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Conserved domains on  [gi|1161026737|ref|WP_079839751|]
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LysR family transcriptional regulator [Salmonella enterica]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 11426520)

LysR family transcriptional regulator negatively or positively regulates the transcription of specific genes; contains 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

CATH:  3.40.190.10
Gene Ontology:  GO:0003700|GO:0006355|GO:0003677
PubMed:  8257110|19047729
SCOP:  3000083|4000316

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
10-202 1.75e-19

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 86.07  E-value: 1.75e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1161026737  10 IDYNLIKVFDTVITEGNATRAARKLDVTPAAISQALLRLQNLYGEELFIRTRKGLVPSSKGKSLHQVFRQAIESIESTL- 88
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEa 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1161026737  89 -CDKTDAQESNELIVLGGDITENYYFPALLDTvLMNRY--IikHYAIKKTGEYSPASMLTHGYADVIMGILEIKNEMIES 165
Cdd:COG0583    81 eLRALRGGPRGTLRIGAPPSLARYLLPPLLAR-FRARHpgV--RLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVA 157

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1161026737 166 YLIDNlSDFVCVCGEKSPLVGLEKISLyNFYAARHAV 202
Cdd:COG0583   158 RPLGE-ERLVLVASPDHPLARRAPLVN-SLEALLAAV 192
Periplasmic_Binding_Protein_Type_2 super family cl21456
Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent ...
 149-289 1.63e-11

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 cd08466:

Pssm-ID: 473866 [Multi-domain]  Cd Length: 200  Bit Score: 62.65  E-value: 1.63e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1161026737 149 ADVIMGILEIKNEMIESYLI--DNLsdfVCVCGEKSPLVGlEKISLYNFYAARHAVYHSDMFSSFTADSIDLfksstPYA 226
Cdd:cd08466    50 VDLVIDYVPFRDPSFKSELLfeDEL---VCVARKDHPRIQ-GSLSLEQYLAEKHVVLSLRRGNLSALDLLTE-----EVL 120

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1161026737 227 GRREIGYYSDSLFGVIGVVEKSDMVAILPGKIATYFRDVrrYNIKILRMPDEMifRRLPVYAY 289
Cdd:cd08466   121 PQRNIAYEVSSLLSMLAVVSQTDLIAIAPRWLADQYAEQ--LNLQILPLPFKT--KPIPLYMV 179
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
10-202 1.75e-19

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 86.07  E-value: 1.75e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1161026737  10 IDYNLIKVFDTVITEGNATRAARKLDVTPAAISQALLRLQNLYGEELFIRTRKGLVPSSKGKSLHQVFRQAIESIESTL- 88
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEa 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1161026737  89 -CDKTDAQESNELIVLGGDITENYYFPALLDTvLMNRY--IikHYAIKKTGEYSPASMLTHGYADVIMGILEIKNEMIES 165
Cdd:COG0583    81 eLRALRGGPRGTLRIGAPPSLARYLLPPLLAR-FRARHpgV--RLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVA 157

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1161026737 166 YLIDNlSDFVCVCGEKSPLVGLEKISLyNFYAARHAV 202
Cdd:COG0583   158 RPLGE-ERLVLVASPDHPLARRAPLVN-SLEALLAAV 192
leuO PRK09508
leucine transcriptional activator; Reviewed
 10-278 2.90e-16

leucine transcriptional activator; Reviewed


Pssm-ID: 181918 [Multi-domain]  Cd Length: 314  Bit Score: 78.14  E-value: 2.90e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1161026737  10 IDYNLIKVFDTVITEGNATRAARKLDVTPAAISQALLRLQNLYGEELFIRTRKGLVPSSKGKSLHQVFRQAIESIEstlc 89
Cdd:PRK09508   22 VDLNLLTVFDAVMQEQNITRAAHNLGMSQPAVSNAVARLKVMFNDELFVRYGRGIQPTARARQLFGPVRQALQLVQ---- 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1161026737  90 dktdaqesNELIVLGgditenyyFPALLDTVLMNRYIIkhyaikktgeySPASMLthgYADVIMGilEIKNE------MI 163
Cdd:PRK09508   98 --------NELPGSG--------FEPESSERVFNLCIC-----------SPLDIR---LTSQIYN--RIEQIapnihvVF 145

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1161026737 164 ESYLIDNLS--------DF----------------------VCVCGEKSPLVGlEKISLYNFYAARHAVYHSDMFSSFTA 213
Cdd:PRK09508  146 KSSLNQNIEhqlryqetEFvisyeefdrpeftsvplfkdelVLVASKNHPRIK-GPITEEQLYNEQHAVVSLDRFASFSQ 224

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1161026737 214 ---DSIDLfksstpyagRREIGYYSDSLFGVIGVVEKSDMVAILPGKIATYFRDvrRYNIKILRMPDE 278
Cdd:PRK09508  225 pwyDTVDK---------QASIAYQGTALSSVLNVVSQTHLVAIAPRWLAEEFAE--SLELQILPLPLK 281
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
13-71 1.15e-14

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 67.41  E-value: 1.15e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1161026737  13 NLIKVFDTVITEGNATRAARKLDVTPAAISQALLRLQNLYGEELFIRTRKGLVPSSKGK 71
Cdd:pfam00126   2 RQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PBP2_LeuO cd08466
The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an ...
 149-289 1.63e-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: 62.65  E-value: 1.63e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1161026737 149 ADVIMGILEIKNEMIESYLI--DNLsdfVCVCGEKSPLVGlEKISLYNFYAARHAVYHSDMFSSFTADSIDLfksstPYA 226
Cdd:cd08466    50 VDLVIDYVPFRDPSFKSELLfeDEL---VCVARKDHPRIQ-GSLSLEQYLAEKHVVLSLRRGNLSALDLLTE-----EVL 120

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1161026737 227 GRREIGYYSDSLFGVIGVVEKSDMVAILPGKIATYFRDVrrYNIKILRMPDEMifRRLPVYAY 289
Cdd:cd08466   121 PQRNIAYEVSSLLSMLAVVSQTDLIAIAPRWLADQYAEQ--LNLQILPLPFKT--KPIPLYMV 179
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 106-289 3.48e-09

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: 55.68  E-value: 3.48e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1161026737 106 DITENYYFPALLdtvlmnRYIIKHY-----AIKKTGEYSPASMLTHGYADVIMGILEIKNEMIESYLIdnLSD-FVCVCG 179
Cdd:cd08417     8 DYLEALLLPPLL------ARLRQEApgvrlRFVPLDRDDLEEALESGEIDLAIGVFPELPPGLRSQPL--FEDrFVCVAR 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1161026737 180 EKSPLVGlEKISLYNFYAARHA-VYHSDMFSSFTADSIDLFKsstpyaGRREIGYYSDSLFGVIGVVEKSDMVAILPGKI 258
Cdd:cd08417    80 KDHPLAG-GPLTLEDYLAAPHVlVSPRGRGHGLVDDALAELG------LSRRVALTVPHFLAAPALVAGTDLIATVPRRL 152

                         170       180       190
                  ....*....|....*....|....*....|.
gi 1161026737 259 ATYFRdvRRYNIKILRMPDEMifRRLPVYAY 289
Cdd:cd08417   153 AEALA--ERLGLRVLPLPFEL--PPFTVSLY 179
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
10-202 1.75e-19

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 86.07  E-value: 1.75e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1161026737  10 IDYNLIKVFDTVITEGNATRAARKLDVTPAAISQALLRLQNLYGEELFIRTRKGLVPSSKGKSLHQVFRQAIESIESTL- 88
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEa 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1161026737  89 -CDKTDAQESNELIVLGGDITENYYFPALLDTvLMNRY--IikHYAIKKTGEYSPASMLTHGYADVIMGILEIKNEMIES 165
Cdd:COG0583    81 eLRALRGGPRGTLRIGAPPSLARYLLPPLLAR-FRARHpgV--RLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVA 157

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1161026737 166 YLIDNlSDFVCVCGEKSPLVGLEKISLyNFYAARHAV 202
Cdd:COG0583   158 RPLGE-ERLVLVASPDHPLARRAPLVN-SLEALLAAV 192
leuO PRK09508
leucine transcriptional activator; Reviewed
 10-278 2.90e-16

leucine transcriptional activator; Reviewed


Pssm-ID: 181918 [Multi-domain]  Cd Length: 314  Bit Score: 78.14  E-value: 2.90e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1161026737  10 IDYNLIKVFDTVITEGNATRAARKLDVTPAAISQALLRLQNLYGEELFIRTRKGLVPSSKGKSLHQVFRQAIESIEstlc 89
Cdd:PRK09508   22 VDLNLLTVFDAVMQEQNITRAAHNLGMSQPAVSNAVARLKVMFNDELFVRYGRGIQPTARARQLFGPVRQALQLVQ---- 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1161026737  90 dktdaqesNELIVLGgditenyyFPALLDTVLMNRYIIkhyaikktgeySPASMLthgYADVIMGilEIKNE------MI 163
Cdd:PRK09508   98 --------NELPGSG--------FEPESSERVFNLCIC-----------SPLDIR---LTSQIYN--RIEQIapnihvVF 145

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1161026737 164 ESYLIDNLS--------DF----------------------VCVCGEKSPLVGlEKISLYNFYAARHAVYHSDMFSSFTA 213
Cdd:PRK09508  146 KSSLNQNIEhqlryqetEFvisyeefdrpeftsvplfkdelVLVASKNHPRIK-GPITEEQLYNEQHAVVSLDRFASFSQ 224

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1161026737 214 ---DSIDLfksstpyagRREIGYYSDSLFGVIGVVEKSDMVAILPGKIATYFRDvrRYNIKILRMPDE 278
Cdd:PRK09508  225 pwyDTVDK---------QASIAYQGTALSSVLNVVSQTHLVAIAPRWLAEEFAE--SLELQILPLPLK 281
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
13-71 1.15e-14

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 67.41  E-value: 1.15e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1161026737  13 NLIKVFDTVITEGNATRAARKLDVTPAAISQALLRLQNLYGEELFIRTRKGLVPSSKGK 71
Cdd:pfam00126   2 RQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK11482 PRK11482
DNA-binding transcriptional regulator;
8-264 1.42e-12

DNA-binding transcriptional regulator;


Pssm-ID: 183159 [Multi-domain]  Cd Length: 317  Bit Score: 67.44  E-value: 1.42e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1161026737   8 KKIDYNLIKVFDTVITEGNATRAARKLDVTPAAISQALLRLQNLYGEELFIRTRKGLVPSSKGKSLHQVFRQAIESIEST 87
Cdd:PRK11482   27 RNIDLNLLTIFEAVYVHKGIVNAAKILNLTPSAISQSIQKLRVIFPDPLFIRKGQGVTPTAYATHLHEYISQGLESILGA 106

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1161026737  88 LcDKTDAQESNELIVLGGDitenyyfPALLDTVLMNRY--IIKHYA---IKKTGEYSPASMLTHGYADVIMGILEIKNEM 162
Cdd:PRK11482  107 L-DITGSYDKQRTITIATT-------PSVGALVMPVIYqaIKTHYPqllLRNIPISDAENQLSQFQTDLIIDTHSCSNRT 178

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1161026737 163 IESYLI--DNLsdfVCVCGEKSPLVGLEKISlYNFYAARHAVYHSD--MFSSFTADSIDLFksstpyaGRREIGYYSDSL 238
Cdd:PRK11482  179 IQHHVLftDNV---VLVCRQGHPLLSLEDDE-ETLDNAEHTLLLPEgqNFSGLRQRLQEMF-------PDRQISFSSYNI 247

                         250       260
                  ....*....|....*....|....*.
gi 1161026737 239 FGVIGVVEKSDMVAILPGKIATYFRD 264
Cdd:PRK11482  248 LTIAALIASSDMLGIMPSRFYNLFSR 273
PBP2_LeuO cd08466
The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an ...
 149-289 1.63e-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: 62.65  E-value: 1.63e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1161026737 149 ADVIMGILEIKNEMIESYLI--DNLsdfVCVCGEKSPLVGlEKISLYNFYAARHAVYHSDMFSSFTADSIDLfksstPYA 226
Cdd:cd08466    50 VDLVIDYVPFRDPSFKSELLfeDEL---VCVARKDHPRIQ-GSLSLEQYLAEKHVVLSLRRGNLSALDLLTE-----EVL 120

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1161026737 227 GRREIGYYSDSLFGVIGVVEKSDMVAILPGKIATYFRDVrrYNIKILRMPDEMifRRLPVYAY 289
Cdd:cd08466   121 PQRNIAYEVSSLLSMLAVVSQTDLIAIAPRWLADQYAEQ--LNLQILPLPFKT--KPIPLYMV 179
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 106-289 3.48e-09

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: 55.68  E-value: 3.48e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1161026737 106 DITENYYFPALLdtvlmnRYIIKHY-----AIKKTGEYSPASMLTHGYADVIMGILEIKNEMIESYLIdnLSD-FVCVCG 179
Cdd:cd08417     8 DYLEALLLPPLL------ARLRQEApgvrlRFVPLDRDDLEEALESGEIDLAIGVFPELPPGLRSQPL--FEDrFVCVAR 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1161026737 180 EKSPLVGlEKISLYNFYAARHA-VYHSDMFSSFTADSIDLFKsstpyaGRREIGYYSDSLFGVIGVVEKSDMVAILPGKI 258
Cdd:cd08417    80 KDHPLAG-GPLTLEDYLAAPHVlVSPRGRGHGLVDDALAELG------LSRRVALTVPHFLAAPALVAGTDLIATVPRRL 152

                         170       180       190
                  ....*....|....*....|....*....|.
gi 1161026737 259 ATYFRdvRRYNIKILRMPDEMifRRLPVYAY 289
Cdd:cd08417   153 AEALA--ERLGLRVLPLPFEL--PPFTVSLY 179
PRK10216 PRK10216
HTH-type transcriptional regulator YidZ;
5-75 1.82e-08

HTH-type transcriptional regulator YidZ;


Pssm-ID: 182312 [Multi-domain]  Cd Length: 319  Bit Score: 54.83  E-value: 1.82e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1161026737   5 KNAKKIDYNLIKVFDTVITEGNATRAARKLDVTPAAISQALLRLQNLYGEELFIRTRKGLVPSSKGKSLHQ 75
Cdd:PRK10216    3 KSLTTLDLNLLLCLQLLMQERSVTKAAKRMNVTPSAVSKSLAKLRAWFDDPLFVNTPLGLSPTPLMVSMEQ 73
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
10-79 4.54e-08

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 53.44  E-value: 4.54e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1161026737  10 IDYNLIKVFDTVITEGNATRAARKLDVTPAAISQALLRLQNLYGEELFIRTRKgLVPSSKGKSLHQVFRQ 79
Cdd:PRK13348    2 LDYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRGRP-CRPTPAGQRLLRHLRQ 70
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
10-79 5.28e-07

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 50.54  E-value: 5.28e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1161026737  10 IDYNLIKVFDTVITEGNATRAARKLDVTPAAISQALLRLQNLYGEELFIRTRKgLVPSSKGKSLHQVFRQ 79
Cdd:PRK03635    2 LDYKQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVRTQP-CRPTEAGQRLLRHARQ 70
PRK10341 PRK10341
transcriptional regulator TdcA;
17-307 6.01e-06

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 47.16  E-value: 6.01e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1161026737  17 VFDTVITEGNATRAARKLDVTPAAISQALLRLQNLYGEELFIRTRKGLVPSSKGkslhQVFRQAIESIESTLcdKTDAQE 96
Cdd:PRK10341   14 VFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAG----QVLLSRSESITREM--KNMVNE 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1161026737  97 SNELivLGGDITE-NYYFPALLDTVLMNRYIIKHYAIKKTGEYS----------PAsmLTHGYADVIMGILeiKNEM-IE 164
Cdd:PRK10341   88 INGM--SSEAVVDvSFGFPSLIGFTFMSDMINKFKEVFPKAQVSmyeaqlssflPA--IRDGRLDFAIGTL--SNEMkLQ 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1161026737 165 SYLIDNL--SDFVCVCGEKSPLVGLEkislyNFYAARHAV---------YHSDMFSSFTADSIDlfksstpyagrREIGY 233
Cdd:PRK10341  162 DLHVEPLfeSEFVLVASKSRTCTGTT-----TLESLKNEQwvlpqtnmgYYSELLTTLQRNGIS-----------IENIV 225

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1161026737 234 YSDSLFGVIGVVEKSDMVAILPGKIATYFRDVRrynIKILRMPDEmifrrLPVYAYLATNSTHYKnVKKLISTF 307
Cdd:PRK10341  226 KTDSVVTIYNLVLNADFLTVIPCDMTSPFGSNQ---FITIPIEET-----LPVAQYAAVWSKNYR-IKKAASVL 290
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 15-73 1.66e-05

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 45.75  E-value: 1.66e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1161026737  15 IKVFDTVITEGNATRAARKLDVTPAAISQALLRLQNLYGEELFIRTRKGLVPSSKGKSL 73
Cdd:PRK11013    9 IEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRL 67
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 6-74 9.37e-05

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 43.52  E-value: 9.37e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1161026737   6 NAKKIDYnLIKVFDTviteGNATRAARKLDVTPAAISQALLRLQNLYGEELFIRTRKGLVPSSKGKSLH 74
Cdd:PRK11233    2 NFRRLKY-FVKIVDI----GSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILY 65
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
10-86 2.18e-04

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 42.49  E-value: 2.18e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1161026737  10 IDYNLIKVFDTVITEGNATRAARKLDVTPAAISQALLRLQNLYGEELFIRTRKGLVPSSKGKSLHQVFRQAIESIES 86
Cdd:PRK10094    2 FDPETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLES 78
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 15-117 2.71e-04

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 41.98  E-value: 2.71e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1161026737  15 IKVFDTVITEGNATRAARKLDVTPAAISQALLRLQNLYGEELFIRTRKGLVPSSKGKSLH----QVFRQAIEsIESTLcd 90
Cdd:PRK10837    8 LEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYpralALLEQAVE-IEQLF-- 84

                          90       100
                  ....*....|....*....|....*...
gi 1161026737  91 ktdaQESNELIVLGGDIT-ENYYFPALL 117
Cdd:PRK10837   85 ----REDNGALRIYASSTiGNYILPAMI 108
PBP2_NodD cd08462
The C-terminal substsrate binding domain of NodD family of LysR-type transcriptional ...
 173-276 3.26e-04

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: 41.08  E-value: 3.26e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1161026737 173 DFVCVCGEKSPLVGlEKISLYNFYAARHAV--YHSDMFSSFTadsiDLFKSSTPYAGRREIGYYSdslFGVI-GVVEKSD 249
Cdd:cd08462    72 EFVCVVWADNPLVG-GELTAEQYFSAGHVVvrFGRNRRPSFE----DWFLNEYGLKRRVEVVTPS---FSSIpPLLVGTN 143

                          90       100
                  ....*....|....*....|....*..
gi 1161026737 250 MVAILPGKIATYFrdVRRYNIKILRMP 276
Cdd:cd08462   144 RIATLHRRLAEQF--ARRLPLRILPLP 168
PRK09986 PRK09986
LysR family transcriptional regulator;
9-88 4.24e-04

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 41.63  E-value: 4.24e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1161026737   9 KIDYNLIKVFDTVITEGNATRAARKLDVTPAAISQALLRLQNLYGEELFIRTRKGLVPSSKGKSLHQVFRQAIESIESTL 88
Cdd:PRK09986    6 RIDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSL 85
PBP2_DntR_NahR_LinR_like cd08459
The C-terminal substrate binding domain of LysR-type transcriptional regulators that are ...
 173-276 6.47e-04

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: 40.25  E-value: 6.47e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1161026737 173 DFVCVCGEKSPLVGlEKISLYNFYAARHAVYHSDmfSSFTADSIDLFKSstpyAG-RREIgyysdSL----FGVIG-VVE 246
Cdd:cd08459    73 RYVCLVRKDHPRIG-STLTLEQFLAARHVVVSAS--GTGHGLVEQALRE----AGiRRRI-----ALrvphFLALPlIVA 140

                          90       100       110
                  ....*....|....*....|....*....|
gi 1161026737 247 KSDMVAILPGKIATYFRdvRRYNIKILRMP 276
Cdd:cd08459   141 QTDLVATVPERLARLFA--RAGGLRIVPLP 168
PRK09791 PRK09791
LysR family transcriptional regulator;
7-75 2.69e-03

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 38.97  E-value: 2.69e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1161026737   7 AKKIDYNLIKVFDTVITEGNATRAARKLDVTPAAISQALLRLQNLYGEELFIRTRKGLVPSSKGKSLHQ 75
Cdd:PRK09791    2 AFQVKIHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQ 70
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 2-59 6.03e-03

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 38.09  E-value: 6.03e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1161026737   2 RPIKNakkIDYNLIKVFDTViTEGNaTRAARKLDV--TPAAISQALLRLQNLYGEELFIR 59
Cdd:PRK15092    6 RPIIN---LDLDLLRTFVAV-ADLN-TFAAAAAAVcrTQSAVSQQMQRLEQLVGKELFAR 60
 
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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