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Conserved domains on  [gi|446457053|ref|WP_000534907|]
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MULTISPECIES: LysR family transcriptional regulator [Salmonella]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 10444297)

LysR family transcriptional regulator containing an N-terminal helix-turn-helix DNA-binding domain and a C-terminal substrate binding domain; similar to CbbR, AmpR, GalR, YhaJ, and NmcR, which are positive transcriptional regulators of various genes

Gene Ontology:  GO:0003677|GO:0003700|GO:0001216
PubMed:  8257110|19047729
SCOP:  4000316

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Periplasmic_Binding_Protein_Type_2 super family cl21456
Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent ...
 101-292 1.14e-13

Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent the ligand-binding domains found in solute binding proteins that serve as initial receptors in the transport, signal transduction and channel gating. The PBP2 proteins share the same architecture as periplasmic binding proteins type 1 (PBP1), but have a different topology. They are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The origin of PBP module can be traced across the distant phyla, including eukaryotes, archebacteria, and prokaryotes. The majority of PBP2 proteins are involved in the uptake of a variety of soluble substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. 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 family includes ionotropic glutamate receptors and unorthodox sensor proteins involved in signal transduction. The substrate binding domain of the LysR transcriptional regulators and the oligopeptide-like transport systems also contain the type 2 periplasmic binding fold and thus they are significantly homologous to that of the PBP2; however, these two families are grouped into a separate hierarchy of the PBP2 superfamily due to the large number of protein sequences.


The actual alignment was detected with superfamily member cd08417:

Pssm-ID: 473866 [Multi-domain]  Cd Length: 200  Bit Score: 68.39  E-value: 1.14e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446457053 101 TLLGSDIVESYYLSQLYNsdIFDRILIN-HFTVRNMSREHISELLFTAQGDLLISAEPLLESGIENQIIdsFK-SFVCIC 178
Cdd:cd08417    3 RIAASDYLEALLLPPLLA--RLRQEAPGvRLRFVPLDRDDLEEALESGEIDLAIGVFPELPPGLRSQPL--FEdRFVCVA 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446457053 179 SSKHMLSTlSQLSLHHFYSSRHALYQP-GMGASVIyhDSELFKDDLYytgRRIVgYRSDSLNGLMSMIERTSLIALMPLK 257
Cdd:cd08417   79 RKDHPLAG-GPLTLEDYLAAPHVLVSPrGRGHGLV--DDALAELGLS---RRVA-LTVPHFLAAPALVAGTDLIATVPRR 151

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 446457053 258 LALFYknHRKYDIKFIQPPpeLALKSVQVYASWNK 292
Cdd:cd08417  152 LAEAL--AERLGLRVLPLP--FELPPFTVSLYWHP 182
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
13-68 2.10e-10

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


:

Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 55.47  E-value: 2.10e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 446457053   13 NLIKILDAVILSGNAAMAAKKLGITPAAVSLALKRLQSYYPEELFSRGKGGLIPTA 68
Cdd:pfam00126   2 RQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTE 57
 
Name Accession Description Interval E-value
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 101-292 1.14e-13

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: 68.39  E-value: 1.14e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446457053 101 TLLGSDIVESYYLSQLYNsdIFDRILIN-HFTVRNMSREHISELLFTAQGDLLISAEPLLESGIENQIIdsFK-SFVCIC 178
Cdd:cd08417    3 RIAASDYLEALLLPPLLA--RLRQEAPGvRLRFVPLDRDDLEEALESGEIDLAIGVFPELPPGLRSQPL--FEdRFVCVA 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446457053 179 SSKHMLSTlSQLSLHHFYSSRHALYQP-GMGASVIyhDSELFKDDLYytgRRIVgYRSDSLNGLMSMIERTSLIALMPLK 257
Cdd:cd08417   79 RKDHPLAG-GPLTLEDYLAAPHVLVSPrGRGHGLV--DDALAELGLS---RRVA-LTVPHFLAAPALVAGTDLIATVPRR 151

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 446457053 258 LALFYknHRKYDIKFIQPPpeLALKSVQVYASWNK 292
Cdd:cd08417  152 LAEAL--AERLGLRVLPLP--FELPPFTVSLYWHP 182
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
10-212 1.05e-12

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 66.81  E-value: 1.05e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446457053  10 FDYNLIKILDAVILSGNAAMAAKKLGITPAAVSLALKRLQSYYPEELFSRGKGGLIPTAKAVDIHQNFSQVMKLVDDTF- 88
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEa 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446457053  89 -LCNSKKDEAFQITLLGSDIVESYYLSQLynsdiFDRILINH----FTVRNMSREHISELLFTAQGDLLISAEPLLESGI 163
Cdd:COG0583   81 eLRALRGGPRGTLRIGAPPSLARYLLPPL-----LARFRARHpgvrLELREGNSDRLVDALLEGELDLAIRLGPPPDPGL 155

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 446457053 164 ENQIIDSFKsFVCICSSKHMLSTLSQLSlHHFYSSRHALYQpGMGASVI 212
Cdd:COG0583  156 VARPLGEER-LVLVASPDHPLARRAPLV-NSLEALLAAVAA-GLGIALL 201
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
13-68 2.10e-10

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 55.47  E-value: 2.10e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 446457053   13 NLIKILDAVILSGNAAMAAKKLGITPAAVSLALKRLQSYYPEELFSRGKGGLIPTA 68
Cdd:pfam00126   2 RQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTE 57
PRK11482 PRK11482
DNA-binding transcriptional regulator;
8-261 1.42e-09

DNA-binding transcriptional regulator;


Pssm-ID: 183159 [Multi-domain]  Cd Length: 317  Bit Score: 58.20  E-value: 1.42e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446457053   8 KSFDYNLIKILDAVILSGNAAMAAKKLGITPAAVSLALKRLQSYYPEELFSRGKGGLIPTAKAVDIHQNFSQVMKLVDDT 87
Cdd:PRK11482  27 RNIDLNLLTIFEAVYVHKGIVNAAKILNLTPSAISQSIQKLRVIFPDPLFIRKGQGVTPTAYATHLHEYISQGLESILGA 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446457053  88 FLCNSKKDEAFQITLLGSDIVESYYLSQLYNS--DIFDRILINHFTVRNMSREhiselLFTAQGDLLISAEPLLESGIEN 165
Cdd:PRK11482 107 LDITGSYDKQRTITIATTPSVGALVMPVIYQAikTHYPQLLLRNIPISDAENQ-----LSQFQTDLIIDTHSCSNRTIQH 181

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446457053 166 QIIDSfKSFVCICSSKHMLSTLSQLSlHHFYSSRHALYQP--GMGASVIYHDSELFKDdlyytgrRIVGYRSDSLNGLMS 243
Cdd:PRK11482 182 HVLFT-DNVVLVCRQGHPLLSLEDDE-ETLDNAEHTLLLPegQNFSGLRQRLQEMFPD-------RQISFSSYNILTIAA 252

                        250
                 ....*....|....*....
gi 446457053 244 MIERTSLIALMPLKL-ALF 261
Cdd:PRK11482 253 LIASSDMLGIMPSRFyNLF 271
PRK10216 PRK10216
HTH-type transcriptional regulator YidZ;
9-83 2.31e-06

HTH-type transcriptional regulator YidZ;


Pssm-ID: 182312 [Multi-domain]  Cd Length: 319  Bit Score: 48.28  E-value: 2.31e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446457053   9 SFDYNLIKILDAVILSGNAAMAAKKLGITPAAVSLALKRLQSYYPEELFSRGKGGLIPTAKAVDIHQNFSQVMKL 83
Cdd:PRK10216   7 TLDLNLLLCLQLLMQERSVTKAAKRMNVTPSAVSKSLAKLRAWFDDPLFVNTPLGLSPTPLMVSMEQNLAEWMQM 81
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 129-308 9.20e-05

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: 42.66  E-value: 9.20e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446457053  129 HFTVRNMSREHISELLftAQG--DLLISAEPLLESGIENQIIDSFKsFVCICSSKHMLSTLSQLSLHHFYSSRHALYQPG 206
Cdd:pfam03466  32 ELELTEGNSEELLDLL--LEGelDLAIRRGPPDDPGLEARPLGEEP-LVLVAPPDHPLARGEPVSLEDLADEPLILLPPG 108

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446457053  207 MGasviYHDseLFKDDLYYTGRRI-VGYRSDSLNGLMSMIERTSLIALMPLKLAL-FYKNHRkydIKFIqPPPELALKSv 284
Cdd:pfam03466 109 SG----LRD--LLDRALRAAGLRPrVVLEVNSLEALLQLVAAGLGIALLPRSAVArELADGR---LVAL-PLPEPPLPR- 177

                         170       180
                  ....*....|....*....|....
gi 446457053  285 QVYASWNKNSRNISTINEMVSMLQ 308
Cdd:pfam03466 178 ELYLVWRKGRPLSPAVRAFIEFLR 201
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 10-48 2.45e-04

transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity. [Cellular processes, Toxin production and resistance, DNA metabolism, DNA replication, recombination, and repair, Regulatory functions, DNA interactions]


Pssm-ID: 274509 [Multi-domain]  Cd Length: 292  Bit Score: 42.21  E-value: 2.45e-04
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 446457053   10 FDYNLIKILDAVILSGNAAMAAKKLGITPAAVSLALKRL 48
Cdd:TIGR03298   1 LDYRQLAALAAVVEEGSFERAAAALSVTPSAVSQRIKAL 39
 
Name Accession Description Interval E-value
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 101-292 1.14e-13

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: 68.39  E-value: 1.14e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446457053 101 TLLGSDIVESYYLSQLYNsdIFDRILIN-HFTVRNMSREHISELLFTAQGDLLISAEPLLESGIENQIIdsFK-SFVCIC 178
Cdd:cd08417    3 RIAASDYLEALLLPPLLA--RLRQEAPGvRLRFVPLDRDDLEEALESGEIDLAIGVFPELPPGLRSQPL--FEdRFVCVA 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446457053 179 SSKHMLSTlSQLSLHHFYSSRHALYQP-GMGASVIyhDSELFKDDLYytgRRIVgYRSDSLNGLMSMIERTSLIALMPLK 257
Cdd:cd08417   79 RKDHPLAG-GPLTLEDYLAAPHVLVSPrGRGHGLV--DDALAELGLS---RRVA-LTVPHFLAAPALVAGTDLIATVPRR 151

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 446457053 258 LALFYknHRKYDIKFIQPPpeLALKSVQVYASWNK 292
Cdd:cd08417  152 LAEAL--AERLGLRVLPLP--FELPPFTVSLYWHP 182
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
10-212 1.05e-12

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 66.81  E-value: 1.05e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446457053  10 FDYNLIKILDAVILSGNAAMAAKKLGITPAAVSLALKRLQSYYPEELFSRGKGGLIPTAKAVDIHQNFSQVMKLVDDTF- 88
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEa 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446457053  89 -LCNSKKDEAFQITLLGSDIVESYYLSQLynsdiFDRILINH----FTVRNMSREHISELLFTAQGDLLISAEPLLESGI 163
Cdd:COG0583   81 eLRALRGGPRGTLRIGAPPSLARYLLPPL-----LARFRARHpgvrLELREGNSDRLVDALLEGELDLAIRLGPPPDPGL 155

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 446457053 164 ENQIIDSFKsFVCICSSKHMLSTLSQLSlHHFYSSRHALYQpGMGASVI 212
Cdd:COG0583  156 VARPLGEER-LVLVASPDHPLARRAPLV-NSLEALLAAVAA-GLGIALL 201
PBP2_LeuO cd08466
The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an ...
 129-296 2.83e-11

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: 61.88  E-value: 2.83e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446457053 129 HFTVRNMSR--EHISELLFTAQGDLLISAEPLLESGIENQIIdSFKSFVCICSSKHMLSTlSQLSLHHFYSSRHALYQPG 206
Cdd:cd08466   28 NISLRESPSseEDLFEDLRLQEVDLVIDYVPFRDPSFKSELL-FEDELVCVARKDHPRIQ-GSLSLEQYLAEKHVVLSLR 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446457053 207 MGASviYHDSELFKDDLYytgRRIVGYRSDSLNGLMSMIERTSLIALMPLKLALFYKNhrKYDIKfIQPPPeLALKSVQV 286
Cdd:cd08466  106 RGNL--SALDLLTEEVLP---QRNIAYEVSSLLSMLAVVSQTDLIAIAPRWLADQYAE--QLNLQ-ILPLP-FKTKPIPL 176

                        170
                 ....*....|.
gi 446457053 287 YASW-NKNSRN 296
Cdd:cd08466  177 YMVWhKSRERD 187
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
13-68 2.10e-10

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 55.47  E-value: 2.10e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 446457053   13 NLIKILDAVILSGNAAMAAKKLGITPAAVSLALKRLQSYYPEELFSRGKGGLIPTA 68
Cdd:pfam00126   2 RQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTE 57
PRK11482 PRK11482
DNA-binding transcriptional regulator;
8-261 1.42e-09

DNA-binding transcriptional regulator;


Pssm-ID: 183159 [Multi-domain]  Cd Length: 317  Bit Score: 58.20  E-value: 1.42e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446457053   8 KSFDYNLIKILDAVILSGNAAMAAKKLGITPAAVSLALKRLQSYYPEELFSRGKGGLIPTAKAVDIHQNFSQVMKLVDDT 87
Cdd:PRK11482  27 RNIDLNLLTIFEAVYVHKGIVNAAKILNLTPSAISQSIQKLRVIFPDPLFIRKGQGVTPTAYATHLHEYISQGLESILGA 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446457053  88 FLCNSKKDEAFQITLLGSDIVESYYLSQLYNS--DIFDRILINHFTVRNMSREhiselLFTAQGDLLISAEPLLESGIEN 165
Cdd:PRK11482 107 LDITGSYDKQRTITIATTPSVGALVMPVIYQAikTHYPQLLLRNIPISDAENQ-----LSQFQTDLIIDTHSCSNRTIQH 181

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446457053 166 QIIDSfKSFVCICSSKHMLSTLSQLSlHHFYSSRHALYQP--GMGASVIYHDSELFKDdlyytgrRIVGYRSDSLNGLMS 243
Cdd:PRK11482 182 HVLFT-DNVVLVCRQGHPLLSLEDDE-ETLDNAEHTLLLPegQNFSGLRQRLQEMFPD-------RQISFSSYNILTIAA 252

                        250
                 ....*....|....*....
gi 446457053 244 MIERTSLIALMPLKL-ALF 261
Cdd:PRK11482 253 LIASSDMLGIMPSRFyNLF 271
leuO PRK09508
leucine transcriptional activator; Reviewed
 8-294 5.93e-09

leucine transcriptional activator; Reviewed


Pssm-ID: 181918 [Multi-domain]  Cd Length: 314  Bit Score: 56.18  E-value: 5.93e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446457053   8 KSFDYNLIKILDAVILSGNAAMAAKKLGITPAAVSLALKRLQSYYPEELFSRGKGGLIPTAKAvdiHQNFS---QVMKLV 84
Cdd:PRK09508  20 RMVDLNLLTVFDAVMQEQNITRAAHNLGMSQPAVSNAVARLKVMFNDELFVRYGRGIQPTARA---RQLFGpvrQALQLV 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446457053  85 DD-----TFLCNSkKDEAFQITLLG-SDIvesYYLSQLYNsDIFDRILINHFTVRNMSREHISELLFTAQGDLLISAEPL 158
Cdd:PRK09508  97 QNelpgsGFEPES-SERVFNLCICSpLDI---RLTSQIYN-RIEQIAPNIHVVFKSSLNQNIEHQLRYQETEFVISYEEF 171

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446457053 159 LESGIENQIIdsFK-SFVCICSSKHmlSTLSQ-LSLHHFYSSRHALyqpgmgasVIYHDSELFKDDLYYTGRRI--VGYR 234
Cdd:PRK09508 172 DRPEFTSVPL--FKdELVLVASKNH--PRIKGpITEEQLYNEQHAV--------VSLDRFASFSQPWYDTVDKQasIAYQ 239

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 446457053 235 SDSLNGLMSMIERTSLIALMPLKLALFYKNhrKYDIKFIQPPpeLALKSVQVYASWNKNS 294
Cdd:PRK09508 240 GTALSSVLNVVSQTHLVAIAPRWLAEEFAE--SLELQILPLP--LKNNSRTCYLSWHESA 295
PRK10216 PRK10216
HTH-type transcriptional regulator YidZ;
9-83 2.31e-06

HTH-type transcriptional regulator YidZ;


Pssm-ID: 182312 [Multi-domain]  Cd Length: 319  Bit Score: 48.28  E-value: 2.31e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446457053   9 SFDYNLIKILDAVILSGNAAMAAKKLGITPAAVSLALKRLQSYYPEELFSRGKGGLIPTAKAVDIHQNFSQVMKL 83
Cdd:PRK10216   7 TLDLNLLLCLQLLMQERSVTKAAKRMNVTPSAVSKSLAKLRAWFDDPLFVNTPLGLSPTPLMVSMEQNLAEWMQM 81
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
10-61 1.10e-05

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 46.12  E-value: 1.10e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 446457053  10 FDYNLIKILDAVILSGNAAMAAKKLGITPAAVSLALKRLQSYYPEELFSRGK 61
Cdd:PRK13348   2 LDYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRGR 53
PBP2_DntR_NahR_LinR_like cd08459
The C-terminal substrate binding domain of LysR-type transcriptional regulators that are ...
 98-287 2.16e-05

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: 44.49  E-value: 2.16e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446457053  98 FQITLlgSDIVESYYLSQLYN--SDIFDRIlinHFTVRNMSREHISELLFTAQGDLLISAEPLLESGIENQIIdsFK-SF 174
Cdd:cd08459    2 FRIAM--SDIGEMYFLPRLLAalREVAPGV---RIETVRLPVDELEEALESGEIDLAIGYLPDLGAGFFQQRL--FReRY 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446457053 175 VCICSSKHMLSTlSQLSLHHFYSSRHALYQPGMGASVIYhDSELFKDDLyytGRRIVgYRSDSLNGLMSMIERTSLIALM 254
Cdd:cd08459   75 VCLVRKDHPRIG-STLTLEQFLAARHVVVSASGTGHGLV-EQALREAGI---RRRIA-LRVPHFLALPLIVAQTDLVATV 148

                        170       180       190
                 ....*....|....*....|....*....|...
gi 446457053 255 PLKLALFYknHRKYDIKFIQPPPELALKSVQVY 287
Cdd:cd08459  149 PERLARLF--ARAGGLRIVPLPFPLPPFEVKLY 179
PBP2_TdcA cd08418
The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is ...
 154-315 6.80e-05

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


Pssm-ID: 176110 [Multi-domain]  Cd Length: 201  Bit Score: 43.11  E-value: 6.80e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446457053 154 SAEPLLEsgienqiidsfKSFVCICSSKHMLSTLSqlSLHHFYSSRHALYQPGMGAsviYHD-SELFKDdLYYTGRRIVg 232
Cdd:cd08418   67 ISEPLFE-----------SDFVVVARKDHPLQGAR--SLEELLDASWVLPGTRMGY---YNNlLEALRR-LGYNPRVAV- 128

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446457053 233 yRSDSLNGLMSMIERTSLIALMPlKLALFYKNHRKydiKFIQPPPELALKSVQVYASWNKNSRnistINEMVSMLQTLss 312
Cdd:cd08418  129 -RTDSIVSIINLVEKADFLTILS-RDMGRGPLDSF---RLITIPVEEPLPSADYYLIYRKKSR----LTPLAEQLVEL-- 197


                 ...
gi 446457053 313 FRR 315
Cdd:cd08418  198 FRR 200
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 129-308 9.20e-05

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: 42.66  E-value: 9.20e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446457053  129 HFTVRNMSREHISELLftAQG--DLLISAEPLLESGIENQIIDSFKsFVCICSSKHMLSTLSQLSLHHFYSSRHALYQPG 206
Cdd:pfam03466  32 ELELTEGNSEELLDLL--LEGelDLAIRRGPPDDPGLEARPLGEEP-LVLVAPPDHPLARGEPVSLEDLADEPLILLPPG 108

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446457053  207 MGasviYHDseLFKDDLYYTGRRI-VGYRSDSLNGLMSMIERTSLIALMPLKLAL-FYKNHRkydIKFIqPPPELALKSv 284
Cdd:pfam03466 109 SG----LRD--LLDRALRAAGLRPrVVLEVNSLEALLQLVAAGLGIALLPRSAVArELADGR---LVAL-PLPEPPLPR- 177

                         170       180
                  ....*....|....*....|....
gi 446457053  285 QVYASWNKNSRNISTINEMVSMLQ 308
Cdd:pfam03466 178 ELYLVWRKGRPLSPAVRAFIEFLR 201
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 10-48 2.45e-04

transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity. [Cellular processes, Toxin production and resistance, DNA metabolism, DNA replication, recombination, and repair, Regulatory functions, DNA interactions]


Pssm-ID: 274509 [Multi-domain]  Cd Length: 292  Bit Score: 42.21  E-value: 2.45e-04
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 446457053   10 FDYNLIKILDAVILSGNAAMAAKKLGITPAAVSLALKRL 48
Cdd:TIGR03298   1 LDYRQLAALAAVVEEGSFERAAAALSVTPSAVSQRIKAL 39
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
10-48 1.30e-03

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 39.76  E-value: 1.30e-03
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 446457053  10 FDYNLIKILDAVILSGNAAMAAKKLGITPAAVSLALKRL 48
Cdd:PRK03635   2 LDYKQLEALAAVVREGSFERAAQKLHITQSAVSQRIKAL 40
PBP2_NodD cd08462
The C-terminal substsrate binding domain of NodD family of LysR-type transcriptional ...
 138-276 2.52e-03

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: 38.38  E-value: 2.52e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446457053 138 EHISELLFTAQGDLLISAEPLLESGIENQIIdsFK-SFVCICSSKHMLsTLSQLSLHHFYSSRHALYQPGMGASVIYHDS 216
Cdd:cd08462   38 DQPHELLERGEVDLLIAPERFMSDGHPSEPL--FEeEFVCVVWADNPL-VGGELTAEQYFSAGHVVVRFGRNRRPSFEDW 114

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 446457053 217 ELfkddLYYTGRRIVGYRSDSLNGLMSMIERTSLIALMPLKLALFYKNHrkYDIKFIQPP 276
Cdd:cd08462  115 FL----NEYGLKRRVEVVTPSFSSIPPLLVGTNRIATLHRRLAEQFARR--LPLRILPLP 168
PRK10341 PRK10341
transcriptional regulator TdcA;
21-313 4.10e-03

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 38.30  E-value: 4.10e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446457053  21 VILSGNAAMAAKKLGITPAAVSLALKRLQSYYPEELFSRGKGGLIPTAKAVDIH---QNFSQVMK-LVDD--TFLCNSKK 94
Cdd:PRK10341  18 VIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLsrsESITREMKnMVNEinGMSSEAVV 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446457053  95 DEAFQI-TLLG----SDIVE-----------SYYLSQLynSDIFDRILINH--FTVRNMSREhisELLFtaqgDLliSAE 156
Cdd:PRK10341  98 DVSFGFpSLIGftfmSDMINkfkevfpkaqvSMYEAQL--SSFLPAIRDGRldFAIGTLSNE---MKLQ----DL--HVE 166

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446457053 157 PLLESgienqiidsfkSFVCICSSKHMLSTLSQL-SLHHfysSRHALYQPGMGasviYHdSELFkDDLYYTGRRIVG-YR 234
Cdd:PRK10341 167 PLFES-----------EFVLVASKSRTCTGTTTLeSLKN---EQWVLPQTNMG----YY-SELL-TTLQRNGISIENiVK 226

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446457053 235 SDSLNGLMSMIERTSLIALMPLKLALFYKNHRkydikFIQPPPELALKSVQVYASWNKNSRNISTINEMVSMLQTLSSF 313
Cdd:PRK10341 227 TDSVVTIYNLVLNADFLTVIPCDMTSPFGSNQ-----FITIPIEETLPVAQYAAVWSKNYRIKKAASVLVELAKEYSSY 300
 
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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