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Conserved domains on  [gi|1590257263|ref|WP_131631590|]
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MULTISPECIES: LysR family transcriptional regulator [Rhizobium]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 10444048)

LysR family transcriptional regulator containing an N-terminal HTH (helix-turn-helix) DNA-binding domain and a C-terminal substrate binding domain, which is structurally homologous to the type 2 periplasmic binding proteins; similar to Vibrio cholerae YidZ, a putative transcriptional regulator involved in anaerobic NO protection, as well other transcriptional regulators of different genes

Gene Ontology:  GO:0003677|GO:0003700
PubMed:  8257110|19047729
SCOP:  4000316

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 102-300 8.46e-51

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: 167.01  E-value: 8.46e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263 102 FRIGLSDYTAVTYLPELIENFSMLAPNASLNVVHAREPDALGSLKNREVECAVLGNPKLDAEhFEVVELSRDRMVCAGWA 181
Cdd:cd08417     2 FRIAASDYLEALLLPPLLARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELPPG-LRSQPLFEDRFVCVARK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263 182 GNPAMAD-MSLDRYLASPHLQISADGIAAGIADITLQKLGLHRKVVATIPHYLVAPWVIKGTELISAFGDGVLLALSEES 260
Cdd:cd08417    81 DHPLAGGpLTLEDYLAAPHVLVSPRGRGHGLVDDALAELGLSRRVALTVPHFLAAPALVAGTDLIATVPRRLAEALAERL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 1590257263 261 ETAIVPPPLELPDVTISLIFDRSNELDPGHVWFRNLIKDV 300
Cdd:cd08417   161 GLRVLPLPFELPPFTVSLYWHPRRDRDPAHRWLRELIAEL 200
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
11-70 1.02e-15

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


:

Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 70.11  E-value: 1.02e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263  11 LNLLRTFDVLMRERSVTRAADRLGRTQSAISHSLGRLRDVFKDDLFTREAGIMEPTARAK 70
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
 
Name Accession Description Interval E-value
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 102-300 8.46e-51

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: 167.01  E-value: 8.46e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263 102 FRIGLSDYTAVTYLPELIENFSMLAPNASLNVVHAREPDALGSLKNREVECAVLGNPKLDAEhFEVVELSRDRMVCAGWA 181
Cdd:cd08417     2 FRIAASDYLEALLLPPLLARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELPPG-LRSQPLFEDRFVCVARK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263 182 GNPAMAD-MSLDRYLASPHLQISADGIAAGIADITLQKLGLHRKVVATIPHYLVAPWVIKGTELISAFGDGVLLALSEES 260
Cdd:cd08417    81 DHPLAGGpLTLEDYLAAPHVLVSPRGRGHGLVDDALAELGLSRRVALTVPHFLAAPALVAGTDLIATVPRRLAEALAERL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 1590257263 261 ETAIVPPPLELPDVTISLIFDRSNELDPGHVWFRNLIKDV 300
Cdd:cd08417   161 GLRVLPLPFELPPFTVSLYWHPRRDRDPAHRWLRELIAEL 200
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
9-299 1.58e-35

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 128.83  E-value: 1.58e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263   9 LDLNLLRTFDVLMRERSVTRAADRLGRTQSAISHSLGRLRDVFKDDLFTREAGIMEPTARAKELAEVISQALHEIRVAVD 88
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263  89 RHLNFDPTTTSRnFRIGLSDYTAVTYLPELIENFSMLAPNASLNVVHAREPDALGSLKNREVECAVLGNPkLDAEHFEVV 168
Cdd:COG0583    81 ELRALRGGPRGT-LRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGP-PPDPGLVAR 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263 169 ELSRDRMVCAGWAGNPAmadmsLDRYLASPHLQISADGIAAGIAditlqklglhrkvVATIPHYLVAPWVikgtelisaf 248
Cdd:COG0583   159 PLGEERLVLVASPDHPL-----ARRAPLVNSLEALLAAVAAGLG-------------IALLPRFLAADEL---------- 210

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1590257263 249 GDGVLlalseesetAIVPPPLELPDVTISLIFDRSNELDPGHVWFRNLIKD 299
Cdd:COG0583   211 AAGRL---------VALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLRE 252
leuO PRK09508
leucine transcriptional activator; Reviewed
 1-303 8.56e-27

leucine transcriptional activator; Reviewed


Pssm-ID: 181918 [Multi-domain]  Cd Length: 314  Bit Score: 107.03  E-value: 8.56e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263   1 MAEFSLNQLDLNLLRTFDVLMRERSVTRAADRLGRTQSAISHSLGRLRDVFKDDLFTREAGIMEPTARAKELAEVISQAL 80
Cdd:PRK09508   14 SSEPQLRMVDLNLLTVFDAVMQEQNITRAAHNLGMSQPAVSNAVARLKVMFNDELFVRYGRGIQPTARARQLFGPVRQAL 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263  81 HEIRvavdrhlN------FDPTTTSRNFRIGLSDYTAVTYLPELIENFSMLAPNASLNVVHAREPDALGSLKNREVEcAV 154
Cdd:PRK09508   94 QLVQ-------NelpgsgFEPESSERVFNLCICSPLDIRLTSQIYNRIEQIAPNIHVVFKSSLNQNIEHQLRYQETE-FV 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263 155 LGNPKLDAEHFEVVELSRDRMVCAGWAGNPAMAD-MSLDRYLASPHLQISADGIaAGIADITLQKLGLHRKVVatiphYl 233
Cdd:PRK09508  166 ISYEEFDRPEFTSVPLFKDELVLVASKNHPRIKGpITEEQLYNEQHAVVSLDRF-ASFSQPWYDTVDKQASIA-----Y- 238

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263 234 vapwviKGTELISAF---GDGVLLAL---------SEESETAIVPPPLELPDVTISLIFDRSNELDPGHVWFRNLIKDVS 301
Cdd:PRK09508  239 ------QGTALSSVLnvvSQTHLVAIaprwlaeefAESLELQILPLPLKNNSRTCYLSWHESAGRDKGHQWMEELLVSIC 312


                  ..
gi 1590257263 302 DR 303
Cdd:PRK09508  313 KR 314
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
11-70 1.02e-15

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 70.11  E-value: 1.02e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263  11 LNLLRTFDVLMRERSVTRAADRLGRTQSAISHSLGRLRDVFKDDLFTREAGIMEPTARAK 70
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK11482 PRK11482
DNA-binding transcriptional regulator;
6-88 2.48e-11

DNA-binding transcriptional regulator;


Pssm-ID: 183159 [Multi-domain]  Cd Length: 317  Bit Score: 63.59  E-value: 2.48e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263   6 LNQLDLNLLRTFDVLMRERSVTRAADRLGRTQSAISHSLGRLRDVFKDDLFTREAGIMEPTARAKELAEVISQALHEIRV 85
Cdd:PRK11482   26 LRNIDLNLLTIFEAVYVHKGIVNAAKILNLTPSAISQSIQKLRVIFPDPLFIRKGQGVTPTAYATHLHEYISQGLESILG 105


                  ...
gi 1590257263  86 AVD 88
Cdd:PRK11482  106 ALD 108
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 102-300 1.28e-10

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: 60.00  E-value: 1.28e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263 102 FRIGLSDYTAVTYLPELIENFSMLAPNASLNVVHAREPDALGSLKNREVECAVLGNPKLDAEhFEVVELSRDRMVCAGWA 181
Cdd:pfam03466   4 LRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPG-LEARPLGEEPLVLVAPP 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263 182 GNP--AMADMSLDRYLASPHLQISADGIAAGIADITLQKLGLHRKVVATIPHYLVAPWVIKGTELISAFGDGVLLALSEE 259
Cdd:pfam03466  83 DHPlaRGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARELAD 162

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1590257263 260 SETAIVPPPLELPDVTISLIFDRSNELDPGHVWFRNLIKDV 300
Cdd:pfam03466 163 GRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREA 203
 
Name Accession Description Interval E-value
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 102-300 8.46e-51

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: 167.01  E-value: 8.46e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263 102 FRIGLSDYTAVTYLPELIENFSMLAPNASLNVVHAREPDALGSLKNREVECAVLGNPKLDAEhFEVVELSRDRMVCAGWA 181
Cdd:cd08417     2 FRIAASDYLEALLLPPLLARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELPPG-LRSQPLFEDRFVCVARK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263 182 GNPAMAD-MSLDRYLASPHLQISADGIAAGIADITLQKLGLHRKVVATIPHYLVAPWVIKGTELISAFGDGVLLALSEES 260
Cdd:cd08417    81 DHPLAGGpLTLEDYLAAPHVLVSPRGRGHGLVDDALAELGLSRRVALTVPHFLAAPALVAGTDLIATVPRRLAEALAERL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 1590257263 261 ETAIVPPPLELPDVTISLIFDRSNELDPGHVWFRNLIKDV 300
Cdd:cd08417   161 GLRVLPLPFELPPFTVSLYWHPRRDRDPAHRWLRELIAEL 200
PBP2_DntR_like_2 cd08464
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 102-300 4.64e-37

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


Pssm-ID: 176153 [Multi-domain]  Cd Length: 200  Bit Score: 131.20  E-value: 4.64e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263 102 FRIGLSDYTAVTYLPELIENFSMLAPNASLNVVHAREPDALGSLKNREVECAVLGNPKLDAEHFEVVeLSRDRMVCAgWA 181
Cdd:cd08464     2 FRIGLSDDVESWLAPPLLAALRAEAPGVRLVFRQVDPFNVGDMLDRGEIDLAIGVFGELPAWLKREV-LYTEGYACL-FD 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263 182 GNPAMAD--MSLDRYLASPHLQISADGIAAGIADITLQKLGLHRKVVATIPHYLVAPWVIKGTELISAFGDGVLLALSEE 259
Cdd:cd08464    80 PQQLSLSapLTLEDYVARPHVLVSYRGGLRGFVDDALAELGRSRRVVASTPHFAALPALLRGTPLIATVPARLARAWAAA 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1590257263 260 SETAIVPPPLELPDVTISLIFDRSNELDPGHVWFRNLIKDV 300
Cdd:cd08464   160 LGLRASPPPLDLPEFPISLLWHARTDNDPALVWLREQIVQA 200
PBP2_DntR_NahR_LinR_like cd08459
The C-terminal substrate binding domain of LysR-type transcriptional regulators that are ...
 101-300 3.73e-36

The C-terminal substrate binding domain of LysR-type transcriptional regulators that are involved in the catabolism of dinitrotoluene, naphthalene and gamma-hexachlorohexane; contains the type 2 periplasmic binding fold; This CD includes LysR-like bacterial transcriptional regulators, DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. DntR from Burkholderia species controls genes encoding enzymes for oxidative degradation of the nitro-aromatic compound 2,4-dinitrotoluene. The active form of DntR is homotetrameric, consisting of a dimer of dimers. NahR is a salicylate-dependent transcription activator of the nah and sal operons for naphthalene degradation. Salicylic acid is an intermediate of the oxidative degradation of the aromatic ring in soil bacteria. LinR positively regulates expression of the genes (linD and linE) encoding enzymes for gamma-hexachlorocyclohexane (a haloorganic insecticide) degradation. Expression of linD and linE are induced by their substrates, 2,5-dichlorohydroquinone (2,5-DCHQ) and chlorohydroquinone (CHQ). The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176148 [Multi-domain]  Cd Length: 201  Bit Score: 128.85  E-value: 3.73e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263 101 NFRIGLSDYTAVTYLPELIENFSMLAPNASLNVVHAREPDALGSLKNREVEcAVLGNPKLDAEHFEVVELSRDRMVCAGW 180
Cdd:cd08459     1 TFRIAMSDIGEMYFLPRLLAALREVAPGVRIETVRLPVDELEEALESGEID-LAIGYLPDLGAGFFQQRLFRERYVCLVR 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263 181 AGNPAMAD-MSLDRYLASPHLQISADGIAAGIADITLQKLGLHRKVVATIPHYLVAPWVIKGTELISAFGDGVLLALSEE 259
Cdd:cd08459    80 KDHPRIGStLTLEQFLAARHVVVSASGTGHGLVEQALREAGIRRRIALRVPHFLALPLIVAQTDLVATVPERLARLFARA 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1590257263 260 SETAIVPPPLELPDVTISLIFDRSNELDPGHVWFRNLIKDV 300
Cdd:cd08459   160 GGLRIVPLPFPLPPFEVKLYWHRRFHRDPGNRWLRQLVAEL 200
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
9-299 1.58e-35

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 128.83  E-value: 1.58e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263   9 LDLNLLRTFDVLMRERSVTRAADRLGRTQSAISHSLGRLRDVFKDDLFTREAGIMEPTARAKELAEVISQALHEIRVAVD 88
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263  89 RHLNFDPTTTSRnFRIGLSDYTAVTYLPELIENFSMLAPNASLNVVHAREPDALGSLKNREVECAVLGNPkLDAEHFEVV 168
Cdd:COG0583    81 ELRALRGGPRGT-LRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGP-PPDPGLVAR 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263 169 ELSRDRMVCAGWAGNPAmadmsLDRYLASPHLQISADGIAAGIAditlqklglhrkvVATIPHYLVAPWVikgtelisaf 248
Cdd:COG0583   159 PLGEERLVLVASPDHPL-----ARRAPLVNSLEALLAAVAAGLG-------------IALLPRFLAADEL---------- 210

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1590257263 249 GDGVLlalseesetAIVPPPLELPDVTISLIFDRSNELDPGHVWFRNLIKD 299
Cdd:COG0583   211 AAGRL---------VALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLRE 252
PBP2_ToxR cd08465
The C-terminal substrate binding domain of LysR-type transcriptional regulator ToxR regulates ...
 102-300 2.33e-31

The C-terminal substrate binding domain of LysR-type transcriptional regulator ToxR regulates the expression of the toxoflavin biosynthesis genes; contains the type 2 periplasmic bindinig fold; In soil bacterium Burkholderia glumae, ToxR regulates the toxABCDE and toxFGHI operons in the presence of toxoflavin as a coinducer. Additionally, the expression of both operons requires a transcriptional activator, ToxJ, whose expression is regulated by the TofI or TofR quorum-sensing system. The biosynthesis of toxoflavin is suggested to be synthesized in a pathway common to the synthesis of riboflavin. 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: 176154  Cd Length: 200  Bit Score: 116.26  E-value: 2.33e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263 102 FRIGLSDYTAVTYLPELIENFSMLAPNASLNVVHAREPDALGSLKNREVECAVLGNPKLDAEhFEVVELSRDRMVC-AGW 180
Cdd:cd08465     2 FRLAMSDYGARLVLPALMRQLRAEAPGIDLAVSQASREAMLAQVADGEIDLALGVFPELPEE-LHAETLFEERFVClADR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263 181 AGNPAMADMSLDRYLASPHLQISADGIAAGIADITLQKLGLHRKVVATIPHYLVAPWVIKGTELISAFGDGVLLALSEES 260
Cdd:cd08465    81 ATLPASGGLSLDAWLARPHVLVAMRGDAANEIDRALAARGLRRRVALTLPHWGVAPELIAGTDLILTVARRALDALRLDE 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 1590257263 261 ETAIVPPPLELPDVTISLIFDRSNELDPGHVWFRNLIKDV 300
Cdd:cd08465   161 RLAVFAPPFPIPPFAFQQIWHQRREGDPAHRWLRERIQEA 200
PBP2_DntR_like_4 cd08463
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 102-300 1.08e-28

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


Pssm-ID: 176152 [Multi-domain]  Cd Length: 203  Bit Score: 109.33  E-value: 1.08e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263 102 FRIGLSDYTAVTYLPELIENFSMLAPNASLnVVHAREPDA--LGSLKNREVEcAVLGNPKLDAEHFEVVELSRDRMVCAG 179
Cdd:cd08463     2 FRIAAPDYLNALFLPELVARFRREAPGARL-EIHPLGPDFdyERALASGELD-LVIGNWPEPPEHLHLSPLFSDEIVCLM 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263 180 WAGNPAMAD--MSLDRYLASPHLQISADGIAA-GIADITLQKLGLHRKVVATIPHYLVAPWVIKGTELIsaFGDGVLLAL 256
Cdd:cd08463    80 RADHPLARRglMTLDDYLEAPHLAPTPYSVGQrGVIDSHLARLGLKRNIVVTVPYFGLAPYMLAQSDLV--FTTGRHFAE 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1590257263 257 SEES--ETAIVPPPLELPDVTISLIFDRSNELDPGHVWFRNLIKDV 300
Cdd:cd08463   158 HYAKllPLAVVDAPIEFPRMRYYQLWHERSHRSPEHRWLRRLVASV 203
leuO PRK09508
leucine transcriptional activator; Reviewed
 1-303 8.56e-27

leucine transcriptional activator; Reviewed


Pssm-ID: 181918 [Multi-domain]  Cd Length: 314  Bit Score: 107.03  E-value: 8.56e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263   1 MAEFSLNQLDLNLLRTFDVLMRERSVTRAADRLGRTQSAISHSLGRLRDVFKDDLFTREAGIMEPTARAKELAEVISQAL 80
Cdd:PRK09508   14 SSEPQLRMVDLNLLTVFDAVMQEQNITRAAHNLGMSQPAVSNAVARLKVMFNDELFVRYGRGIQPTARARQLFGPVRQAL 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263  81 HEIRvavdrhlN------FDPTTTSRNFRIGLSDYTAVTYLPELIENFSMLAPNASLNVVHAREPDALGSLKNREVEcAV 154
Cdd:PRK09508   94 QLVQ-------NelpgsgFEPESSERVFNLCICSPLDIRLTSQIYNRIEQIAPNIHVVFKSSLNQNIEHQLRYQETE-FV 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263 155 LGNPKLDAEHFEVVELSRDRMVCAGWAGNPAMAD-MSLDRYLASPHLQISADGIaAGIADITLQKLGLHRKVVatiphYl 233
Cdd:PRK09508  166 ISYEEFDRPEFTSVPLFKDELVLVASKNHPRIKGpITEEQLYNEQHAVVSLDRF-ASFSQPWYDTVDKQASIA-----Y- 238

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263 234 vapwviKGTELISAF---GDGVLLAL---------SEESETAIVPPPLELPDVTISLIFDRSNELDPGHVWFRNLIKDVS 301
Cdd:PRK09508  239 ------QGTALSSVLnvvSQTHLVAIaprwlaeefAESLELQILPLPLKNNSRTCYLSWHESAGRDKGHQWMEELLVSIC 312


                  ..
gi 1590257263 302 DR 303
Cdd:PRK09508  313 KR 314
PBP2_Pa0477 cd08468
The C-terminal substrate biniding domain of an uncharacterized LysR-like transcriptional ...
 102-300 1.78e-24

The C-terminal substrate biniding domain of an uncharacterized LysR-like transcriptional regulator Pa0477 related to DntR, contains the type 2 periplasmic binding fold; LysR-type transcriptional regulator Pa0477 is related to DntR, which controls genes encoding enzymes for oxidative degradation of the nitro-aromatic compound 2,4-dinitrotoluene. 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. 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: 176157 [Multi-domain]  Cd Length: 202  Bit Score: 98.28  E-value: 1.78e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263 102 FRIGLSDYTAVTYLPELIENFSMLAPNASLNVVHAREPDALGSLKNREVECAvlgnpkLDAEHFEVVELSR--------D 173
Cdd:cd08468     2 FRFAVTDYTALAVMPRLMARLEELAPSVRLNLVHAEQKLPLDALLAGEIDFA------LGYSHDDGAEPRLieerdwweD 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263 174 RMVCAGWAGNPAMADMSLDRYLASPHLQISADGIAAGIADITLQKLGLHRKVVATIPHYLVAPWVIKGTELISAFGDGVL 253
Cdd:cd08468    76 TYVVIASRDHPRLSRLTLDAFLAERHLVVTPWNEDRGVVDQVLEKQGLEREIALQLPNVLNAPFIVASSDLLMTLPRQAA 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 1590257263 254 LALSEESETAIVPPPLELPDVTISLIFDRSNELDPGHVWFRNLIKDV 300
Cdd:cd08468   156 RALAEALPLELFDLPFDMPPYRLKLYSHRQHENSAANQWLIEQLDGL 202
PBP2_NodD cd08462
The C-terminal substsrate binding domain of NodD family of LysR-type transcriptional ...
 102-300 1.67e-23

The C-terminal substsrate binding domain of NodD family of LysR-type transcriptional regulators that regulates the expression of nodulation (nod) genes; contains the type 2 periplasmic binding fold; The nodulation (nod) genes in soil bacteria play important roles in the development of nodules. nod genes are involved in synthesis of Nod factors that are required for bacterial entry into root hairs. Thirteen nod genes have been identified and are classified into five transcription units: nodD, nodABCIJ, nodFEL, nodMNT, and nodO. NodD is negatively auto-regulates its own expression of nodD gene, while other nod genes are inducible and positively regulated by NodD in the presence of flavonoids released by plant roots. 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: 176151 [Multi-domain]  Cd Length: 200  Bit Score: 95.39  E-value: 1.67e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263 102 FRIGLSDYTAVTYLPELIENFSMLAPNASLNVVhAREPDALGSLKNREVECAVLGNPKLDAEH-FEvvELSRDRMVCAGW 180
Cdd:cd08462     2 FRIIASDYVITVLLPPVIERVAREAPGVRFELL-PPDDQPHELLERGEVDLLIAPERFMSDGHpSE--PLFEEEFVCVVW 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263 181 AGNPAMAD-MSLDRYLASPHLQISADGIAA-GIADITLQKLGLHRKVVATIPHYLVAPWVIKGTELISAfgdgVLLALSE 258
Cdd:cd08462    79 ADNPLVGGeLTAEQYFSAGHVVVRFGRNRRpSFEDWFLNEYGLKRRVEVVTPSFSSIPPLLVGTNRIAT----LHRRLAE 154

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1590257263 259 ESET----AIVPPPLELPDVTISLIFDRSNELDPGHVWFRNLIKDV 300
Cdd:cd08462   155 QFARrlplRILPLPFPLPPMREALQWHRYRNNDPGLIWLRELIIEA 200
PBP2_PnbR cd08469
The C-terminal substrate binding domain of LysR-type transcriptional regulator PnbR, which is ...
 102-300 3.18e-19

The C-terminal substrate binding domain of LysR-type transcriptional regulator PnbR, which is involved in regulating the pnb genes encoding enzymes for 4-nitrobenzoate catabolism, contains the type 2 periplasmic binding fold; PnbR is the regulator of one or both of the two pnb genes that encoding enzymes for 4-nitrobenzoate catabolism. In Pseudomonas putida strain, pnbA encodes a 4-nitrobenzoate reductase, which is responsible for catalyzing the direct reduction of 4-nitrobenzoate to 4-hydroxylaminobenzoate, and pnbB encodes a 4-hydroxylaminobenzoate lyase, which catalyzes the conversion of 4-hydroxylaminobenzoate to 3, 4-dihydroxybenzoic acid and ammonium. 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: 176158  Cd Length: 221  Bit Score: 84.38  E-value: 3.18e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263 102 FRIGLSDYTAVTYLPELIENFSMLAPNASLNVVHAREPDALGSLKNREVECAVLGNPKLdAEHFEVVELSRDRMVCAGWA 181
Cdd:cd08469     2 FVIAANDYVTAVLLPALVRRLETEAPGIDLRIRPVTRLDLAEQLDLGRIDLVIGIFEQI-PPRFRRRTLFDEDEVWVMRK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263 182 GNPAM-ADMSLDRYLASPHLQISADGIAAGIADITLQKLGLHRKVV---------------------ATIPHYLVAPWVI 239
Cdd:cd08469    81 DHPAArGALTIETLARYPHIVVSLGGEEEGAVSGFISERGLARQTEmfdrraleeafresglvprvaVTVPHALAVPPLL 160

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1590257263 240 KGTELISAFGDGVLLALSEESETAIVPPPLELPDVTISLIFDRSNELDPGHVWFRNLIKDV 300
Cdd:cd08469   161 ADSDMLALLPRSLARAFAERGGLVMKEPPYPPPPVQIRAVWHERHDNDPAVAWLREMIRDV 221
PBP2_DntR_like_1 cd08460
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 102-300 8.80e-19

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


Pssm-ID: 176149 [Multi-domain]  Cd Length: 200  Bit Score: 82.64  E-value: 8.80e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263 102 FRIGLSDYTAVTYLPELIENFSMLAPNASLNVVHAREPDAlGSLKNREVECAVLGNPKLDAEhFEVVELSRDRMVCAGWA 181
Cdd:cd08460     2 FTIRANDGFVAAFGPALLAAVAAEAPGVRLRFVPESDKDV-DALREGRIDLEIGVLGPTGPE-IRVQTLFRDRFVGVVRA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263 182 GNP-AMADMSLDRYLASPHLQISADGIAAGIADITLQKLGLHRKVVATIPHYLVAPWVIKGTELISAFGDGVLLALSEES 260
Cdd:cd08460    80 GHPlARGPITPERYAAAPHVSVSRRGRLHGPIDDALAALGLTRRVVAVVPTFAAALFLARGSDLIALVPERVTAAARAGL 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 1590257263 261 ETAIVPPPLELPDVTISLIFDRSNELDPGHVWFRNLIKDV 300
Cdd:cd08460   160 GLRTFPLPLELPAVTVSQAWHPRFDADPAHRWLRECVREV 199
PBP2_SyrM cd08467
The C-terminal substrate binding of LysR-type symbiotic regulator SyrM, which activates ...
 102-297 1.48e-16

The C-terminal substrate binding of LysR-type symbiotic regulator SyrM, which activates expression of nodulation gene NodD3, contains the type 2 periplasmic binding fold; Rhizobium is a nitrogen fixing bacteria present in the roots of leguminous plants, which fixes atmospheric nitrogen to the soil. Most Rhizobium species possess multiple nodulation (nod) genes for the development of nodules. For example, Rhizobium meliloti possesses three copies of nodD genes. NodD1 and NodD2 activate nod operons when Rhizobium is exposed to inducers synthesized by the host plant, while NodD3 acts independent of plant inducers and requires the symbiotic regulator SyrM for nod gene expression. SyrM activates the expression of the regulatory nodulation gene nodD3. In turn, NodD3 activates expression of syrM. In addition, SyrM is involved in exopolysaccharide synthesis. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176156 [Multi-domain]  Cd Length: 200  Bit Score: 76.71  E-value: 1.48e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263 102 FRIGLSDYTAVTYLPELIENFSMLAPNASLNVVHAREPDALGSLKNREVECAVlGNPKLDAEHFEVVELSRDRMVCAGWA 181
Cdd:cd08467     2 FTLAMPDYAEVALLPRLAPRLRERAPGLDLRLCPIGDDLAERGLEQGTIDLAV-GRFAVPPDGLVVRRLYDDGFACLVRH 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263 182 GNPAMAD-MSLDRYLASPHLQISADG-IAAGIADItLQKLGLHRKVVATIPHYLVAPWVIKGTELISAFGDGVLLALSEE 259
Cdd:cd08467    81 GHPALAQeWTLDDFATLRHVAIAPPGrLFGGIYKR-LENLGLKRNVAIAVSSFLTAAATVAATDLIATVPRRVATQVAAM 159

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 1590257263 260 SETAIVPPPLELPDVTISLIFDRSNELDPGHVWFRNLI 297
Cdd:cd08467   160 LPLRVVPPPVDLGTFPVMLIWHERYQHDPAHRWLRKLI 197
PBP2_DntR_like_3 cd08461
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 102-300 3.30e-16

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


Pssm-ID: 176150 [Multi-domain]  Cd Length: 198  Bit Score: 75.40  E-value: 3.30e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263 102 FRIGLSDYTAVTYLPELIENFSMLAPNASLNVVHArEPDALGSLKNR-EVECAVLgNPKLDAEHFEVVELSRDRMVCAGW 180
Cdd:cd08461     2 LVIAATDYAQKAILPPLLAALRQEAPGVRVAIRDL-ESDNLEAQLERgEVDLALT-TPEYAPDGLRSRPLFEERYVCVTR 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263 181 AGNP-AMADMSLDRYLASPHLQISADGIA-AGIADITLQKLGLHRKVVATIPHYLVAPWVIKGTELIsAFGDGVLLAlsE 258
Cdd:cd08461    80 RGHPlLQGPLSLDQFCALDHIVVSPSGGGfAGSTDEALAALGLTRNVVLSVPSFLVVPEILAATDMV-AFVPSRLVP--N 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1590257263 259 ESETAIVPPPLELPDVTISLIFDRSNELDPGHVWFRNLIKDV 300
Cdd:cd08461   157 LEGLQEVELPLEPPGFDVVMAWHERTHRDPAHRWLRELLAAA 198
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
11-70 1.02e-15

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 70.11  E-value: 1.02e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263  11 LNLLRTFDVLMRERSVTRAADRLGRTQSAISHSLGRLRDVFKDDLFTREAGIMEPTARAK 70
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK10216 PRK10216
HTH-type transcriptional regulator YidZ;
5-298 1.13e-15

HTH-type transcriptional regulator YidZ;


Pssm-ID: 182312 [Multi-domain]  Cd Length: 319  Bit Score: 76.40  E-value: 1.13e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263   5 SLNQLDLNLLRTFDVLMRERSVTRAADRLGRTQSAISHSLGRLRDVFKDDLFTREAGIMEPTARAKELAEVISQALHEIR 84
Cdd:PRK10216    4 SLTTLDLNLLLCLQLLMQERSVTKAAKRMNVTPSAVSKSLAKLRAWFDDPLFVNTPLGLSPTPLMVSMEQNLAEWMQMGN 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263  85 VAVDRHLNFDPTTTSrnFRIGLSDYTAVTYLPELIENFSMLAPNASLNVVHArEPDALGSLKNREVECAVLG---NPK-- 159
Cdd:PRK10216   84 QLLDKPHHQTPRGLK--FELAAESPLMMIMLNALSKRIYQRYPQATIKLRNW-DYDSLDAITRGEVDIGFTGresHPRsr 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263 160 --LD----AEHFEV-------VELSRDrmvcagwagNPAMAD-MSLDRYLASPHLQISADGIAAGIADITLQKLGLHRKV 225
Cdd:PRK10216  161 elLSllplAIDFEVlfsdlpcVWLRKD---------HPALHEeWNLDTFLRYPHISICWEQSDTWALDDVLQELGRERTI 231

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263 226 VATIPHYlvapwviKGTELISAFGDGVLLALS--------EESETAIVPPPLELPD-------VTISLIFDRSNELDPGH 290
Cdd:PRK10216  232 ALSLPEF-------EQSLFMAAQPDHLLLATAprycqyynQLHQLPLVALPLPFDEsqqkkleVPFTLLWHKRNSHNPKI 304


                  ....*...
gi 1590257263 291 VWFRNLIK 298
Cdd:PRK10216  305 VWLRETIK 312
PBP2_LeuO cd08466
The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an ...
 101-300 1.00e-12

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: 65.74  E-value: 1.00e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263 101 NFRIGLSDYTAVTYLPELIENFSMLAPNASLNVVHAREPDALGSLKNREVECaVLGNPKLDAEHFEVVELSRDRMVCAGW 180
Cdd:cd08466     1 TFNIAANETLDLLLLPRLLARLKQLAPNISLRESPSSEEDLFEDLRLQEVDL-VIDYVPFRDPSFKSELLFEDELVCVAR 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263 181 AGNPAMAD-MSLDRYLASPHLQISADGIAAGIADITLQKLGLHRKVVATIPHYLVAPWVIKGTELIsAFGDGVLLALSEE 259
Cdd:cd08466    80 KDHPRIQGsLSLEQYLAEKHVVLSLRRGNLSALDLLTEEVLPQRNIAYEVSSLLSMLAVVSQTDLI-AIAPRWLADQYAE 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1590257263 260 S-ETAIVPPPLELPDVTISLIFDRSNELDPGHVWFRNLIKDV 300
Cdd:cd08466   159 QlNLQILPLPFKTKPIPLYMVWHKSRERDPAHQWLREQIKQL 200
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 9-154 6.41e-12

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 65.05  E-value: 6.41e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263   9 LDLNLLRTFDVLMRERSVTRAADRLGRTQSAISHSLGRLRDVFKDDLFTREAgimeptaRAKELAEVISQALHEIRvavd 88
Cdd:PRK15092   11 LDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHG-------RNKLLTEHGIQLLGYAR---- 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1590257263  89 RHLNF-DPTTTSRNF-------RIGLSDYTAVTYLPELIENFSMLAPNASLNVVHAREPDALGSLKNREVECAV 154
Cdd:PRK15092   80 KILRFnDEACSSLMYsnlqgvlTIGASDDTADTILPFLLNRVSSVYPKLALDVRVKRNAFMMEMLESQEVDLAV 153
PRK11482 PRK11482
DNA-binding transcriptional regulator;
6-88 2.48e-11

DNA-binding transcriptional regulator;


Pssm-ID: 183159 [Multi-domain]  Cd Length: 317  Bit Score: 63.59  E-value: 2.48e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263   6 LNQLDLNLLRTFDVLMRERSVTRAADRLGRTQSAISHSLGRLRDVFKDDLFTREAGIMEPTARAKELAEVISQALHEIRV 85
Cdd:PRK11482   26 LRNIDLNLLTIFEAVYVHKGIVNAAKILNLTPSAISQSIQKLRVIFPDPLFIRKGQGVTPTAYATHLHEYISQGLESILG 105


                  ...
gi 1590257263  86 AVD 88
Cdd:PRK11482  106 ALD 108
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 102-300 1.28e-10

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: 60.00  E-value: 1.28e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263 102 FRIGLSDYTAVTYLPELIENFSMLAPNASLNVVHAREPDALGSLKNREVECAVLGNPKLDAEhFEVVELSRDRMVCAGWA 181
Cdd:pfam03466   4 LRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPG-LEARPLGEEPLVLVAPP 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263 182 GNP--AMADMSLDRYLASPHLQISADGIAAGIADITLQKLGLHRKVVATIPHYLVAPWVIKGTELISAFGDGVLLALSEE 259
Cdd:pfam03466  83 DHPlaRGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARELAD 162

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1590257263 260 SETAIVPPPLELPDVTISLIFDRSNELDPGHVWFRNLIKDV 300
Cdd:pfam03466 163 GRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREA 203
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 103-297 5.47e-09

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: 54.91  E-value: 5.47e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263 103 RIGLSDYTAVTYLPELIENFSMLAPNASLNVVHAREPDALGSLKNREVECAVLGNPkLDAEHFEVVELSRDRMVCAG--- 179
Cdd:cd05466     3 RIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALP-VDDPGLESEPLFEEPLVLVVppd 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263 180 --WAGNPAMADMSLDRYlasPHLQISADGIAAGIADITLQKLGLHRKVVATIPHYLvapwVIKgtELISAfGDGV----- 252
Cdd:cd05466    82 hpLAKRKSVTLADLADE---PLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLE----AIK--ALVAA-GLGIallpe 151

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1590257263 253 -LLALSEESETAIVPPPLELPDVTISLIFDRSNELDPGHVWFRNLI 297
Cdd:cd05466   152 sAVEELADGGLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 11-89 4.03e-06

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 47.53  E-value: 4.03e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1590257263  11 LNLLRTFDVLMRERSVTRAADRLGRTQSAISHSLGRLRDVFKDDLFTREAGIMEPTARAKELAEVISQALHEIRVAVDR 89
Cdd:PRK11139    8 LNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEATRK 86
PRK10341 PRK10341
transcriptional regulator TdcA;
14-154 2.01e-05

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 45.62  E-value: 2.01e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263  14 LRTFDVLMRERSVTRAADRLGRTQSAISHSLGRLRDVFKDDLFTREAGIMEPTARAKELAEVISQALHEIRVAVDRhLNF 93
Cdd:PRK10341   12 LVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNE-ING 90

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1590257263  94 DPTTTSRNFRIGLSDYTAVTYLPELIENFSMLAPNASLNVVHAREPDALGSLKNREVECAV 154
Cdd:PRK10341   91 MSSEAVVDVSFGFPSLIGFTFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAI 151
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
9-151 4.01e-05

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 44.62  E-value: 4.01e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263   9 LDLNLLRTFDVLMRERSVTRAADRLGRTQSAISHSLGRLRDVFKDDLFTREAGIMEPTARAKELAEVISQALHEIRVAVd 88
Cdd:PRK15421    2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQAL- 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1590257263  89 RHLNfDPTTTsrNFRIGLSDYTAVTYLPELIENFSMLAPNASLNVVHAREPDALGSLKNREVE 151
Cdd:PRK15421   81 QACN-EPQQT--RLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELD 140
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
5-84 6.51e-05

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 43.84  E-value: 6.51e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263   5 SLNQLDLNLLRTFDVLMRERSVTRAADRLGRTQSAISHSLGRLRDVFKDDLFTREAGIMEPTARAKEL-------AEVIS 77
Cdd:PRK10086   10 LLNGWQLSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVfwalkssLDTLN 89


                  ....*..
gi 1590257263  78 QALHEIR 84
Cdd:PRK10086   90 QEILDIK 96
PBP2_LrhA_like cd08439
The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of ...
 103-165 2.74e-04

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: 41.16  E-value: 2.74e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1590257263 103 RIGLSDYTAVTYLPELIENFSMLAPNASLNVVHAREPDALGSLKNREVECAVLGNPKLDAEHF 165
Cdd:cd08439     3 RIGCPDDYADTILPFLLNRFASVYPRLAIEVVCKRTPRLMEMLERGEVDLALITHPPPGASAT 65
PBP2_TdcA cd08418
The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is ...
 102-154 3.27e-04

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: 41.18  E-value: 3.27e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1590257263 102 FRIGLSDYTAVTYLPELIENFSMLAPNASLNVVHAREPDALGSLKNREVECAV 154
Cdd:cd08418     2 VSIGVSSLIAHTLMPAVINRFKEQFPDVQISIYEGQLSSLLPELRDGRLDFAI 54
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
8-41 5.75e-04

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 40.91  E-value: 5.75e-04
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1590257263   8 QLDLNLLRTFDVLMRERSVTRAADRLGRTQSAIS 41
Cdd:PRK03635    1 MLDYKQLEALAAVVREGSFERAAQKLHITQSAVS 34
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 1-134 9.14e-04

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 40.36  E-value: 9.14e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263   1 MAEFSLNQLDLnllrtFDVLMRERSVTRAADRLGRTQSAISHSLGRLRDVFKDDLFTREAGIMEPTARAKELAEVISQAL 80
Cdd:PRK11013    1 MAAVSLRHIEI-----FHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLFEEVQRSY 75

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1590257263  81 heirVAVDRHLNFdpTTTSRNFRIGLSDYTAV-----TYLPELIENFSMLAPNASLNVV 134
Cdd:PRK11013   76 ----YGLDRIVSA--AESLREFRQGQLSIACLpvfsqSLLPGLCQPFLARYPDVSLNIV 128
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
9-100 1.51e-03

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 39.79  E-value: 1.51e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1590257263   9 LDLNLLRTFDVLMRERSVTRAADRLGRTQSAISHSLGRLRDVFKDDLFTREAGIMEPTARAKELAEVISQ---------- 78
Cdd:PRK10094    2 FDPETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDwlswlesmps 81

                          90       100
                  ....*....|....*....|....*....
gi 1590257263  79 ALHEIRVAVDRHLN-------FDPTTTSR 100
Cdd:PRK10094   82 ELQQVNDGVERQVNivinnllYNPQAVAQ 110
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
9-59 5.17e-03

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 38.03  E-value: 5.17e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1590257263   9 LDLNLLRTFDVLMRERSVTRAADRLGRTQSAISHSLGRLRDVFKDDLFTRE 59
Cdd:PRK13348    2 LDYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRG 52
 
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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