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Conserved domains on  [gi|2171225192|ref|WP_233109035|]
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MULTISPECIES: LysR family transcriptional regulator [Rhizobium/Agrobacterium group]

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];
50-331 1.45e-49

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 166.20  E-value: 1.45e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192  50 FVAVAEELHFGRAAVRLRLTQSTLSQRIRRLESEVGVPLFLRSTRNVELTEAGKTFLPLARDILIKLDEATLLSRIAAGG 129
Cdd:COG0583     9 FVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAELRALRGG 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 130 VSPgdeQLNIATIGPAAYRLLPLILRRFCAGRPKTGLDVKICDSTELVRLLEHGDYHVGLMRAPSNVNFLRFKPLISERF 209
Cdd:COG0583    89 PRG---TLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPLGEERL 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 210 LAVIPKQSDLANATSLhledfvghrcftlkrfeISGFEEVHQMVLHagveidnrisasttsaalalasaGVGVTFLPSWV 289
Cdd:COG0583   166 VLVASPDHPLARRAPL-----------------VNSLEALLAAVAA-----------------------GLGIALLPRFL 205

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*
gi 2171225192 290 --RNISDGNVVLRQVEDLTTELILGVVWRADSPA-PGIAPFIEYA 331
Cdd:COG0583   206 aaDELAAGRLVALPLPDPPPPRPLYLVWRRRRHLsPAVRAFLDFL 250
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
50-331 1.45e-49

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 166.20  E-value: 1.45e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192  50 FVAVAEELHFGRAAVRLRLTQSTLSQRIRRLESEVGVPLFLRSTRNVELTEAGKTFLPLARDILIKLDEATLLSRIAAGG 129
Cdd:COG0583     9 FVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAELRALRGG 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 130 VSPgdeQLNIATIGPAAYRLLPLILRRFCAGRPKTGLDVKICDSTELVRLLEHGDYHVGLMRAPSNVNFLRFKPLISERF 209
Cdd:COG0583    89 PRG---TLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPLGEERL 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 210 LAVIPKQSDLANATSLhledfvghrcftlkrfeISGFEEVHQMVLHagveidnrisasttsaalalasaGVGVTFLPSWV 289
Cdd:COG0583   166 VLVASPDHPLARRAPL-----------------VNSLEALLAAVAA-----------------------GLGIALLPRFL 205

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*
gi 2171225192 290 --RNISDGNVVLRQVEDLTTELILGVVWRADSPA-PGIAPFIEYA 331
Cdd:COG0583   206 aaDELAAGRLVALPLPDPPPPRPLYLVWRRRRHLsPAVRAFLDFL 250
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 50-329 8.91e-37

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 134.13  E-value: 8.91e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192  50 FVAVAEELHFGRAAVRLRLTQSTLSQRIRRLESEVGVPLFLRSTRNVELTEAGKTFLPLARDILIKLDEATLLSRiaagG 129
Cdd:PRK09906    9 FVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKLRAR----K 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 130 VSPGDEQLNIATIGPAAYRLLPLILRRFCAGRPKTGLDVKICDSTELVRLLEHGDYHVGLMRAPSNVNFLRFKPLISERF 209
Cdd:PRK09906   85 IVQEDRQLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPVYSDEIDYLELLDEPL 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 210 LAVIPKQSDLAN-----ATSLHLEDFV---GHRCFTLKRFeISGFEEVHQMVLHAGVEIDNRIsasttsAALALASAGVG 281
Cdd:PRK09906  165 VVVLPVDHPLAHekeitAAQLDGVNFIstdPAYSGSLAPI-IKAWFAQHNSQPNIVQVATNIL------VTMNLVGMGLG 237

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*...
gi 2171225192 282 VTFLPSWVRNISDGNVVLRQVEDLTTELILGVVWRADSPAPGIAPFIE 329
Cdd:PRK09906  238 CTIIPGYMNNFNTGQVVFRPLAGNVPSIALLMAWKKGEMKPALRDFIA 285
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 136-331 1.37e-25

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: 101.43  E-value: 1.37e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 136 QLNIATIGPAAYRLLPLILRRFCAGRPKTGLDVKICDSTELVRLLEHGDYHVGLMRAPSNVNFLRFKPLISERFLAVIPK 215
Cdd:cd08414     1 RLRIGFVGSALYGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPPPDPPGLASRPLLREPLVVALPA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 216 QSDLANATSLHLEDFVGHRCFTLKRFEISGF-EEVHQMVLHAGVEIDNRISASTTSAALALASAGVGVTFLPSWVRNISD 294
Cdd:cd08414    81 DHPLAARESVSLADLADEPFVLFPREPGPGLyDQILALCRRAGFTPRIVQEASDLQTLLALVAAGLGVALVPASVARLQR 160

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 2171225192 295 GNVVLRQVEDLTTELILGVVWRADSPAPGIAPFIEYA 331
Cdd:cd08414   161 PGVVYRPLADPPPRSELALAWRRDNASPALRAFLELA 197
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 136-331 5.55e-23

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: 94.66  E-value: 5.55e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 136 QLNIATIGPAAYRLLPLILRRFCAGRPKTGLDVKICDSTELVRLLEHGDYHVGLMRAPSNVNFLRFKPLISERFLAVIPK 215
Cdd:pfam03466   3 RLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVAPP 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 216 QSDLANATSLHLEDFVGHRCFTLKRfEISGFEEVHQMVLHAGVEIDNRISASTTSAALALASAGVGVTFLPSWV--RNIS 293
Cdd:pfam03466  83 DHPLARGEPVSLEDLADEPLILLPP-GSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAvaRELA 161

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 2171225192 294 DGNVVLRQVEDLTTELILGVVWRADSPA-PGIAPFIEYA 331
Cdd:pfam03466 162 DGRLVALPLPEPPLPRELYLVWRKGRPLsPAVRAFIEFL 200
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 42-128 9.91e-12

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


Pssm-ID: 274509 [Multi-domain]  Cd Length: 292  Bit Score: 64.55  E-value: 9.91e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192  42 LDLWSVKGFVAVAEELHFGRAAVRLRLTQSTLSQRIRRLESEVGVPLFLRsTRNVELTEAGKTFLPLARDilIKLDEATL 121
Cdd:TIGR03298   1 LDYRQLAALAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVR-TQPCRATEAGQRLLRHARQ--VRLLEAEL 77


                  ....*..
gi 2171225192 122 LSRIAAG 128
Cdd:TIGR03298  78 LAELPGL 84
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 48-239 4.24e-11

multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, including founding member GSU2202 from Geobacter sulfurreducens PCA, are LysR family transcriptional regulators found regularly in the vicinity of multiheme cytochromes such as GSU2203, a decaheme c-type cytochrome.


Pssm-ID: 468965 [Multi-domain]  Cd Length: 301  Bit Score: 62.83  E-value: 4.24e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192  48 KGFVAVAEELHFGRAAVRLRLTQSTLSQRIRRLESEVGVPLFLRSTRNVELTEAGKTFLPLARDILIKldEATLLSRIAA 127
Cdd:NF041036    7 KTLVIVAEEGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRILDI--EDSLMDELKS 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 128 ggvSPGDEQLNI---ATIGPAAyrlLPLILRRFCAgRPKTGLDVKICDST--ELVRLLEHGDYHVGLMRAPSNVNFLRFK 202
Cdd:NF041036   85 ---FKGRQRLSIcctPTFGMAH---LPGVLNRFML-RNADVVDLKFLFHSpaQALEGIQNKEFDLAIIEHCADLDLGRFH 157

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 2171225192 203 --PLISERFLAVIPKQSDLAnATSLHLEDFVGHRCFTLK 239
Cdd:NF041036  158 tyPLPQDELVFVSAPSLGLP-TPNVTLERLLELCLITRR 195
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
50-331 1.45e-49

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 166.20  E-value: 1.45e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192  50 FVAVAEELHFGRAAVRLRLTQSTLSQRIRRLESEVGVPLFLRSTRNVELTEAGKTFLPLARDILIKLDEATLLSRIAAGG 129
Cdd:COG0583     9 FVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAELRALRGG 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 130 VSPgdeQLNIATIGPAAYRLLPLILRRFCAGRPKTGLDVKICDSTELVRLLEHGDYHVGLMRAPSNVNFLRFKPLISERF 209
Cdd:COG0583    89 PRG---TLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPLGEERL 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 210 LAVIPKQSDLANATSLhledfvghrcftlkrfeISGFEEVHQMVLHagveidnrisasttsaalalasaGVGVTFLPSWV 289
Cdd:COG0583   166 VLVASPDHPLARRAPL-----------------VNSLEALLAAVAA-----------------------GLGIALLPRFL 205

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*
gi 2171225192 290 --RNISDGNVVLRQVEDLTTELILGVVWRADSPA-PGIAPFIEYA 331
Cdd:COG0583   206 aaDELAAGRLVALPLPDPPPPRPLYLVWRRRRHLsPAVRAFLDFL 250
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 50-329 8.91e-37

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 134.13  E-value: 8.91e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192  50 FVAVAEELHFGRAAVRLRLTQSTLSQRIRRLESEVGVPLFLRSTRNVELTEAGKTFLPLARDILIKLDEATLLSRiaagG 129
Cdd:PRK09906    9 FVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKLRAR----K 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 130 VSPGDEQLNIATIGPAAYRLLPLILRRFCAGRPKTGLDVKICDSTELVRLLEHGDYHVGLMRAPSNVNFLRFKPLISERF 209
Cdd:PRK09906   85 IVQEDRQLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPVYSDEIDYLELLDEPL 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 210 LAVIPKQSDLAN-----ATSLHLEDFV---GHRCFTLKRFeISGFEEVHQMVLHAGVEIDNRIsasttsAALALASAGVG 281
Cdd:PRK09906  165 VVVLPVDHPLAHekeitAAQLDGVNFIstdPAYSGSLAPI-IKAWFAQHNSQPNIVQVATNIL------VTMNLVGMGLG 237

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*...
gi 2171225192 282 VTFLPSWVRNISDGNVVLRQVEDLTTELILGVVWRADSPAPGIAPFIE 329
Cdd:PRK09906  238 CTIIPGYMNNFNTGQVVFRPLAGNVPSIALLMAWKKGEMKPALRDFIA 285
PRK09986 PRK09986
LysR family transcriptional regulator;
38-329 9.10e-30

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 115.21  E-value: 9.10e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192  38 RNHPLDLWSVKGFVAVAEELHFGRAAVRLRLTQSTLSQRIRRLESEVGVPLFLRSTRNVELTEAGKTFLPLARDILIKLD 117
Cdd:PRK09986    3 RLYRIDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAE 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 118 EAtlLSRIAAGGVSPGdEQLNIATIGPAAY-RLLPLiLRRFCAGRPKTGLDVKICDSTELVRLLEHGDYHVGLMR----- 191
Cdd:PRK09986   83 QS--LARVEQIGRGEA-GRIEIGIVGTALWgRLRPA-MRHFLKENPNVEWLLRELSPSMQMAALERRELDAGIWRmadle 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 192 APSNVNFLRfkpLISERFLAVIPKQSDLANATSLHLEDFVGHRCFTLKrFEISGF-EEVHQMVLHAGVEIDNRISASTTS 270
Cdd:PRK09986  159 PNPGFTSRR---LHESAFAVAVPEEHPLASRSSVPLKALRNEYFITLP-FVHSDWgKFLQRVCQQAGFSPQIIRQVNEPQ 234

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 271 AALALASAGVGVTFLPSWVRNISDGNVVLRQV-EDLTTELIlgVVWRADSPAPGIAPFIE 329
Cdd:PRK09986  235 TVLAMVSMGIGITLLPDSYAQIPWPGVVFRPLkERIPADLY--AVYHPDQVTPALNKLLA 292
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 136-331 1.37e-25

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: 101.43  E-value: 1.37e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 136 QLNIATIGPAAYRLLPLILRRFCAGRPKTGLDVKICDSTELVRLLEHGDYHVGLMRAPSNVNFLRFKPLISERFLAVIPK 215
Cdd:cd08414     1 RLRIGFVGSALYGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPPPDPPGLASRPLLREPLVVALPA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 216 QSDLANATSLHLEDFVGHRCFTLKRFEISGF-EEVHQMVLHAGVEIDNRISASTTSAALALASAGVGVTFLPSWVRNISD 294
Cdd:cd08414    81 DHPLAARESVSLADLADEPFVLFPREPGPGLyDQILALCRRAGFTPRIVQEASDLQTLLALVAAGLGVALVPASVARLQR 160

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 2171225192 295 GNVVLRQVEDLTTELILGVVWRADSPAPGIAPFIEYA 331
Cdd:cd08414   161 PGVVYRPLADPPPRSELALAWRRDNASPALRAFLELA 197
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 136-331 5.55e-23

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: 94.66  E-value: 5.55e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 136 QLNIATIGPAAYRLLPLILRRFCAGRPKTGLDVKICDSTELVRLLEHGDYHVGLMRAPSNVNFLRFKPLISERFLAVIPK 215
Cdd:pfam03466   3 RLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVAPP 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 216 QSDLANATSLHLEDFVGHRCFTLKRfEISGFEEVHQMVLHAGVEIDNRISASTTSAALALASAGVGVTFLPSWV--RNIS 293
Cdd:pfam03466  83 DHPLARGEPVSLEDLADEPLILLPP-GSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAvaRELA 161

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 2171225192 294 DGNVVLRQVEDLTTELILGVVWRADSPA-PGIAPFIEYA 331
Cdd:pfam03466 162 DGRLVALPLPEPPLPRELYLVWRKGRPLsPAVRAFIEFL 200
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
50-103 8.10e-22

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 87.06  E-value: 8.10e-22
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2171225192  50 FVAVAEELHFGRAAVRLRLTQSTLSQRIRRLESEVGVPLFLRSTRNVELTEAGK 103
Cdd:pfam00126   7 FVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 137-331 1.22e-20

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: 88.04  E-value: 1.22e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 137 LNIATIGPAAYRLLPLILRRFCAGRPKTGLDVKICDSTELVRLLEHGDYHVGLMRAPSNVNFLRFKPLISERFLAVIPKQ 216
Cdd:cd05466     2 LRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPPD 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 217 SDLANATSLHLEDFVGHRCFTLKRFEiSGFEEVHQMVLHAGVEIDNRISASTTSAALALASAGVGVTFLPSW-VRNISDG 295
Cdd:cd05466    82 HPLAKRKSVTLADLADEPLILFERGS-GLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESaVEELADG 160

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 2171225192 296 NVVLRQVEDLTTELILGVVWRADSP-APGIAPFIEYA 331
Cdd:cd05466   161 GLVVLPLEDPPLSRTIGLVWRKGRYlSPAARAFLELL 197
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 42-183 1.43e-19

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 87.78  E-value: 1.43e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192  42 LDLWSVKGFVAVAEELHFGRAAVRLRLTQSTLSQRIRRLESEVGVPLFLRSTRNVELTEAGKTFLPLARDILIKLDEATL 121
Cdd:PRK15092   11 LDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEACS 90

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2171225192 122 -LSRIAAGGVspgdeqLNIATIGPAAYRLLPLILRRFCAGRPKTGLDVKICDSTELVRLLEHG 183
Cdd:PRK15092   91 sLMYSNLQGV------LTIGASDDTADTILPFLLNRVSSVYPKLALDVRVKRNAFMMEMLESQ 147
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 46-226 5.17e-18

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 82.97  E-value: 5.17e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192  46 SVKGFVAVAEELHFGRAAVRLRLTQSTLSQRIRRLESEVGVPLFLRSTRNVELTEAGKTFLPLARDILIKLDEAT--LLS 123
Cdd:PRK11139   10 ALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEATrkLRA 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 124 RIAAGgvspgdeQLNIATiGP--AAYRLLPLiLRRFCAGRPktGLDVKICDSTELVRLLEhGDYHVGLMRAPSNVNFLRF 201
Cdd:PRK11139   90 RSAKG-------ALTVSL-LPsfAIQWLVPR-LSSFNEAHP--DIDVRLKAVDRLEDFLR-DDVDVAIRYGRGNWPGLRV 157

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 2171225192 202 KPLISERFLAV-----------IPKQSDLANATSLH 226
Cdd:PRK11139  158 EKLLDEYLLPVcspallnggkpLKTPEDLARHTLLH 193
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 50-119 4.51e-17

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 80.39  E-value: 4.51e-17
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192  50 FVAVAEELHFGRAAVRLRLTQSTLSQRIRRLESEVGVPLFLRSTRNVELTEAGKTFLPLARDILIKLDEA 119
Cdd:PRK11242    9 FLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAG 78
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
42-184 1.84e-16

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 78.47  E-value: 1.84e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192  42 LDLWSVKGFVAVAEELHFGRAAVRLRLTQSTLSQRIRRLESEVGVPLFLRsTRNVELTEAGKTFLPLARDilIKLDEATL 121
Cdd:PRK13348    2 LDYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQRLLRHLRQ--VALLEADL 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2171225192 122 LSRIAAGGVSPgdEQLNIATigpAAYRL----LPlILRRFCAGRpKTGLDVKICDSTELVRLLEHGD 184
Cdd:PRK13348   79 LSTLPAERGSP--PTLAIAV---NADSLatwfLP-ALAAVLAGE-RILLELIVDDQDHTFALLERGE 138
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 51-287 8.10e-16

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 76.61  E-value: 8.10e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192  51 VAVAEELHFGRAAVRLRLTQSTLSQRIRRLESEVGVPLFLRSTRNVELTEAGKTFLPLARDILIkldEATLLSRIAA--G 128
Cdd:PRK11151   10 VALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLR---EVKVLKEMASqqG 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 129 GVSPGDEQLN-IATIGPaaYrLLPLILRRFCAGRPKTGLDVKICDSTELVRLLEHGDYHVGLMRAPSNVNFLRFKPLISE 207
Cdd:PRK11151   87 ETMSGPLHIGlIPTVGP--Y-LLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCAILALVKESEAFIEVPLFDE 163

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 208 RFLAVIPKQ-----------SDLANATSLHLEDfvGH--R------CFTL-----KRFEISGFEEVHQMVlhagveidnr 263
Cdd:PRK11151  164 PMLLAVYEDhpwanrdrvpmSDLAGEKLLMLED--GHclRdqamgfCFEAgadedTHFRATSLETLRNMV---------- 231

                         250       260
                  ....*....|....*....|....
gi 2171225192 264 isasttsaalalaSAGVGVTFLPS 287
Cdd:PRK11151  232 -------------AAGSGITLLPA 242
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
42-117 2.29e-15

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 75.61  E-value: 2.29e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2171225192  42 LDLWSVKGFVAVAEELHFGRAAVRLRLTQSTLSQRIRRLESEVGVPLFLRSTRNVELTEAGKTFLPLARDILIKLD 117
Cdd:PRK10094    2 FDPETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLE 77
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
48-109 8.37e-15

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 73.51  E-value: 8.37e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2171225192  48 KGFVAVAEELHFGRAAVRLRLTQSTLSQRIRRLESEVGVPLFLRSTRNVELTEAGKTFLPLA 109
Cdd:PRK03601    7 KTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYA 68
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
71-163 1.50e-14

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 72.54  E-value: 1.50e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192  71 STLSQRIRRLESEVGVPLFLRSTRNVELTEAGKTFLPLARDIL---------IKLDEATLlsriaAGgvspgdeQLNIAT 141
Cdd:PRK11716    6 STLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLlqwqqlrhtLDQQGPSL-----SG-------ELSLFC 73

                          90       100
                  ....*....|....*....|..
gi 2171225192 142 IGPAAYRLLPLILRRFCAGRPK 163
Cdd:PRK11716   74 SVTAAYSHLPPILDRFRAEHPL 95
PBP2_LTTR_aromatics_like_2 cd08448
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 136-329 6.34e-13

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: 66.52  E-value: 6.34e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 136 QLNIATIGPAAYRLLPLILRRFCAGRPktglDVKIC----DSTELVRLLEHGDYHVGLMRAPSNVNFLRFKPLISERFLA 211
Cdd:cd08448     1 RLRIGFVGSMLYRGLPRILRAFRAEYP----GIEVAlhemSSAEQIEALLRGELDLGFVHSRRLPAGLSARLLHREPFVC 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 212 VIPKQSDLANATSLHL-----EDFVghrcFTLKRFEISGFEEVHQMVLHAGVEIDNRISASTTSAALALASAGVGVTFLP 286
Cdd:cd08448    77 CLPAGHPLAARRRIDLrelagEPFV----LFSREVSPDYYDQIIALCMDAGFHPKIRHEVRHWLTVVALVAAGMGVALVP 152

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 2171225192 287 SWVRNISDGNVVLRQVEDLTTELILGVVWRADSPAPGIAPFIE 329
Cdd:cd08448   153 RSLARAGLAGVRFLPLKGATQRSELYAAWKASAPNPALQAFLA 195
rbcR CHL00180
LysR transcriptional regulator; Provisional
 41-240 6.42e-13

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 68.51  E-value: 6.42e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192  41 PLDLWSVKGFVAVAEELHFGRAAVRLRLTQSTLSQRIRRLESEVGVPLFLRSTRNVELTEAGKTFLPLARDILIKLDEAT 120
Cdd:CHL00180    4 PFTLDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETC 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 121 L----LSRIAAGGVSPGDEQlniaTIGpaAYrLLPLILRRFCAGRPKTGLDVKICDSTELVRLLEHGDYHVGLM--RAPS 194
Cdd:CHL00180   84 RaledLKNLQRGTLIIGASQ----TTG--TY-LMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVggEVPT 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 2171225192 195 NV-NFLRFKPLISERFLAVIPKQSDLANATSLHLEDFVGHRCFTLKR 240
Cdd:CHL00180  157 ELkKILEITPYVEDELALIIPKSHPFAKLKKIQKEDLYRLNFITLDS 203
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
38-103 2.02e-12

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 66.95  E-value: 2.02e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2171225192  38 RNHPLDLWSVKG---FVAVAEELHFGRAAVRLRLTQSTLSQRIRRLESEVGVPLFLRSTRNVELTEAGK 103
Cdd:PRK10086    7 RNRLLNGWQLSKlhtFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGK 75
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 52-233 2.78e-12

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 66.61  E-value: 2.78e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192  52 AVAEELHFGRAAVRLRLTQSTLSQRIRRLESEVGVPLFLRS-TRNVELTEAGKTFLPLARDILikLDEATLlsRIAAGGV 130
Cdd:PRK12683   12 AVRQNFNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRgKRLTGLTEPGKELLQIVERML--LDAENL--RRLAEQF 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 131 SPGDE-QLNIATIGPAAYRLLPLILRRFCAGRPKTGLDVKICDSTELVRLLEHGDYHVG-----LMRAPSNVNFlrfkPL 204
Cdd:PRK12683   88 ADRDSgHLTVATTHTQARYALPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGiateaLDREPDLVSF----PY 163

                         170       180
                  ....*....|....*....|....*....
gi 2171225192 205 ISERFLAVIPKQSDLANATSLHLEDFVGH 233
Cdd:PRK12683  164 YSWHHVVVVPKGHPLTGRENLTLEAIAEY 192
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 50-140 9.19e-12

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 64.96  E-value: 9.19e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192  50 FVAVAEELHFGRAAVrlrltqstlSQRIRRLESEVGVPLFLRSTRNVELTEAGKTFLPLARDILIKLDEATLLSRIAAGG 129
Cdd:PRK11074   19 FSAAAQELHRVPSAV---------SYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRRQCQQVANG 89

                          90
                  ....*....|.
gi 2171225192 130 VSPgdeQLNIA 140
Cdd:PRK11074   90 WRG---QLSIA 97
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 42-128 9.91e-12

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


Pssm-ID: 274509 [Multi-domain]  Cd Length: 292  Bit Score: 64.55  E-value: 9.91e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192  42 LDLWSVKGFVAVAEELHFGRAAVRLRLTQSTLSQRIRRLESEVGVPLFLRsTRNVELTEAGKTFLPLARDilIKLDEATL 121
Cdd:TIGR03298   1 LDYRQLAALAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVR-TQPCRATEAGQRLLRHARQ--VRLLEAEL 77


                  ....*..
gi 2171225192 122 LSRIAAG 128
Cdd:TIGR03298  78 LAELPGL 84
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
42-141 1.50e-11

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 64.02  E-value: 1.50e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192  42 LDLWSVKGFVAVAEELHFGRAAVRLRLTQSTLSQRIRRLESEVGVPLFLRsTRNVELTEAGKTFLPLARDilIKLDEATL 121
Cdd:PRK03635    2 LDYKQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRLLRHARQ--VRLLEAEL 78

                          90       100
                  ....*....|....*....|
gi 2171225192 122 LSRIAAGGVSPgdEQLNIAT 141
Cdd:PRK03635   79 LGELPALDGTP--LTLSIAV 96
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 48-239 4.24e-11

multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, including founding member GSU2202 from Geobacter sulfurreducens PCA, are LysR family transcriptional regulators found regularly in the vicinity of multiheme cytochromes such as GSU2203, a decaheme c-type cytochrome.


Pssm-ID: 468965 [Multi-domain]  Cd Length: 301  Bit Score: 62.83  E-value: 4.24e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192  48 KGFVAVAEELHFGRAAVRLRLTQSTLSQRIRRLESEVGVPLFLRSTRNVELTEAGKTFLPLARDILIKldEATLLSRIAA 127
Cdd:NF041036    7 KTLVIVAEEGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRILDI--EDSLMDELKS 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 128 ggvSPGDEQLNI---ATIGPAAyrlLPLILRRFCAgRPKTGLDVKICDST--ELVRLLEHGDYHVGLMRAPSNVNFLRFK 202
Cdd:NF041036   85 ---FKGRQRLSIcctPTFGMAH---LPGVLNRFML-RNADVVDLKFLFHSpaQALEGIQNKEFDLAIIEHCADLDLGRFH 157

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 2171225192 203 --PLISERFLAVIPKQSDLAnATSLHLEDFVGHRCFTLK 239
Cdd:NF041036  158 tyPLPQDELVFVSAPSLGLP-TPNVTLERLLELCLITRR 195
PRK09791 PRK09791
LysR family transcriptional regulator;
41-225 8.10e-11

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 62.09  E-value: 8.10e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192  41 PLDLWSVKGFVAVAEELHFgRAAVR-LRLTQSTLSQRIRRLESEVGVPLFLRSTRNVELTEAGKTFLPLARDILIKLDEA 119
Cdd:PRK09791    4 QVKIHQIRAFVEVARQGSI-RGASRmLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAA 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 120 T--LLSRIA-AGGvspgdeQLNIATIGPAAYRLLPLILRRFCAGRPKTGLDVKICDSTELVRLLEHG--DYHVGLMRAPS 194
Cdd:PRK09791   83 QedIRQRQGqLAG------QINIGMGASIARSLMPAVISRFHQQHPQVKVRIMEGQLVSMINELRQGelDFTINTYYQGP 156

                         170       180       190
                  ....*....|....*....|....*....|.
gi 2171225192 195 NVNFLRFKPLISERFLAVIPKQSDLANATSL 225
Cdd:PRK09791  157 YDHEFTFEKLLEKQFAVFCRPGHPAIGARSL 187
PBP2_IlvR cd08453
The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved ...
 136-331 9.44e-11

The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved in the biosynthesis of isoleucine, leucine and valine; contains type 2 periplasmic binding fold; The IlvR is an activator of the upstream and divergently transcribed ilvD gene, which encodes dihydroxy acid dehydratase that participates in isoleucine, leucine, and valine biosynthesis. As in the case of other members of the LysR family, the expression of ilvR gene is repressed in the presence of its own gene product. 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: 176144 [Multi-domain]  Cd Length: 200  Bit Score: 60.45  E-value: 9.44e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 136 QLNIATIGPAAYRLLPLILRRFCAGRPKTGLDVKicDSTELVRL--LEHGDYHVGLMRAPSNVNF---LRFKPLISERFL 210
Cdd:cd08453     1 RLSLAFVSTADYSVLPELVRRFREAYPDVELQLR--EATSDVQLeaLLAGEIDAGIVIPPPGASAppaLAYRPLLSEPLV 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 211 AVIPKQSDLANATSLHLEDFVGHRCFTLKRFEISGFeevHQMVLH----AGVEIDNRISASTTSAALALASAGVGVTFLP 286
Cdd:cd08453    79 LAVPAAWAAEGGAPLALAAVAAEPLVIFPRRIAPAF---HDAVTGyyraAGQTPRIAQEAIQMQTIISLVSAGMGVALVP 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 2171225192 287 SWVRNISDGNVVLRQVEDLTTELILGVVWRADSPAPGIAPFIEYA 331
Cdd:cd08453   156 ASLRNLARPGVVYRELADPAPVLETGLVWRRDDASPVLARFLDLV 200
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 62-229 1.53e-10

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 61.16  E-value: 1.53e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192  62 AAVRLRLTQSTLSQRIRRLESEVGVPLFLRSTRNVE-LTEAGKTFLPLARDIlikLDEATLLSRIAAGGVSPGDEQLNIA 140
Cdd:PRK12682   22 AAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKgLTEPGKAVLDVIERI---LREVGNIKRIGDDFSNQDSGTLTIA 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 141 TIGPAAYRLLPLILRRFCAGRPKTGLDVKICDSTELVRLLEHGDYHVG-----LMRAPSNVNFlrfkPLISERFLAVIPK 215
Cdd:PRK12682   99 TTHTQARYVLPRVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGiatesLADDPDLATL----PCYDWQHAVIVPP 174

                         170
                  ....*....|....
gi 2171225192 216 QSDLANATSLHLED 229
Cdd:PRK12682  175 DHPLAQEERITLED 188
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 137-234 2.83e-09

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: 56.03  E-value: 2.83e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 137 LNIATIGPAAYRLLPLILRRFCAGRPKTGLDVKICDSTELVRLLEHGDYHVGLMRAPSNVNFLRFKPLISERFLAVIPKQ 216
Cdd:cd08415     2 LRIAALPALALSLLPRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPLDHPGLESEPLASGRAVCVLPPG 81

                          90
                  ....*....|....*...
gi 2171225192 217 SDLANATSLHLEDFVGHR 234
Cdd:cd08415    82 HPLARKDVVTPADLAGEP 99
PBP2_HcaR cd08450
The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in ...
 149-328 2.85e-09

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: 56.23  E-value: 2.85e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 149 LLPLILRRFCAGRPKTGLDVKICDSTELVRLLEHGDYHVGLMRAPSNVNFLRFKPLISERFLAVIPKQSDLANATSLHLE 228
Cdd:cd08450    14 WLPEVLPILREEHPDLDVELSSLFSPQLAEALMRGKLDVAFMRPEIQSDGIDYQLLLKEPLIVVLPADHRLAGREKIPPQ 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 229 DFVGHRCFTLKRFE------ISGFEEVHQMVLHAGVEIDNrisastTSAALALASAGVGVTFLPSWVRNISDGNVVLRQV 302
Cdd:cd08450    94 DLAGENFISPAPTApvlqqvIENYAAQHNIQPNIIQEADN------LLSAMSLVASTLGCALLPLYANNLLPPSVVARPL 167

                         170       180
                  ....*....|....*....|....*.
gi 2171225192 303 EDLTTELILGVVWRADSPAPGIAPFI 328
Cdd:cd08450   168 SGETPTIDLVMGYNKANTSPLLKRFL 193
cbl PRK12679
HTH-type transcriptional regulator Cbl;
66-229 2.93e-09

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 57.51  E-value: 2.93e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192  66 LRLTQSTLSQRIRRLESEVGVPLFLR-STRNVELTEAGKTFLPLARDIlikLDEATLLSRIAAGGVSPGDEQLNIATIGP 144
Cdd:PRK12679   26 LFTSQSGVSRHIRELEDELGIEIFIRrGKRLLGMTEPGKALLVIAERI---LNEASNVRRLADLFTNDTSGVLTIATTHT 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 145 AAYRLLPLILRRFCAGRPKTGLDVKICDSTELVRLLEHGDYHVG-----LMRAPSNVNFlrfkPLISERFLAVIPKQSDL 219
Cdd:PRK12679  103 QARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGiaserLSNDPQLVAF----PWFRWHHSLLVPHDHPL 178

                         170
                  ....*....|
gi 2171225192 220 ANATSLHLED 229
Cdd:PRK12679  179 TQITPLTLES 188
PRK12680 PRK12680
LysR family transcriptional regulator;
42-215 4.21e-09

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 56.94  E-value: 4.21e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192  42 LDLWSVKGFVAVAE-ELHFGRAAVRLRLTQSTLSQRIRRLESEVGVPLFLRSTRNVE-LTEAGKTFLPLARDILIkldEA 119
Cdd:PRK12680    1 MTLTQLRYLVAIADaELNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLEsVTPAGVEVIERARAVLS---EA 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 120 TLLSRIAAGGVSPGDEQLNIATIGPAAYRLLPLILRRFCAGRPKTGLDVKICDSTELVRLLEHGDYHVGLMRAPSNVNFL 199
Cdd:PRK12680   78 NNIRTYAANQRRESQGQLTLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVSTAGGEPSA 157

                         170
                  ....*....|....*..
gi 2171225192 200 RFK-PLISERFLAVIPK 215
Cdd:PRK12680  158 GIAvPLYRWRRLVVVPR 174
PBP2_AlsR cd08452
The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which ...
 137-331 4.26e-09

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: 55.59  E-value: 4.26e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 137 LNIATIGPAAYRLLPLILRRFCAGRPKTGLDVKICDSTELVRLLEHGDYHVGLMRAPSNVNFLRFKPLISERFLAVIPKQ 216
Cdd:cd08452     2 LVIGFVGAAIYEFLPPIVREYRKKFPSVKVELRELSSPDQVEELLKGRIDIGFLHPPIQHTALHIETVQSSPCVLALPKQ 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 217 SDLANATSLHLEDFVGHRCFTLKRfEI--SGFEEVHQMVLHAGVEIDNRISASTTSAALALASAGVGVTFLPSWVRNISD 294
Cdd:cd08452    82 HPLASKEEITIEDLRDEPIITVAR-EAwpTLYDEIIQLCEQAGFRPKIVQEATEYQTVIGLVSAGIGVTFVPSSAKKLFN 160

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 2171225192 295 GNVVLRQVEDLTTELILGVVWRADSPAPGIAPFIEYA 331
Cdd:cd08452   161 LEVAYRKIDQINLNAEWSIAYRKDNHNPLLKHFIHIS 197
PBP2_LTTR_aromatics_like_1 cd08447
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 136-329 5.20e-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: 176138 [Multi-domain]  Cd Length: 198  Bit Score: 55.35  E-value: 5.20e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 136 QLNIATIGPAAYRLLPLILRRFCAGRPKTGLDVKICDSTELVRLLEHGDYHVGLMRAPSNVNFLRFKPLISERFLAVIPK 215
Cdd:cd08447     1 SLRIGFTAASAYSFLPRLLAAARAALPDVDLVLREMVTTDQIEALESGRIDLGLLRPPFARPGLETRPLVREPLVAAVPA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 216 QSDLANATSLHLEDF----------VGHRCF---TLKRFEISGFEE--VHQMV-LHAGVEIDNrisasttsaalalasAG 279
Cdd:cd08447    81 GHPLAGAERLTLEDLdgqpfimyspTEARYFhdlVVRLFASAGVQPryVQYLSqIHTMLALVR---------------AG 145

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2171225192 280 VGVTFLPSWVRNISDGNVVLRQVEDLTTELI-LGVVWRADSPAPGIAPFIE 329
Cdd:cd08447   146 LGVALVPASASRLRFEGVVFRPLDLPRDVPVeLHLAWRRDNDNPALRALLD 196
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 136-240 1.06e-08

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


Pssm-ID: 176131 [Multi-domain]  Cd Length: 197  Bit Score: 54.45  E-value: 1.06e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 136 QLNIATIGPAAYRLLPLILRRFCAGRPKTGLDVKICDSTELVRLLEHGDYHVGLMRAPSNVNFLRFKPLISERFLAVIPK 215
Cdd:cd08440     1 RVRVAALPSLAATLLPPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEADPDLEFEPLLRDPFVLVCPK 80

                          90       100
                  ....*....|....*....|....*
gi 2171225192 216 QSDLANATSLHLEDFVGHRCFTLKR 240
Cdd:cd08440    81 DHPLARRRSVTWAELAGYPLIALGR 105
PRK10341 PRK10341
transcriptional regulator TdcA;
50-264 1.97e-08

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 54.87  E-value: 1.97e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192  50 FVAVAEELHFGRAAVRLRLTQSTLSQRIRRLESEVGVPLFLRSTRNVELTEAGKTFL----PLARDILIKLDEATLLSRI 125
Cdd:PRK10341   15 FQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLsrseSITREMKNMVNEINGMSSE 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 126 AAGGVSPGDEQLniatIGpaaYRLLPLILRRFCAGRPKTGLDVKICDSTELVRLLEHG--DYHVGLMRAPSNVNFLRFKP 203
Cdd:PRK10341   95 AVVDVSFGFPSL----IG---FTFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGrlDFAIGTLSNEMKLQDLHVEP 167

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2171225192 204 LISERFLAVIPKQSDLANATSLhleDFVGHRCFTLKRFEISGFEEVHQMVLHAGVEIDNRI 264
Cdd:PRK10341  168 LFESEFVLVASKSRTCTGTTTL---ESLKNEQWVLPQTNMGYYSELLTTLQRNGISIENIV 225
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
50-183 2.80e-08

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 54.29  E-value: 2.80e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192  50 FVAVAEELHFGRAAVRLRLTQSTLSQRIRRLESEVGVPLFLRSTRNVELTEAGKTFLPLARDILIKLDEATLLSRiaaGG 129
Cdd:PRK10082   19 FLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESNLAELR---GG 95

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2171225192 130 VSPGDEQLNIATIGPAAYRLLPLILRRFcagRPKTGLDVKICDSTELVRLLEHG 183
Cdd:PRK10082   96 SDYAQRKIKIAAAHSLSLGLLPSIISQM---PPLFTWAIEAIDVDEAVDKLREG 146
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 139-320 3.11e-08

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: 52.91  E-value: 3.11e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 139 IATIGPaaYrLLPLILRRFCAGRPKTGLDVKICDSTELVRLLEHGDYHVGLMRAPSNVNFLRFKPLISERFLAVIPKQSD 218
Cdd:cd08411     8 IPTIAP--Y-LLPRLLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAALLALPVDEPGLEEEPLFDEPFLLAVPKDHP 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 219 LANATSLHLEDFVGHR--------CFT--------------LKRFEISGFEEVHQMVlhagveidnrisasttsaalala 276
Cdd:cd08411    85 LAKRKSVTPEDLAGERlllleeghCLRdqalelcrlagareQTDFEATSLETLRQMV----------------------- 141

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 2171225192 277 SAGVGVTFLPS---WVRNISDGNVVLRQVEDLTTELILGVVWRADSP 320
Cdd:cd08411   142 AAGLGITLLPElavPSEELRGDRLVVRPFAEPAPSRTIGLVWRRSSP 188
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
52-189 4.72e-08

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 53.83  E-value: 4.72e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192  52 AVAEELHFGRAAVRLRLTQSTLSQRIRRLESEVGVPLFLR-STRNVELTEAGKTFLPLARDILIKLDEatlLSRIAAGGV 130
Cdd:PRK12684   12 AVRQNFNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRhGKRLRGLTEPGRIILASVERILQEVEN---LKRVGKEFA 88

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2171225192 131 SPGDEQLNIATIGPAAYRLLPLILRRFCAGRPKTGLDVKICDSTELVRLLEHGDYHVGL 189
Cdd:PRK12684   89 AQDQGNLTIATTHTQARYALPAAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAI 147
cysB PRK12681
HTH-type transcriptional regulator CysB;
62-166 5.52e-08

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 53.75  E-value: 5.52e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192  62 AAVRLRLTQSTLSQRIRRLESEVGVPLFLRSTRNV-ELTEAGKTFLPLARDILIKLDEatlLSRIAAGGVSPGDEQLNIA 140
Cdd:PRK12681   22 TAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLtQVTPAGEEIIRIAREILSKVES---IKSVAGEHTWPDKGSLYIA 98

                          90       100
                  ....*....|....*....|....*.
gi 2171225192 141 TIGPAAYRLLPLILRRFCAGRPKTGL 166
Cdd:PRK12681   99 TTHTQARYALPPVIKGFIERYPRVSL 124
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
50-113 8.01e-08

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 53.23  E-value: 8.01e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2171225192  50 FVAVAEELHFGRAAVRLRLTQSTLSQRIRRLESEVGVPLFLRSTRNVELTEAGKTFLPLARDIL 113
Cdd:PRK10632   10 FAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRML 73
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 43-119 2.37e-07

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 51.53  E-value: 2.37e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2171225192  43 DLWSVKGFVAVAEELHFGRAAVRLRLTQSTLSQRIRRLESEVGVPLFLRSTRNVELTEAGKTFLPLARDILIKLDEA 119
Cdd:PRK14997    3 DLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAA 79
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 61-220 3.88e-07

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 50.84  E-value: 3.88e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192  61 RAAVRLRLTQSTLSQRIRRLESEVGVPLFLRSTRNVELTEAGKTFLPLARDILIKLDEATlLSRIAAGGVSPGDEQLNIA 140
Cdd:PRK11233   20 QAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQ-LAVHNVGQALSGQVSIGLA 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 141 TiGPAAYRL-LPLiLRRFCAGRPKTGLDVKICDSTELVRLLEHGDYHVGLMRAPSNVNFLRFKPLISERFLAV----IPK 215
Cdd:PRK11233   99 P-GTAASSLtMPL-LQAVRAEFPGIVLYLHENSGATLNEKLMNGQLDMAVIYEHSPVAGLSSQPLLKEDLFLVgtqdCPG 176


                  ....*.
gi 2171225192 216 QS-DLA 220
Cdd:PRK11233  177 QSvDLA 182
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 137-329 6.69e-07

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


Pssm-ID: 176115 [Multi-domain]  Cd Length: 200  Bit Score: 49.13  E-value: 6.69e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 137 LNIATIGPAAYRLLPLILRRFCAGRPKTGLDVKICDSTELVRLLEHG--------DYHVGLMRAPSNvnfLRFKPLISER 208
Cdd:cd08423     2 LRVGAFPTAAAALLPPALAALRARHPGLEVRLREAEPPESLDALRAGeldlavvfDYPVTPPPDDPG---LTRVPLLDDP 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 209 FLAVIPKQSDLANATSLHLEDFV---------GHRC------------FTLK-RFEISGFEEVHQMVLHagveidnrisa 266
Cdd:cd08423    79 LDLVLPADHPLAGREEVALADLAdepwiagcpGSPChrwlvracraagFTPRiAHEADDYATVLALVAA----------- 147

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2171225192 267 sttsaalalasaGVGVTFLPSWVRNISDGNVVLRQVEDLTTELILgVVWRADSPA-PGIAPFIE 329
Cdd:cd08423   148 ------------GLGVALVPRLALGARPPGVVVRPLRPPPTRRIY-AAVRAGAARrPAVAAALE 198
PBP2_XapR cd08449
The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved ...
 136-329 2.64e-06

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: 47.27  E-value: 2.64e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 136 QLNIATIGPAAYRLLPLILRRFCAGRPKTGLDVKICDSTELVRLLEHGDYHVGLMRAPSNVNF--LRFKPLISERFLAVI 213
Cdd:cd08449     1 HLNIGMVGSVLWGGLGPALRRFKRQYPNVTVRFHELSPEAQKAALLSKRIDLGFVRFADTLNDppLASELLWREPMVVAL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 214 PKQSDLANATSLHLEDFVGHRcFTLKRFEISGFEE-VHQMVLHAGVEIDNRISASTTSAALALASAGVGVTFLPSWVRNI 292
Cdd:cd08449    81 PEEHPLAGRKSLTLADLRDEP-FVFLRLANSRFADfLINCCLQAGFTPQITQEVVEPQTLMALVAAGFGVALVPESYARL 159

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 2171225192 293 SDGNVVLRQV-EDLTTELILgvVWRADSPAPGIAPFIE 329
Cdd:cd08449   160 PWPGVRFIPLkQAISADLYA--VYHPDSATPVIQAFLA 195
PBP2_BudR cd08451
The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is ...
 136-329 4.26e-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: 46.79  E-value: 4.26e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 136 QLNIATIGPAAYR-LLPLILRRFCAGRPKTGLDVKICDSTELVRLLEHGDYHVGLMRAP-SNVNFLRFKPLISERFLAVI 213
Cdd:cd08451     1 RLRVGFTSSAAFHpLVPGLIRRFREAYPDVELTLEEANTAELLEALREGRLDAAFVRPPvARSDGLVLELLLEEPMLVAL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 214 PKQSDLANATSLHL-----EDFVghrcftLKRFEISG--FEEVHQMVLHAGVEIdnRISAST--TSAALALASAGVGVTF 284
Cdd:cd08451    81 PAGHPLARERSIPLaaladEPFI------LFPRPVGPglYDAIIAACRRAGFTP--RIGQEApqMASAINLVAAGLGVSI 152

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 2171225192 285 LPSWVRNISDGNVVLRQVED--LTTELILgvVWRADSPAPGIAPFIE 329
Cdd:cd08451   153 VPASMRQLQAPGVVYRPLAGapLTAPLAL--AYRRGERSPAVRNFIA 197
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 148-331 2.37e-05

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


Pssm-ID: 176125 [Multi-domain]  Cd Length: 195  Bit Score: 44.45  E-value: 2.37e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 148 RLLPLILRRFCAGRPKTGLDVKICDSTELVRLLEHGDYHVGLMRAPSNVNFLRFKPLISERFLAVIPKQSDLANATSLHL 227
Cdd:cd08434    13 SLVPDLIRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLALCSPVPDEPDIEWIPLFTEELVLVVPKDHPLAGRDSVDL 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 228 ED-----FV------GHRCFTLKRFEISGF--------EEVHQMvlhAGVeidnrisasttsaalalASAGVGVTFLPSw 288
Cdd:cd08434    93 AEladepFVllspgfGLRPIVDELCAAAGFtpkiafegEEDSTI---AGL-----------------VAAGLGVAILPE- 151

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 2171225192 289 VRNISDGNVVLRQVEDLTTELILGVVWRADSP-APGIAPFIEYA 331
Cdd:cd08434   152 MTLLNPPGVKKIPIKDPDAERTIGLAWLKDRYlSPAARRFKDFV 195
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
62-230 5.17e-05

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 44.62  E-value: 5.17e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192  62 AAVRLRLTQSTLSQRIRRLESEVGVPLFLRSTRNVELTEAGKTFLPLARDILIKldeatlLSRIAAGGVSPGDEQLNIAT 141
Cdd:PRK15421   22 AAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQ------ISQALQACNEPQQTRLRIAI 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 142 IGPAAYRLLPLILRRFCAGRPKTGLDVKICDSTELVRLLEHGDYHVGLMRAPSNVNFLRFKPLISERFLAVIPKQSDLAN 221
Cdd:PRK15421   96 ECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLHYSPMFDYEVRLVLAPDHPLAA 175


                  ....*....
gi 2171225192 222 ATSLHLEDF 230
Cdd:PRK15421  176 KTRITPEDL 184
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 136-234 5.41e-05

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: 43.42  E-value: 5.41e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 136 QLNIATIGPAAYRLLPLILRRFCAGRPKTGLDVKICDSTELVRLLEHG--DYHVGLMRAPSNVNFLRFKPLISERFLAVI 213
Cdd:cd08435     1 TVRVGAVPAAAPVLLPPAIARLLARHPRLTVRVVEGTSDELLEGLRAGelDLAIGRLADDEQPPDLASEELADEPLVVVA 80

                          90       100
                  ....*....|....*....|.
gi 2171225192 214 PKQSDLANATSLHLEDFVGHR 234
Cdd:cd08435    81 RPGHPLARRARLTLADLADYP 101
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 50-177 8.22e-05

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 43.52  E-value: 8.22e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192  50 FVAVAEELHFGRAAVRLRLTQSTLSQRIRRLESEVGVPLFLRSTRNVELTEAGKTFLPLAR-------DI--LIKLDEAT 120
Cdd:PRK10837   11 FAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALalleqavEIeqLFREDNGA 90

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2171225192 121 LlsRIAAGgvspgdeqlniATIGpaAYrLLPLILRRFCAGRPKTGLDVKICDSTELV 177
Cdd:PRK10837   91 L--RIYAS-----------STIG--NY-ILPAMIARYRRDYPQLPLELSVGNSQDVI 131
PBP2_CbnR cd08486
The C-terminal substrate binding domain of LysR-type transcriptional regulator, CbnR, involved ...
 136-330 5.70e-04

The C-terminal substrate binding domain of LysR-type transcriptional regulator, CbnR, involved in the chlorocatechol catabolism, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of LysR-type regulator CbnR which is 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. 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: 176175  Cd Length: 198  Bit Score: 40.46  E-value: 5.70e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 136 QLNIATIGPAAYRLLPLILRRFCAGRPKTGLDVKICDSTELVRLLEHGDYHVGLMR-APSNVNFLRFKPLISERFLAVIP 214
Cdd:cd08486     2 ELSVAYFGTPIYRSLPLLLRAFLTSTPTATVSLTHMTKDEQVEGLLAGTIHVGFSRfFPRHPGIEIVNIAQEDLYLAVHR 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 215 KQSDLANATSlHLEDFvghRCFTLKRFEISG----FEEVHQMVLHAGVEIDNRISASTTSAALALASAGVGVTFLPSWVR 290
Cdd:cd08486    82 SQSGKFGKTC-KLADL---RAVELTLFPRGGrpsfADEVIGLFKHAGIEPRIARVVEDATAALALTMAGAASSIVPASVA 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 2171225192 291 NISDGNVVLRQVEDLTTELILGVVWRADSPAPGIAPFIEY 330
Cdd:cd08486   158 AIRWPDIAFARIVGTRVKVPISCIFRKEKQPPILARFVEH 197
PBP2_Chlorocatechol cd08446
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 136-329 1.53e-03

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: 39.19  E-value: 1.53e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 136 QLNIATIGPAAYRLLPLILRRFCAGRPKTGLDVKICDSTELVRLLEHGDYHVGLMRAPSNVNFLRFKPLISERFLAVIPK 215
Cdd:cd08446     2 ELDVGYFGSAILDTVPRLLRAFLTARPDVTVSLHNMTKDEQIEALRAGRIHIGFGRFYPVEPDIAVENVAQERLYLAVPK 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 216 QSDLANATSLHLEDFVGHRCFTLKRFEISGF-EEVHQMVLHAGVEIDNRISASTTSAALALASAGVGVTFLPSWVRNISD 294
Cdd:cd08446    82 SHPLAARPAVSLADLRNEPLILFPRGGRPSFaDEVLGLFRRAGVEPRVAQEVEDVVAALALVAAGFGVCIVPESVAALRW 161

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 2171225192 295 GNVVLRQVEDLTTELILGVVWRADSPAPGIAPFIE 329
Cdd:cd08446   162 PGVVFRPLADAEAKVPLSCIYRKDDRSPILRAFLD 196
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 136-234 3.71e-03

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: 37.86  E-value: 3.71e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 136 QLNI-ATIGPAAYrLLPLILRRFCAGRPKTGLDVKICDSTELVRLLEHGDYHVGLMRAPSNVNFLRFKPLISERFLAVIP 214
Cdd:cd08420     1 TLRIgASTTIGEY-LLPRLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLVEGPVDHPDLIVEPFAEDELVLVVP 79

                          90       100
                  ....*....|....*....|
gi 2171225192 215 KQSDLANATSLHLEDFVGHR 234
Cdd:cd08420    80 PDHPLAGRKEVTAEELAAEP 99
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 136-234 5.95e-03

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


Pssm-ID: 176117 [Multi-domain]  Cd Length: 199  Bit Score: 37.29  E-value: 5.95e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 136 QLNIATIGPAAYRLLPLILRRFCAGRPKTGLDVKICDSTELVRLLEHGDYHVGL---MRAPSNVNFLRFKPLiseRFLAV 212
Cdd:cd08426     1 RVRVATGEGLAAELLPSLIARFRQRYPGVFFTVDVASTADVLEAVLSGEADIGLafsPPPEPGIRVHSRQPA---PIGAV 77

                          90       100
                  ....*....|....*....|..
gi 2171225192 213 IPKQSDLANATSLHLEDFVGHR 234
Cdd:cd08426    78 VPPGHPLARQPSVTLAQLAGYP 99
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 203-322 5.99e-03

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: 37.54  E-value: 5.99e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 203 PLISERFLAVIPKQSDLANATSLHLEDFVGHRcFTLkrFEiSGFEeVHQMVL----HAGVEIDNRISASTTSAALALASA 278
Cdd:cd08438    68 PLCNEPLVAVLPRGHPLAGRKTVSLADLADEP-FIL--FN-EDFA-LHDRIIdacqQAGFTPNIAARSSQWDFIAELVAA 142

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 2171225192 279 GVGVTFLP-SWVRNISDGNVVLRQVEDLTTELILGVVWRADSPAP 322
Cdd:cd08438   143 GLGVALLPrSIAQRLDNAGVKVIPLTDPDLRWQLALIWRKGRYLS 187
nhaR PRK11062
transcriptional activator NhaR; Provisional
 39-102 6.89e-03

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 37.68  E-value: 6.89e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2171225192  39 NHPLDLWSV--KGFVAvaeelhfgRAAVRLRLTQSTLSQRIRRLESEVGVPLFLRSTRNVELTEAG 102
Cdd:PRK11062    7 NHLYYFWMVckEGSVV--------GAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELG 64
PBP2_YofA_SoxR_like cd08442
The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, ...
 145-329 8.90e-03

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


Pssm-ID: 176133  Cd Length: 193  Bit Score: 36.82  E-value: 8.90e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 145 AAYRLlPLILRRFCAGRPKTGLDVKICDSTELVRLLEHGDYHVGLMRAPSNVNFLRFKPLISERFLAVIPKQ-------S 217
Cdd:cd08442    11 AAVRL-PPLLAAYHARYPKVDLSLSTGTTGALIQAVLEGRLDGAFVAGPVEHPRLEQEPVFQEELVLVSPKGhppvsraE 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171225192 218 DLANATSLhledFVGHRCFTLKRFE------------ISGFEEVHQMVlhAGVEidnrisasttsaalalasAGVGVTFL 285
Cdd:cd08442    90 DLAGSTLL----AFRAGCSYRRRLEdwlaeegvspgkIMEFGSYHAIL--GCVA------------------AGMGIALL 145

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 2171225192 286 PSWVRNISDGNVVLRQVE------DLTTELilgvVWRADSPAPGIAPFIE 329
Cdd:cd08442   146 PRSVLDSLQGRGSVSIHPlpepfaDVTTWL----VWRKDSFTAALQAFLD 191
 
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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