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Conserved domains on  [gi|499208303|ref|WP_010905843|]
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MULTISPECIES: LysR family transcriptional regulator [Lactococcus]

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];
1-148 9.30e-38

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 134.22  E-value: 9.30e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303   1 MKLSTLRYFVEVATENSFTKASQNLFISQPTLSRRIQELESELGVTLFNRnNTNNIILSPEGKQLLVKVRDVLDQIESIS 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFER-TGRGLRLTEAGERLLERARRILAELEEAE 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 499208303  81 GMFD-----PEGPnknnkasIKIGCLTNFDFSKLYDLIEQFKTQYPNVKFIIEQGSPMELNDGLLNRTYDLVL 148
Cdd:COG0583   80 AELRalrggPRGT-------LRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAI 145
LysR_Sec_metab super family cl49002
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-298 5.08e-27

selenium metabolism-associated LysR family transcriptional regulator; LysR family transcriptional regulators regularly appear encoded adjacent to selenecysteine incorporation proteins such as SelB. This model represents one especially well-conserved subgroup of such transcription factors from species such as Merdimonas faecis, Sellimonas intestinalis, Syntrophotalea acetylenica, and Hydrogenivirga caldilitoris. Seed alignment members were selected by proximity to selB, but not all family members are expected to have similar genomic locations.


The actual alignment was detected with superfamily member NF040786:

Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 106.93  E-value: 5.08e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303   1 MKLSTLRYFVEVATENSFTKASQNLFISQPTLSRRIQELESELGVTLFNRnNTNNIILSPEGKQLLVKVRDVLDQIESIS 80
Cdd:NF040786   1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVR-NTKEVSLTEDGKLLYEYAKEMLDLWEKLE 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303  81 GMFDPEGpnKNNKASIKIGCLTNFDFSKLYDLIEQFKTQYPNVKFIIEQGSPMELNDGLLNRTYDLVLNLDNyISNNDVL 160
Cdd:NF040786  80 EEFDRYG--KESKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTK-LEKKRLV 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303 161 KTSLYKnNNLQVAIQNNHRLAS--KQEIQFSDLTDETLILIErNKSplvfdyvinqclkhGFHAKANYYVKNLdeGLSKT 238
Cdd:NF040786 157 YTPFYK-DRLVLITPNGTEKYRmlKEEISISELQKEPFIMRE-EGS--------------GTRKEAEKALKSL--GISLE 218

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 499208303 239 SLG--------EGI-SFLYSGMDNGYLSK----KY----RVKFLNLNEEKSSQNLVYAFQENNN--PMLDEFLNFVHQN 298
Cdd:NF040786 219 DLNvvaslgstEAIkQSVEAGLGISVISElaaeKEvergRVLIFPIPGLPKNRDFYLVYNKNRQlsPTAEAFLQFVKER 297
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-148 9.30e-38

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 134.22  E-value: 9.30e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303   1 MKLSTLRYFVEVATENSFTKASQNLFISQPTLSRRIQELESELGVTLFNRnNTNNIILSPEGKQLLVKVRDVLDQIESIS 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFER-TGRGLRLTEAGERLLERARRILAELEEAE 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 499208303  81 GMFD-----PEGPnknnkasIKIGCLTNFDFSKLYDLIEQFKTQYPNVKFIIEQGSPMELNDGLLNRTYDLVL 148
Cdd:COG0583   80 AELRalrggPRGT-------LRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAI 145
PRK09986 PRK09986
LysR family transcriptional regulator;
3-293 6.56e-32

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 120.21  E-value: 6.56e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303   3 LSTLRYFVEVATENSFTKASQNLFISQPTLSRRIQELESELGVTLFNRnNTNNIILSPEGKQLLVKVRDVLDQIE-SISG 81
Cdd:PRK09986   9 LKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIR-HSRSVVLTHAGKILMEESRRLLDNAEqSLAR 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303  82 MfdpEGPNKNNKASIKIGCLTNFDFSKLYDLIEQFKTQYPNVKFIIEQGSPMELNDGLLNRTYDLVLNLDNYISNNDVLK 161
Cdd:PRK09986  88 V---EQIGRGEAGRIEIGIVGTALWGRLRPAMRHFLKENPNVEWLLRELSPSMQMAALERRELDAGIWRMADLEPNPGFT 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303 162 TSLYKNNNLQVAIQNNHRLASKQEIQFSDLTDETLILIERNKSPLVfDYVINQCLKHGFHAKANYYVKNLDEGLSKTSLG 241
Cdd:PRK09986 165 SRRLHESAFAVAVPEEHPLASRSSVPLKALRNEYFITLPFVHSDWG-KFLQRVCQQAGFSPQIIRQVNEPQTVLAMVSMG 243

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 499208303 242 EGISFL---YSGMD-NGylskkyrVKFLNLNEEKSSQNLVYAFQENNNPMLDEFLN 293
Cdd:PRK09986 244 IGITLLpdsYAQIPwPG-------VVFRPLKERIPADLYAVYHPDQVTPALNKLLA 292
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-298 5.08e-27

selenium metabolism-associated LysR family transcriptional regulator; LysR family transcriptional regulators regularly appear encoded adjacent to selenecysteine incorporation proteins such as SelB. This model represents one especially well-conserved subgroup of such transcription factors from species such as Merdimonas faecis, Sellimonas intestinalis, Syntrophotalea acetylenica, and Hydrogenivirga caldilitoris. Seed alignment members were selected by proximity to selB, but not all family members are expected to have similar genomic locations.


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 106.93  E-value: 5.08e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303   1 MKLSTLRYFVEVATENSFTKASQNLFISQPTLSRRIQELESELGVTLFNRnNTNNIILSPEGKQLLVKVRDVLDQIESIS 80
Cdd:NF040786   1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVR-NTKEVSLTEDGKLLYEYAKEMLDLWEKLE 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303  81 GMFDPEGpnKNNKASIKIGCLTNFDFSKLYDLIEQFKTQYPNVKFIIEQGSPMELNDGLLNRTYDLVLNLDNyISNNDVL 160
Cdd:NF040786  80 EEFDRYG--KESKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTK-LEKKRLV 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303 161 KTSLYKnNNLQVAIQNNHRLAS--KQEIQFSDLTDETLILIErNKSplvfdyvinqclkhGFHAKANYYVKNLdeGLSKT 238
Cdd:NF040786 157 YTPFYK-DRLVLITPNGTEKYRmlKEEISISELQKEPFIMRE-EGS--------------GTRKEAEKALKSL--GISLE 218

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 499208303 239 SLG--------EGI-SFLYSGMDNGYLSK----KY----RVKFLNLNEEKSSQNLVYAFQENNN--PMLDEFLNFVHQN 298
Cdd:NF040786 219 DLNvvaslgstEAIkQSVEAGLGISVISElaaeKEvergRVLIFPIPGLPKNRDFYLVYNKNRQlsPTAEAFLQFVKER 297
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-63 1.00e-20

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 83.59  E-value: 1.00e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 499208303    3 LSTLRYFVEVATENSFTKASQNLFISQPTLSRRIQELESELGVTLFNRnNTNNIILSPEGK 63
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFER-TTRGVRLTEAGE 60
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 95-297 3.86e-20

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: 86.19  E-value: 3.86e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303   95 SIKIGCLTNFDFSKLYDLIEQFKTQYPNVKFIIEQGSPMELNDGLLNRTYDLVLNLDNyISNNDVLKTSLYkNNNLQVAI 174
Cdd:pfam03466   3 RLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGP-PDDPGLEARPLG-EEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303  175 QNNHRLASKQEIQFSDLTDETLILIERnkSPLVFDYVINQCLKHGFHAKANYYVKNLDEGLSKTSLGEGISFLYSGMDNG 254
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLPP--GSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAR 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 499208303  255 YLSKKyRVKFLNLNEEKSSQNLVYAFQEN--NNPMLDEFLNFVHQ 297
Cdd:pfam03466 159 ELADG-RLVALPLPEPPLPRELYLVWRKGrpLSPAVRAFIEFLRE 202
TF_pcaQ TIGR02424
pca operon transcription factor PcaQ; Members of this family are LysR-family transcription ...
 1-198 9.89e-16

pca operon transcription factor PcaQ; Members of this family are LysR-family transcription factors associated with operons for catabolism of protocatechuate. Members occur only in Proteobacteria. [Energy metabolism, Other, Regulatory functions, DNA interactions]


Pssm-ID: 274127 [Multi-domain]  Cd Length: 300  Bit Score: 75.91  E-value: 9.89e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303    1 MKLSTLRYFVEVATENSFTKASQNLFISQPTLSRRIQELESELGVTLFNRNNtNNIILSPEGKQLL----VKVRDVLDQI 76
Cdd:TIGR02424   3 IKFRHLQCFVEVARQGSVKRAAEALHITQPAVSKTLRELEEILGTPLFERDR-RGIRLTRYGELFLrhagASLAALRQGV 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303   77 ESISGMFDPEGPnknnkaSIKIGCLTNFDFSKLYDLIEQFKTQYPNVKFIIEQGSPMELNDGLLNRTYDLVLN-LDNYIS 155
Cdd:TIGR02424  82 ASLSQLGEGEGP------TVRIGALPTVAARLMPEVVKRFLARAPRLRVRIMTGPNAYLLDQLRVGALDLVVGrLGAPET 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 499208303  156 NNDVLKTSLYkNNNLQVAIQNNHRLASKQEIQFSDLTDETLIL 198
Cdd:TIGR02424 156 MQGLSFEHLY-NEPVVFVVRAGHPLLAAPSLPVASLADYPVLL 197
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 95-247 3.04e-14

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: 69.84  E-value: 3.04e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303  95 SIKIGCLTNFDFSKLYDLIEQFKTQYPNVKFIIEQGSPMELNDGLLNRTYDLVLnLDNYISNNDVLKTSLYKNNnLQVAI 174
Cdd:cd08414    1 RLRIGFVGSALYGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGF-VRPPPDPPGLASRPLLREP-LVVAL 78

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 499208303 175 QNNHRLASKQEIQFSDLTDETLILIERNKSPLVFDYVINQCLKHGFHAKANYYVKNLDEGLSKTSLGEGISFL 247
Cdd:cd08414   79 PADHPLAARESVSLADLADEPFVLFPREPGPGLYDQILALCRRAGFTPRIVQEASDLQTLLALVAAGLGVALV 151
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 96-199 1.28e-07

The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator PAO1-like, a member of the type 2 periplasmic binding fold protein superfamily; This family includes the C-terminal substrate domain of a putative LysR-type transcriptional regulator from the plant pathogen Pseudomonas aeruginosa PAO1and its closely related homologs. The LysR-type transcriptional regulators (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 N2 fixing bacteria, and synthesis of virulence factors, to a 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: 176104 [Multi-domain]  Cd Length: 198  Bit Score: 51.01  E-value: 1.28e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303  96 IKIGCLTNFDFSKLYDLIEQFKTQYPNVKFIIEQGSPMELNDGLLNRTYDLVLNLDnyISNNDVLKTSLYKNNNLQVAIQ 175
Cdd:cd08412    2 LRIGCFSTLAPYYLPGLLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALTYD--LDLPEDIAFEPLARLPPYVWLP 79

                         90       100
                 ....*....|....*....|....
gi 499208303 176 NNHRLASKQEIQFSDLTDETLILI 199
Cdd:cd08412   80 ADHPLAGKDEVSLADLAAEPLILL 103
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-148 9.30e-38

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 134.22  E-value: 9.30e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303   1 MKLSTLRYFVEVATENSFTKASQNLFISQPTLSRRIQELESELGVTLFNRnNTNNIILSPEGKQLLVKVRDVLDQIESIS 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFER-TGRGLRLTEAGERLLERARRILAELEEAE 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 499208303  81 GMFD-----PEGPnknnkasIKIGCLTNFDFSKLYDLIEQFKTQYPNVKFIIEQGSPMELNDGLLNRTYDLVL 148
Cdd:COG0583   80 AELRalrggPRGT-------LRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAI 145
PRK09986 PRK09986
LysR family transcriptional regulator;
3-293 6.56e-32

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 120.21  E-value: 6.56e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303   3 LSTLRYFVEVATENSFTKASQNLFISQPTLSRRIQELESELGVTLFNRnNTNNIILSPEGKQLLVKVRDVLDQIE-SISG 81
Cdd:PRK09986   9 LKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIR-HSRSVVLTHAGKILMEESRRLLDNAEqSLAR 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303  82 MfdpEGPNKNNKASIKIGCLTNFDFSKLYDLIEQFKTQYPNVKFIIEQGSPMELNDGLLNRTYDLVLNLDNYISNNDVLK 161
Cdd:PRK09986  88 V---EQIGRGEAGRIEIGIVGTALWGRLRPAMRHFLKENPNVEWLLRELSPSMQMAALERRELDAGIWRMADLEPNPGFT 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303 162 TSLYKNNNLQVAIQNNHRLASKQEIQFSDLTDETLILIERNKSPLVfDYVINQCLKHGFHAKANYYVKNLDEGLSKTSLG 241
Cdd:PRK09986 165 SRRLHESAFAVAVPEEHPLASRSSVPLKALRNEYFITLPFVHSDWG-KFLQRVCQQAGFSPQIIRQVNEPQTVLAMVSMG 243

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 499208303 242 EGISFL---YSGMD-NGylskkyrVKFLNLNEEKSSQNLVYAFQENNNPMLDEFLN 293
Cdd:PRK09986 244 IGITLLpdsYAQIPwPG-------VVFRPLKERIPADLYAVYHPDQVTPALNKLLA 292
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-298 5.08e-27

selenium metabolism-associated LysR family transcriptional regulator; LysR family transcriptional regulators regularly appear encoded adjacent to selenecysteine incorporation proteins such as SelB. This model represents one especially well-conserved subgroup of such transcription factors from species such as Merdimonas faecis, Sellimonas intestinalis, Syntrophotalea acetylenica, and Hydrogenivirga caldilitoris. Seed alignment members were selected by proximity to selB, but not all family members are expected to have similar genomic locations.


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 106.93  E-value: 5.08e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303   1 MKLSTLRYFVEVATENSFTKASQNLFISQPTLSRRIQELESELGVTLFNRnNTNNIILSPEGKQLLVKVRDVLDQIESIS 80
Cdd:NF040786   1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVR-NTKEVSLTEDGKLLYEYAKEMLDLWEKLE 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303  81 GMFDPEGpnKNNKASIKIGCLTNFDFSKLYDLIEQFKTQYPNVKFIIEQGSPMELNDGLLNRTYDLVLNLDNyISNNDVL 160
Cdd:NF040786  80 EEFDRYG--KESKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTK-LEKKRLV 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303 161 KTSLYKnNNLQVAIQNNHRLAS--KQEIQFSDLTDETLILIErNKSplvfdyvinqclkhGFHAKANYYVKNLdeGLSKT 238
Cdd:NF040786 157 YTPFYK-DRLVLITPNGTEKYRmlKEEISISELQKEPFIMRE-EGS--------------GTRKEAEKALKSL--GISLE 218

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 499208303 239 SLG--------EGI-SFLYSGMDNGYLSK----KY----RVKFLNLNEEKSSQNLVYAFQENNN--PMLDEFLNFVHQN 298
Cdd:NF040786 219 DLNvvaslgstEAIkQSVEAGLGISVISElaaeKEvergRVLIFPIPGLPKNRDFYLVYNKNRQlsPTAEAFLQFVKER 297
cysB PRK12681
HTH-type transcriptional regulator CysB;
1-191 5.22e-21

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 91.11  E-value: 5.22e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303   1 MKLSTLRYFVEVATEN-SFTKASQNLFISQPTLSRRIQELESELGVTLFNRNNTNNIILSPEGKQLLVKVRDVLDQIESI 79
Cdd:PRK12681   1 MKLQQLRYIVEVVNHNlNVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTQVTPAGEEIIRIAREILSKVESI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303  80 ---SGMFdpegpNKNNKASIKIGCLTNFDFSKLYDLIEQFKTQYPNVKFIIEQGSPMELNDGLLNRTYDLVL---NLDNY 153
Cdd:PRK12681  81 ksvAGEH-----TWPDKGSLYIATTHTQARYALPPVIKGFIERYPRVSLHMHQGSPTQIAEAAAKGNADFAIateALHLY 155

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 499208303 154 isnNDVLKTSLYKNNNlQVAIQNNHRLASKQEIQFSDL 191
Cdd:PRK12681 156 ---DDLIMLPCYHWNR-SVVVPPDHPLAKKKKLTIEEL 189
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-63 1.00e-20

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 83.59  E-value: 1.00e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 499208303    3 LSTLRYFVEVATENSFTKASQNLFISQPTLSRRIQELESELGVTLFNRnNTNNIILSPEGK 63
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFER-TTRGVRLTEAGE 60
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 95-297 3.86e-20

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: 86.19  E-value: 3.86e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303   95 SIKIGCLTNFDFSKLYDLIEQFKTQYPNVKFIIEQGSPMELNDGLLNRTYDLVLNLDNyISNNDVLKTSLYkNNNLQVAI 174
Cdd:pfam03466   3 RLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGP-PDDPGLEARPLG-EEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303  175 QNNHRLASKQEIQFSDLTDETLILIERnkSPLVFDYVINQCLKHGFHAKANYYVKNLDEGLSKTSLGEGISFLYSGMDNG 254
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLPP--GSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAR 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 499208303  255 YLSKKyRVKFLNLNEEKSSQNLVYAFQEN--NNPMLDEFLNFVHQ 297
Cdd:pfam03466 159 ELADG-RLVALPLPEPPLPRELYLVWRKGrpLSPAVRAFIEFLRE 202
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 1-197 3.90e-20

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 88.51  E-value: 3.90e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303   1 MKLSTLRYFVEVATEN-SFTKASQNLFISQPTLSRRIQELESELGVTLFNRNNTNNIILSPEGKQLLVKV----RDVlDQ 75
Cdd:PRK12682   1 MNLQQLRFVREAVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKGLTEPGKAVLDVIerilREV-GN 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303  76 IESISGMFdpegpNKNNKASIKIGCL-TNFDFSkLYDLIEQFKTQYPNVKFIIEQGSPMELNDGLLNRTYDLVLNLDNYI 154
Cdd:PRK12682  80 IKRIGDDF-----SNQDSGTLTIATThTQARYV-LPRVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGIATESLA 153

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 499208303 155 SNNDVLKTSLYKnNNLQVAIQNNHRLASKQEIQFSDLTDETLI 197
Cdd:PRK12682 154 DDPDLATLPCYD-WQHAVIVPPDHPLAQEERITLEDLAEYPLI 195
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
1-197 4.54e-20

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 88.11  E-value: 4.54e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303   1 MKLSTLRYFVEVATEN-SFTKASQNLFISQPTLSRRIQELESELGVTLFNRNNTNNIILSPEGKQLLVKVRDVLDQIESI 79
Cdd:PRK12684   1 MNLHQLRFVREAVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRGLTEPGRIILASVERILQEVENL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303  80 SGMfdpeGPNKNNKASikiGCLT--------NFdfsKLYDLIEQFKTQYPNVKFIIEQGSPMELNDGLLNRTYDLVLNLD 151
Cdd:PRK12684  81 KRV----GKEFAAQDQ---GNLTiatthtqaRY---ALPAAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAIATE 150

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 499208303 152 nYISNNDVLkTSL--YKNNNlQVAIQNNHRLASKQEIQFSDLTDETLI 197
Cdd:PRK12684 151 -AIADYKEL-VSLpcYQWNH-CVVVPPDHPLLERKPLTLEDLAQYPLI 195
TF_pcaQ TIGR02424
pca operon transcription factor PcaQ; Members of this family are LysR-family transcription ...
 1-198 9.89e-16

pca operon transcription factor PcaQ; Members of this family are LysR-family transcription factors associated with operons for catabolism of protocatechuate. Members occur only in Proteobacteria. [Energy metabolism, Other, Regulatory functions, DNA interactions]


Pssm-ID: 274127 [Multi-domain]  Cd Length: 300  Bit Score: 75.91  E-value: 9.89e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303    1 MKLSTLRYFVEVATENSFTKASQNLFISQPTLSRRIQELESELGVTLFNRNNtNNIILSPEGKQLL----VKVRDVLDQI 76
Cdd:TIGR02424   3 IKFRHLQCFVEVARQGSVKRAAEALHITQPAVSKTLRELEEILGTPLFERDR-RGIRLTRYGELFLrhagASLAALRQGV 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303   77 ESISGMFDPEGPnknnkaSIKIGCLTNFDFSKLYDLIEQFKTQYPNVKFIIEQGSPMELNDGLLNRTYDLVLN-LDNYIS 155
Cdd:TIGR02424  82 ASLSQLGEGEGP------TVRIGALPTVAARLMPEVVKRFLARAPRLRVRIMTGPNAYLLDQLRVGALDLVVGrLGAPET 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 499208303  156 NNDVLKTSLYkNNNLQVAIQNNHRLASKQEIQFSDLTDETLIL 198
Cdd:TIGR02424 156 MQGLSFEHLY-NEPVVFVVRAGHPLLAAPSLPVASLADYPVLL 197
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 1-197 1.95e-15

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 75.19  E-value: 1.95e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303   1 MKLSTLRYFVEVATENSFTKASQNLFISQPTLSRRIQELESELGVTLFNRNNtNNIILSPEGKQLLVKVRDVLDQIESIS 80
Cdd:PRK09906   1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDK-RKVALTAAGEVFLQDARAILEQAEKAK 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303  81 GMfdpegPNKNNKASI--KIGCLTNFDFSKLYDLIEQFKTQYPNVKFIIEQGSPMELNDGLLNRTYDLVLNLDNyiSNND 158
Cdd:PRK09906  80 LR-----ARKIVQEDRqlTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHP--VYSD 152

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 499208303 159 VLKTSLYKNNNLQVAIQNNHRLASKQEIQFSDLTDETLI 197
Cdd:PRK09906 153 EIDYLELLDEPLVVVLPVDHPLAHEKEITAAQLDGVNFI 191
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 1-141 6.05e-15

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 73.92  E-value: 6.05e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303   1 MKLSTLRYFVEVATEN-SFTKASQNLFISQPTLSRRIQELESELGVTLFNRNNTNNIILSPEGKQLLVKVRDVLDQIESI 79
Cdd:PRK12683   1 MNFQQLRIIREAVRQNfNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTGLTEPGKELLQIVERMLLDAENL 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 499208303  80 ---SGMFdpegpNKNNKASIKIGCLTNFDFSKLYDLIEQFKTQYPNVKFIIEQGSPMELNDGLLN 141
Cdd:PRK12683  81 rrlAEQF-----ADRDSGHLTVATTHTQARYALPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLN 140
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 95-247 3.04e-14

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: 69.84  E-value: 3.04e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303  95 SIKIGCLTNFDFSKLYDLIEQFKTQYPNVKFIIEQGSPMELNDGLLNRTYDLVLnLDNYISNNDVLKTSLYKNNnLQVAI 174
Cdd:cd08414    1 RLRIGFVGSALYGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGF-VRPPPDPPGLASRPLLREP-LVVAL 78

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 499208303 175 QNNHRLASKQEIQFSDLTDETLILIERNKSPLVFDYVINQCLKHGFHAKANYYVKNLDEGLSKTSLGEGISFL 247
Cdd:cd08414   79 PADHPLAARESVSLADLADEPFVLFPREPGPGLYDQILALCRRAGFTPRIVQEASDLQTLLALVAAGLGVALV 151
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
26-132 7.63e-14

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 70.23  E-value: 7.63e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303  26 FISQPTLSRRIQELESELGVTLFNRNNtNNIILSPEGKQLLVKVRDVLDQIESISGMFDPEGPNKnnKASIKIGCLTNFD 105
Cdd:PRK11716   2 HVSPSTLSRQIQRLEEELGQPLFVRDN-RSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSL--SGELSLFCSVTAA 78

                         90       100
                 ....*....|....*....|....*..
gi 499208303 106 FSKLYDLIEQFKTQYPNVKFIIEQGSP 132
Cdd:PRK11716  79 YSHLPPILDRFRAEHPLVEIKLTTGDA 105
rbcR CHL00180
LysR transcriptional regulator; Provisional
 3-214 8.14e-14

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 70.43  E-value: 8.14e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303   3 LSTLRYFVEVATENSFTKASQNLFISQPTLSRRIQELESELGVTLFNRNNtNNIILSPEGKQLLVKVRDVLDQIESISGM 82
Cdd:CHL00180   7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSK-NKASLTEAGELLLRYGNRILALCEETCRA 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303  83 FDPEgpnKN-NKASIKIGCLTNFDFSKLYDLIEQFKTQYPNVKFIIEQGSPMELNDGLLNRTYDLVLnLDNYISNN--DV 159
Cdd:CHL00180  86 LEDL---KNlQRGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAI-VGGEVPTElkKI 161

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 499208303 160 LKTSLYKNNNLQVAIQNNHRLASKQEIQFSDLTDETLILIERN-KSPLVFDYVINQ 214
Cdd:CHL00180 162 LEITPYVEDELALIIPKSHPFAKLKKIQKEDLYRLNFITLDSNsTIRKVIDNILIQ 217
cbl PRK12679
HTH-type transcriptional regulator Cbl;
1-197 1.25e-13

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 70.22  E-value: 1.25e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303   1 MKLSTLRYFVEVA-TENSFTKASQNLFISQPTLSRRIQELESELGVTLFNRNNTNNIILSPEGKQLLVKVRDVLDQIESI 79
Cdd:PRK12679   1 MNFQQLKIIREAArQDYNLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRLLGMTEPGKALLVIAERILNEASNV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303  80 SGMFDpegpNKNNKASIKIGCLTNFDFSK--LYDLIEQFKTQYPNVKFIIEQGSPMELNDGLLNRTYDLVLNLDNyISNN 157
Cdd:PRK12679  81 RRLAD----LFTNDTSGVLTIATTHTQARysLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASER-LSND 155

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 499208303 158 DVLKTSLYKNNNLQVAIQNNHRLASKQEIQFSDLTDETLI 197
Cdd:PRK12679 156 PQLVAFPWFRWHHSLLVPHDHPLTQITPLTLESIAKWPLI 195
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 1-201 1.46e-13

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 69.60  E-value: 1.46e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303   1 MKLSTLRYFVEVATENSFTKASQNLFISQPTLSRRIQELESELGVTLFNRNNtNNIILSPEGKQLLVKVRDVLDQIE--- 77
Cdd:PRK11242   1 MLLRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSG-RTVRLTDAGEVYLRYARRALQDLEagr 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303  78 -SISGMFDPEgpnknnKASIKIGCLTNFDFSKLYDLIEQFKTQYPNVKFIIEQGSPMELNDGLLNRTYDLVLNLDNyISN 156
Cdd:PRK11242  80 rAIHDVADLS------RGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMSQERIEALLADDELDVGIAFAP-VHS 152

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 499208303 157 NDVLKTSLYkNNNLQVAIQNNHRLASKQE-IQFSDLTDETLILIER 201
Cdd:PRK11242 153 PEIEAQPLF-TETLALVVGRHHPLAARRKaLTLDELADEPLVLLSA 197
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
5-148 1.73e-13

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 69.45  E-value: 1.73e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303   5 TLRYFVEVATENSFTKASQNLFISQPTLSRRIQELESELGVTLFNRnNTNNIILSPEGKQLLVKVRDVLDQIESISGMFD 84
Cdd:PRK10094   6 TLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFR-TTRSVTLTAAGEHLLSQARDWLSWLESMPSELQ 84

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 499208303  85 PEGPNKNNKASIKIGCLTnFDFSKLYDLIEQFKTQYPNVKFIIEQGSPMELNDGLLNRTYDLVL 148
Cdd:PRK10094  85 QVNDGVERQVNIVINNLL-YNPQAVAQLLAWLNERYPFTQFHISRQIYMGVWDSLLYEGFSLAI 147
PRK09791 PRK09791
LysR family transcriptional regulator;
1-143 6.02e-12

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 64.78  E-value: 6.02e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303   1 MKLSTLRYFVEVATENSFTKASQNLFISQPTLSRRIQELESELGVTLFNRNNtNNIILSPEGK-----------QLLVKV 69
Cdd:PRK09791   5 VKIHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRS-KGVTLTDAGEsfyqhaslileELRAAQ 83

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 499208303  70 RDVLDQIESISGmfdpegpnknnkaSIKIGCLTNFDFSKLYDLIEQFKTQYPNVKFIIEQGSPM----ELNDGLLNRT 143
Cdd:PRK09791  84 EDIRQRQGQLAG-------------QINIGMGASIARSLMPAVISRFHQQHPQVKVRIMEGQLVsminELRQGELDFT 148
PBP2_XapR cd08449
The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved ...
 111-292 1.34e-11

The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved in xanthosine catabolism, contains the type 2 periplasmic binding fold; In Escherichia coli, XapR is a positive regulator for the expression of xapA gene, encoding xanthosine phosphorylase, and xapB gene, encoding a polypeptide similar to the nucleotide transport protein NupG. As an operon, the expression of both xapA and xapB is fully dependent on the presence of both XapR and the inducer xanthosine. Expression of the xapR is constitutive but not auto-regulated, unlike many other LysR family proteins. 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: 176140 [Multi-domain]  Cd Length: 197  Bit Score: 62.29  E-value: 1.34e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303 111 DLIEQFKTQYPNVKFIIEQGSPMELNDGLLNRTYDLVLNLDNYISNNDVLKTSLYKNNNLQVAIQNNHRLASKQEIQFSD 190
Cdd:cd08449   17 PALRRFKRQYPNVTVRFHELSPEAQKAALLSKRIDLGFVRFADTLNDPPLASELLWREPMVVALPEEHPLAGRKSLTLAD 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303 191 LTDETLILIERNKSPLVfDYVINQCLKHGFHAKANYYVknlDEGLSKTSL---GEGISFLYSGMDNgylSKKYRVKFLNL 267
Cdd:cd08449   97 LRDEPFVFLRLANSRFA-DFLINCCLQAGFTPQITQEV---VEPQTLMALvaaGFGVALVPESYAR---LPWPGVRFIPL 169

                        170       180
                 ....*....|....*....|....*..
gi 499208303 268 NEEKSSQnlVYAF--QENNNPMLDEFL 292
Cdd:cd08449  170 KQAISAD--LYAVyhPDSATPVIQAFL 194
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
9-247 2.25e-11

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 63.15  E-value: 2.25e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303   9 FVEVATENSFTKASQNLFISQPTLSRRIQELESELGVTLFNRNNTnNIILSPEGKQLLVKVRDVLDQIEsiSGMFDPEGP 88
Cdd:PRK10082  19 FLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVT-PLQLSEQGKIFHSQIRHLLQQLE--SNLAELRGG 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303  89 NKNNKASIKIGCLTNFDFSKLYDLIEQFKTQYpnvKFIIEQGSPMELNDGLLNRTYDLVLNldnyisnndvlktslYKNN 168
Cdd:PRK10082  96 SDYAQRKIKIAAAHSLSLGLLPSIISQMPPLF---TWAIEAIDVDEAVDKLREGQSDCIFS---------------FHDE 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303 169 NLQVAIQNNHRLASKQ--EIQFSDLTDETLILIERNKSPLVfDY--------VINQCL-KHGFHAKANYYVKNLDEGLSK 237
Cdd:PRK10082 158 DLLEAPFDHIRLFESQlfPVCASDEHGEALFNLAQPHFPLL-NYsrnsymgrLINRTLtRHSELSFSTFFVSSMSELLKQ 236

                        250
                 ....*....|.
gi 499208303 238 TSL-GEGISFL 247
Cdd:PRK10082 237 VALdGCGIAWL 247
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 111-247 2.64e-11

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: 61.40  E-value: 2.64e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303 111 DLIEQFKTQYPNVKFIIEQGSPMELNDGLLNRTYDLVLnldnyIS----NNDVLKTSLYKnNNLQVAIQNNHRLASKQEI 186
Cdd:cd08434   17 DLIRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLAL-----CSpvpdEPDIEWIPLFT-EELVLVVPKDHPLAGRDSV 90

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 499208303 187 QFSDLTDETLILIERNKS--PLVFDYvinqCLKHGFHAKANYYVKNLD--EGLskTSLGEGISFL 247
Cdd:cd08434   91 DLAELADEPFVLLSPGFGlrPIVDEL----CAAAGFTPKIAFEGEEDStiAGL--VAAGLGVAIL 149
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 1-200 5.17e-11

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 62.35  E-value: 5.17e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303   1 MKLSTLRYFVEVATENSFTKASQNLFISQPTLSRRIQELESELGVTLFNRnNTNNIILSPEGKQLLVKVRDVLDQIESIS 80
Cdd:PRK11151   1 MNIRDLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLER-TSRKVLFTQAGLLLVDQARTVLREVKVLK 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303  81 GMFDPEGpnKNNKASIKIGCLTNFDFSKLYDLIEQFKTQYPNVKFIIEQGSPMELNDGLLNRTYD-LVLNLdnyisnndV 159
Cdd:PRK11151  80 EMASQQG--ETMSGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDcAILAL--------V 149

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 499208303 160 LKTSLYK-----NNNLQVAIQNNHRLASKQEIQFSDLTDETLILIE 200
Cdd:PRK11151 150 KESEAFIevplfDEPMLLAVYEDHPWANRDRVPMSDLAGEKLLMLE 195
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 3-76 6.07e-11

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 61.78  E-value: 6.07e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 499208303   3 LSTLRYFVEVATENSFTKASQNLFISQPTLSRRIQELESELGVTLFNRNNtNNIILSPEGKQLLVKVRDVLDQI 76
Cdd:PRK11139   8 LNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRN-RSLLLTEEGQRYFLDIREIFDQL 80
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 95-295 7.45e-11

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: 60.31  E-value: 7.45e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303  95 SIKIGCLTNFDFSKLYDLIEQFKTQYPNVKFIIEQGSPMELNDGLLNRTYDLVLNLDNyISNNDVLKTSLYKnNNLQVAI 174
Cdd:cd05466    1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALP-VDDPGLESEPLFE-EPLVLVV 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303 175 QNNHRLASKQEIQFSDLTDETLILIERNKSPlvFDYVINQCLKHGFHAKANYYVKNLDEGLSKTSLGEGISFLYSGMDNG 254
Cdd:cd05466   79 PPDHPLAKRKSVTLADLADEPLILFERGSGL--RRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEE 156

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 499208303 255 YLSKkyRVKFLNLNEEKSSQNLVYAFQENN--NPMLDEFLNFV 295
Cdd:cd05466  157 LADG--GLVVLPLEDPPLSRTIGLVWRKGRylSPAARAFLELL 197
PBP2_AlsR cd08452
The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which ...
 95-295 1.25e-10

The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which regulates acetoin formation under stationary phase growth conditions; contains the type 2 periplasmic binding fold; AlsR is responsible for activating the expression of the acetoin operon (alsSD) in response to inducing signals such as glucose and acetate. Like many other LysR family proteins, AlsR is transcribed divergently from the alsSD operon. The alsS gene encodes acetolactate synthase, an enzyme involved in the production of acetoin in cells of stationary-phase. AlsS catalyzes the conversion of two pyruvate molecules to acetolactate and carbon dioxide. Acetolactate is then converted to acetoin at low pH by acetolactate decarboxylase which encoded by the alsD gene. Acetoin is an important physiological metabolite excreted by many microorganisms grown on glucose or other fermentable carbon sources. 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: 176143 [Multi-domain]  Cd Length: 197  Bit Score: 59.82  E-value: 1.25e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303  95 SIKIGCLTNFDFSKLYDLIEQFKTQYPNVKFIIEQGSPMELNDGLLNRtydlvlNLDNYISNNDVLKTSLY----KNNNL 170
Cdd:cd08452    1 LLVIGFVGAAIYEFLPPIVREYRKKFPSVKVELRELSSPDQVEELLKG------RIDIGFLHPPIQHTALHietvQSSPC 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303 171 QVAIQNNHRLASKQEIQFSDLTDETLILIERNKSPLVFDYVINQCLKHGFHAKAnyyVKNLDE-----GLskTSLGEGIS 245
Cdd:cd08452   75 VLALPKQHPLASKEEITIEDLRDEPIITVAREAWPTLYDEIIQLCEQAGFRPKI---VQEATEyqtviGL--VSAGIGVT 149

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|.
gi 499208303 246 FLYSGMDNGYlskKYRVKFLNLNEEKSSQNLVYAFQENN-NPMLDEFLNFV 295
Cdd:cd08452  150 FVPSSAKKLF---NLEVAYRKIDQINLNAEWSIAYRKDNhNPLLKHFIHIS 197
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 5-204 2.51e-10

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 60.39  E-value: 2.51e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303   5 TLRY---FVEVATENSFTKASQNLFISQPTLSRRIQELESELGVTLFNRNNTNniiLSP--EGKQLLVKVRDV---LDQI 76
Cdd:PRK11013   5 SLRHieiFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGR---LHPtvQGLRLFEEVQRSyygLDRI 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303  77 ESISgmfdpEGPNKNNKASIKIGCLTNFDFSKLYDLIEQFKTQYPNVKF-IIEQGSPMeLNDGLLNRTYDLVLNlDNYIS 155
Cdd:PRK11013  82 VSAA-----ESLREFRQGQLSIACLPVFSQSLLPGLCQPFLARYPDVSLnIVPQESPL-LEEWLSAQRHDLGLT-ETLHT 154

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 499208303 156 NNDVLKTSLYKNNNLQVaIQNNHRLASKQEIQFSDLTDETLILIERNKS 204
Cdd:PRK11013 155 PAGTERTELLTLDEVCV-LPAGHPLAAKKVLTPDDFAGENFISLSRTDS 202
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
17-254 2.96e-10

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 60.03  E-value: 2.96e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303  17 SFTKASQNLFISQPTLSRRIQELESELGVTLFNRnNTNNIILSPEGKQLLVKVRDVLDQI-ESISGMFDPEgpnkNNKAS 95
Cdd:PRK15421  18 SLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVR-KSQPLRFTPQGEILLQLANQVLPQIsQALQACNEPQ----QTRLR 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303  96 IKIGCLTNFDFskLYDLIEQFKTQYPNVKFIIEQGSPMELNDGLLNRTYDLVLNLDnyISNNDVLKTSLYKNNNLQVAIQ 175
Cdd:PRK15421  93 IAIECHSCIQW--LTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSD--ILPRSGLHYSPMFDYEVRLVLA 168

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303 176 NNHRLASKQEIQFSDLTDETLIL--IERNK-------------SPLVfDYVINQCL-------KHGFHAKANYYVKNLD- 232
Cdd:PRK15421 169 PDHPLAAKTRITPEDLASETLLIypVQRSRldvwrhflqpagvSPSL-KSVDNTLLliqmvaaRMGIAALPHWVVESFEr 247

                        250       260
                 ....*....|....*....|....
gi 499208303 233 EGLSKT-SLGEGI-SFLYSGMDNG 254
Cdd:PRK15421 248 QGLVVTkTLGEGLwSRLYAAVRDG 271
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
3-76 1.68e-09

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 57.70  E-value: 1.68e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 499208303   3 LSTLRYFVEVATENSFTKASQNLFISQPTLSRRIQELESELGVTLFNRnNTNNIILSPEGKQLLVKVRDVLDQI 76
Cdd:PRK10086  16 LSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVR-SHRKVELTEEGKRVFWALKSSLDTL 88
PBP2_LTTR_aromatics_like_2 cd08448
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 95-295 1.86e-09

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


Pssm-ID: 176139 [Multi-domain]  Cd Length: 197  Bit Score: 56.51  E-value: 1.86e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303  95 SIKIGCLTNFDFSKLYDLIEQFKTQYPNVKFIIEQGSPMELNDGLLNRTYDLVL----NLDNYISNNDVLKTSLYknnnl 170
Cdd:cd08448    1 RLRIGFVGSMLYRGLPRILRAFRAEYPGIEVALHEMSSAEQIEALLRGELDLGFvhsrRLPAGLSARLLHREPFV----- 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303 171 qVAIQNNHRLASKQEIQFSDLTDETLILIERNKSPLVFDYVINQCLKHGFHAKANYYVKNLDEGLSKTSLGEGISFLYSG 250
Cdd:cd08448   76 -CCLPAGHPLAARRRIDLRELAGEPFVLFSREVSPDYYDQIIALCMDAGFHPKIRHEVRHWLTVVALVAAGMGVALVPRS 154

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 499208303 251 MDNGYLSKkyrVKFLNLNEEKSSQNLVYAFQENN-NPMLDEFLNFV 295
Cdd:cd08448  155 LARAGLAG---VRFLPLKGATQRSELYAAWKASApNPALQAFLAAL 197
PRK10341 PRK10341
transcriptional regulator TdcA;
2-141 3.15e-09

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 56.79  E-value: 3.15e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303   2 KLSTLRYFVEVATENSFTKASQNLFISQPTLSRRIQELESELGVTLFNRNNTnNIILSPEGKQLLVKV----RDVLDQIE 77
Cdd:PRK10341   8 KTQHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNT-GVTLTPAGQVLLSRSesitREMKNMVN 86

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 499208303  78 SISGMFDpegpNKNNKASIKIGCLTNFDFskLYDLIEQFKTQYPNVKFIIEQGS-----PMeLNDGLLN 141
Cdd:PRK10341  87 EINGMSS----EAVVDVSFGFPSLIGFTF--MSDMINKFKEVFPKAQVSMYEAQlssflPA-IRDGRLD 148
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
6-66 4.76e-09

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 56.18  E-value: 4.76e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 499208303   6 LRYFVEVATENSFTKASQNLFISQPTLSRRIQELESELGVTLFNRNNtNNIILSPEGKQLL 66
Cdd:PRK03601   6 LKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHR-NNIRLTAAGERLL 65
PRK12680 PRK12680
LysR family transcriptional regulator;
1-79 1.78e-08

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 54.63  E-value: 1.78e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303   1 MKLSTLRYFVEVA-TENSFTKASQNLFISQPTLSRRIQELESELGVTLFNRNNTNNIILSPEGKQLLVKVRDVLDQIESI 79
Cdd:PRK12680   1 MTLTQLRYLVAIAdAELNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLESVTPAGVEVIERARAVLSEANNI 80
PRK09801 PRK09801
LysR family transcriptional regulator;
6-158 6.23e-08

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 53.12  E-value: 6.23e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303   6 LRYFVEVATENSFTKASQNLFISQPTLSRRIQELESELGVTLFNRnNTNNIILSPEGK-------QLLVKVRDVLDQIES 78
Cdd:PRK09801  11 LQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNR-SARGVALTESGQrcyehalEILTQYQRLVDDVTQ 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303  79 ISGMfdPEGpnknnkaSIKIGCLTNFDFSKLYDLIEQFKTQYPNVKFIIEqgspmelndgLLNRTYDLVL-NLDNYISNN 157
Cdd:PRK09801  90 IKTR--PEG-------MIRIGCSFGFGRSHIAPAITELMRNYPELQVHFE----------LFDRQIDLVQdNIDLDIRIN 150


                 .
gi 499208303 158 D 158
Cdd:PRK09801 151 D 151
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 3-138 1.07e-07

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 52.38  E-value: 1.07e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303   3 LSTLRYFVEVATENSFTKASQNLFISQPTLSRRIQELESELGVTLFNRNNtNNIILSPEGKQLLVKVRDVLDQIESISGM 82
Cdd:PRK10837   5 LRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVG-KRLVVNEHGRLLYPRALALLEQAVEIEQL 83

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 499208303  83 FdpegpnKNNKASIKIGCLTNFDFSKLYDLIEQFKTQYPnvkfiieqGSPMELNDG 138
Cdd:PRK10837  84 F------REDNGALRIYASSTIGNYILPAMIARYRRDYP--------QLPLELSVG 125
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 96-199 1.28e-07

The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator PAO1-like, a member of the type 2 periplasmic binding fold protein superfamily; This family includes the C-terminal substrate domain of a putative LysR-type transcriptional regulator from the plant pathogen Pseudomonas aeruginosa PAO1and its closely related homologs. The LysR-type transcriptional regulators (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 N2 fixing bacteria, and synthesis of virulence factors, to a 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: 176104 [Multi-domain]  Cd Length: 198  Bit Score: 51.01  E-value: 1.28e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303  96 IKIGCLTNFDFSKLYDLIEQFKTQYPNVKFIIEQGSPMELNDGLLNRTYDLVLNLDnyISNNDVLKTSLYKNNNLQVAIQ 175
Cdd:cd08412    2 LRIGCFSTLAPYYLPGLLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALTYD--LDLPEDIAFEPLARLPPYVWLP 79

                         90       100
                 ....*....|....*....|....
gi 499208303 176 NNHRLASKQEIQFSDLTDETLILI 199
Cdd:cd08412   80 ADHPLAGKDEVSLADLAAEPLILL 103
PBP2_BudR cd08451
The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is ...
 111-220 1.26e-06

The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is responsible for activation of the expression of the butanediol operon genes; contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of BudR regulator, which is responsible for induction of the butanediol formation pathway under fermentative growth conditions. Three enzymes are involved in the production of 1 mol of 2,3 butanediol from the condensation of 2 mol of pyruvate with acetolactate and acetoin as intermediates: acetolactate synthetase, acetolactate decarboxylase, and acetoin reductase. In Klebsiella terrigena, BudR regulates the expression of the budABC operon genes, encoding these three enzymes of the butanediol pathway. In many bacterial species, the use of this pathway can prevent intracellular acidification by diverting metabolism from acid production to the formation of neutral compounds (acetoin and butanediol). 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: 176142 [Multi-domain]  Cd Length: 199  Bit Score: 47.94  E-value: 1.26e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303 111 DLIEQFKTQYPNVKFIIEQGSPMELNDGLLNRTYDLV-LNLDNYISNNDVLKTSLykNNNLQVAIQNNHRLASKQEIQFS 189
Cdd:cd08451   18 GLIRRFREAYPDVELTLEEANTAELLEALREGRLDAAfVRPPVARSDGLVLELLL--EEPMLVALPAGHPLARERSIPLA 95

                         90       100       110
                 ....*....|....*....|....*....|.
gi 499208303 190 DLTDETLILIERNKSPLVFDYVINQCLKHGF 220
Cdd:cd08451   96 ALADEPFILFPRPVGPGLYDAIIAACRRAGF 126
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 112-221 2.91e-06

The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold; This CD includes the substrate binding domain of CidR which positively up-regulates the expression of cidABC operon in the presence of acetic acid produced by the metabolism of excess glucose. The CidR affects the control of murein hydrolase activity by enhancing cidABC expression in the presence of acetic acid. Thus, up-regulation of cidABC expression results in increased murein hydrolase activity. 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: 176129 [Multi-domain]  Cd Length: 197  Bit Score: 47.17  E-value: 2.91e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303 112 LIEQFKTQYPNVKF-IIEQGSpMELNDGLLNRTYDL---VLNLDNyisnnDVLKTSLYKNNNLQVAIQNNHRLASKQEIQ 187
Cdd:cd08438   18 LLAAFRQRYPNIELeLVEYGG-KKVEQAVLNGELDVgitVLPVDE-----EEFDSQPLCNEPLVAVLPRGHPLAGRKTVS 91

                         90       100       110
                 ....*....|....*....|....*....|....
gi 499208303 188 FSDLTDETLILIERNKSplVFDYVINQCLKHGFH 221
Cdd:cd08438   92 LADLADEPFILFNEDFA--LHDRIIDACQQAGFT 123
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 1-147 4.14e-06

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 47.29  E-value: 4.14e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303   1 MKLSTLRYFVEVATENSFTKASQNLFISQPTLSRRIQELESELGVTLFNRnNTNNIILSPEG-------KQLLVKVRDVL 73
Cdd:PRK14997   2 TDLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQR-TTRQFNVTEVGqtfyehcKAMLVEAQAAQ 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 499208303  74 DQIESISGmfDPEGpnknnkaSIKIGCLTNFDFSKLYDLIEQFKTQYPNVKFIIEQgspmelndglLNRTYDLV 147
Cdd:PRK14997  81 DAIAALQV--EPRG-------IVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLEA----------TNRRVDVV 135
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 1-77 5.25e-06

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 46.98  E-value: 5.25e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 499208303   1 MKLSTLRYFVEVATENSFTKASQNLFISQPTLSRRIQELESELGVTLFNRnnTNNIILSPE-GKQLLVKVRDVLDQIE 77
Cdd:PRK11233   1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIR--TKRGVTPTEaGKILYTHARAILRQCE 76
PBP2_Chlorocatechol cd08446
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 112-245 1.17e-05

The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the chlorocatechol catabolism, contains the type 2 periplasmic binding fold; This CD includes the substrate binding domain of LysR-type regulators CbnR, ClcR and TfdR, which are involved in the regulation of chlorocatechol breakdown. The chlorocatechol-degradative pathway is often found in bacteria that can use chlorinated aromatic compounds as carbon and energy sources. CbnR is found in the 3-chlorobenzoate degradative bacterium Ralstonia eutropha NH9 and forms a tetramer. CbnR activates the expression of the cbnABCD genes, which are responsible for the degradation of chlorocatechol converted from 3-chlorobenzoate and are transcribed divergently from cbnR. In soil bacterium Pseudomonas putida, the 3-chlorocatechol-degradative pathway is encoded by clcABD operon, which requires the divergently transcribed clcR for activation. TfdR is involved in the activation of tfdA and tfdB gene expression. These genes encode enzymes for the conversion of 2,4-dichlorophenoxyacetic acid and 2,4-dichlorophenol. 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: 176137 [Multi-domain]  Cd Length: 198  Bit Score: 45.35  E-value: 1.17e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303 112 LIEQFKTQYPNVKFIIEQGSPMELNDGLLNRTYDLVLN----LDNYISNNDVLKTSLYknnnlqVAIQNNHRLASKQEIQ 187
Cdd:cd08446   19 LLRAFLTARPDVTVSLHNMTKDEQIEALRAGRIHIGFGrfypVEPDIAVENVAQERLY------LAVPKSHPLAARPAVS 92

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 499208303 188 FSDLTDETLILIERNKSPLVFDYVINQCLKHGFHAKANYYVKNLDEGLSKTSLGEGIS 245
Cdd:cd08446   93 LADLRNEPLILFPRGGRPSFADEVLGLFRRAGVEPRVAQEVEDVVAALALVAAGFGVC 150
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 3-73 1.34e-05

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 45.79  E-value: 1.34e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 499208303   3 LSTLRYFVEVATENSFTKASQNLFISQPTLSRRIQELESELGVTLFNRNNTNNiILSPEGKQLLVKVRDVL 73
Cdd:PRK15092  13 LDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNK-LLTEHGIQLLGYARKIL 82
PBP2_CysB_like cd08413
The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains ...
 113-197 2.80e-05

The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; CysB is a transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the regulation of transcription in response to sulfur source is attributed to two transcriptional regulators, CysB and Cbl. CysB, in association with Cbl, downregulates the expression of ssuEADCB operon which is required for the utilization of sulfur from aliphatic sulfonates, in the presence of cysteine. Also, Cbl and CysB together directly function as transcriptional activators of tauABCD genes, which are required for utilization of taurine as sulfur source for growth. Like many other members of the LTTR family, CysB 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 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: 176105 [Multi-domain]  Cd Length: 198  Bit Score: 44.15  E-value: 2.80e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303 113 IEQFKTQYPNVKFIIEQGSPMELNDGLLNRTYDLVLN---LDNYIsnnDVLKTSLYKNNNLqVAIQNNHRLASKQEIQFS 189
Cdd:cd08413   19 IAAFRKRYPKVKLSLHQGTPSQIAEMVLKGEADIAIAteaLDDHP---DLVTLPCYRWNHC-VIVPPGHPLADLGPLTLE 94


                 ....*...
gi 499208303 190 DLTDETLI 197
Cdd:cd08413   95 DLAQYPLI 102
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
6-72 2.97e-05

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 44.96  E-value: 2.97e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 499208303   6 LRYFVEVATENSFTKASQNLFISQPTLSRRIQELESELGVTLFNRnnTNNIILSPEGKQLLVKVRDV 72
Cdd:PRK13348   7 LEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR--GRPCRPTPAGQRLLRHLRQV 71
PBP2_MleR cd08437
The substrate binding domain of LysR-type transcriptional regulator MleR which required for ...
 111-247 3.81e-05

The substrate binding domain of LysR-type transcriptional regulator MleR which required for malolactic fermentation, contains type 2 periplasmic binidning fold; MleR, a transcription activator of malolactic fermentation system, is found in gram-positive bacteria and belongs to the lysR family of bacterial transcriptional regulators. The mleR gene is required for the expression and induction of malolactic fermentation. 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: 176128  Cd Length: 198  Bit Score: 43.86  E-value: 3.81e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303 111 DLIEQFKTQYPNVKFIIEQGSPMELNDGLLNRTYDLVLNLDNYISNNDVLKTSLYKNNNLQVAIQNNHRLASKQEIQFSD 190
Cdd:cd08437   17 KLAKDLIKTGLMIQIDTYEGGSAELLEQLLQGDLDIALLGSLTPLENSALHSKIIKTQHFMIIVSKDHPLAKAKKVNFAD 96

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 499208303 191 LTDETLILI-ERNKSPLVFDYVinqCLKHGFHAKANYYVKNLDEGLSKTSLGEGISFL 247
Cdd:cd08437   97 LKKENFILLnEHFVHPKAFDSL---CQQANFQPNIVYRTNDIHILKSMVRENVGIGFL 151
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 111-201 4.34e-05

C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which activates the transcription of the cysJI operon encoding sulfite reductase, contains the type 2 periplasmic binding fold; CysL, also known as YwfK, is a regular of sulfur metabolism in Bacillus subtilis. Sulfur is required for the synthesis of proteins and essential cofactors in all living organism. Sulfur can be assimilated either from inorganic sources (sulfate and thiosulfate), or from organic sources (sulfate esters, sulfamates, and sulfonates). CysL activates the transcription of the cysJI operon encoding sulfite reductase, which reduces sulfite to sulfide. Both cysL mutant and cysJI mutant are unable to grow using sulfate or sulfite as the sulfur source. Like other LysR-type regulators, CysL also negatively regulates its own transcription. In Escherichia coli, three LysR-type activators are involved in the regulation of sulfur metabolism: CysB, Cbl and MetR. 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: 176112 [Multi-domain]  Cd Length: 201  Bit Score: 43.63  E-value: 4.34e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303 111 DLIEQFKTQYPNVKFIIEQGSPMELNDGLLNRTYDLVLnldnyI---SNNDVLKTSLYKNNNLQVAIQNNHRLASKQEIQ 187
Cdd:cd08420   17 RLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGL-----VegpVDHPDLIVEPFAEDELVLVVPPDHPLAGRKEVT 91

                         90
                 ....*....|....
gi 499208303 188 FSDLTDETLILIER 201
Cdd:cd08420   92 AEELAAEPWILREP 105
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 95-202 5.12e-05

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: 43.32  E-value: 5.12e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303  95 SIKIGCLTNFDFSKLYDLIEQFKTQYPNVKFIIEQGSPMELNDGLLNRTYDLVLNldNYISNNDVLKTSLYKNNNLQVAI 174
Cdd:cd08415    1 TLRIAALPALALSLLPRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLA--SLPLDHPGLESEPLASGRAVCVL 78

                         90       100
                 ....*....|....*....|....*...
gi 499208303 175 QNNHRLASKQEIQFSDLTDETLILIERN 202
Cdd:cd08415   79 PPGHPLARKDVVTPADLAGEPLISLGRG 106
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
2-148 9.16e-05

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 43.21  E-value: 9.16e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303   2 KLSTLRYFVEVATENSFTKASQNLFISQPTLSRRIQELESELGVTLFNRnNTNNIILSPEGK-------QLLVKVRDVLD 74
Cdd:PRK10632   3 RLKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNR-STRSIGLTEAGRiyyqgcrRMLHEVQDVHE 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 499208303  75 QIESIsgmfdpegpNKNNKASIKIGCLTNFDFSKLYDLIEQFKTQYPNVKFIIEQGSPME--LNDGLlnrtyDLVL 148
Cdd:PRK10632  82 QLYAF---------NNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTGIPAPdlIADGL-----DVVI 143
PBP2_HcaR cd08450
The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in ...
 98-247 1.60e-04

The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in involved in 3-phenylpropionic acid catabolism, contains the type2 periplasmic binding fold; HcaR, a member of the LysR family of transcriptional regulators, controls the expression of the hcA1, A2, B, C, and D operon, encoding for the 3-phenylpropionate dioxygenase complex and 3-phenylpropionate-2',3'-dihydrodiol dehydrogenase, that oxidizes 3-phenylpropionate to 3-(2,3-dihydroxyphenyl) propionate. Dioxygenases play an important role in protecting the cell against the toxic effects of dioxygen. The expression of hcaR is negatively auto-regulated, as for other members of the LysR family, and is strongly repressed in the presence of glucose. 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: 176141 [Multi-domain]  Cd Length: 196  Bit Score: 41.98  E-value: 1.60e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303  98 IGCLTNFDFSKLYDLIEQFKTQYPNVKFIIEQGSPMELNDGLLNRTYDLVLNLDNyiSNNDVLKTSLYKNNNLQVAIQNN 177
Cdd:cd08450    4 IGFLPGAEVQWLPEVLPILREEHPDLDVELSSLFSPQLAEALMRGKLDVAFMRPE--IQSDGIDYQLLLKEPLIVVLPAD 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303 178 HRLASKQEIQFSDLTDETLIlIERNKSPLVFDYVINQCLKHGFHAKANYYVKNLDEGLSKTSLGEGISFL 247
Cdd:cd08450   82 HRLAGREKIPPQDLAGENFI-SPAPTAPVLQQVIENYAAQHNIQPNIIQEADNLLSAMSLVASTLGCALL 150
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
6-72 1.66e-04

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 42.45  E-value: 1.66e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 499208303   6 LRYFVEVATENSFTKASQNLFISQPTLSRRIQELESELGVTLFNRnnTNNIILSPEGKQLLVKVRDV 72
Cdd:PRK03635   7 LEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR--TQPCRPTEAGQRLLRHARQV 71
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 95-198 1.90e-04

The C-terminal substrate binding domain of galactose-binding protein regulator contains the type 2 periplasmic binding fold; Galactose-binding protein regulator (GbpR), a member of the LysR family of bacterial transcriptional regulators, regulates the expression of chromosomal virulence gene chvE. The chvE gene is involved in the uptake of specific sugars, in chemotaxis to these sugars, and in the VirA-VirG two-component signal transduction system. In the presence of an inducing sugar such as L-arabinose, D-fucose, or D-galactose, GbpR activates chvE expression, while in the absence of an inducing sugar, GbpR represses expression. 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: 176126 [Multi-domain]  Cd Length: 201  Bit Score: 41.49  E-value: 1.90e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303  95 SIKIGCLTNFDFSKLYDLIEQFKTQYPNVKFIIEQGSPMELNDGLLNRTYDLVLN-LDNYISNNDVLKTSLYKnNNLQVA 173
Cdd:cd08435    1 TVRVGAVPAAAPVLLPPAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAIGrLADDEQPPDLASEELAD-EPLVVV 79

                         90       100
                 ....*....|....*....|....*
gi 499208303 174 IQNNHRLASKQEIQFSDLTDETLIL 198
Cdd:cd08435   80 ARPGHPLARRARLTLADLADYPWVL 104
PBP2_LysR cd08456
The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine ...
 96-201 7.16e-04

The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine biosynthesis, contains the type 2 periplasmic binding fold; LysR, the transcriptional activator of lysA encoding diaminopimelate decarboxylase, catalyses the decarboxylation of diaminopimelate to produce lysine. The 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: 176145 [Multi-domain]  Cd Length: 196  Bit Score: 40.09  E-value: 7.16e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303  96 IKIGCLTNFDFSKLYDLIEQFKTQYPNVKFIIEQGSPMELNDGLLNRTYDLvlNLDNYISNNDVLKTSLYKNNNLQVAIQ 175
Cdd:cd08456    2 LRIAVLPALSQSFLPRAIKAFLQRHPDVTISIHTRDSPTVEQWLSAQQCDL--GLVSTLHEPPGIERERLLRIDGVCVLP 79

                         90       100
                 ....*....|....*....|....*.
gi 499208303 176 NNHRLASKQEIQFSDLTDETLILIER 201
Cdd:cd08456   80 PGHRLAVKKVLTPSDLEGEPFISLAR 105
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 12-79 2.06e-03

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 39.15  E-value: 2.06e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 499208303  12 VATENSFTKASQNLFISQPTLSRRIQELESELGVTLFNRNNtNNIILSPEGKQLLVKVRDVLDQIESI 79
Cdd:PRK11074  13 VARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRH-RDVELTPAGEWFVKEARSVIKKMQET 79
nhaR PRK11062
transcriptional activator NhaR; Provisional
 6-51 2.48e-03

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 38.84  E-value: 2.48e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 499208303   6 LRYFVEVATENSFTKASQNLFISQPTLSRRIQELESELGVTLFNRN 51
Cdd:PRK11062   9 LYYFWMVCKEGSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRK 54
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 112-200 2.88e-03

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: 38.27  E-value: 2.88e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303 112 LIEQFKTQYPNVKFIIEQGSPMELNDGLLNRTYDLVLnLDNYISNNDVLKTSLYKNNnLQVAIQNNHRLASKQEIQFSDL 191
Cdd:cd08411   19 LLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAAL-LALPVDEPGLEEEPLFDEP-FLLAVPKDHPLAKRKSVTPEDL 96


                 ....*....
gi 499208303 192 TDETLILIE 200
Cdd:cd08411   97 AGERLLLLE 105
PBP2_CysB cd08443
The C-terminal substrate domain of LysR-type transcriptional regulator CysB contains type 2 ...
 113-197 9.45e-03

The C-terminal substrate domain of LysR-type transcriptional regulator CysB contains type 2 periplasmic binding fold; CysB is a transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the regulation of transcription in response to sulfur source is attributed to two transcriptional regulators, CysB and Cbl. CysB, in association with Cbl, downregulates the expression of ssuEADCB operon which is required for the utilization of sulfur from aliphatic sulfonates, in the presence of cysteine. Also, Cbl and CysB together directly function as transcriptional activators of tauABCD genes, which are required for utilization of taurine as sulfur source for growth. Like many other members of the LTTR family, CysB 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 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: 176134  Cd Length: 198  Bit Score: 36.77  E-value: 9.45e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499208303 113 IEQFKTQYPNVKFIIEQGSPMELNDGLLNRTYDLVL---NLDNYIsnnDVLKTSLYKNNNLqVAIQNNHRLASKQEIQFS 189
Cdd:cd08443   19 IKGFIERYPRVSLQMHQGSPTQIAEMVSKGLVDFAIateALHDYD---DLITLPCYHWNRC-VVVKRDHPLADKQSISIE 94


                 ....*...
gi 499208303 190 DLTDETLI 197
Cdd:cd08443   95 ELATYPIV 102
 
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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