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Conserved domains on  [gi|15596461|ref|NP_249955|]
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transcriptional regulator [Pseudomonas aeruginosa PAO1]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 10444297)

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

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Periplasmic_Binding_Protein_Type_2 super family cl21456
Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent ...
 94-282 5.96e-27

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 cd08439:

Pssm-ID: 473866  Cd Length: 185  Bit Score: 103.57  E-value: 5.96e-27
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596461  94 RVRFGISEEYAGKLLGRLLPRLGAELPALELEVLTDASGRLAGRLRRGQLDLALLVqaqdeTPYDGHSREIGGTQP-VWV 172
Cdd:cd08439   1 TLRIGCPDDYADTILPFLLNRFASVYPRLAIEVVCKRTPRLMEMLERGEVDLALIT-----HPPPGASATILRRSPtVWY 75

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596461 173 AGHGLRIDPQRPLPLALHGQGCPYRQALLEALGATGRRWRTVVSSPGATALEAAIEGGLAIGVIDRARVGPTMRVLGPAE 252
Cdd:cd08439  76 CAAGYILAPGEPLPLALLDEPTLDRRAALAALDAAGIPWRIAYAASSLSGLRAAVRAGLGITARTQEMVPPDLRILGESE 155

                       170       180       190
                ....*....|....*....|....*....|
gi 15596461 253 GFAELPAHRIRLAFAPGERPPALERLGELI 282
Cdd:cd08439 156 GLPPLPDTGYTLCLDPNRPSELAQAFFEAL 185
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
7-66 1.07e-14

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


:

Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 67.02  E-value: 1.07e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596461     7 IELLRTFHAILRFGRFLAAASHLNRSPSAVSTHVRRLEELAGGRLFERDNQSVRLTPLGQ 66
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
 
Name Accession Description Interval E-value
PBP2_LrhA_like cd08439
The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of ...
 94-282 5.96e-27

The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of closely related homologs, contains the type 2 periplasmic binding fold; This CD represents the LrhA subfamily of LysR-like bacterial transcriptional regulators, including LrhA, HexA, PecT, and DgdR. LrhA is involved in control of the transcription of flagellar, motility, and chemotaxis genes by regulating the synthesis and concentration of FlhD(2)C(2), the master regulator for the expression of flagellar and chemotaxis genes. The LrhA protein has strong homology to HexA and PecT from plant pathogenic bacteria, in which HexA and PecT act as repressors of motility and of virulence factors, such as exoenzymes required for lytic reactions. DgdR also shares similar characteristics to those of LrhA, HexA and PecT. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176130  Cd Length: 185  Bit Score: 103.57  E-value: 5.96e-27
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596461  94 RVRFGISEEYAGKLLGRLLPRLGAELPALELEVLTDASGRLAGRLRRGQLDLALLVqaqdeTPYDGHSREIGGTQP-VWV 172
Cdd:cd08439   1 TLRIGCPDDYADTILPFLLNRFASVYPRLAIEVVCKRTPRLMEMLERGEVDLALIT-----HPPPGASATILRRSPtVWY 75

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596461 173 AGHGLRIDPQRPLPLALHGQGCPYRQALLEALGATGRRWRTVVSSPGATALEAAIEGGLAIGVIDRARVGPTMRVLGPAE 252
Cdd:cd08439  76 CAAGYILAPGEPLPLALLDEPTLDRRAALAALDAAGIPWRIAYAASSLSGLRAAVRAGLGITARTQEMVPPDLRILGESE 155

                       170       180       190
                ....*....|....*....|....*....|
gi 15596461 253 GFAELPAHRIRLAFAPGERPPALERLGELI 282
Cdd:cd08439 156 GLPPLPDTGYTLCLDPNRPSELAQAFFEAL 185
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
5-206 1.28e-25

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 101.87  E-value: 1.28e-25
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596461   5 LDIELLRTFHAILRFGRFLAAASHLNRSPSAVSTHVRRLEELAGGRLFERDNQSVRLTPLGQRFQRQTAELLETHDRVLA 84
Cdd:COG0583   1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596461  85 GLRRREEPL--RVRFGISEEYAGKLLGRLLPRLGAELPALELEVLTDASGRLAGRLRRGQLDLALLVQAQDETpyDGHSR 162
Cdd:COG0583  81 ELRALRGGPrgTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDP--GLVAR 158

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....
gi 15596461 163 EIGGTQPVWVAGHGlridpqrpLPLALHGQGCPYRQALLEALGA 206
Cdd:COG0583 159 PLGEERLVLVASPD--------HPLARRAPLVNSLEALLAAVAA 194
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 4-264 2.28e-24

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 99.72  E-value: 2.28e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596461    4 NLDIELLRTFHAILRFGRFLAAASHLNRSPSAVSTHVRRLEELAGGRLFERDNQSVRLTPLGQRFQRQTAELLETHDRVL 83
Cdd:PRK15092  10 NLDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEAC 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596461   84 AGLRRREEPLRVRFGISEEYAGKLLGRLLPRLGAELPALELEVLTDASGRLAGRLRRGQLDLALLVQAQdetpyDGHSRE 163
Cdd:PRK15092  90 SSLMYSNLQGVLTIGASDDTADTILPFLLNRVSSVYPKLALDVRVKRNAFMMEMLESQEVDLAVTTHRP-----SSFPAL 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596461  164 IGGTQPV-WVAGHGLRIDPQRPLPLALHGQGCPYRQALLEALGATGRRWRTVVSSPGATALEAAIEGGLAIGVIDRARVG 242
Cdd:PRK15092 165 NLRTSPTlWYCAAEYVLQKGEPIPLVLLDEPSPFRDMALATLNAAGIPWRIAYVASTLSAVRAAVKAGLGVTARPVEMMS 244

                        250       260
                 ....*....|....*....|..
gi 15596461  243 PTMRVLGPAEGFAELPAHRIRL 264
Cdd:PRK15092 245 PDLRVLGESEGLPPLPDTEYLL 266
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
7-66 1.07e-14

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 67.02  E-value: 1.07e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596461     7 IELLRTFHAILRFGRFLAAASHLNRSPSAVSTHVRRLEELAGGRLFERDNQSVRLTPLGQ 66
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
5-77 5.44e-11

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 62.13  E-value: 5.44e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15596461    5 LDIELLRTFHAILRFGRFLAAASHLNRSPSAVSTHVRRLEELAGGRLFERDNQSVRLTPLGQRFQRQTAELLE 77
Cdd:PRK10094   2 FDPETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLS 74
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 120-287 2.30e-10

LysR substrate binding domain; The structure of this domain is known and is similar to the periplasmic binding proteins. This domain binds a variety of ligands that caries in size and structure, such as amino acids, sugar phosphates, organic acids, metal cations, flavonoids, C6-ring carboxylic acids, H2O2, HOCl, homocysteine, NADPH, ATP, sulphate, muropeptides, acetate, salicylate, citrate, phenol- and quinolone derivatives, acetylserines, fatty acid CoA, shikimate, chorismate, homocysteine, indole-3-acetic acid, Na(I), c-di-GMP, ppGpp and hydrogen peroxide (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 460931 [Multi-domain]  Cd Length: 205  Bit Score: 58.84  E-value: 2.30e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596461   120 PALELEVLTDASGRLAGRLRRGQLDLALLvqAQDETPYDGHSREIGGTQPVWVAGHGLRIDPQRPL--------PLALHG 191
Cdd:pfam03466  29 PDVELELTEGNSEELLDLLLEGELDLAIR--RGPPDDPGLEARPLGEEPLVLVAPPDHPLARGEPVsledladePLILLP 106

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596461   192 QGCPYRQALLEALGATGRRWRTVVSSPGATALEAAIEGGLAIGVIDRARVGPTMRV--LGPAEGFAELPAHRIRLAFAPG 269
Cdd:pfam03466 107 PGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARELADgrLVALPLPEPPLPRELYLVWRKG 186

                         170
                  ....*....|....*....
gi 15596461   270 -ERPPALERLGELIAEEFR 287
Cdd:pfam03466 187 rPLSPAVRAFIEFLREALA 205
 
Name Accession Description Interval E-value
PBP2_LrhA_like cd08439
The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of ...
 94-282 5.96e-27

The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of closely related homologs, contains the type 2 periplasmic binding fold; This CD represents the LrhA subfamily of LysR-like bacterial transcriptional regulators, including LrhA, HexA, PecT, and DgdR. LrhA is involved in control of the transcription of flagellar, motility, and chemotaxis genes by regulating the synthesis and concentration of FlhD(2)C(2), the master regulator for the expression of flagellar and chemotaxis genes. The LrhA protein has strong homology to HexA and PecT from plant pathogenic bacteria, in which HexA and PecT act as repressors of motility and of virulence factors, such as exoenzymes required for lytic reactions. DgdR also shares similar characteristics to those of LrhA, HexA and PecT. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176130  Cd Length: 185  Bit Score: 103.57  E-value: 5.96e-27
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596461  94 RVRFGISEEYAGKLLGRLLPRLGAELPALELEVLTDASGRLAGRLRRGQLDLALLVqaqdeTPYDGHSREIGGTQP-VWV 172
Cdd:cd08439   1 TLRIGCPDDYADTILPFLLNRFASVYPRLAIEVVCKRTPRLMEMLERGEVDLALIT-----HPPPGASATILRRSPtVWY 75

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596461 173 AGHGLRIDPQRPLPLALHGQGCPYRQALLEALGATGRRWRTVVSSPGATALEAAIEGGLAIGVIDRARVGPTMRVLGPAE 252
Cdd:cd08439  76 CAAGYILAPGEPLPLALLDEPTLDRRAALAALDAAGIPWRIAYAASSLSGLRAAVRAGLGITARTQEMVPPDLRILGESE 155

                       170       180       190
                ....*....|....*....|....*....|
gi 15596461 253 GFAELPAHRIRLAFAPGERPPALERLGELI 282
Cdd:cd08439 156 GLPPLPDTGYTLCLDPNRPSELAQAFFEAL 185
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
5-206 1.28e-25

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 101.87  E-value: 1.28e-25
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596461   5 LDIELLRTFHAILRFGRFLAAASHLNRSPSAVSTHVRRLEELAGGRLFERDNQSVRLTPLGQRFQRQTAELLETHDRVLA 84
Cdd:COG0583   1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596461  85 GLRRREEPL--RVRFGISEEYAGKLLGRLLPRLGAELPALELEVLTDASGRLAGRLRRGQLDLALLVQAQDETpyDGHSR 162
Cdd:COG0583  81 ELRALRGGPrgTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDP--GLVAR 158

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....
gi 15596461 163 EIGGTQPVWVAGHGlridpqrpLPLALHGQGCPYRQALLEALGA 206
Cdd:COG0583 159 PLGEERLVLVASPD--------HPLARRAPLVNSLEALLAAVAA 194
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 4-264 2.28e-24

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 99.72  E-value: 2.28e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596461    4 NLDIELLRTFHAILRFGRFLAAASHLNRSPSAVSTHVRRLEELAGGRLFERDNQSVRLTPLGQRFQRQTAELLETHDRVL 83
Cdd:PRK15092  10 NLDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEAC 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596461   84 AGLRRREEPLRVRFGISEEYAGKLLGRLLPRLGAELPALELEVLTDASGRLAGRLRRGQLDLALLVQAQdetpyDGHSRE 163
Cdd:PRK15092  90 SSLMYSNLQGVLTIGASDDTADTILPFLLNRVSSVYPKLALDVRVKRNAFMMEMLESQEVDLAVTTHRP-----SSFPAL 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596461  164 IGGTQPV-WVAGHGLRIDPQRPLPLALHGQGCPYRQALLEALGATGRRWRTVVSSPGATALEAAIEGGLAIGVIDRARVG 242
Cdd:PRK15092 165 NLRTSPTlWYCAAEYVLQKGEPIPLVLLDEPSPFRDMALATLNAAGIPWRIAYVASTLSAVRAAVKAGLGVTARPVEMMS 244

                        250       260
                 ....*....|....*....|..
gi 15596461  243 PTMRVLGPAEGFAELPAHRIRL 264
Cdd:PRK15092 245 PDLRVLGESEGLPPLPDTEYLL 266
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
7-66 1.07e-14

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 67.02  E-value: 1.07e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596461     7 IELLRTFHAILRFGRFLAAASHLNRSPSAVSTHVRRLEELAGGRLFERDNQSVRLTPLGQ 66
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
5-77 5.44e-11

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 62.13  E-value: 5.44e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15596461    5 LDIELLRTFHAILRFGRFLAAASHLNRSPSAVSTHVRRLEELAGGRLFERDNQSVRLTPLGQRFQRQTAELLE 77
Cdd:PRK10094   2 FDPETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLS 74
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 15-76 8.39e-11

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 61.50  E-value: 8.39e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15596461   15 AILRFGRFLAAASHLNRSPSAVSTHVRRLEELAGGRLFERDNQSVRLTPLGQRFQRQTAELL 76
Cdd:PRK11074  12 AVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVI 73
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 120-287 2.30e-10

LysR substrate binding domain; The structure of this domain is known and is similar to the periplasmic binding proteins. This domain binds a variety of ligands that caries in size and structure, such as amino acids, sugar phosphates, organic acids, metal cations, flavonoids, C6-ring carboxylic acids, H2O2, HOCl, homocysteine, NADPH, ATP, sulphate, muropeptides, acetate, salicylate, citrate, phenol- and quinolone derivatives, acetylserines, fatty acid CoA, shikimate, chorismate, homocysteine, indole-3-acetic acid, Na(I), c-di-GMP, ppGpp and hydrogen peroxide (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 460931 [Multi-domain]  Cd Length: 205  Bit Score: 58.84  E-value: 2.30e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596461   120 PALELEVLTDASGRLAGRLRRGQLDLALLvqAQDETPYDGHSREIGGTQPVWVAGHGLRIDPQRPL--------PLALHG 191
Cdd:pfam03466  29 PDVELELTEGNSEELLDLLLEGELDLAIR--RGPPDDPGLEARPLGEEPLVLVAPPDHPLARGEPVsledladePLILLP 106

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596461   192 QGCPYRQALLEALGATGRRWRTVVSSPGATALEAAIEGGLAIGVIDRARVGPTMRV--LGPAEGFAELPAHRIRLAFAPG 269
Cdd:pfam03466 107 PGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARELADgrLVALPLPEPPLPRELYLVWRKG 186

                         170
                  ....*....|....*....
gi 15596461   270 -ERPPALERLGELIAEEFR 287
Cdd:pfam03466 187 rPLSPAVRAFIEFLREALA 205
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
32-70 2.22e-09

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 56.75  E-value: 2.22e-09
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 15596461   32 SPSAVSTHVRRLEELAGGRLFERDNQSVRLTPLGQRFQR 70
Cdd:PRK11716   4 SPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRP 42
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 10-89 3.54e-09

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 56.39  E-value: 3.54e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596461   10 LRTFHAILRFGRFLAAASHLNRSPSAVSTHVRRLEELAGGRLFERDNQSVRLTPLGQR-FQRQTA---ELLETHDRVLAG 85
Cdd:PRK11139  11 LRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRyFLDIREifdQLAEATRKLRAR 90


                 ....
gi 15596461   86 LRRR 89
Cdd:PRK11139  91 SAKG 94
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
5-77 2.43e-08

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 54.01  E-value: 2.43e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15596461    5 LDIELLRTFHAILRFGRFLAAASHLNRSPSAVSTHVRRLEELAGGRLFERDnQSVRLTPLGQ---RFQRQTAeLLE 77
Cdd:PRK03635   2 LDYKQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVRT-QPCRPTEAGQrllRHARQVR-LLE 75
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
4-77 3.45e-08

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 53.44  E-value: 3.45e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15596461    4 NLDIELLRTFHAILRFGRFLAAASHLNRSPSAVSTHVRRLEELAGGRLFERDNQsVRLTPLGQRFQR--QTAELLE 77
Cdd:PRK13348   1 MLDYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRGRP-CRPTPAGQRLLRhlRQVALLE 75
PRK09791 PRK09791
LysR family transcriptional regulator;
1-98 4.50e-08

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 53.23  E-value: 4.50e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596461    1 MSANLDIELLRTFHAILRFGRFLAAASHLNRSPSAVSTHVRRLEELAGGRLFERDNQSVRLTPLGQRFQRQTAELLEThd 80
Cdd:PRK09791   1 MAFQVKIHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEE-- 78

                         90
                 ....*....|....*...
gi 15596461   81 rvlagLRRREEPLRVRFG 98
Cdd:PRK09791  79 -----LRAAQEDIRQRQG 91
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
5-147 2.97e-07

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 50.79  E-value: 2.97e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596461    5 LDIELLRTFHAILRFGRFLAAASHLNRSPSAVSTHVRRLEELAGGRLFERDNQSVRLTPLGQRFQRQTAELLETHDRVLA 84
Cdd:PRK15421   2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQ 81

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15596461   85 GLRRREEPlRVRFGISEEYAGKLLGRLLPRLGAELPALELEVLTDASGRLAGRLRRGQLDLAL 147
Cdd:PRK15421  82 ACNEPQQT-RLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVM 143
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
10-67 3.17e-07

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 50.77  E-value: 3.17e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 15596461   10 LRTFHAILRFGRFLAAASHLNRSPSAVSTHVRRLEELAGGRLFERDNQSVRLTPLGQR 67
Cdd:PRK10086  19 LHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKR 76
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
5-67 1.17e-06

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 48.86  E-value: 1.17e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15596461    5 LDIELLRTFHAILR---FGRflaAASHLNRSPSAVSTHVRRLEELAGGRLFERDNQSVRLTPLGQR 67
Cdd:PRK03601   1 MDTELLKTFLEVSRtrhFGR---AAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGER 63
PRK09986 PRK09986
LysR family transcriptional regulator;
5-99 1.71e-06

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 48.57  E-value: 1.71e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596461    5 LDIELLRTFHAI---LRFGRflaAASHLNRSPSAVSTHVRRLEELAGGRLFERDNQSVRLTPLGQRFQRQTAELLETHDR 81
Cdd:PRK09986   7 IDLKLLRYFLAVaeeLHFGR---AAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQ 83

                         90       100
                 ....*....|....*....|
gi 15596461   82 VLAGLRR--REEPLRVRFGI 99
Cdd:PRK09986  84 SLARVEQigRGEAGRIEIGI 103
rbcR CHL00180
LysR transcriptional regulator; Provisional
 10-87 3.81e-06

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 47.32  E-value: 3.81e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596461   10 LRTFHAILRFGRFLAAASHLNRSPSAVSTHVRRLEELAGGRLFERDNQSVRLTPLGQ---RFQRQTAELLETHDRVLAGL 86
Cdd:CHL00180  10 LRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGElllRYGNRILALCEETCRALEDL 89


                 .
gi 15596461   87 R 87
Cdd:CHL00180  90 K 90
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 120-236 2.47e-05

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: 44.13  E-value: 2.47e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596461 120 PALELEVLTDASGRLAGRLRRGQLDLALLVQAQDETPYdgHSREIgGTQPVWVA---GHGL----RIDPQ--RPLPLALH 190
Cdd:cd05466  27 PGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGL--ESEPL-FEEPLVLVvppDHPLakrkSVTLAdlADEPLILF 103

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*.
gi 15596461 191 GQGCPYRQALLEALGATGRRWRTVVSSPGATALEAAIEGGLAIGVI 236
Cdd:cd05466 104 ERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALL 149
PRK09801 PRK09801
LysR family transcriptional regulator;
10-100 1.40e-04

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 42.71  E-value: 1.40e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596461   10 LRTFHAILRFGRFLAAASHLNRSPSAVSTHVRRLEELAGGRLFERDNQSVRLTPLGQRFQRQTAELLETHDRV---LAGL 86
Cdd:PRK09801  11 LQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLvddVTQI 90

                         90
                 ....*....|....
gi 15596461   87 RRREEPLrVRFGIS 100
Cdd:PRK09801  91 KTRPEGM-IRIGCS 103
PRK10341 PRK10341
transcriptional regulator TdcA;
10-68 1.92e-04

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 42.16  E-value: 1.92e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 15596461   10 LRTFHAILRFGRFLAAASHLNRSPSAVSTHVRRLEELAGGRLFERDNQSVRLTPLGQRF 68
Cdd:PRK10341  12 LVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVL 70
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 10-148 2.13e-04

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 42.06  E-value: 2.13e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596461   10 LRTFHAILRFGRFLAAASHLNRSPSAVSTHVRRLEELAGGRLFERDNQSVRLTPLGQRFQRQTAELLETHDRVLAGLRR- 88
Cdd:PRK09906   6 LRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKLRARKi 85

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596461   89 REEPLRVRFGISEEYAGKLLGRLLPRLGAELPALELEVLTDASGRLAGRLRRGQLDLALL 148
Cdd:PRK09906  86 VQEDRQLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFM 145
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
4-87 8.34e-04

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 40.42  E-value: 8.34e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596461    4 NLDIELLRTFHAILRFGRFLAAASHLNRSPSAVSTHVRRLEELAGGRLFERDNQSVRLTPLGQRFQRQTAELLETHDRVL 83
Cdd:PRK10082  10 NIETKWLYDFLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESNL 89


                 ....
gi 15596461   84 AGLR 87
Cdd:PRK10082  90 AELR 93
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
13-84 1.07e-03

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 40.13  E-value: 1.07e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15596461   13 FHAILRFGRFLAAASHLNRSPSAVSTHVRRLEELAGGRLFERDNQSVRLTPLG----QRFQRQTAELLETHDRVLA 84
Cdd:PRK10632  10 FAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGriyyQGCRRMLHEVQDVHEQLYA 85
PRK10216 PRK10216
HTH-type transcriptional regulator YidZ;
3-102 1.29e-03

HTH-type transcriptional regulator YidZ;


Pssm-ID: 182312 [Multi-domain]  Cd Length: 319  Bit Score: 39.80  E-value: 1.29e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596461    3 ANLDIELLRTFHAILRFGRFLAAASHLNRSPSAVSTHVRRLEELAGGRLFERDNQSVRLTPLGQRFQRQTAELLETHDRV 82
Cdd:PRK10216   6 TTLDLNLLLCLQLLMQERSVTKAAKRMNVTPSAVSKSLAKLRAWFDDPLFVNTPLGLSPTPLMVSMEQNLAEWMQMGNQL 85

                         90       100
                 ....*....|....*....|
gi 15596461   83 LaGLRRREEPLRVRFGISEE 102
Cdd:PRK10216  86 L-DKPHHQTPRGLKFELAAE 104
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 117-275 3.06e-03

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: 37.93  E-value: 3.06e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596461 117 AELPALELEVLTDASGRLAGRLRRGQLDLALLVQAQDETpyDGHSREIGGTQPVWV--AGHGL----RIDPQ--RPLPLA 188
Cdd:cd08415  24 ARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPLDHP--GLESEPLASGRAVCVlpPGHPLarkdVVTPAdlAGEPLI 101

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596461 189 LHGQGCPYRQALLEALGATGRRWRTVVSSPGATALEAAIEGGLAIGVID----RARVGPTMRVLgPaegFAELPAHRIRL 264
Cdd:cd08415 102 SLGRGDPLRQRVDAAFERAGVEPRIVIETQLSHTACALVAAGLGVAIVDpltaAGYAGAGLVVR-P---FRPAIPFEFAL 177

                       170
                ....*....|.
gi 15596461 265 AFAPGERPPAL 275
Cdd:cd08415 178 VRPAGRPLSRL 188
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 10-70 4.34e-03

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 38.01  E-value: 4.34e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15596461   10 LRTFHAILRFGRFLAAASHLNRSPSAVSTHVRRLEELAGGRLFERDNQSVRLTPLGQRFQR 70
Cdd:PRK11242   6 IRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLR 66
 
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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