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Conserved domains on  [gi|740864843|ref|WP_038650094|]
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LysR family transcriptional regulator [Roseibacterium elongatum]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 11426483)

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 (PBP2) fold proteins

CATH:  3.40.190.10
Gene Ontology:  GO:0003700|GO:0003677|GO:0006355
PubMed:  19047729|8257110|15808743
SCOP:  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];
9-277 9.70e-38

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 134.99  E-value: 9.70e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740864843   9 LTLRGLEVFEALARTGSVAATAAELGMSAPAVSQQMKNLAQVLGVDLIDHSRRPMIPTPAGRLFLPRAEAALSALRSGQR 88
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740864843  89 DLTALDLSGLSALSLGVIEDFENEVTPRLAARLAEALSQCAFRLRTGASHNLVAGVVARDLDMAMCASPGAHPgGTTAYP 168
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDP-GLVARP 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740864843 169 ILTDPYIVAVPQGtdmtggltglsHLVFLRRDLTqvmgrqietyltrvqldlpqrfemDSNQSISALVASGTGWTItTPL 248
Cdd:COG0583  160 LGEERLVLVASPD-----------HPLARRAPLV------------------------NSLEALLAAVAAGLGIAL-LPR 203

                        250       260
                 ....*....|....*....|....*....
gi 740864843 249 SLLRAGRFAGGIDAHPLPDADIARDIVLL 277
Cdd:COG0583  204 FLAADELAAGRLVALPLPDPPPPRPLYLV 232
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
9-277 9.70e-38

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 134.99  E-value: 9.70e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740864843   9 LTLRGLEVFEALARTGSVAATAAELGMSAPAVSQQMKNLAQVLGVDLIDHSRRPMIPTPAGRLFLPRAEAALSALRSGQR 88
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740864843  89 DLTALDLSGLSALSLGVIEDFENEVTPRLAARLAEALSQCAFRLRTGASHNLVAGVVARDLDMAMCASPGAHPgGTTAYP 168
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDP-GLVARP 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740864843 169 ILTDPYIVAVPQGtdmtggltglsHLVFLRRDLTqvmgrqietyltrvqldlpqrfemDSNQSISALVASGTGWTItTPL 248
Cdd:COG0583  160 LGEERLVLVASPD-----------HPLARRAPLV------------------------NSLEALLAAVAAGLGIAL-LPR 203

                        250       260
                 ....*....|....*....|....*....
gi 740864843 249 SLLRAGRFAGGIDAHPLPDADIARDIVLL 277
Cdd:COG0583  204 FLAADELAAGRLVALPLPDPPPPRPLYLV 232
PBP2_LTTR_like_2 cd08427
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 101-300 1.60e-19

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


Pssm-ID: 176118 [Multi-domain]  Cd Length: 195  Bit Score: 84.55  E-value: 1.60e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740864843 101 LSLGVIEDFENEVTPRLAARLAEALSQCAFRLRTGASHNLVAGVVARDLDMAMCASP-GAHPGGTTAYPILTDPYIVAVP 179
Cdd:cd08427    2 LRLGAIATVLTGLLPRALARLRRRHPDLEVHIVPGLSAELLARVDAGELDAAIVVEPpFPLPKDLVWTPLVREPLVLIAP 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740864843 180 QGTDMTGGLTGLSHLVFLRRDLTQVMGRQIETYLTRVQLDLPQRFEMDSNQSISALVASGTGWTItTPLSlLRAGRFAGG 259
Cdd:cd08427   82 AELAGDDPRELLATQPFIRYDRSAWGGRLVDRFLRRQGIRVREVMELDSLEAIAAMVAQGLGVAI-VPDI-AVPLPAGPR 159

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 740864843 260 IDAHPLPDADIARDIVLLAGADWSGaipaqiASLARELIEA 300
Cdd:cd08427  160 VRVLPLGDPAFSRRVGLLWRRSSPR------SRLIQALLEA 194
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
11-70 1.97e-17

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 75.11  E-value: 1.97e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 740864843   11 LRGLEVFEALARTGSVAATAAELGMSAPAVSQQMKNLAQVLGVDLIDHSRRPMIPTPAGR 70
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
rbcR CHL00180
LysR transcriptional regulator; Provisional
 10-241 3.14e-12

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 66.20  E-value: 3.14e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740864843  10 TLRGLEVFEALARTGSVAATAAELGMSAPAVSQQMKNLAQVLGVDLIDHSRRPMIPTPAGRLFLPRAEAALSALRSGQRD 89
Cdd:CHL00180   6 TLDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRA 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740864843  90 LtaLDLSGLSA--LSLGVIEDFENEVTPRLAARLAEALSQCAFRLRTGASHNLVAGVVARDLDMAMCAspGAHPggTTAY 167
Cdd:CHL00180  86 L--EDLKNLQRgtLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVG--GEVP--TELK 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740864843 168 PILT------DPYIVAVPQG---TDMTGGLT-GLSHLVFLRRDLTQVMGRQIETYLTRVQLDLPQ---RFEMDSNQSISA 234
Cdd:CHL00180 160 KILEitpyveDELALIIPKShpfAKLKKIQKeDLYRLNFITLDSNSTIRKVIDNILIQNGIDSKRfkiEMELNSIEAIKN 239


                 ....*..
gi 740864843 235 LVASGTG 241
Cdd:CHL00180 240 AVQSGLG 246
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
9-277 9.70e-38

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 134.99  E-value: 9.70e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740864843   9 LTLRGLEVFEALARTGSVAATAAELGMSAPAVSQQMKNLAQVLGVDLIDHSRRPMIPTPAGRLFLPRAEAALSALRSGQR 88
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740864843  89 DLTALDLSGLSALSLGVIEDFENEVTPRLAARLAEALSQCAFRLRTGASHNLVAGVVARDLDMAMCASPGAHPgGTTAYP 168
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDP-GLVARP 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740864843 169 ILTDPYIVAVPQGtdmtggltglsHLVFLRRDLTqvmgrqietyltrvqldlpqrfemDSNQSISALVASGTGWTItTPL 248
Cdd:COG0583  160 LGEERLVLVASPD-----------HPLARRAPLV------------------------NSLEALLAAVAAGLGIAL-LPR 203

                        250       260
                 ....*....|....*....|....*....
gi 740864843 249 SLLRAGRFAGGIDAHPLPDADIARDIVLL 277
Cdd:COG0583  204 FLAADELAAGRLVALPLPDPPPPRPLYLV 232
PBP2_LTTR_like_2 cd08427
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 101-300 1.60e-19

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


Pssm-ID: 176118 [Multi-domain]  Cd Length: 195  Bit Score: 84.55  E-value: 1.60e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740864843 101 LSLGVIEDFENEVTPRLAARLAEALSQCAFRLRTGASHNLVAGVVARDLDMAMCASP-GAHPGGTTAYPILTDPYIVAVP 179
Cdd:cd08427    2 LRLGAIATVLTGLLPRALARLRRRHPDLEVHIVPGLSAELLARVDAGELDAAIVVEPpFPLPKDLVWTPLVREPLVLIAP 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740864843 180 QGTDMTGGLTGLSHLVFLRRDLTQVMGRQIETYLTRVQLDLPQRFEMDSNQSISALVASGTGWTItTPLSlLRAGRFAGG 259
Cdd:cd08427   82 AELAGDDPRELLATQPFIRYDRSAWGGRLVDRFLRRQGIRVREVMELDSLEAIAAMVAQGLGVAI-VPDI-AVPLPAGPR 159

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 740864843 260 IDAHPLPDADIARDIVLLAGADWSGaipaqiASLARELIEA 300
Cdd:cd08427  160 VRVLPLGDPAFSRRVGLLWRRSSPR------SRLIQALLEA 194
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
11-70 1.97e-17

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 75.11  E-value: 1.97e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 740864843   11 LRGLEVFEALARTGSVAATAAELGMSAPAVSQQMKNLAQVLGVDLIDHSRRPMIPTPAGR 70
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 101-277 7.65e-15

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: 71.94  E-value: 7.65e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740864843  101 LSLGVIEDFENEVTPRLAARLAEALSQCAFRLRTGASHNLVAGVVARDLDMAMCASPGAHPgGTTAYPILTDPYIVAVPQ 180
Cdd:pfam03466   4 LRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDP-GLEARPLGEEPLVLVAPP 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740864843  181 GTDMTGG----LTGLSHLVFLRRDLTQVMGRQIETYLTRVQLDLPQRFEMDSNQSISALVASGTGWTItTPLSLLRAGRF 256
Cdd:pfam03466  83 DHPLARGepvsLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIAL-LPRSAVARELA 161

                         170       180
                  ....*....|....*....|.
gi 740864843  257 AGGIDAHPLPDADIARDIVLL 277
Cdd:pfam03466 162 DGRLVALPLPEPPLPRELYLV 182
rbcR CHL00180
LysR transcriptional regulator; Provisional
 10-241 3.14e-12

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 66.20  E-value: 3.14e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740864843  10 TLRGLEVFEALARTGSVAATAAELGMSAPAVSQQMKNLAQVLGVDLIDHSRRPMIPTPAGRLFLPRAEAALSALRSGQRD 89
Cdd:CHL00180   6 TLDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRA 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740864843  90 LtaLDLSGLSA--LSLGVIEDFENEVTPRLAARLAEALSQCAFRLRTGASHNLVAGVVARDLDMAMCAspGAHPggTTAY 167
Cdd:CHL00180  86 L--EDLKNLQRgtLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVG--GEVP--TELK 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740864843 168 PILT------DPYIVAVPQG---TDMTGGLT-GLSHLVFLRRDLTQVMGRQIETYLTRVQLDLPQ---RFEMDSNQSISA 234
Cdd:CHL00180 160 KILEitpyveDELALIIPKShpfAKLKKIQKeDLYRLNFITLDSNSTIRKVIDNILIQNGIDSKRfkiEMELNSIEAIKN 239


                 ....*..
gi 740864843 235 LVASGTG 241
Cdd:CHL00180 240 AVQSGLG 246
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 101-276 4.18e-12

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: 64.16  E-value: 4.18e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740864843 101 LSLGVIEDFENEVTPRLAARLAEALSQCAFRLRTGASHNLVAGVVARDLDMAMCASPGAHPGGTTaYPILTDPYIVAVPQ 180
Cdd:cd05466    2 LRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLES-EPLFEEPLVLVVPP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740864843 181 GTDMTGG----LTGLSHLVFLRRDLTQVMGRQIETYLTRVQLDLPQRFEMDSNQSISALVASGTGWTItTPLSLLRAGRf 256
Cdd:cd05466   81 DHPLAKRksvtLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIAL-LPESAVEELA- 158

                        170       180
                 ....*....|....*....|
gi 740864843 257 AGGIDAHPLPDADIARDIVL 276
Cdd:cd05466  159 DGGLVVLPLEDPPLSRTIGL 178
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 9-194 5.34e-10

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 59.32  E-value: 5.34e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740864843   9 LTLRGLEVFEALARTGSVAATAAELGMSAPAVSQQMKNLAQVLGVDLIDHSRRPMIPTPAGRLFLPRA----EAALSALR 84
Cdd:PRK10837   3 ITLRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRAlallEQAVEIEQ 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740864843  85 SGQRDLTALDLSGLSALSlgviedfeNEVTPRLAARLAEALSQCAFRLRTGASHNLVAGVVARDLDMAMCASPGAHPgGT 164
Cdd:PRK10837  83 LFREDNGALRIYASSTIG--------NYILPAMIARYRRDYPQLPLELSVGNSQDVINAVLDFRVDIGLIEGPCHSP-EL 153

                        170       180       190
                 ....*....|....*....|....*....|
gi 740864843 165 TAYPILTDPYIVAVPQGTDMTGGLTGLSHL 194
Cdd:PRK10837 154 ISEPWLEDELVVFAAPDSPLARGPVTLEQL 183
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 11-103 5.04e-09

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 56.50  E-value: 5.04e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740864843  11 LRGLEVFEALARTGSVAATAAELGMSAPAVSQQMKNLAQVLGVDLIDHSRRPMIPTPAGRLFLPRAEAALSALRSGQRDL 90
Cdd:PRK11242   3 LRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRRAI 82

                         90
                 ....*....|...
gi 740864843  91 TalDLSGLSALSL 103
Cdd:PRK11242  83 H--DVADLSRGSL 93
PRK10341 PRK10341
transcriptional regulator TdcA;
14-135 4.02e-08

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 53.71  E-value: 4.02e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740864843  14 LEVFEALARTGSVAATAAELGMSAPAVSQQMKNLAQVLGVDLIDHSRRPMIPTPAGRLFLPRAEAALSALRSGQRDLTAL 93
Cdd:PRK10341  12 LVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEINGM 91

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 740864843  94 DLSGLSALSLG------------VIEDFEnEVTPRLAARLAEA-LSQCAFRLRTG 135
Cdd:PRK10341  92 SSEAVVDVSFGfpsligftfmsdMINKFK-EVFPKAQVSMYEAqLSSFLPAIRDG 145
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 113-276 5.48e-08

The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) protein, contains the type 2 periplasmic binding fold; The NAC is a LysR-type transcription regulator that activates expression of operons such as hut (histidine utilization) and ure (urea utilization), allowing use of non-preferred (poor) nitrogen sources, and represses expression of operons, such as glutamate dehydrogenase (gdh), allowing assimilation of the preferred nitrogen source. The expression of the nac gene is fully dependent on the nitrogen regulatory system (NTR) and the sigma54-containing RNA polymerase (sigma54-RNAP). In response to nitrogen starvation, NTR system activates the expression of nac, and NAC activates the expression of hut, ure, and put (proline utilization). NAC is not involved in the transcription of Sigma70-RNAP operons such as glnA, which directly respond by the NTR system, but activates the transcription of sigma70-RNAP dependent operons such as hut. Hence, NAC allows the coupling of sigma70-RNAP dependent operons to the sigma54-RNAP dependent NTR system. This substrate-binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176124  Cd Length: 198  Bit Score: 52.21  E-value: 5.48e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740864843 113 VTPRLAARLAEALSQCAFRLRTGASHNLVAGVVARDLDMAMCASPGAHPGGTTAyPILTDP-YIVAVPQGTDMTGGLTGL 191
Cdd:cd08433   14 LAVPLLRAVRRRYPGIRLRIVEGLSGHLLEWLLNGRLDLALLYGPPPIPGLSTE-PLLEEDlFLVGPADAPLPRGAPVPL 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740864843 192 SHLVFLRRDLT---QVMGRQIETYLTRVQLDLPQRFEMDSNQSISALVASGTGWTItTPLSLLRAGRFAGGIDAHPLPDA 268
Cdd:cd08433   93 AELARLPLILPsrgHGLRRLVDEAAARAGLTLNVVVEIDSVATLKALVAAGLGYTI-LPASAVAAEVAAGRLVAAPIVDP 171


                 ....*...
gi 740864843 269 DIARDIVL 276
Cdd:cd08433  172 ALTRTLSL 179
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
11-149 6.76e-07

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 50.14  E-value: 6.76e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740864843  11 LRGLEVFEALARTGSVAATAAELGMSAPAVSQQMKNLAQVLGVDLIDHSRRPMIPTPAGRLFLPRAEAALSALRSGQRDL 90
Cdd:PRK10632   4 LKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQL 83

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 740864843  91 TALDLSGLSALSLGVIEDFENEVTPRLAARLaealsqcaFRLRTGASHNLVAGVVARDL 149
Cdd:PRK10632  84 YAFNNTPIGTLRIGCSSTMAQNVLAGLTAKM--------LKEYPGLSVNLVTGIPAPDL 134
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 14-76 8.00e-07

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 49.94  E-value: 8.00e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 740864843  14 LEVFEALARTGSVAATAAELGMSAPAVSQQMKNLAQVLGVDLIDHSRRPMIPTPAGRLFLPRA 76
Cdd:PRK11074   7 LEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEA 69
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
1-72 8.62e-07

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 49.62  E-value: 8.62e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 740864843   1 MPAPLHKGLTLRGLEVFEALARTGSVAATAAELGMSAPAVSQQMKNLAQVLGVDLIDHSRRPMIPTPAG-RLF 72
Cdd:PRK10086   6 MRNRLLNGWQLSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGkRVF 78
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 11-94 1.01e-06

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 49.46  E-value: 1.01e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740864843  11 LRGLEVFEALARTGSVAATAAELGMSAPAVSQQMKNLAQVLGVDL-IDHSRRPMIpTPAGRLFLPRAEAALSALRSGQRD 89
Cdd:PRK11139   8 LNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLfRRRNRSLLL-TEEGQRYFLDIREIFDQLAEATRK 86


                 ....*
gi 740864843  90 LTALD 94
Cdd:PRK11139  87 LRARS 91
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 101-276 1.75e-06

The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; This CD includes the C-terminal substrate binding domain of LTTRs involved in degradation of aromatic compounds, such as CbnR, BenM, CatM, ClcR and TfdR, as well as that of other transcriptional regulators clustered together in phylogenetic trees, including XapR, HcaR, MprR, IlvR, BudR, AlsR, LysR, and OccR. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 176106 [Multi-domain]  Cd Length: 197  Bit Score: 47.89  E-value: 1.75e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740864843 101 LSLGVIEDFENEVTPRLAARLAEALSQCAFRLRTGASHNLVAGVVARDLDMAMCASPGAHPgGTTAYPILTDPYIVAVPQ 180
Cdd:cd08414    2 LRIGFVGSALYGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPPPDPP-GLASRPLLREPLVVALPA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740864843 181 GTDMTG----GLTGLSH--LVFLRRDLTQVMGRQIETYLTRVQLDLPQRFEMDSNQSISALVASGTGWTItTPLSLLRAG 254
Cdd:cd08414   81 DHPLAAresvSLADLADepFVLFPREPGPGLYDQILALCRRAGFTPRIVQEASDLQTLLALVAAGLGVAL-VPASVARLQ 159

                        170       180
                 ....*....|....*....|..
gi 740864843 255 RfaGGIDAHPLPDADIARDIVL 276
Cdd:cd08414  160 R--PGVVYRPLADPPPRSELAL 179
PRK09791 PRK09791
LysR family transcriptional regulator;
1-90 3.52e-06

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 47.83  E-value: 3.52e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740864843   1 MPAPLhkglTLRGLEVFEALARTGSVAATAAELGMSAPAVSQQMKNLAQVLGVDLIDHSRRPMIPTPAGRLFLPRAEAAL 80
Cdd:PRK09791   1 MAFQV----KIHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLIL 76

                         90
                 ....*....|
gi 740864843  81 SALRSGQRDL 90
Cdd:PRK09791  77 EELRAAQEDI 86
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
12-78 1.04e-05

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 46.50  E-value: 1.04e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 740864843  12 RGLEVFEALARTGSVAATAAELGMSAPAVSQQMKNLAQVLGVDLIDHSrRPMIPTPAGRLFLPRAEA 78
Cdd:PRK13348   5 KQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRG-RPCRPTPAGQRLLRHLRQ 70
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 8-84 1.61e-05

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 45.75  E-value: 1.61e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740864843   8 GLTLRGLEVFEALARTGSVAATAAELGMSAPAVSQQMKNLAQVLGVDLIDHSRRPMIPTPAG-RLF---------LPRAE 77
Cdd:PRK11013   3 AVSLRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGlRLFeevqrsyygLDRIV 82


                 ....*..
gi 740864843  78 AALSALR 84
Cdd:PRK11013  83 SAAESLR 89
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 115-252 1.71e-05

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


Pssm-ID: 176125 [Multi-domain]  Cd Length: 195  Bit Score: 44.83  E-value: 1.71e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740864843 115 PRLAARLAEALSQCAFRLRTGASHNLVAGVVARDLDMAMCaSPGAHPGGTTAYPILTDPYIVAVP------QGTDMTggL 188
Cdd:cd08434   16 PDLIRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLALC-SPVPDEPDIEWIPLFTEELVLVVPkdhplaGRDSVD--L 92

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 740864843 189 TGLSH--LVFLRRDLtqVMGRQIETYLTRVQLDLPQRFEMDSNQSISALVASGTGWTITTPLSLLR 252
Cdd:cd08434   93 AELADepFVLLSPGF--GLRPIVDELCAAAGFTPKIAFEGEEDSTIAGLVAAGLGVAILPEMTLLN 156
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
9-80 2.06e-05

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 45.39  E-value: 2.06e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 740864843   9 LTLRGLEVFEALARTGSVAATAAELGMSAPAVSQQMKNLAQVLGVDLIDHSRRPMIPTPAGRLFLPRAEAAL 80
Cdd:PRK15421   2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVL 73
PRK12680 PRK12680
LysR family transcriptional regulator;
9-181 7.97e-05

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 43.84  E-value: 7.97e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740864843   9 LTLRGLEVFEALARTG-SVAATAAELGMSAPAVSQQMKNLAQVLGVDLIDHSRRPM-IPTPAGRLFLPRAEAALSALRSG 86
Cdd:PRK12680   1 MTLTQLRYLVAIADAElNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLeSVTPAGVEVIERARAVLSEANNI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740864843  87 QRDLTALDLSGLSALSLGVIEDFENEVTPRLAARLAEALSQCAFRLRTGASHNLVAGVVARDLDMAMCASPGAHPGGTTA 166
Cdd:PRK12680  81 RTYAANQRRESQGQLTLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVSTAGGEPSAGIA 160

                        170
                 ....*....|....*
gi 740864843 167 YPILTDPYIVAVPQG 181
Cdd:PRK12680 161 VPLYRWRRLVVVPRG 175
PBP2_YofA_SoxR_like cd08442
The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, ...
 115-268 1.17e-04

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


Pssm-ID: 176133  Cd Length: 193  Bit Score: 42.21  E-value: 1.17e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740864843 115 PRLAARLAEALSQCAFRLRTGASHNLVAGVVARDLDMAMCASPGAHPgGTTAYPILTDPYIVAVPQG-------TDMTGg 187
Cdd:cd08442   16 PPLLAAYHARYPKVDLSLSTGTTGALIQAVLEGRLDGAFVAGPVEHP-RLEQEPVFQEELVLVSPKGhppvsraEDLAG- 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740864843 188 ltglSHLVFLR-----RDLtqvmgrqIETYLtRVQLDLPQR-FEMDSNQSISALVASGTGWTItTPLSLLRAGRFAGGID 261
Cdd:cd08442   94 ----STLLAFRagcsyRRR-------LEDWL-AEEGVSPGKiMEFGSYHAILGCVAAGMGIAL-LPRSVLDSLQGRGSVS 160


                 ....*..
gi 740864843 262 AHPLPDA 268
Cdd:cd08442  161 IHPLPEP 167
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 93-265 1.37e-04

The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the catabolism of opines and that of related regulators, contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulators, OccR and NocR, involved in the catabolism of opines and that of LysR for lysine biosynthesis which clustered together in phylogenetic trees. Opines, such as octopine and nopaline, are low molecular weight compounds found in plant crown gall tumors that are produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. NocR and OccR belong to the family of LysR-type transcriptional regulators that positively regulates the catabolism of nopaline and octopine, respectively. Both nopaline and octopalin are arginine derivatives. In Agrobacterium tumefaciens, NocR regulates expression of the divergently transcribed nocB and nocR genes of the nopaline catabolism (noc) region. OccR protein activates the occQ operon of the Ti plasmid in response to octopine. This operon encodes proteins required for the uptake and catabolism of octopine. The occ operon also encodes the TraR protein, which is a quorum-sensing transcriptional regulator of the Ti plasmid tra regulon. LysR is the transcriptional activator of lysA gene encoding diaminopimelate decarboxylase, an enzyme that catalyses the decarboxylation of diaminopimelate to produce lysine. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176107 [Multi-domain]  Cd Length: 196  Bit Score: 42.16  E-value: 1.37e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740864843  93 LDLSGLSALSLGVIedfenevtPRLAARLAEALSQCAFRLRTGASHNLVAGVVARDLDMAMCASPGAHPGGTTAyPILTD 172
Cdd:cd08415    2 LRIAALPALALSLL--------PRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPLDHPGLESE-PLASG 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740864843 173 PYIVAVPQGTDMTGG-------LTGLSHLVFLRRDLtqvMGRQIETYLTRVQLDLPQRFEMDSNQSISALVASGTGWTIT 245
Cdd:cd08415   73 RAVCVLPPGHPLARKdvvtpadLAGEPLISLGRGDP---LRQRVDAAFERAGVEPRIVIETQLSHTACALVAAGLGVAIV 149

                        170       180
                 ....*....|....*....|
gi 740864843 246 TPLSLlrAGRFAGGIDAHPL 265
Cdd:cd08415  150 DPLTA--AGYAGAGLVVRPF 167
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 115-293 1.51e-04

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


Pssm-ID: 176115 [Multi-domain]  Cd Length: 200  Bit Score: 42.20  E-value: 1.51e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740864843 115 PRLAARLAEALSQCAFRLRTGASHNLVAGVVARDLDMAMC----ASPGAHPGGTTAYPILTDPYIVAVPQGTDMTGGLT- 189
Cdd:cd08423   16 PPALAALRARHPGLEVRLREAEPPESLDALRAGELDLAVVfdypVTPPPDDPGLTRVPLLDDPLDLVLPADHPLAGREEv 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740864843 190 GLSHLvflrRDLTQVMGRQIETYlTRVQLDLPQR--------FEMDSNQSISALVASGTGWTIttpLSLLRAGRFAGGID 261
Cdd:cd08423   96 ALADL----ADEPWIAGCPGSPC-HRWLVRACRAagftpriaHEADDYATVLALVAAGLGVAL---VPRLALGARPPGVV 167

                        170       180       190
                 ....*....|....*....|....*....|....
gi 740864843 262 AHPLPDAdIARDIVLL--AGADWSGAIPAQIASL 293
Cdd:cd08423  168 VRPLRPP-PTRRIYAAvrAGAARRPAVAAALEAL 200
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 11-80 2.06e-04

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 42.45  E-value: 2.06e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740864843  11 LRGLEVFEALARTGSVAATAAELGMSAPAVSQQMKNLAQVLGVDLIDHSRRPMIPTPAGRLFLPRAEAAL 80
Cdd:PRK09906   3 LRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAIL 72
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
17-137 3.57e-04

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 41.58  E-value: 3.57e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740864843  17 FEALARTGSVAATAAELGMSAPAVSQQMKNLAQVLGVDLIDHSRRPMIPTPAGRLF-------LPRAEAALSALRSGQR- 88
Cdd:PRK10082  19 FLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFhsqirhlLQQLESNLAELRGGSDy 98

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 740864843  89 DLTALDLSGLSALSLGVIEDFENEVTPRLA-ARLAEALSQCAFRLRTGAS 137
Cdd:PRK10082  99 AQRKIKIAAAHSLSLGLLPSIISQMPPLFTwAIEAIDVDEAVDKLREGQS 148
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 9-162 4.08e-04

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 41.55  E-value: 4.08e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740864843   9 LTLRGLEVFEALARTGSVAATAAELGMSAPAVSQQMKNLAQVLGVDLIDHSRRPMIPTPAGRLFLPRA--------EAAL 80
Cdd:PRK15092  11 LDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYArkilrfndEACS 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740864843  81 SALRSgqrdltalDLSGlsALSLGVIEDFENEVTPRLAARLAEALSQCAFRLRTGASHNLVAGVVARDLDMAM-CASPGA 159
Cdd:PRK15092  91 SLMYS--------NLQG--VLTIGASDDTADTILPFLLNRVSSVYPKLALDVRVKRNAFMMEMLESQEVDLAVtTHRPSS 160


                 ...
gi 740864843 160 HPG 162
Cdd:PRK15092 161 FPA 163
PRK09986 PRK09986
LysR family transcriptional regulator;
11-197 7.85e-04

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 40.48  E-value: 7.85e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740864843  11 LRGLEVFEALARTGSVAATAAELGMSAPAVSQQMKNLAQVLGVDLIDHSRRPMIPTPAGRLF-------LPRAEAALSAL 83
Cdd:PRK09986   9 LKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILmeesrrlLDNAEQSLARV 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740864843  84 RS-GQRDLTALDlsglsalsLGVI-EDFENEVTPRLAARLAEAlSQCAFRLRTGASHNLVAGVVARDLDMAM--CASPGA 159
Cdd:PRK09986  89 EQiGRGEAGRIE--------IGIVgTALWGRLRPAMRHFLKEN-PNVEWLLRELSPSMQMAALERRELDAGIwrMADLEP 159

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 740864843 160 HPgGTTAYPILTDPYIVAVPQGTDMTG----GLTGLSHLVFL 197
Cdd:PRK09986 160 NP-GFTSRRLHESAFAVAVPEEHPLASrssvPLKALRNEYFI 200
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 101-181 8.51e-04

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


Pssm-ID: 176127 [Multi-domain]  Cd Length: 194  Bit Score: 39.89  E-value: 8.51e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740864843 101 LSLGVIEDFENEVTPRLAARLAEALSQCAFRLRTGASHNLVAGVVARDLDMAMCASPGAHPGGTTAYPILTDPYIVAVPQ 180
Cdd:cd08436    2 LAIGTITSLAAVDLPELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAFVGLPERRPPGLASRELAREPLVAVVAP 81


                 .
gi 740864843 181 G 181
Cdd:cd08436   82 D 82
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 101-181 9.60e-04

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


Pssm-ID: 176103 [Multi-domain]  Cd Length: 200  Bit Score: 39.82  E-value: 9.60e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740864843 101 LSLGVIEDFENEVTPRLAARLAEALSQCAFRLRTGASHNLVAGVVARDLDMAMCASPGAHPgGTTAYPILTDPYIVAVPQ 180
Cdd:cd08411    3 LRLGVIPTIAPYLLPRLLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAALLALPVDEP-GLEEEPLFDEPFLLAVPK 81


                 .
gi 740864843 181 G 181
Cdd:cd08411   82 D 82
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 9-253 2.04e-03

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 39.28  E-value: 2.04e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740864843   9 LTLRGLEVFEALARTGSVAATAAELGMSAPAVSQQMKNLAQVLGVDLIDHSRRPMIPTPAGRLFLPRAEAALSALRSGQR 88
Cdd:PRK11233   1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740864843  89 DLTA--LDLSG-----------LSALSLGVIEDFENEVtPRLAARLAEALSqcafrlrTGASHNLVAGvvarDLDMAMCA 155
Cdd:PRK11233  81 AVHNvgQALSGqvsiglapgtaASSLTMPLLQAVRAEF-PGIVLYLHENSG-------ATLNEKLMNG----QLDMAVIY 148

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740864843 156 SpGAHPGGTTAYPILTDP-YIVAVPQGTDMTGGLTGLSHL-VFLRRDLTqVMGRQIETYLTRVQLDLPQRFEMDSNQSIS 233
Cdd:PRK11233 149 E-HSPVAGLSSQPLLKEDlFLVGTQDCPGQSVDLAAVAQMnLFLPRDYS-AVRLRVDEAFSLRRLTAKVIGEIESIATLT 226

                        250       260
                 ....*....|....*....|
gi 740864843 234 ALVASGTGWTItTPLSLLRA 253
Cdd:PRK11233 227 AAIASGMGVTV-LPESAARS 245
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
14-73 5.95e-03

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 37.83  E-value: 5.95e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 740864843  14 LEVFEALARTGSVAATAAELGMSAPAVSQQMKNLAQVLGVDLIDHSRrPMIPTPAGRLFL 73
Cdd:PRK03635   7 LEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVRTQ-PCRPTEAGQRLL 65
 
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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