSQHN-ELSIGA---SASLWECMLTPWLGRLYQN 114
PRK10341 PRK10341
transcriptional regulator TdcA;
4-241 5.91e-15

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 73.74  E-value: 5.91e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743   4 QLLQVFLTTAREGSISKAAQTLNYAQSNVTNKIQQLENDLQTKLFYRHSRGITLTPPGQILVSYSEKILNTIEEARAAM- 82
Cdd:PRK10341   10 QHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEIn 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  83 GESSAPSGPLRIGSMETTAAVWLPQLLAHYNSLYPNVDLNLVTGPTEQQIQAVLHYELNGAF--VSGPIEHPDLVQEKVL 160
Cdd:PRK10341   90 GMSSEAVVDVSFGFPSLIGFTFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIgtLSNEMKLQDLHVEPLF 169

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 161 EEEMVLVTSASHP--DISTIHDVQTQTMLVFREGCSYRAKLNHILQEEGLSPVKLMEFGILEAIIGCVSAGLGISLLPRS 238
Cdd:PRK10341  170 ESEFVLVASKSRTctGTTTLESLKNEQWVLPQTNMGYYSELLTTLQRNGISIENIVKTDSVVTIYNLVLNADFLTVIPCD 249


                  ...
gi 1713952743 239 IIA 241
Cdd:PRK10341  250 MTS 252
PBP2_IlvR cd08453
The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved ...
 105-283 8.26e-15

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: 71.24  E-value: 8.26e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 105 LPQLLAHYNSLYPNVDLNLVTGPTEQQIQAVLHYELNGAFV--SGPIEHP-DLVQEKVLEEEMVLVTSASHPDIS----T 177
Cdd:cd08453    15 LPELVRRFREAYPDVELQLREATSDVQLEALLAGEIDAGIVipPPGASAPpALAYRPLLSEPLVLAVPAAWAAEGgaplA 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 178 IHDVQTQTMLVF--REGCSYRAKLNHILQEEGLSPVKLMEFGILEAIIGCVSAGLGISLLPRSIiaSHEKEGRIRSHTIS 255
Cdd:cd08453    95 LAAVAAEPLVIFprRIAPAFHDAVTGYYRAAGQTPRIAQEAIQMQTIISLVSAGMGVALVPASL--RNLARPGVVYRELA 172

                         170       180
                  ....*....|....*....|....*...
gi 1713952743 256 DKYSFVSTMFIRRKDTlITPALSAFLTH 283
Cdd:cd08453   173 DPAPVLETGLVWRRDD-ASPVLARFLDL 199
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 1-236 3.55e-14

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 71.21  E-value: 3.55e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743   1 MNIQLLQVFLTTAREGSISKAAQTLNYAQSNVTNKIQQLENDLQTKLFYRHSRGITLTPPGQILVSYSEKILNTIEEAR- 79
Cdd:PRK11151    1 MNIRDLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVLKe 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  80 AAMGESSAPSGPLRIGSMETTAAVWLPQLLAHYNSLYPNVDLNLVTGPTEQQIQAVLHYELNGAFVSGPIEHPDLVQEKV 159
Cdd:PRK11151   81 MASQQGETMSGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCAILALVKESEAFIEVPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 160 LEEEMVLVTSASHP----DISTIHDVQTQTMLVFREGcsyraklnHILQEEglspvkLMEFGI--------------LEA 221
Cdd:PRK11151  161 FDEPMLLAVYEDHPwanrDRVPMSDLAGEKLLMLEDG--------HCLRDQ------AMGFCFeagadedthfratsLET 226

                         250
                  ....*....|....*
gi 1713952743 222 IIGCVSAGLGISLLP 236
Cdd:PRK11151  227 LRNMVAAGSGITLLP 241
PBP2_MetR cd08441
The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which ...
 104-282 8.25e-14

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


Pssm-ID: 176132  Cd Length: 198  Bit Score: 68.75  E-value: 8.25e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 104 WLPQLLAHYNSLYPNVDLNLVTGPTEQQIQAVLHYELNGAFVSGPIEHPDLVQEKVLEEEMVLVTSASHP----DISTIH 179
Cdd:cd08441    14 WLMPVLDQFRERWPDVELDLSSGFHFDPLPALLRGELDLVITSDPLPLPGIAYEPLFDYEVVLVVAPDHPlaakEFITPE 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 180 DVQTQTMLvfregcSY---RAKL---NHILQEEGLSPVKLMEFGILEAIIGCVSAGLGISLLPRSIIASHEKEGRIRSHT 253
Cdd:cd08441    94 DLADETLI------TYpveRERLdvfRHFLQPAGIEPKRRRTVELTLMILQLVASGRGVAALPNWAVREYLDQGLVVARP 167

                         170       180       190
                  ....*....|....*....|....*....|
gi 1713952743 254 ISDKYSFvSTMFI-RRKDTLITPALSAFLT 282
Cdd:cd08441   168 LGEEGLW-RTLYAaVRTEDADQPYLQDFLE 196
PBP2_LTTR_like_2 cd08427
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 91-238 1.10e-13

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


Pssm-ID: 176118 [Multi-domain]  Cd Length: 195  Bit Score: 67.98  E-value: 1.10e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  91 PLRIGSMETTAAVWLPQLLAHYNSLYPNVDLNLVTGPTEQQIQAVLHYELNGAFVSGPIE--HPDLVQEKVLEEEMVLVT 168
Cdd:cd08427     1 RLRLGAIATVLTGLLPRALARLRRRHPDLEVHIVPGLSAELLARVDAGELDAAIVVEPPFplPKDLVWTPLVREPLVLIA 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1713952743 169 SASHPdistIHDV----QTQTMLVFREgcsyRAKLNHILQEE----GLSPVKLMEFGILEAIIGCVSAGLGISLLPRS 238
Cdd:cd08427    81 PAELA----GDDPrellATQPFIRYDR----SAWGGRLVDRFlrrqGIRVREVMELDSLEAIAAMVAQGLGVAIVPDI 150
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 5-124 1.23e-13

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 69.67  E-value: 1.23e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743   5 LLQVFLTTAREGSISKAAQTLNYAQSNVTNKIQQLENDLQTKLFYRHSRGITLTPPGQILVSYSEKILNTIEEARAAMGE 84
Cdd:PRK15092   15 LLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEACSSLMY 94

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1713952743  85 SSApSGPLRIGSMETTAAVWLPQLLAHYNSLYPNVDLNLV 124
Cdd:PRK15092   95 SNL-QGVLTIGASDDTADTILPFLLNRVSSVYPKLALDVR 133
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 1-260 1.98e-13

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 69.33  E-value: 1.98e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743   1 MNIQLLQVFLTTAREGSISKAAQTLNYAQSNVTNKIQQLENDLQTKLFYRHSRGITLTPPGQILVSYSEKILNTIEEARA 80
Cdd:PRK11233    1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  81 AMGESS-APSGPLRIGSMETTAA--VWLPqLLAHYNSLYPNV--DLNLVTGPTEQQIqaVLHYELNGAFVSGPIEHPDLV 155
Cdd:PRK11233   81 AVHNVGqALSGQVSIGLAPGTAAssLTMP-LLQAVRAEFPGIvlYLHENSGATLNEK--LMNGQLDMAVIYEHSPVAGLS 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 156 QEKVLEEEMVLVTSASHPDIS-TIHDVQTQTMLVFREGCSYRAKLNHILQEEGLSPVKLMEFGILEAIIGCVSAGLGISL 234
Cdd:PRK11233  158 SQPLLKEDLFLVGTQDCPGQSvDLAAVAQMNLFLPRDYSAVRLRVDEAFSLRRLTAKVIGEIESIATLTAAIASGMGVTV 237

                         250       260       270
                  ....*....|....*....|....*....|.
gi 1713952743 235 LPRS-----IIASHEKEGRIRSHTISDKYSF 260
Cdd:PRK11233  238 LPESaarslCGAVNGWMARITTPSMSLSLSL 268
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 6-169 4.75e-13

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 67.95  E-value: 4.75e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743   6 LQVFLTTAREGSISKAAQTLNYAQSNVTNKIQQLENDLQTKLFYRHSRGITLTPPGQILVSYSEKILNTIEEARAAMGES 85
Cdd:PRK11139   11 LRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEATRKLRAR 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  86 SAPsGPLRIGSMETTAAVWLPQLLAHYNSLYPNVDLNLVT-----GPTEQQIQAVLHYelngafvsGPIEHPDLVQEKVL 160
Cdd:PRK11139   91 SAK-GALTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLKAvdrleDFLRDDVDVAIRY--------GRGNWPGLRVEKLL 161


                  ....*....
gi 1713952743 161 EEEMVLVTS 169
Cdd:PRK11139  162 DEYLLPVCS 170
PBP2_BudR cd08451
The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is ...
 92-256 2.98e-12

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: 64.12  E-value: 2.98e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  92 LRIGSMETTAA-VWLPQLLAHYNSLYPNVDLNLVTGPTEQQIQAVLHYELNGAFVSGPIEHP-DLVQEKVLEEEMVLVTS 169
Cdd:cd08451     2 LRVGFTSSAAFhPLVPGLIRRFREAYPDVELTLEEANTAELLEALREGRLDAAFVRPPVARSdGLVLELLLEEPMLVALP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 170 ASHP-------DISTIHDvqtQTMLVF-REGCS--YRAklnhILQ---EEGLSPVKLMEFGILEAIIGCVSAGLGISLLP 236
Cdd:cd08451    82 AGHPlarersiPLAALAD---EPFILFpRPVGPglYDA----IIAacrRAGFTPRIGQEAPQMASAINLVAAGLGVSIVP 154

                         170       180
                  ....*....|....*....|
gi 1713952743 237 RSiIASHEKEGrIRSHTISD 256
Cdd:cd08451   155 AS-MRQLQAPG-VVYRPLAG 172
PBP2_XapR cd08449
The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved ...
 92-239 4.97e-12

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: 63.44  E-value: 4.97e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  92 LRIGSMETtaAVW--LPQLLAHYNSLYPNVDLNLVTGPTEQQIQAVLHYELNGAFVSGPIEH--PDLVQEKVLEEEMVLV 167
Cdd:cd08449     2 LNIGMVGS--VLWggLGPALRRFKRQYPNVTVRFHELSPEAQKAALLSKRIDLGFVRFADTLndPPLASELLWREPMVVA 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1713952743 168 TSASHP----DISTIHDVQTQTMLVFREGCSYRAK-LNHILQEEGLSPVKLMEFGILEAIIGCVSAGLGISLLPRSI 239
Cdd:cd08449    80 LPEEHPlagrKSLTLADLRDEPFVFLRLANSRFADfLINCCLQAGFTPQITQEVVEPQTLMALVAAGFGVALVPESY 156
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
6-126 8.69e-12

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 64.40  E-value: 8.69e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743   6 LQVFLTTAREGSISKAAQTLNYAQSNVTNKIQQLENDLQTKLFYRHSRGITLTPPGQILVSYSEKILNTIEEARAAM-GE 84
Cdd:PRK10632    7 MSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQLyAF 86

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1713952743  85 SSAPSGPLRIGSMETTAAVWLPQLLAHYNSLYPNVDLNLVTG 126
Cdd:PRK10632   87 NNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTG 128
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
36-236 3.68e-11

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 62.14  E-value: 3.68e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  36 IQQLENDLQTKLFYRHSRGITLTPPGQILVSYSEKILNTIEEARAAMGESSAP-SGPLRIGSMETTAAVWLPQLLAHYNS 114
Cdd:PRK11716   12 IQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSlSGELSLFCSVTAAYSHLPPILDRFRA 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 115 LYPNVDLNLVTGPTEQQIQAVLHYELNGAFVSGPIEHP-DLVQEKVLEEEMVLV-----------TSASHPDISTIhdvq 182
Cdd:PRK11716   92 EHPLVEIKLTTGDAADAVEKVQSGEADLAIAAKPETLPaSVAFSPIDEIPLVLIapalpcpvrqqLSQEKPDWSRI---- 167

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1713952743 183 tqTMLVFREGCSyRAKLNHILQEEGLSPVKLMEFGILEAIIGCVSAGLGISLLP 236
Cdd:PRK11716  168 --PFILPEHGPA-RRRIDLWFRRHKIKPNIYATVSGHEAIVSMVALGCGVGLLP 218
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 91-281 4.32e-11

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: 61.13  E-value: 4.32e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  91 PLRIGSMETTAAVWLPQLLAHYNSLYPNVDLNLVTGPTEQQIQAVLHYELNgaFVSG----PIEHPDLVQEKVLEEEMVL 166
Cdd:cd08435     1 TVRVGAVPAAAPVLLPPAIARLLARHPRLTVRVVEGTSDELLEGLRAGELD--LAIGrladDEQPPDLASEELADEPLVV 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 167 VTSASHP----DISTIHDVQTQTMLVFREGCSYRAKLNHILQEEGLS-PVKLMEFGILEAIIGCVSAGLGISLLPRSIIA 241
Cdd:cd08435    79 VARPGHPlarrARLTLADLADYPWVLPPPGTPLRQRLEQLFAAAGLPlPRNVVETASISALLALLARSDMLAVLPRSVAE 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 1713952743 242 SHEKEGRIRSHTISDKYSFVSTMFIRRKDTLITPALSAFL 281
Cdd:cd08435   159 DELRAGVLRELPLPLPTSRRPIGITTRRGGPLSPAARALL 198
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 91-284 1.02e-10

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: 59.87  E-value: 1.02e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  91 PLRIGSMETTAAVWLPQLLAHYNSLYPNVDLNLVTGPTEQQIQAVLHYELNGAFVSGPIEHPDLVQEKVLEEEMVLVTSA 170
Cdd:cd08412     1 TLRIGCFSTLAPYYLPGLLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALTYDLDLPEDIAFEPLARLPPYVWLPA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 171 SHP----DISTIHDVQTQTMLVFREGCSyRAKLNHILQEEGLSPVKLMEFGILEAIIGCVSAGLGISLLPRSIIASHEKE 246
Cdd:cd08412    81 DHPlagkDEVSLADLAAEPLILLDLPHS-REYFLSLFAAAGLTPRIAYRTSSFEAVRSLVANGLGYSLLNDRPYRPWSYD 159

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 1713952743 247 G-RIRSHTISDKYSFVSTMFIRRKDTLITPALSAFLTHM 284
Cdd:cd08412   160 GkRLVRRPLADPVPPLRLGLAWRRGARLTRAARAFVDFA 198
PBP2_OccR cd08457
The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the ...
 91-235 1.44e-10

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


Pssm-ID: 176146 [Multi-domain]  Cd Length: 196  Bit Score: 59.43  E-value: 1.44e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  91 PLRIGSMETTAAVWLPQLLAHYNSLYPNVDLNLVTGPTEQQIQAVLHYELNGAFVSGPIEHPDLVQEKVLEEEMVLVTSA 170
Cdd:cd08457     1 TLRIAAMPALANGFLPRFLAAFLRLRPNLHLSLMGLSSSQVLEAVASGRADLGIADGPLEERQGFLIETRSLPAVVAVPM 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1713952743 171 SHP----DISTIHDVQTQTMLVFREGCSYRAKLNHILQEEGLSPVKLMEFGILEAIIGCVSAGLGISLL 235
Cdd:cd08457    81 GHPlaqlDVVSPQDLAGERIITLENGYLFRMRVEVALGKIGVKRRPIIEVNLSHTALSLVREGLGIAII 149
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 4-80 6.67e-10

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 58.80  E-value: 6.67e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1713952743   4 QLLQVFLTTAREGSISKAAQTLNYAQSNVTNKIQQLENDLQTKLFYRHSRGITLTPPGQILVSYSEKILNTIEEARA 80
Cdd:PRK11074    5 YSLEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRR 81
PBP2_Chlorocatechol cd08446
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 90-283 7.92e-10

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


Pssm-ID: 176137 [Multi-domain]  Cd Length: 198  Bit Score: 57.29  E-value: 7.92e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  90 GPLRIGSMETTAAVWLPQLLAHYNSLYPNVDLNLVTGPTEQQIQAVLHYELNGAFVSGPIEHPDLVQEKVLEEEMVLVTS 169
Cdd:cd08446     1 GELDVGYFGSAILDTVPRLLRAFLTARPDVTVSLHNMTKDEQIEALRAGRIHIGFGRFYPVEPDIAVENVAQERLYLAVP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 170 ASHP----DISTIHDVQTQTMLVFREGC--SYRAKLNHILQEEGLSPVKLMEFGILEAIIGCVSAGLGISLLPRSIIASH 243
Cdd:cd08446    81 KSHPlaarPAVSLADLRNEPLILFPRGGrpSFADEVLGLFRRAGVEPRVAQEVEDVVAALALVAAGFGVCIVPESVAALR 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 1713952743 244 EKEGRIRShtISDKYSFVSTMFIRRKDTlITPALSAFLTH 283
Cdd:cd08446   161 WPGVVFRP--LADAEAKVPLSCIYRKDD-RSPILRAFLDV 197
PBP2_AlsR cd08452
The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which ...
 92-281 9.68e-10

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: 57.13  E-value: 9.68e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  92 LRIGSMETTAAVWLPQLLAHYNSLYPNVDLNLVTGPTEQQIQAVLHYELNGAFVSGPIEHPDLVQEKVLEEEMVLVTSAS 171
Cdd:cd08452     2 LVIGFVGAAIYEFLPPIVREYRKKFPSVKVELRELSSPDQVEELLKGRIDIGFLHPPIQHTALHIETVQSSPCVLALPKQ 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 172 HPDIS----TIHDVQTQTMLVFREGCS---YRAKLNhILQEEGLSPVKLMEFGILEAIIGCVSAGLGISLLPRSiiASHE 244
Cdd:cd08452    82 HPLASkeeiTIEDLRDEPIITVAREAWptlYDEIIQ-LCEQAGFRPKIVQEATEYQTVIGLVSAGIGVTFVPSS--AKKL 158

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1713952743 245 KEGRIRSHTISDKYSFVSTMFIRRKDTLiTPALSAFL 281
Cdd:cd08452   159 FNLEVAYRKIDQINLNAEWSIAYRKDNH-NPLLKHFI 194
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
4-76 1.08e-09

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 58.28  E-value: 1.08e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1713952743   4 QLLQVFLTTAREGSISKAAQTLNYAQSNVTNKIQQLENDLQTKLFYRHSRGITLTPPGQILVSYSEKILNTIE 76
Cdd:PRK10094    5 ETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLE 77
PBP2_LTTR_aromatics_like_1 cd08447
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-283 1.17e-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: 176138 [Multi-domain]  Cd Length: 198  Bit Score: 56.89  E-value: 1.17e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  92 LRIGSmeTTAAVW--LPQLLAHYNSLYPNVDLNLVTGPTEQQIQAVLHYELNGAFVSGPIEHPDLVQEKVLEEEMVLVTS 169
Cdd:cd08447     2 LRIGF--TAASAYsfLPRLLAAARAALPDVDLVLREMVTTDQIEALESGRIDLGLLRPPFARPGLETRPLVREPLVAAVP 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 170 ASHP----DISTIHDVQTQTMLVF--REGCSYRAKLNHILQEEGLSPVKLMEFGILEAIIGCVSAGLGISLLPRSiiASH 243
Cdd:cd08447    80 AGHPlagaERLTLEDLDGQPFIMYspTEARYFHDLVVRLFASAGVQPRYVQYLSQIHTMLALVRAGLGVALVPAS--ASR 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1713952743 244 EKEGRIRSHTISD-KYSFVSTMFIRRKDTlITPALSAFLTH 283
Cdd:cd08447   158 LRFEGVVFRPLDLpRDVPVELHLAWRRDN-DNPALRALLDL 197
PBP2_CynR cd08425
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, ...
 90-243 2.50e-09

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


Pssm-ID: 176116  Cd Length: 197  Bit Score: 55.80  E-value: 2.50e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  90 GPLRIGSMETTAAVWLPQLLAHYNSLYPNVDLNLVTGPTEQQIQAVLHYELNGAFVSGPIEHPDLVQEKVLEEEMVLVTS 169
Cdd:cd08425     1 GSLRLAMTPTFTAYLIGPLIDRFHARYPGIALSLREMPQERIEAALADDRLDLGIAFAPVRSPDIDAQPLFDERLALVVG 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1713952743 170 ASHP-----DISTIHDVQTQTMLVFREGCSYRAKLNHILQEEGLSPVKLMEFGILEAIIGCVSAGLGISLLPRSIIASH 243
Cdd:cd08425    81 ATHPlaqrrTALTLDDLAAEPLALLSPDFATRQHIDRYFQKQGIKPRIAIEANSISAVLEVVRRGRLATILPDAIAREQ 159
PRK09801 PRK09801
LysR family transcriptional regulator;
6-95 2.51e-09

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 57.35  E-value: 2.51e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743   6 LQVFLTTAREGSISKAAQTLNYAQSNVTNKIQQLENDLQTKLFYRHSRGITLTPPGQILVSYSEKILNTIEEARAAMGE- 84
Cdd:PRK09801   11 LQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVTQi 90

                          90
                  ....*....|.
gi 1713952743  85 SSAPSGPLRIG 95
Cdd:PRK09801   91 KTRPEGMIRIG 101
cysB PRK12681
HTH-type transcriptional regulator CysB;
18-132 2.80e-09

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 57.22  E-value: 2.80e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  18 ISKAAQTLNYAQSNVTNKIQQLENDLQTKLFYRHSRGIT-LTPPGQILVSYSEKILNTIEEARAAMGESSAPS-GPLRIG 95
Cdd:PRK12681   19 VSATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTqVTPAGEEIIRIAREILSKVESIKSVAGEHTWPDkGSLYIA 98

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1713952743  96 SMETTAAVWLPQLLAHYNSLYPNVDLNLVTGpTEQQI 132
Cdd:PRK12681   99 TTHTQARYALPPVIKGFIERYPRVSLHMHQG-SPTQI 134
PBP2_LTTR_aromatics_like_2 cd08448
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-238 6.13e-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: 54.58  E-value: 6.13e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  92 LRIGSMETTAAVWLPQLLAHYNSLYPNVDLNLVTGPTEQQIQAVLHYELNGAFVSGPIEHPDLVQEKVLEEEMVLVTSAS 171
Cdd:cd08448     2 LRIGFVGSMLYRGLPRILRAFRAEYPGIEVALHEMSSAEQIEALLRGELDLGFVHSRRLPAGLSARLLHREPFVCCLPAG 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1713952743 172 HP-----DIStIHDVQTQTMLVF-RE-GCSYRAKLNHILQEEGLSPVKLMEFGILEAIIGCVSAGLGISLLPRS 238
Cdd:cd08448    82 HPlaarrRID-LRELAGEPFVLFsREvSPDYYDQIIALCMDAGFHPKIRHEVRHWLTVVALVAAGMGVALVPRS 154
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 91-276 6.65e-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: 54.52  E-value: 6.65e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  91 PLRIGsMETTAAVWL-PQLLAHYNSLYPNVDLNLVTGPTEQQIQAVLHYELNGAFVSGPIEHPDLVQEKVLEEEMVLVTS 169
Cdd:cd08433     1 RVSVG-LPPSAASVLaVPLLRAVRRRYPGIRLRIVEGLSGHLLEWLLNGRLDLALLYGPPPIPGLSTEPLLEEDLFLVGP 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 170 ASHP---DIS-TIHDVQTQTMLVFREGCSYRAKLNHILQEEGLSPVKLMEFGILEAIIGCVSAGLGISLLPRSIIASHEK 245
Cdd:cd08433    80 ADAPlprGAPvPLAELARLPLILPSRGHGLRRLVDEAAARAGLTLNVVVEIDSVATLKALVAAGLGYTILPASAVAAEVA 159

                         170       180       190
                  ....*....|....*....|....*....|.
gi 1713952743 246 EGRIRSHTISDKYsfvstmfIRRKDTLITPA 276
Cdd:cd08433   160 AGRLVAAPIVDPA-------LTRTLSLATPR 183
PBP2_TdcA cd08418
The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is ...
 105-287 2.01e-08

The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is involved in the degradation of L-serine and L-threonine, contains the type 2 periplasmic binding fold; TdcA, a member of the LysR family, activates the expression of the anaerobically-regulated tdcABCDEFG operon which is involved in the degradation of L-serine and L-threonine to acetate and propionate, respectively. The tdc operon is comprised of one regulatory gene tdcA and six structural genes, tdcB to tdcG. The expression of the tdc operon is affected by several transcription factors including the cAMP receptor protein (CRP), integration host factor (IHF), histone-like protein (HU), and the operon specific regulators TdcA and TcdR. TcdR is divergently transcribed from the operon and encodes a small protein that is required for efficient expression of the Escherichia coli tdc operon. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176110 [Multi-domain]  Cd Length: 201  Bit Score: 53.51  E-value: 2.01e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 105 LPQLLAHYNSLYPNVDLNLvtgpTEQQIQAVLHyELN--------GAFVSGPIEHpDLVQEKVLEEEMVLVTSASHPDI- 175
Cdd:cd08418    15 MPAVINRFKEQFPDVQISI----YEGQLSSLLP-ELRdgrldfaiGTLPDEMYLK-ELISEPLFESDFVVVARKDHPLQg 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 176 -STIHDVQTQTMLVFREGCSYRAKLNHILQEEGLSPVKLMEFGILEAIIGCVSAGLGISLLPRSIIASHEKEGRIRSHTI 254
Cdd:cd08418    89 aRSLEELLDASWVLPGTRMGYYNNLLEALRRLGYNPRVAVRTDSIVSIINLVEKADFLTILSRDMGRGPLDSFRLITIPV 168

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1713952743 255 SDKYSFVSTMFIRRKDTLITPALSAFLTHMRDH 287
Cdd:cd08418   169 EEPLPSADYYLIYRKKSRLTPLAEQLVELFRRY 201
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 9-123 3.84e-08

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 53.46  E-value: 3.84e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743   9 FLTTAREGSISKAAQTLNYAQSNVTNKIQQLENDLQTKLFYRHSRGITLTPPGQILVSYSEKILNTIEEARAAMGESSA- 87
Cdd:PRK14997   10 FVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDAIAALQVe 89

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1713952743  88 PSGPLRIGSMETTAAVWLPQLLAHYNSLYPNVDLNL 123
Cdd:PRK14997   90 PRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQL 125
PBP2_LysR cd08456
The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine ...
 92-284 3.99e-08

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: 52.42  E-value: 3.99e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  92 LRIGSMETTAAVWLPQLLAHYNSLYPNVDLNLVTG--PTEQQIQAVLHYELngAFVSGPIEHPDLVQEKVLEEEMVLVTS 169
Cdd:cd08456     2 LRIAVLPALSQSFLPRAIKAFLQRHPDVTISIHTRdsPTVEQWLSAQQCDL--GLVSTLHEPPGIERERLLRIDGVCVLP 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 170 ASHP----DISTIHDVQTQTMLVFREGCSYRAKLNHILQEEGLSPVKLMEFGILEAIIGCVSAGLGISLLPRSIIASHEK 245
Cdd:cd08456    80 PGHRlavkKVLTPSDLEGEPFISLARTDGTRQRVDALFEQAGVKRRIVVETSYAATICALVAAGVGVSVVNPLTALDYAA 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 1713952743 246 EG-RIRSHTISDKYSFvstMFIRRKDTLITPALSAFLTHM 284
Cdd:cd08456   160 AGlVVRRFSPAVPFEV---SLIRPKHRPSSALVAAFSACL 196
PBP2_BenM_CatM_CatR cd08445
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 105-239 4.64e-08

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: 52.23  E-value: 4.64e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 105 LPQLLAHYNSLYPNVDLNLVTGPTEQQIQAVLHYELNGAFVSGPIEHPDLVQEKVLEEEMVLVTSASHP-----DISTIH 179
Cdd:cd08445    16 LPELIRRFRQAAPDVEIELIEMTTVQQIEALKEGRIDVGFGRLRIEDPAIRRIVLREEPLVVALPAGHPlaqekAPLTLA 95

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1713952743 180 DVQTQTMLVFREGC--SYRAKLNHILQEEGLSPVKLMEFGILEAIIGCVSAGLGISLLPRSI 239
Cdd:cd08445    96 QLADEPLILYPASPrpSFADQVLSLFRDHGLRPRVIQEVRELQTALGLVAAGEGVTLVPASV 157
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 90-248 1.11e-07

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


Pssm-ID: 176114 [Multi-domain]  Cd Length: 197  Bit Score: 50.90  E-value: 1.11e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  90 GPLRIGSMETTAAVWLPQLLAHYNSLYPNVDLNLVTgpTEQQIQAVLH-YELngAFVSGPIEHPDLVQEKVLEEEMVLVT 168
Cdd:cd08422     1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVL--SDRLVDLVEEgFDL--AIRIGELPDSSLVARRLGPVRRVLVA 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 169 S----ASHPDISTIHDVQTQTMLVFRegcsYRAKLN--HILQEEGLSPVKL---MEFGILEAIIGCVSAGLGISLLPRSI 239
Cdd:cd08422    77 SpaylARHGTPQTPEDLARHRCLGYR----LPGRPLrwRFRRGGGEVEVRVrgrLVVNDGEALRAAALAGLGIALLPDFL 152


                  ....*....
gi 1713952743 240 IASHEKEGR 248
Cdd:cd08422   153 VAEDLASGR 161
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 93-176 1.23e-07

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


Pssm-ID: 176109 [Multi-domain]  Cd Length: 200  Bit Score: 51.06  E-value: 1.23e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  93 RIGSMETTAAVWLPQLLAHYNSLYPNVDLNLVTGPTEQQIQAVLHYELNGAFVSGPIEHPDLVQEKVLEEEMVLVTSASH 172
Cdd:cd08417     3 RIAASDYLEALLLPPLLARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELPPGLRSQPLFEDRFVCVARKDH 82


                  ....
gi 1713952743 173 PDIS 176
Cdd:cd08417    83 PLAG 86
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
4-82 1.85e-07

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 51.51  E-value: 1.85e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743   4 QLLQVFLTTAREGSISKAAQTLNYAQSNVTNKIQQLENDLQTKLFYRhSRGITLTPPGQILVSYSEKI-------LNTIE 76
Cdd:PRK13348    5 KQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQRLLRHLRQValleadlLSTLP 83


                  ....*.
gi 1713952743  77 EARAAM 82
Cdd:PRK13348   84 AERGSP 89
nhaR PRK11062
transcriptional activator NhaR; Provisional
 1-70 2.21e-07

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 51.16  E-value: 2.21e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743   1 MNIQLLQVFLTTAREGSISKAAQTLNYAQSNVTNKIQQLENDLQTKLFYRHSRGITLTPPGQILVSYSEK 70
Cdd:PRK11062    4 INYNHLYYFWMVCKEGSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGELVFRYADK 73
PBP2_LTTR_like_1 cd08421
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 99-287 2.57e-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: 176113  Cd Length: 198  Bit Score: 50.21  E-value: 2.57e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  99 TTAAV--WLPQLLAHYNSLYPNVDLNLVTGPTEQQIQAVLHYELNGAFVSGPIEHPDLVQEKVLEEEMVLVTSASHPDIS 176
Cdd:cd08421     7 NTSAIveFLPEDLASFLAAHPDVRIDLEERLSADIVRAVAEGRADLGIVAGNVDAAGLETRPYRTDRLVVVVPRDHPLAG 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 177 TIH----DVQTQTMLVFREGCSYRAKLNHILQEEGLsPVKL-MEFGILEAIIGCVSAGLGISLLPRSIIASHEKEGRIRS 251
Cdd:cd08421    87 RASvafaDTLDHDFVGLPAGSALHTFLREAAARLGR-RLRLrVQVSSFDAVCRMVAAGLGIGIVPESAARRYARALGLRV 165

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 1713952743 252 HTISDKYSfvstmfiRRKDTLIT---PALSAFLTHMRDH 287
Cdd:cd08421   166 VPLDDAWA-------RRRLLLCVrsfDALPPAARALVDH 197
PBP2_HcaR cd08450
The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in ...
 92-236 1.68e-06

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: 47.76  E-value: 1.68e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  92 LRIGSMETTAAVWLPQLLAHYNSLYPNVDLNLVTGPTEQQIQAVLHYELNGAFVSGPIEHPDLVQEKVLEEEMVLVTSAS 171
Cdd:cd08450     2 LTIGFLPGAEVQWLPEVLPILREEHPDLDVELSSLFSPQLAEALMRGKLDVAFMRPEIQSDGIDYQLLLKEPLIVVLPAD 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 172 HP----DISTIHDVQTQTML-VFREGCSYRAKLNHILQEEGLSPVKLMEFGILEAIIGCVSAGLGISLLP 236
Cdd:cd08450    82 HRlagrEKIPPQDLAGENFIsPAPTAPVLQQVIENYAAQHNIQPNIIQEADNLLSAMSLVASTLGCALLP 151
PBP2_MdcR cd08416
The C-terminal substrate-binding domian of LysR-type transcriptional regulator MdcR, which ...
 92-281 1.74e-06

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: 47.73  E-value: 1.74e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  92 LRIGSMETTAAVWLPQLLAHYNSLYPNVDLNLVTGPTEQQIQAVLHYELNGAFVSGPIEH--PDLVQEKVLEEEMVLVTS 169
Cdd:cd08416     2 LRLGSLYSLTVNTVPRIIMGLKLRRPELDIELTLGSNKDLLKKLKDGELDAILVATPEGLndPDFEVVPLFEDDIFLAVP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 170 ASHPDIST----IHDVQTQTMLVFREGCSYRAKLNHILQEEGLSPVKLMEFGILEAIIGCVSAGLGISLLPRSIIASHEK 245
Cdd:cd08416    82 ATSPLAASseidLRDLKDEKFVTLSEGFATYRGFDEAFEIAGFEPNVVMRVNDIFSLMSMVSGGVGYALLPGRIADVYED 161

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1713952743 246 EGRIRSHTISDKYS-FVSTMFIRRKDTliTPALSAFL 281
Cdd:cd08416   162 KVQLIPLAEPYQIRqTIGLVFLRSRER--DPNLLALA 196
leuO PRK09508
leucine transcriptional activator; Reviewed
 5-176 1.98e-06

leucine transcriptional activator; Reviewed


Pssm-ID: 181918 [Multi-domain]  Cd Length: 314  Bit Score: 48.48  E-value: 1.98e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743   5 LLQVFLTTAREGSISKAAQTLNYAQSNVTNKIQQLE---NDlqtKLFYRHSRGITLTPPGQILVSYSEKILNTIEEARAA 81
Cdd:PRK09508   26 LLTVFDAVMQEQNITRAAHNLGMSQPAVSNAVARLKvmfND---ELFVRYGRGIQPTARARQLFGPVRQALQLVQNELPG 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  82 MG---ESSAPSGPLRIGS---METTaavwlPQLLAHYNSLYPNVDLNLvTGPTEQQIQAVLHYElNGAFVSG--PIEHPD 153
Cdd:PRK09508  103 SGfepESSERVFNLCICSpldIRLT-----SQIYNRIEQIAPNIHVVF-KSSLNQNIEHQLRYQ-ETEFVISyeEFDRPE 175

                         170       180
                  ....*....|....*....|...
gi 1713952743 154 LVQEKVLEEEMVLVTSASHPDIS 176
Cdd:PRK09508  176 FTSVPLFKDELVLVASKNHPRIK 198
PRK12680 PRK12680
LysR family transcriptional regulator;
3-123 5.92e-06

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 46.92  E-value: 5.92e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743   3 IQLLQVFLTTAREGSISKAAQTLNYAQSNVTNKIQQLENDLQTKLFYRHSRGI-TLTPPGQILVSYSEKILNTIEEARA- 80
Cdd:PRK12680    4 TQLRYLVAIADAELNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLeSVTPAGVEVIERARAVLSEANNIRTy 83

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1713952743  81 AMGESSAPSGPLRIGSMETTAAVWLPQLLAHYNSLYPNVDLNL 123
Cdd:PRK12680   84 AANQRRESQGQLTLTTTHTQARFVLPPAVAQIKQAYPQVSVHL 126
PBP2_LrhA_like cd08439
The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of ...
 92-238 1.03e-05

The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of closely related homologs, contains the type 2 periplasmic binding fold; This CD represents the LrhA subfamily of LysR-like bacterial transcriptional regulators, including LrhA, HexA, PecT, and DgdR. LrhA is involved in control of the transcription of flagellar, motility, and chemotaxis genes by regulating the synthesis and concentration of FlhD(2)C(2), the master regulator for the expression of flagellar and chemotaxis genes. The LrhA protein has strong homology to HexA and PecT from plant pathogenic bacteria, in which HexA and PecT act as repressors of motility and of virulence factors, such as exoenzymes required for lytic reactions. DgdR also shares similar characteristics to those of LrhA, HexA and PecT. 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: 176130  Cd Length: 185  Bit Score: 45.02  E-value: 1.03e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  92 LRIGSMETTAAVWLPQLLAHYNSLYPNVDLNLVTGPTeQQIQAVLH-YELNGAFVSGPIEHpdlvqekvlEEEMVLVTSA 170
Cdd:cd08439     2 LRIGCPDDYADTILPFLLNRFASVYPRLAIEVVCKRT-PRLMEMLErGEVDLALITHPPPG---------ASATILRRSP 71

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1713952743 171 SH----PDISTIHDVQTQTMLVFREGCSYRAKLNHiLQEEGLSPVKLMEFGILEAIIGCVSAGLGISLLPRS 238
Cdd:cd08439    72 TVwycaAGYILAPGEPLPLALLDEPTLDRRAALAA-LDAAGIPWRIAYAASSLSGLRAAVRAGLGITARTQE 142
PBP2_CysB_like cd08413
The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains ...
 92-242 1.62e-05

The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; CysB is a transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the regulation of transcription in response to sulfur source is attributed to two transcriptional regulators, CysB and Cbl. CysB, in association with Cbl, downregulates the expression of ssuEADCB operon which is required for the utilization of sulfur from aliphatic sulfonates, in the presence of cysteine. Also, Cbl and CysB together directly function as transcriptional activators of tauABCD genes, which are required for utilization of taurine as sulfur source for growth. Like many other members of the LTTR family, CysB is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 176105 [Multi-domain]  Cd Length: 198  Bit Score: 44.92  E-value: 1.62e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  92 LRIGSMETTAAVWLPQLLAHYNSLYPNVDLNLVTGPTEQQIQAVLHYELNGAFVSGPIE-HPDLVQEKVLEEEMVLVTSA 170
Cdd:cd08413     2 LTIATTHTQARYVLPPVIAAFRKRYPKVKLSLHQGTPSQIAEMVLKGEADIAIATEALDdHPDLVTLPCYRWNHCVIVPP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 171 SHP--DIS--TIHDVQTQTMLVFREGCSYRAKLNHILQEEGLSP-VklmefgILEA-----IIGCVSAGLGIsllprSII 240
Cdd:cd08413    82 GHPlaDLGplTLEDLAQYPLITYDFGFTGRSSIDRAFARAGLEPnI------VLTAldadvIKTYVRLGLGV-----GII 150


                  ..
gi 1713952743 241 AS 242
Cdd:cd08413   151 AE 152
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-284 3.46e-05

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: 43.84  E-value: 3.46e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  93 RIGSMETTAAVWLPQLLAHYNSLYPNVDLNLVTGPTEQQIQAVLHYELNGAFVSGPIEHPDLVQEKVLEEEMVLVTSASH 172
Cdd:cd08426     3 RVATGEGLAAELLPSLIARFRQRYPGVFFTVDVASTADVLEAVLSGEADIGLAFSPPPEPGIRVHSRQPAPIGAVVPPGH 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 173 PDIS----TIHDVQTQTMLVFREGCSYRAKLNHILQEEGLSPVKLMEFGILEAIIGCVSAGLGISLLPRSIIASHEKEGR 248
Cdd:cd08426    83 PLARqpsvTLAQLAGYPLALPPPSFSLRQILDAAFARAGVQLEPVLISNSIETLKQLVAAGGGISLLTELAVRREIRRGQ 162

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1713952743 249 IRSHTISDKYSFVSTMFI-RRKDTLITPALSAFLTHM 284
Cdd:cd08426   163 LVAVPLADPHMNHRQLELqTRAGRQLPAAASAFLQLL 199
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 16-287 3.83e-05

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 44.60  E-value: 3.83e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  16 GSISKAAQTLNYAQSNVTNKIQQLENDLQTKLFYRhSRGiTLTPPGQILV-------SYS--EKILNTIEEARAAMGess 86
Cdd:PRK11013   19 GSLTEAARLLHTSQPTVSRELARFEKVIGLKLFER-VRG-RLHPTVQGLRlfeevqrSYYglDRIVSAAESLREFRQ--- 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  87 apsGPLRIGSMETTAAVWLPQLLAHYNSLYPNVDLNLVT--GPTEQQIQAVLHYELngafvsGPIEH----PDLVQEKVL 160
Cdd:PRK11013   94 ---GQLSIACLPVFSQSLLPGLCQPFLARYPDVSLNIVPqeSPLLEEWLSAQRHDL------GLTETlhtpAGTERTELL 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 161 EEEMVLVTSASHP----DISTIHDVQTQTMLVFREGCSYRAKLNHILQEEGLSPVKLMEFGILEAIIGCVSAGLGISLL- 235
Cdd:PRK11013  165 TLDEVCVLPAGHPlaakKVLTPDDFAGENFISLSRTDSYRQLLDQLFAEHGVKRRMVVETHSAASVCAMVRAGVGVSIVn 244

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1713952743 236 PRSIIASHEKEGRIRSHTISDKYsfvSTMFIRRKDTLITPALSAFLTHMRDH 287
Cdd:PRK11013  245 PLTALDYAGSGLVVRRFSISVPF---TVSLIRPLHRPASALVDAFSEHLQQQ 293
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
5-110 4.33e-05

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 44.38  E-value: 4.33e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743   5 LLQVFLTTAREGSISKAAQTLNYAQSNVTNKIQQLENDLQTKLFYRhSRGITLTPPGQILVSYSEKiLNTIE-EARAAMG 83
Cdd:PRK03635    6 QLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRLLRHARQ-VRLLEaELLGELP 83

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1713952743  84 ESSAPSGPLRIG----SMETtaavWLPQLLA 110
Cdd:PRK03635   84 ALDGTPLTLSIAvnadSLAT----WFLPALA 110
PBP2_GcdR_like cd08481
The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, ...
 92-249 5.52e-05

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


Pssm-ID: 176170 [Multi-domain]  Cd Length: 194  Bit Score: 43.05  E-value: 5.52e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  92 LRIGSMETTAAVWL----PQLLAHYnslyPNVDLNLVTGP-----TEQQIQAVLHYelngafvsGPIEHPDLVQEKVLEE 162
Cdd:cd08481     2 LELAVLPTFGTRWLiprlPDFLARH----PDITVNLVTRDepfdfSQGSFDAAIHF--------GDPVWPGAESEYLMDE 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 163 EMVLVTSASHPD---ISTIHDVQTQTMLVFregcSYRAKL-NHILQEEGLS---PVKLMEFGILEAIIGCVSAGLGISLL 235
Cdd:cd08481    70 EVVPVCSPALLAgraLAAPADLAHLPLLQQ----TTRPEAwRDWFEEVGLEvptAYRGMRFEQFSMLAQAAVAGLGVALL 145

                         170
                  ....*....|....
gi 1713952743 236 PRSIIASHEKEGRI 249
Cdd:cd08481   146 PRFLIEEELARGRL 159
PBP2_LeuO cd08466
The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an ...
 105-175 6.01e-05

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


Pssm-ID: 176155 [Multi-domain]  Cd Length: 200  Bit Score: 43.01  E-value: 6.01e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1713952743 105 LPQLLAHYNSLYPNVDLNLvTGPTEQQIQAVLHY-ELNGAFVSGPIEHPDLVQEKVLEEEMVLVTSASHPDI 175
Cdd:cd08466    15 LPRLLARLKQLAPNISLRE-SPSSEEDLFEDLRLqEVDLVIDYVPFRDPSFKSELLFEDELVCVARKDHPRI 85
PBP2_IlvY cd08430
The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates ...
 105-240 8.13e-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: 42.57  E-value: 8.13e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 105 LPQLLAHYNSLYPNVDLNLVTGPTEQQIQAVLHYELNGAFVSGPIEHP-DLVQEKVLEEEMVLVTSASHPDISTIH---- 179
Cdd:cd08430    15 LPPILERFRAQHPQVEIKLHTGDPADAIDKVLNGEADIAIAARPDKLPaRLAFLPLATSPLVFIAPNIACAVTQQLsqge 94

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1713952743 180 -DVQTQTMLVFREGCSyRAKLNHILQEEGLSPVKLMEFGILEAIIGCVSAGLGISLLPRSII 240
Cdd:cd08430    95 iDWSRLPFILPERGLA-RERLDQWFRRRGIKPNIYAQVAGHEAIVSMVALGCGVGIVPELVL 155
PBP2_CysB cd08443
The C-terminal substrate domain of LysR-type transcriptional regulator CysB contains type 2 ...
 92-242 9.90e-04

The C-terminal substrate domain of LysR-type transcriptional regulator CysB contains type 2 periplasmic binding fold; CysB is a transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the regulation of transcription in response to sulfur source is attributed to two transcriptional regulators, CysB and Cbl. CysB, in association with Cbl, downregulates the expression of ssuEADCB operon which is required for the utilization of sulfur from aliphatic sulfonates, in the presence of cysteine. Also, Cbl and CysB together directly function as transcriptional activators of tauABCD genes, which are required for utilization of taurine as sulfur source for growth. Like many other members of the LTTR family, CysB is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176134  Cd Length: 198  Bit Score: 39.47  E-value: 9.90e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  92 LRIGSMETTAAVWLPQLLAHYNSLYPNVDLNLVTGPTEQQIQAVLHYELNGAFVSGPI-EHPDLVQEKVLEEEMVLVTSA 170
Cdd:cd08443     2 LYVATTHTQARYVLPPVIKGFIERYPRVSLQMHQGSPTQIAEMVSKGLVDFAIATEALhDYDDLITLPCYHWNRCVVVKR 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1713952743 171 SHPDIS----TIHDVQTQTMLVFREGCSYRAKLNHILQEEGLSPVKLMEFGILEAIIGCVSAGLGIsllprSIIAS 242
Cdd:cd08443    82 DHPLADkqsiSIEELATYPIVTYTFGFTGRSELDTAFNRAGLTPNIVLTATDADVIKTYVRLGLGV-----GVIAS 152
PBP2_AmpR cd08488
The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in ...
 91-249 2.81e-03

The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in control of the expression of beta-lactamase gene ampC, contains the type 2 periplasmic binding fold; AmpR acts as a transcriptional activator by binding to a DNA region immediately upstream of the ampC promoter. In the absence of a beta-lactam inducer, AmpR represses the synthesis of beta-lactamase, whereas expression is induced in the presence of a beta-lactam inducer. The AmpD, AmpG, and AmpR proteins are involved in the induction of AmpC-type beta-lactamase (class C) which produced by enterobacterial strains and many other gram-negative bacilli. The activation of ampC by AmpR requires ampG for induction or high-level expression of AmpC. It is probable that the AmpD and AmpG work together to modulate the ability of AmpR to activate ampC expression. 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: 176177 [Multi-domain]  Cd Length: 191  Bit Score: 37.90  E-value: 2.81e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743  91 PLRIGSMETTAAVWLPQLLAHYNSLYPNVDLNLVTGPTEQQIQAV-LHYELNgaFVSGpiEHPDLVQEKVLEEEM-VLVT 168
Cdd:cd08488     1 VLHVGAVGTFAVGWLLPRLADFQNRHPFIDLRLSTNNNRVDIAAEgLDYAIR--FGSG--AWHGIDATRLFEAPLsPLCT 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743 169 SASHPDISTIHDVQTQTMLVfregcSYRA-KLNHILQEEGLSPVKLMEFGIL-EAIIGCVSA---GLGISLLPRSIIASH 243
Cdd:cd08488    77 PELARQLREPADLARHTLLR-----SYRAdEWPQWFEAAGVGHPCGLPNSIMfDSSLGMMEAalqGLGVALAPPSMFSRQ 151


                  ....*.
gi 1713952743 244 EKEGRI 249
Cdd:cd08488   152 LASGAL 157
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
9-116 3.07e-03

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 38.50  E-value: 3.07e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713952743   9 FLTTAREGSISKAAQTLNYAQSNVTNKIQQLENDLQTKLFYRHSRGITLTPPGQILVSYSEKILNTIEEARAAM-GESSA 87
Cdd:PRK10082   19 FLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESNLAELrGGSDY 98

                          90       100
                  ....*....|....*....|....*....
gi 1713952743  88 PSGPLRIGSMETTAAVWLPQLLAHYNSLY 116
Cdd:PRK10082   99 AQRKIKIAAAHSLSLGLLPSIISQMPPLF 127
 
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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