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Conserved domains on  [gi|480205230|gb|ENX41026|]
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hypothetical protein F887_02508 [Acinetobacter sp. NIPH 2100]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 11426483)

LysR family transcriptional regulator containing an N-terminal HTH (helix-turn-helix) DNA-binding domain and a C-terminal substrate binding domain, which is structurally homologous to the type 2 periplasmic-binding (PBP2) fold proteins

CATH:  3.40.190.10
Gene Ontology:  GO:0003700|GO:0003677|GO:0006355
PubMed:  19047729|8257110|15808743
SCOP:  4000316

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-258 1.00e-50

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 168.12  E-value: 1.00e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230   1 MNLKNLEAFYWVVTLNSFNKAAAKLQTTQPAVSQKITALENDLGFKVLDRSFRQLKPTHKGMTLFKYAEKLMRLETELIA 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230  81 ELTD-NQHLTGTIRLGVSETIVYTWLVEYIEKVQQEYPKVSVEIVVDLTPNLQEGVRTGDLDMAFLLGPTLAFECIEQAL 159
Cdd:COG0583   81 ELRAlRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230 160 CDFELSFLASPSfkggvgqmsfktlmshtiltYPkitypykelkakmkeqgLDEPLSITSySLATLLRLAEQGLGIAVVP 239
Cdd:COG0583  161 GEERLVLVASPD--------------------HP-----------------LARRAPLVN-SLEALLAAVAAGLGIALLP 202

                        250
                 ....*....|....*....
gi 480205230 240 TLTALKEITDGRLEILNTP 258
Cdd:COG0583  203 RFLAADELAAGRLVALPLP 221
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-258 1.00e-50

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 168.12  E-value: 1.00e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230   1 MNLKNLEAFYWVVTLNSFNKAAAKLQTTQPAVSQKITALENDLGFKVLDRSFRQLKPTHKGMTLFKYAEKLMRLETELIA 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230  81 ELTD-NQHLTGTIRLGVSETIVYTWLVEYIEKVQQEYPKVSVEIVVDLTPNLQEGVRTGDLDMAFLLGPTLAFECIEQAL 159
Cdd:COG0583   81 ELRAlRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230 160 CDFELSFLASPSfkggvgqmsfktlmshtiltYPkitypykelkakmkeqgLDEPLSITSySLATLLRLAEQGLGIAVVP 239
Cdd:COG0583  161 GEERLVLVASPD--------------------HP-----------------LARRAPLVN-SLEALLAAVAAGLGIALLP 202

                        250
                 ....*....|....*....
gi 480205230 240 TLTALKEITDGRLEILNTP 258
Cdd:COG0583  203 RFLAADELAAGRLVALPLP 221
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-274 1.29e-34

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


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 127.35  E-value: 1.29e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230   1 MNLKNLEAFYWVVTLNSFNKAAAKLQTTQPAVSQKITALENDLGFKVLDRSFRQLKPTHKGMTLFKYAEKLMRLETELIA 80
Cdd:NF040786   1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230  81 ELTDNQ-HLTGTIRLGVSETIVYTWLVEYIEKVQQEYPKVSVEIVVDLTPNLQEGVRTGDLDMAFLLGPTLAFECIEQAL 159
Cdd:NF040786  81 EFDRYGkESKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKKRLVYTPF 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230 160 CDFELSfLASPSFKGGVGQMSFKTLMSHtILTYPKI-------TypYKELKAKMKEQGLDEP-----LSITsySLATLLR 227
Cdd:NF040786 161 YKDRLV-LITPNGTEKYRMLKEEISISE-LQKEPFImreegsgT--RKEAEKALKSLGISLEdlnvvASLG--STEAIKQ 234

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*..
gi 480205230 228 LAEQGLGIAVVPTLTALKEITDGRLEILNTPIQLKTFHFTSIYIQGN 274
Cdd:NF040786 235 SVEAGLGISVISELAAEKEVERGRVLIFPIPGLPKNRDFYLVYNKNR 281
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 89-258 8.20e-29

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: 109.30  E-value: 8.20e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230   89 TGTIRLGVSETIVYTWLVEYIEKVQQEYPKVSVEIVVDLTPNLQEGVRTGDLDMAFLLGPTLAFECIEQALCDFELSFLA 168
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230  169 SPSFK-GGVGQMSFKTLMSHTILTYPKITYPYKELKAKMKEQGLDEPLSITSYSLATLLRLAEQGLGIAVVPTLTALKEI 247
Cdd:pfam03466  81 PPDHPlARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAREL 160

                         170
                  ....*....|.
gi 480205230  248 TDGRLEILNTP 258
Cdd:pfam03466 161 ADGRLVALPLP 171
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 91-255 3.27e-22

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: 91.51  E-value: 3.27e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230  91 TIRLGVSETIVYTWLVEYIEKVQQEYPKVSVEIVVDLTPNLQEGVRTGDLDMAFLLGPTLAFECIEQALCDFELSFLASP 170
Cdd:cd05466    1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230 171 SFK-GGVGQMSFKTLMSHTILTYPKITYPYKELKAKMKEQGLDEPLSITSYSLATLLRLAEQGLGIAVVPTLtALKEITD 249
Cdd:cd05466   81 DHPlAKRKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPES-AVEELAD 159


                 ....*.
gi 480205230 250 GRLEIL 255
Cdd:cd05466  160 GGLVVL 165
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
2-252 3.65e-20

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 88.10  E-value: 3.65e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230   2 NLKNLEAFYWVVTLNSFNKAAAKLQTTQPAVSQKITALENDLGFKVLDRSfRQLKPTHKGMTLFKYAEKLMRLETELIAE 81
Cdd:PRK13348   3 DYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRG-RPCRPTPAGQRLLRHLRQVALLEADLLST 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230  82 LTDNQHLTGTIRLGVSETIVYTWLVEYIEKVQQEyPKVSVEIVVDLTPNLQEGVRTGDLdMAFLLG-PTLAFECIEQALC 160
Cdd:PRK13348  82 LPAERGSPPTLAIAVNADSLATWFLPALAAVLAG-ERILLELIVDDQDHTFALLERGEV-VGCVSTqPKPMRGCLAEPLG 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230 161 DFELSFLASPSF-----KGGVGQmsfktlmsHTILTYPKITYPYKElkaKMKEQGLDE--PLSITSY------SLATLLR 227
Cdd:PRK13348 160 TMRYRCVASPAFaaryfAQGLTR--------HSALKAPAVAFNRKD---TLQDSFLEQlfGLPVGAYprhyvpSTHAHLA 228

                        250       260
                 ....*....|....*....|....*
gi 480205230 228 LAEQGLGIAVVPTLTALKEITDGRL 252
Cdd:PRK13348 229 AIRHGLGYGMVPELLIGPLLAAGRL 253
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 1-252 1.51e-15

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: 75.54  E-value: 1.51e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230   1 MNLKNLEAFYWVVTLNSFNKAAAKLQTTQPAVSQKITALENDLGFKVLDRSFRQLKPTHKGMTLFKYAEKLMRLETELIA 80
Cdd:NF041036   1 METRYLKTLVIVAEEGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRILDIEDSLMD 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230  81 ELtdnQHLTGTIRLGVSETIvyTWLVEYIEKVQQEYPKVSVEIvVDL-----TPnLQ--EGVRTGDLDMAFL-------L 146
Cdd:NF041036  81 EL---KSFKGRQRLSICCTP--TFGMAHLPGVLNRFMLRNADV-VDLkflfhSP-AQalEGIQNKEFDLAIIehcadldL 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230 147 GPTLAFEcieqaLCDFELSFLASPSFKGGVGQMSFKTLMSHTILTYPKITYPYKELKAKMKEQGLDepLS-----ITSYS 221
Cdd:NF041036 154 GRFHTYP-----LPQDELVFVSAPSLGLPTPNVTLERLLELCLITRRDGCSSRDLLRRNLAEQGRD--LDdfrrvVVSDD 226

                        250       260       270
                 ....*....|....*....|....*....|.
gi 480205230 222 LATLLRLAEQGLGIAVVPTLTALKEITDGRL 252
Cdd:NF041036 227 LRLTIQTVLDGGGISFVSRSLVCEYLKNGQL 257
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-258 1.00e-50

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 168.12  E-value: 1.00e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230   1 MNLKNLEAFYWVVTLNSFNKAAAKLQTTQPAVSQKITALENDLGFKVLDRSFRQLKPTHKGMTLFKYAEKLMRLETELIA 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230  81 ELTD-NQHLTGTIRLGVSETIVYTWLVEYIEKVQQEYPKVSVEIVVDLTPNLQEGVRTGDLDMAFLLGPTLAFECIEQAL 159
Cdd:COG0583   81 ELRAlRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230 160 CDFELSFLASPSfkggvgqmsfktlmshtiltYPkitypykelkakmkeqgLDEPLSITSySLATLLRLAEQGLGIAVVP 239
Cdd:COG0583  161 GEERLVLVASPD--------------------HP-----------------LARRAPLVN-SLEALLAAVAAGLGIALLP 202

                        250
                 ....*....|....*....
gi 480205230 240 TLTALKEITDGRLEILNTP 258
Cdd:COG0583  203 RFLAADELAAGRLVALPLP 221
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-274 1.29e-34

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


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 127.35  E-value: 1.29e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230   1 MNLKNLEAFYWVVTLNSFNKAAAKLQTTQPAVSQKITALENDLGFKVLDRSFRQLKPTHKGMTLFKYAEKLMRLETELIA 80
Cdd:NF040786   1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230  81 ELTDNQ-HLTGTIRLGVSETIVYTWLVEYIEKVQQEYPKVSVEIVVDLTPNLQEGVRTGDLDMAFLLGPTLAFECIEQAL 159
Cdd:NF040786  81 EFDRYGkESKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKKRLVYTPF 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230 160 CDFELSfLASPSFKGGVGQMSFKTLMSHtILTYPKI-------TypYKELKAKMKEQGLDEP-----LSITsySLATLLR 227
Cdd:NF040786 161 YKDRLV-LITPNGTEKYRMLKEEISISE-LQKEPFImreegsgT--RKEAEKALKSLGISLEdlnvvASLG--STEAIKQ 234

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*..
gi 480205230 228 LAEQGLGIAVVPTLTALKEITDGRLEILNTPIQLKTFHFTSIYIQGN 274
Cdd:NF040786 235 SVEAGLGISVISELAAEKEVERGRVLIFPIPGLPKNRDFYLVYNKNR 281
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 89-258 8.20e-29

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: 109.30  E-value: 8.20e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230   89 TGTIRLGVSETIVYTWLVEYIEKVQQEYPKVSVEIVVDLTPNLQEGVRTGDLDMAFLLGPTLAFECIEQALCDFELSFLA 168
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230  169 SPSFK-GGVGQMSFKTLMSHTILTYPKITYPYKELKAKMKEQGLDEPLSITSYSLATLLRLAEQGLGIAVVPTLTALKEI 247
Cdd:pfam03466  81 PPDHPlARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAREL 160

                         170
                  ....*....|.
gi 480205230  248 TDGRLEILNTP 258
Cdd:pfam03466 161 ADGRLVALPLP 171
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 91-255 3.27e-22

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: 91.51  E-value: 3.27e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230  91 TIRLGVSETIVYTWLVEYIEKVQQEYPKVSVEIVVDLTPNLQEGVRTGDLDMAFLLGPTLAFECIEQALCDFELSFLASP 170
Cdd:cd05466    1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230 171 SFK-GGVGQMSFKTLMSHTILTYPKITYPYKELKAKMKEQGLDEPLSITSYSLATLLRLAEQGLGIAVVPTLtALKEITD 249
Cdd:cd05466   81 DHPlAKRKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPES-AVEELAD 159


                 ....*.
gi 480205230 250 GRLEIL 255
Cdd:cd05466  160 GGLVVL 165
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
2-252 3.65e-20

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 88.10  E-value: 3.65e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230   2 NLKNLEAFYWVVTLNSFNKAAAKLQTTQPAVSQKITALENDLGFKVLDRSfRQLKPTHKGMTLFKYAEKLMRLETELIAE 81
Cdd:PRK13348   3 DYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRG-RPCRPTPAGQRLLRHLRQVALLEADLLST 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230  82 LTDNQHLTGTIRLGVSETIVYTWLVEYIEKVQQEyPKVSVEIVVDLTPNLQEGVRTGDLdMAFLLG-PTLAFECIEQALC 160
Cdd:PRK13348  82 LPAERGSPPTLAIAVNADSLATWFLPALAAVLAG-ERILLELIVDDQDHTFALLERGEV-VGCVSTqPKPMRGCLAEPLG 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230 161 DFELSFLASPSF-----KGGVGQmsfktlmsHTILTYPKITYPYKElkaKMKEQGLDE--PLSITSY------SLATLLR 227
Cdd:PRK13348 160 TMRYRCVASPAFaaryfAQGLTR--------HSALKAPAVAFNRKD---TLQDSFLEQlfGLPVGAYprhyvpSTHAHLA 228

                        250       260
                 ....*....|....*....|....*
gi 480205230 228 LAEQGLGIAVVPTLTALKEITDGRL 252
Cdd:PRK13348 229 AIRHGLGYGMVPELLIGPLLAAGRL 253
rbcR CHL00180
LysR transcriptional regulator; Provisional
 3-147 3.87e-18

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 82.76  E-value: 3.87e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230   3 LKNLEAFYWVVTLNSFNKAAAKLQTTQPAVSQKITALENDLGFKVLDRSFRQLKPTHKGMTLFKYAEKLMRLETELIAEL 82
Cdd:CHL00180   7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRAL 86

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 480205230  83 TDNQHL-TGTIRLGVSETIvYTWLV-EYIEKVQQEYPKVSVEIVVDLTPNLQEGVRTGDLDMAFLLG 147
Cdd:CHL00180  87 EDLKNLqRGTLIIGASQTT-GTYLMpRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVGG 152
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
1-252 1.00e-16

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 78.66  E-value: 1.00e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230   1 MNLKNLEAFYWVVTLNSFNKAAAKLQTTQPAVSQKITALENDLGFKVLDRSfRQLKPTHKGMTLFKYAEKLMRLETELIA 80
Cdd:PRK03635   2 LDYKQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVRT-QPCRPTEAGQRLLRHARQVRLLEAELLG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230  81 ELTDNQHLTGTIRLGVSETIVYTWLVEYIEKVQQEYPkVSVEIVV---DLTPNLqegVRTGDLDMAFLLGPTLAFECIEQ 157
Cdd:PRK03635  81 ELPALDGTPLTLSIAVNADSLATWFLPALAPVLARSG-VLLDLVVedqDHTAEL---LRRGEVVGAVTTEPQPVQGCRVD 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230 158 ALCDFELSFLASPSF-----KGGVGQmsfktlmsHTILTYPKITY-PYKELKAKMKEQGLDEPLSITSY----SLATLLR 227
Cdd:PRK03635 157 PLGAMRYLAVASPAFaaryfPDGVTA--------EALAKAPAVVFnRKDDLQDRFLRQAFGLPPGSVPChyvpSSEAFVR 228

                        250       260
                 ....*....|....*....|....*
gi 480205230 228 LAEQGLGIAVVPTLTALKEITDGRL 252
Cdd:PRK03635 229 AALAGLGWGMIPELQIEPELASGEL 253
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
3-255 7.06e-16

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 76.34  E-value: 7.06e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230   3 LKNLEAFYWVVTLNSFNKAAAKLQTTQPAVSQKITALENDLGFKVLDRSFRQLKPTHKGMTLFKYAEKLMRLETELIAEL 82
Cdd:PRK10632   4 LKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQL 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230  83 -TDNQHLTGTIRLGVSETIVYTWLVEYIEKVQQEYPKVSVEIVV-----DLTPN-LQEGVRTGDLDMAFLLGPTLAfeCI 155
Cdd:PRK10632  84 yAFNNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTgipapDLIADgLDVVIRVGALQDSSLFSRRLG--AM 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230 156 EQALCDFElSFLASPSFKGGVGQMSfktlmSHTILTYPkiTYPYKELKAkMKEQGLDEPLS-----ITSYSLaTLLRLAE 230
Cdd:PRK10632 162 PMVVCAAK-SYLAQYGTPEKPADLS-----SHSWLEYS--VRPDNEFEL-IAPEGISTRLIpqgrfVTNDPQ-TLVRWLT 231

                        250       260
                 ....*....|....*....|....*
gi 480205230 231 QGLGIAVVPTLTALKEITDGRLEIL 255
Cdd:PRK10632 232 AGAGIAYVPLMWVIDEINRGELEIL 256
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 17-252 7.99e-16

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 76.04  E-value: 7.99e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230  17 SFNKAAAKLQTTQPAVSQKITALENDLGFKVLDRSFRQLKPTHKGMTLF---KYAEKLMRLETELIAELTDNQHLtgTIR 93
Cdd:PRK11139  22 SFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFldiREIFDQLAEATRKLRARSAKGAL--TVS 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230  94 LGVSETIvyTWLVEYIEKVQQEYPKVSVEIvvdLTPNLQEGVRTGDLDMAFLLG----PTLAFEcieqALCDFELSFLAS 169
Cdd:PRK11139 100 LLPSFAI--QWLVPRLSSFNEAHPDIDVRL---KAVDRLEDFLRDDVDVAIRYGrgnwPGLRVE----KLLDEYLLPVCS 170

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230 170 PSFKGgvGQMSFKT---LMSHTILtypKITYPyKELKAKMKEQGLDEpLSI---TSYSLATL-LRLAEQGLGIAVVPTLT 242
Cdd:PRK11139 171 PALLN--GGKPLKTpedLARHTLL---HDDSR-EDWRAWFRAAGLDD-LNVqqgPIFSHSSMaLQAAIHGQGVALGNRVL 243

                        250
                 ....*....|
gi 480205230 243 ALKEITDGRL 252
Cdd:PRK11139 244 AQPEIEAGRL 253
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 1-252 1.51e-15

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: 75.54  E-value: 1.51e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230   1 MNLKNLEAFYWVVTLNSFNKAAAKLQTTQPAVSQKITALENDLGFKVLDRSFRQLKPTHKGMTLFKYAEKLMRLETELIA 80
Cdd:NF041036   1 METRYLKTLVIVAEEGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRILDIEDSLMD 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230  81 ELtdnQHLTGTIRLGVSETIvyTWLVEYIEKVQQEYPKVSVEIvVDL-----TPnLQ--EGVRTGDLDMAFL-------L 146
Cdd:NF041036  81 EL---KSFKGRQRLSICCTP--TFGMAHLPGVLNRFMLRNADV-VDLkflfhSP-AQalEGIQNKEFDLAIIehcadldL 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230 147 GPTLAFEcieqaLCDFELSFLASPSFKGGVGQMSFKTLMSHTILTYPKITYPYKELKAKMKEQGLDepLS-----ITSYS 221
Cdd:NF041036 154 GRFHTYP-----LPQDELVFVSAPSLGLPTPNVTLERLLELCLITRRDGCSSRDLLRRNLAEQGRD--LDdfrrvVVSDD 226

                        250       260       270
                 ....*....|....*....|....*....|.
gi 480205230 222 LATLLRLAEQGLGIAVVPTLTALKEITDGRL 252
Cdd:NF041036 227 LRLTIQTVLDGGGISFVSRSLVCEYLKNGQL 257
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-61 2.49e-15

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 68.95  E-value: 2.49e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 480205230    3 LKNLEAFYWVVTLNSFNKAAAKLQTTQPAVSQKITALENDLGFKVLDRSFRQLKPTHKG 61
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 6-143 4.24e-15

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 74.29  E-value: 4.24e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230   6 LEAFYWVVTLNSFNKAAAKLQTTQPAVSQKITALENDLGFKVLDRSFRQLKPTHKGMTLFKYAEKLMRLETELIAELTDN 85
Cdd:PRK15092  16 LRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEACSSLMYS 95

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 480205230  86 QhLTGTIRLGVSETIVYTWLVEYIEKVQQEYPKVSVEIVVDLTPNLQEGVRTGDLDMA 143
Cdd:PRK15092  96 N-LQGVLTIGASDDTADTILPFLLNRVSSVYPKLALDVRVKRNAFMMEMLESQEVDLA 152
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
3-143 1.39e-14

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 72.73  E-value: 1.39e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230   3 LKNLEAFYWVVTLNSFNKAAAKLQTTQPAVSQKITALENDLGFKVLDRSFRQLKPTHKGMTLFKYAEKLMRletELIAEL 82
Cdd:PRK10086  16 LSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLD---TLNQEI 92

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 480205230  83 TD--NQHLTGTIRLGVSETIVYTWLVEYIEKVQQEYPKVSVEIvvdLTPNLQEGVRTGDLDMA 143
Cdd:PRK10086  93 LDikNQELSGTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTI---LTGNENVNFQRAGIDLA 152
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 1-147 1.78e-12

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 66.63  E-value: 1.78e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230   1 MNLKNLEAFYWVVTLNSFNKAAAKLQTTQPAVSQKITALENDLGFKVLDRSFRQLKPTHKGMTLFKYAEKLMR-LETELI 79
Cdd:PRK11233   1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRqCEQAQL 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 480205230  80 AELTDNQHLTGTIRLGVSE-TIVYTWLVEYIEKVQQEYPkvsvEIVVDLTPN----LQEGVRTGDLDMAFLLG 147
Cdd:PRK11233  81 AVHNVGQALSGQVSIGLAPgTAASSLTMPLLQAVRAEFP----GIVLYLHENsgatLNEKLMNGQLDMAVIYE 149
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 3-171 2.04e-12

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 66.25  E-value: 2.04e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230   3 LKNLEAFYWVVTLNSFNKAAAKLQTTQPAVSQKITALENDLGFKVLDRSFRQLKPTHKGMTLFKYAEKLMRLETElIAEL 82
Cdd:PRK10837   5 LRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQAVE-IEQL 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230  83 TdnQHLTGTIRLGVSETIVYTWLVEYIEKVQQEYPKVSVEIVVDLTPNLQEGVRTGDLDMAFLLGPTLAFECIEQALCDF 162
Cdd:PRK10837  84 F--REDNGALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNSQDVINAVLDFRVDIGLIEGPCHSPELISEPWLED 161


                 ....*....
gi 480205230 163 ELSFLASPS 171
Cdd:PRK10837 162 ELVVFAAPD 170
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 1-123 1.67e-11

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 63.44  E-value: 1.67e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230   1 MNLKNLEAFYWVVTLNSFNKAAAKLQTTQPAVSQKITALENDLGFKVLDRSFRQLKPTHKGMTLFKYAEKLMR-LETELI 79
Cdd:PRK11242   1 MLLRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQdLEAGRR 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 480205230  80 AeLTDNQHLT-GTIRLGVSETIVyTWLV-EYIEKVQQEYPKVSVEI 123
Cdd:PRK11242  81 A-IHDVADLSrGSLRLAMTPTFT-AYLIgPLIDAFHARYPGITLTI 124
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 90-255 3.15e-11

The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; This CD includes the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA and its related homologs. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis further showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. 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: 176114 [Multi-domain]  Cd Length: 197  Bit Score: 61.30  E-value: 3.15e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230  90 GTIRLGVSETIVYTWLVEYIEKVQQEYPKVSVEIV-----VDLtpnLQEGVrtgdlDMAFLLGPTLAFECIEQALCDFEL 164
Cdd:cd08422    1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVlsdrlVDL---VEEGF-----DLAIRIGELPDSSLVARRLGPVRR 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230 165 SFLASPSF--KGGVGQmSFKTLMSHTILTYpkiTYPYKELKAKMKEQGLDEPLSITSY----SLATLLRLAEQGLGIAVV 238
Cdd:cd08422   73 VLVASPAYlaRHGTPQ-TPEDLARHRCLGY---RLPGRPLRWRFRRGGGEVEVRVRGRlvvnDGEALRAAALAGLGIALL 148

                        170
                 ....*....|....*..
gi 480205230 239 PTLTALKEITDGRLEIL 255
Cdd:cd08422  149 PDFLVAEDLASGRLVRV 165
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
1-239 4.53e-11

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 62.34  E-value: 4.53e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230   1 MNLKNLEAFYWVVTLNSFNKAAAKLQTTQPAVSQKITALENDLGFKVLDRSFRQLKPTHKGMTLFKYAEKLMRLETELIA 80
Cdd:PRK15421   2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQ 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230  81 ELTDNQHLtgTIRLGVSETIVYTWLVEYIEKVQQEYPKVSVEIVVDLTPNLQEGVRTGDLDMAfLLGPTLAFECIEQA-L 159
Cdd:PRK15421  82 ACNEPQQT--RLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLV-MTSDILPRSGLHYSpM 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230 160 CDFELSFLASPSFK-GGVGQMSFKTLMSHTILTYPKITYPYKELKAKMKEQGLDEPLSITSYSLaTLLRLAEQGLGIAVV 238
Cdd:PRK15421 159 FDYEVRLVLAPDHPlAAKTRITPEDLASETLLIYPVQRSRLDVWRHFLQPAGVSPSLKSVDNTL-LLIQMVAARMGIAAL 237


                 .
gi 480205230 239 P 239
Cdd:PRK15421 238 P 238
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 1-123 6.32e-11

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 61.93  E-value: 6.32e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230   1 MNLKNLEaFYWVVTLNSFN--KAAAKLQTTQPAVSQKITALENDLGFKVLDRSFRQLKP-THKGMTLFKYAEKLMRLETE 77
Cdd:PRK12682   1 MNLQQLR-FVREAVRRNLNltEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKGlTEPGKAVLDVIERILREVGN 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 480205230  78 L--IAELTDNQHlTGTIRLGVSETIVYTWLVEYIEKVQQEYPKVSVEI 123
Cdd:PRK12682  80 IkrIGDDFSNQD-SGTLTIATTHTQARYVLPRVVAAFRKRYPKVNLSL 126
PRK10341 PRK10341
transcriptional regulator TdcA;
4-270 1.16e-10

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 61.42  E-value: 1.16e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230   4 KNLEAFYWVVTLNSFNKAAAKLQTTQPAVSQKITALENDLGFKVLDRSFRQLKPTHKGMTLFKYAEKLMRLETELIAELt 83
Cdd:PRK10341  10 QHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEI- 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230  84 dnQHLTGT----IRLGVSETIVYTWLVEYIEKVQQEYPKVSVEIVVDLTPNLQEGVRTGDLDMAF--LLGPTLAFECIEQ 157
Cdd:PRK10341  89 --NGMSSEavvdVSFGFPSLIGFTFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIgtLSNEMKLQDLHVE 166

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230 158 ALCDFELSFLASPSfKGGVGQMSFKTL------MSHTILTYpkitypYKELKAKMKEQGLDEPLSITSYSLATLLRLAEQ 231
Cdd:PRK10341 167 PLFESEFVLVASKS-RTCTGTTTLESLkneqwvLPQTNMGY------YSELLTTLQRNGISIENIVKTDSVVTIYNLVLN 239

                        250       260       270
                 ....*....|....*....|....*....|....*....
gi 480205230 232 GLGIAVVPTLTAlKEITDGRLEILNTPIQLKTFHFTSIY 270
Cdd:PRK10341 240 ADFLTVIPCDMT-SPFGSNQFITIPIEETLPVAQYAAVW 277
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 91-259 1.65e-10

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: 59.59  E-value: 1.65e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230  91 TIRLGVSETIVYTWLVEYIEKVQQEYPKVSVEIVVDLTPNLQEGVRTGDLDMAF-LLGPTLAFECIE-QALCDFELSFLA 168
Cdd:cd08435    1 TVRVGAVPAAAPVLLPPAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAIgRLADDEQPPDLAsEELADEPLVVVA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230 169 S---PSFKGgvGQMSFKTLMSHTILTYPKITYPYKELKAKMKEQGLDEPLSIT-SYSLATLLRLAEQGLGIAVVPTLTAL 244
Cdd:cd08435   81 RpghPLARR--ARLTLADLADYPWVLPPPGTPLRQRLEQLFAAAGLPLPRNVVeTASISALLALLARSDMLAVLPRSVAE 158

                        170
                 ....*....|....*
gi 480205230 245 KEITDGRLEILNTPI 259
Cdd:cd08435  159 DELRAGVLRELPLPL 173
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 90-253 2.00e-10

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: 59.08  E-value: 2.00e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230  90 GTIRLGVSETIVYTWLVEYIEKVQQEYPKVSVEIVVDLTPNLQEGVRTGDLDMAFLLGPTLAFECIEQALCDFELsFLAS 169
Cdd:cd08411    1 GPLRLGVIPTIAPYLLPRLLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAALLALPVDEPGLEEEPLFDEPF-LLAV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230 170 PSfkggvgqmsfktlmSHTILTYPKITypYKELKAK----------MKEQ--------GLDEPLSITSYSLATLLRLAEQ 231
Cdd:cd08411   80 PK--------------DHPLAKRKSVT--PEDLAGErlllleeghcLRDQalelcrlaGAREQTDFEATSLETLRQMVAA 143

                        170       180
                 ....*....|....*....|..
gi 480205230 232 GLGIAVVPTLTALKEITDGRLE 253
Cdd:cd08411  144 GLGITLLPELAVPSEELRGDRL 165
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 1-145 2.57e-10

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 60.04  E-value: 2.57e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230   1 MNLKNLEafyWVVTL---NSFNKAAAKLQTTQPAVSQKITALENDLGFKVLDRSFRQLKPTHKGMTLFKYAEKLMRlETE 77
Cdd:PRK11151   1 MNIRDLE---YLVALaehRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLR-EVK 76

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230  78 LIAELTDNQ--HLTGTIRLGVSETIVYTWLVEYIEKVQQEYPKVSVEIVVDLTPNLQEGVRTGDLDMAFL 145
Cdd:PRK11151  77 VLKEMASQQgeTMSGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCAIL 146
PBP2_CrgA_like_7 cd08476
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-252 4.25e-10

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 7. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. 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: 176165  Cd Length: 197  Bit Score: 58.02  E-value: 4.25e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230  93 RLGVSETIVYTWLVEYIEKVQQEYPKVSVEI-----VVDLtpnLQEG----VRTGDLD----MAFLLGPtlafecieqal 159
Cdd:cd08476    2 RLRVSLPLVGGLLLPVLAAFMQRYPEIELDLdfsdrLVDV---IDEGfdavIRTGELPdsrlMSRRLGS----------- 67

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230 160 cdFELSFLASPSFKGGVGQ-MSFKTLMSHTILTYpkiTYPYK------ELKAKMKEQGLDEPLSITSYSLATLLRLAEQG 232
Cdd:cd08476   68 --FRMVLVASPDYLARHGTpETPADLAEHACLRY---RFPTTgklepwPLRGDGGDPELRLPTALVCNNIEALIEFALQG 142

                        170       180
                 ....*....|....*....|
gi 480205230 233 LGIAVVPTLTALKEITDGRL 252
Cdd:cd08476  143 LGIACLPDFSVREALADGRL 162
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
3-260 1.25e-09

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 58.14  E-value: 1.25e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230   3 LKNLEA--FYWVVTLN---SFNKAAAKLQTTQPAVSQKITALENDLGFKVLDRSFRQLKPTHKGMTLFKYAEKLM-RLET 76
Cdd:PRK10082   8 LHNIETkwLYDFLTLEkcrNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLqQLES 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230  77 ELiAELTDNQHLT---------GTIRLGVSETIV------YTWLVEYIEkvqqeypkvsVEIVVDLtpnlqegVRTGDLD 141
Cdd:PRK10082  88 NL-AELRGGSDYAqrkikiaaaHSLSLGLLPSIIsqmpplFTWAIEAID----------VDEAVDK-------LREGQSD 149

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230 142 MAFllgpTLAFECIEQALCD----FElSFLASPSFKGGVGQMSFKTLMSHtiltYPKITYPYKELKAKMKEQGLDE--PL 215
Cdd:PRK10082 150 CIF----SFHDEDLLEAPFDhirlFE-SQLFPVCASDEHGEALFNLAQPH----FPLLNYSRNSYMGRLINRTLTRhsEL 220

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....
gi 480205230 216 SITSY---SLATLLR-LAEQGLGIAVVPTLTALKEITDGRLEILN-----TPIQ 260
Cdd:PRK10082 221 SFSTFfvsSMSELLKqVALDGCGIAWLPEYAIQQEIRSGQLVVLNrdelvIPIQ 274
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 1-167 1.60e-09

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 57.86  E-value: 1.60e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230   1 MNLKNLEAFYWVVTLNSFNKAAAKLQTTQPAVSQKITALENDLGFKVLDRSFRQLKPTHKGMTLFKYAekLMRLETELIA 80
Cdd:PRK09906   1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDA--RAILEQAEKA 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230  81 ELTDNQHLTGTI--RLGVSETIVYTWLVEYIEKVQQEYPKVSVEIVVDLTPNLQEGVRTGDLDMAFLLGPTLAFECIEQA 158
Cdd:PRK09906  79 KLRARKIVQEDRqlTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPVYSDEIDYLE 158


                 ....*....
gi 480205230 159 LCDFELSFL 167
Cdd:PRK09906 159 LLDEPLVVV 167
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 2-65 8.58e-09

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 55.77  E-value: 8.58e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 480205230   2 NLKNLEAFYWVVTLNSFNKAAAKLQTTQPAVSQKITALENDLGFKVLDRSFRQLKPTHKGMTLF 65
Cdd:PRK11013   5 SLRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLF 68
PRK09801 PRK09801
LysR family transcriptional regulator;
4-121 8.76e-09

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 55.81  E-value: 8.76e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230   4 KNLEAFYWVVTLNSFNKAAAKLQTTQPAVSQKITALENDLGFKVLDRSFRQLKPTHKGMTLFKYAEKLMRLETELIAELT 83
Cdd:PRK09801   9 KDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVT 88

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 480205230  84 D-NQHLTGTIRLGVSETIVYTWLVEYIEKVQQEYPKVSV 121
Cdd:PRK09801  89 QiKTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQV 127
PRK09986 PRK09986
LysR family transcriptional regulator;
1-239 1.85e-08

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 54.34  E-value: 1.85e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230   1 MNLKNLEAFYWVVTLNSFNKAAAKLQTTQPAVSQKITALENDLGFKVLDRSFRQLKPTHKGMTLFKYAEKLMRLETELIA 80
Cdd:PRK09986   7 IDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLA 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230  81 ELTD-NQHLTGTIRLGVSETIVYTWLVEYIEKVQQEYPKVSVeIVVDLTPNLQ-EGVRTGDLDMAFLLgptlafECIEQA 158
Cdd:PRK09986  87 RVEQiGRGEAGRIEIGIVGTALWGRLRPAMRHFLKENPNVEW-LLRELSPSMQmAALERRELDAGIWR------MADLEP 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230 159 LCDFELSFLASPSFKGGVGQ---------MSFKTLMSHTILTYPKITYPY-KELKAKMKEQG--------LDEPlsitsy 220
Cdd:PRK09986 160 NPGFTSRRLHESAFAVAVPEehplasrssVPLKALRNEYFITLPFVHSDWgKFLQRVCQQAGfspqiirqVNEP------ 233

                        250
                 ....*....|....*....
gi 480205230 221 slATLLRLAEQGLGIAVVP 239
Cdd:PRK09986 234 --QTVLAMVSMGIGITLLP 250
PRK09791 PRK09791
LysR family transcriptional regulator;
3-141 3.43e-08

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 53.61  E-value: 3.43e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230   3 LKNLEAFYWVVTLNSFNKAAAKLQTTQPAVSQKITALENDLGFKVLDRSFRQLKPTHKGMTLFKYAEKLMRletELIAEL 82
Cdd:PRK09791   7 IHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILE---ELRAAQ 83

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 480205230  83 TDNQ----HLTGTIRLGVSETIVYTWLVEYIEKVQQEYPKVSVEIV----VDLTPNLqegvRTGDLD 141
Cdd:PRK09791  84 EDIRqrqgQLAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRIMegqlVSMINEL----RQGELD 146
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 91-158 7.10e-08

The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator PAO1-like, a member of the type 2 periplasmic binding fold protein superfamily; This family includes the C-terminal substrate domain of a putative LysR-type transcriptional regulator from the plant pathogen Pseudomonas aeruginosa PAO1and its closely related homologs. The LysR-type transcriptional regulators (LTTRs) are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of N2 fixing bacteria, and synthesis of virulence factors, to a name a few. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 176104 [Multi-domain]  Cd Length: 198  Bit Score: 51.78  E-value: 7.10e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 480205230  91 TIRLGVSETIVYTWLVEYIEKVQQEYPKVSVEIVVDLTPNLQEGVRTGDLDMAFL----LGPTLAFECIEQA 158
Cdd:cd08412    1 TLRIGCFSTLAPYYLPGLLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALTydldLPEDIAFEPLARL 72
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 89-253 1.89e-07

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 5. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. 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: 176163 [Multi-domain]  Cd Length: 202  Bit Score: 50.54  E-value: 1.89e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230  89 TGTIRLGVSETIVYTWLVEYIEKVQQEYPKVSVEIVVD--LTPNLQE----GVRTGDL---DM-AFLLGPTLAFECIeqa 158
Cdd:cd08474    2 AGTLRINAPRVAARLLLAPLLARFLARYPDIRLELVVDdgLVDIVAEgfdaGIRLGESvekDMvAVPLGPPLRMAVV--- 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230 159 lcdfelsflASPSFkggvgqmsfktLMSHTILTYPK-------ITY-------PYK-ELKAKMKEQGLDEPLSITSYSLA 223
Cdd:cd08474   79 ---------ASPAY-----------LARHGTPEHPRdllnhrcIRYrfptsgaLYRwEFERGGRELEVDVEGPLILNDSD 138

                        170       180       190
                 ....*....|....*....|....*....|
gi 480205230 224 TLLRLAEQGLGIAVVPTLTALKEITDGRLE 253
Cdd:cd08474  139 LMLDAALDGLGIAYLFEDLVAEHLASGRLV 168
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 1-255 1.96e-07

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 51.53  E-value: 1.96e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230   1 MNLKNLEAFYWVVTLNSFNKAAAKLQTTQPAVSQKITALENDLGFKVLDRSFRQLKPTHKGMTLFKYAeKLMRLETELIA 80
Cdd:PRK14997   2 TDLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHC-KAMLVEAQAAQ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230  81 ELTDNQHLT--GTIRLGVSETIVYTWLVEYIEKVQQEYPKVSVEIV-----VDLtpnLQEGVrtgdlDMAFLLGPTlAFE 153
Cdd:PRK14997  81 DAIAALQVEprGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLEatnrrVDV---VGEGV-----DVAIRVRPR-PFE 151

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230 154 ---CIEQALCDFELSFLASPSFKGGVGQMSFKTLMSHtiltYPKITYPYKELKAKMKEQGLD--------EPLSITSYSL 222
Cdd:PRK14997 152 dsdLVMRVLADRGHRLFASPDLIARMGIPSAPAELSH----WPGLSLASGKHIHRWELYGPQgaraevhfTPRMITTDML 227

                        250       260       270
                 ....*....|....*....|....*....|...
gi 480205230 223 AtLLRLAEQGLGIAVVPTLTALKEITDGRLEIL 255
Cdd:PRK14997 228 A-LREAAMAGVGLVQLPVLMVKEQLAAGELVAV 259
PRK12680 PRK12680
LysR family transcriptional regulator;
21-259 4.53e-07

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 50.39  E-value: 4.53e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230  21 AAAKLQTTQPAVSQKITALENDLGFKVLDRSFRQLKP-THKGMTLFKYAEKLMrLETELIAELTDNQHL--TGTIRLGVS 97
Cdd:PRK12680  22 AAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLESvTPAGVEVIERARAVL-SEANNIRTYAANQRResQGQLTLTTT 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230  98 ETIVYTWLVEYIEKVQQEYPKVSVeivvdltpNLQEGVRTGDLDmafLLGPTLAFECIEQALCDFELSFLASPSF----- 172
Cdd:PRK12680 101 HTQARFVLPPAVAQIKQAYPQVSV--------HLQQAAESAALD---LLGQGDADIAIVSTAGGEPSAGIAVPLYrwrrl 169

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230 173 ----KGGVGQMSFKTLMSHTILTYPKITY-----PYKELKAKMKEQGLDEPLSITSYSLATLLRLAEQGLGIAVVPTLTA 243
Cdd:PRK12680 170 vvvpRGHALDTPRRAPDMAALAEHPLISYesstrPGSSLQRAFAQLGLEPSIALTALDADLIKTYVRAGLGVGLLAEMAV 249

                        250
                 ....*....|....*.
gi 480205230 244 LKEITDGRLEILNTPI 259
Cdd:PRK12680 250 NANDEDLRAWPAPAPI 265
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 109-254 1.35e-06

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


Pssm-ID: 176124  Cd Length: 198  Bit Score: 47.98  E-value: 1.35e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230 109 IEKVQQEYPKVSVEIVVDLTPNLQEGVRTGDLDMAFLLGPT--LAFECieQALCDFELSFLASPSF-KGGVGQMSFKTLm 185
Cdd:cd08433   19 LRAVRRRYPGIRLRIVEGLSGHLLEWLLNGRLDLALLYGPPpiPGLST--EPLLEEDLFLVGPADApLPRGAPVPLAEL- 95

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 480205230 186 shtiLTYPKI-TYPYKELKAKMKE--QGLDEPLSITSY--SLATLLRLAEQGLGIAVVPTLTALKEITDGRLEI 254
Cdd:cd08433   96 ----ARLPLIlPSRGHGLRRLVDEaaARAGLTLNVVVEidSVATLKALVAAGLGYTILPASAVAAEVAAGRLVA 165
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 91-243 2.04e-06

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


Pssm-ID: 176127 [Multi-domain]  Cd Length: 194  Bit Score: 47.60  E-value: 2.04e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230  91 TIRLGVSETIVYTWLVEYIEKVQQEYPKVSVEIVVDLTPNLQEGVRTGDLDMAFL-LGPTLAFECIEQALCDFELSFLAS 169
Cdd:cd08436    1 RLAIGTITSLAAVDLPELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAFVgLPERRPPGLASRELAREPLVAVVA 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 480205230 170 PSFK-GGVGQMSFKTLMSHTILTYPKITYPYKELKAKMKEQGL--DEPLSITsySLATLLRLAEQGLGIAVVPTLTA 243
Cdd:cd08436   81 PDHPlAGRRRVALADLADEPFVDFPPGTGARRQVDRAFAAAGVrrRVAFEVS--DVDLLLDLVARGLGVALLPASVA 155
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 91-266 2.12e-06

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: 47.49  E-value: 2.12e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230  91 TIRLGVSETIVYTWLVEYIEKVQQEYPKVSVEIVVDLTPNLQEGVRTGDLDMAFLLGPTLAFECIEQALCDFELSFLASP 170
Cdd:cd08420    1 TLRIGASTTIGEYLLPRLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLVEGPVDHPDLIVEPFAEDELVLVVPP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230 171 SfkggvgqmsfKTLMSHTILTYPKI-TYPY----------KELKAKMKEQGLDePLSITSY----SLATLLRLAEQGLGI 235
Cdd:cd08420   81 D----------HPLAGRKEVTAEELaAEPWilrepgsgtrEVFERALAEAGLD-GLDLNIVmelgSTEAIKEAVEAGLGI 149

                        170       180       190
                 ....*....|....*....|....*....|...
gi 480205230 236 AVVPTLTALKEITDGRLEILNTP-IQLK-TFHF 266
Cdd:cd08420  150 SILSRLAVRKELELGRLVALPVEgLRLTrPFSL 182
nhaR PRK11062
transcriptional activator NhaR; Provisional
 1-79 7.61e-06

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 46.54  E-value: 7.61e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 480205230   1 MNLKNLEAFYWVVTLNSFNKAAAKLQTTQPAVSQKITALENDLGFKVLDRSFRQLKPTHKGMTLFKYAEKLMRLETELI 79
Cdd:PRK11062   4 INYNHLYYFWMVCKEGSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGELVFRYADKMFTLSQEML 82
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
1-123 1.13e-05

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 46.12  E-value: 1.13e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230   1 MNLKNLEAFYWVVTLNsFN--KAAAKLQTTQPAVSQKITALENDLGFKVLDRSFRQLKP-THKGMTLFKYAEKLMRlETE 77
Cdd:PRK12684   1 MNLHQLRFVREAVRQN-FNltEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRGlTEPGRIILASVERILQ-EVE 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 480205230  78 LIAELTD--NQHLTGTIRLGVSETIVYTWLVEYIEKVQQEYPKVSVEI 123
Cdd:PRK12684  79 NLKRVGKefAAQDQGNLTIATTHTQARYALPAAIKEFKKRYPKVRLSI 126
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
31-123 2.12e-05

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 45.19  E-value: 2.12e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230  31 AVSQKITALENDLGFKVLDRSFRQLKPTHKGMTLFKYAEKLMRLETELIAELTDNQH-LTGTIRLGVSETIVYTWLVEYI 109
Cdd:PRK11716   7 TLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPsLSGELSLFCSVTAAYSHLPPIL 86

                         90
                 ....*....|....
gi 480205230 110 EKVQQEYPKvsVEI 123
Cdd:PRK11716  87 DRFRAEHPL--VEI 98
PBP2_CrgA_like_8 cd08477
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 105-255 3.06e-05

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 8. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. 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: 176166  Cd Length: 197  Bit Score: 44.14  E-value: 3.06e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230 105 LVEYiekvQQEYPKVSVEIV-----VDLTpnlQEGvrtgdLDMAFLLGPTLAFECIEQALCDFELSFLASPSFKGGVGQ- 178
Cdd:cd08477   20 LAEY----LARYPDVRVDLVlsdrlVDLV---EEG-----FDAAFRIGELADSSLVARPLAPYRMVLCASPDYLARHGTp 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230 179 MSFKTLMSHTIL--TYPKITYPYkELKAKMKEQGLDEPLSITSYSLATLLRLAEQGLGIAVVPTLTALKEITDGRL-EIL 255
Cdd:cd08477   88 TTPEDLARHECLgfSYWRARNRW-RLEGPGGEVKVPVSGRLTVNSGQALRVAALAGLGIVLQPEALLAEDLASGRLvELL 166
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 91-239 3.43e-05

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: 43.65  E-value: 3.43e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230  91 TIRLGVSETIVYTWLVEYIEKVQQEYPKVSVEIVVDLTPNLQEGVRTGDLDMAFL----LGPTLAFECIEQ-----ALC- 160
Cdd:cd08414    1 RLRIGFVGSALYGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVrpppDPPGLASRPLLReplvvALPa 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230 161 DFELSFLASPsfkggvgqmSFKTLMSHTILTYPKITYP--YKELKAKMKEQGLDEPLSITSYSLATLLRLAEQGLGIAVV 238
Cdd:cd08414   81 DHPLAARESV---------SLADLADEPFVLFPREPGPglYDQILALCRRAGFTPRIVQEASDLQTLLALVAAGLGVALV 151


                 .
gi 480205230 239 P 239
Cdd:cd08414  152 P 152
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 91-241 3.45e-05

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: 43.67  E-value: 3.45e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230  91 TIRLGVSETIVYTWLVEYIEKVQQEYPKVSVEIVVDLTPNLQEGVRTGDLDMA--FLLG--PTLAFECIeqalcdFELSF 166
Cdd:cd08440    1 RVRVAALPSLAATLLPPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGigSEPEadPDLEFEPL------LRDPF 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230 167 ---------LASPSfkggvgQMSFKTLMSHTILTYPKITYPYKELKAKMKEQGLDEPLSITSYSLATLLRLAEQGLGIAV 237
Cdd:cd08440   75 vlvcpkdhpLARRR------SVTWAELAGYPLIALGRGSGVRALIDRALAAAGLTLRPAYEVSHMSTALGMVAAGLGVAV 148


                 ....
gi 480205230 238 VPTL 241
Cdd:cd08440  149 LPAL 152
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
18-72 3.85e-05

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 44.24  E-value: 3.85e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 480205230  18 FNKAAAKLQTTQPAVSQKITALENDLGFKVLDRSFRQLKPTHKGMTLFKYAEKLM 72
Cdd:PRK03601  18 FGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYAETLM 72
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 1-143 4.65e-05

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 44.26  E-value: 4.65e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230   1 MNLKNLEAFYWVVTLNsFN--KAAAKLQTTQPAVSQKITALENDLGFKVLDRS-FRQLKPTHKGMTLFKYAEKlMRLETE 77
Cdd:PRK12683   1 MNFQQLRIIREAVRQN-FNltEVANALYTSQSGVSKQIKDLEDELGVEIFIRRgKRLTGLTEPGKELLQIVER-MLLDAE 78

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 480205230  78 LIAELTD--NQHLTGTIRLGVSETIVYTWLVEYIEKVQQEYPKVSVEivvdltpnLQEG--------VRTGDLDMA 143
Cdd:PRK12683  79 NLRRLAEqfADRDSGHLTVATTHTQARYALPKVVRQFKEVFPKVHLA--------LRQGspqeiaemLLNGEADIG 146
cysB PRK12681
HTH-type transcriptional regulator CysB;
1-120 5.97e-05

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 44.12  E-value: 5.97e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230   1 MNLKNLEaFYWVVTLNSFN--KAAAKLQTTQPAVSQKITALENDLGFKVLDRSFRQLKP-THKGMTLFKYAEKLMRlETE 77
Cdd:PRK12681   1 MKLQQLR-YIVEVVNHNLNvsATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTQvTPAGEEIIRIAREILS-KVE 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 480205230  78 LI----AELTDNQHltGTIRLGVSETIVYTWLVEYIEKVQQEYPKVS 120
Cdd:PRK12681  79 SIksvaGEHTWPDK--GSLYIATTHTQARYALPPVIKGFIERYPRVS 123
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 91-266 6.66e-05

The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of dinitrotoluene and similar compounds, such as DntR, NahR, and LinR. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. Also included are related LysR-type regulators clustered together in phylogenetic trees, including NodD, ToxR, LeuO, SyrM, TdcA, and PnbR. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176109 [Multi-domain]  Cd Length: 200  Bit Score: 42.97  E-value: 6.66e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230  91 TIRLGVSETIVYTWLVEYIEKVQQEYPKVSVEIVVDLTPNLQEGVRTGDLDMAFLLGPTLAFECIEQALCDFELSFLASP 170
Cdd:cd08417    1 TFRIAASDYLEALLLPPLLARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELPPGLRSQPLFEDRFVCVARK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230 171 SFKGGVGQMSFKTLMS--H-TILTYPKITYPYKELkakMKEQGLDEPLSITSYSLATLLRLAEQGLGIAVVPTLTALKEI 247
Cdd:cd08417   81 DHPLAGGPLTLEDYLAapHvLVSPRGRGHGLVDDA---LAELGLSRRVALTVPHFLAAPALVAGTDLIATVPRRLAEALA 157

                        170
                 ....*....|....*....
gi 480205230 248 TDGRLEILNTPIQLKTFHF 266
Cdd:cd08417  158 ERLGLRVLPLPFELPPFTV 176
PBP2_CrgA cd08478
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains ...
 90-255 1.47e-04

The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains the type 2 periplasmic binding domain; This CD represents the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis further showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. 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: 176167 [Multi-domain]  Cd Length: 199  Bit Score: 41.94  E-value: 1.47e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230  90 GTIRLGVSETIVYTWLVEYIEKVQQEYPKVSVEI-----VVDLtpnLQEgvRTgdlDMAFLLGPTLAFECIEQALCDFEL 164
Cdd:cd08478    3 GLLRVDAATPFVLHLLAPLIAKFRERYPDIELELvsnegIIDL---IER--KT---DVAIRIGELTDSTLHARPLGKSRL 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230 165 SFLASPSF--KGGVGQmSFKTLMSHTIL--TYPKI--TYPYKElkakMKEQGLDEPLSITSYSLATLLRLAEQGLGIAVV 238
Cdd:cd08478   75 RILASPDYlaRHGTPQ-SIEDLAQHQLLgfTEPASlnTWPIKD----ADGNLLKIQPTITASSGETLRQLALSGCGIACL 149

                        170
                 ....*....|....*..
gi 480205230 239 PTLTALKEITDGRLEIL 255
Cdd:cd08478  150 SDFMTDKDIAEGRLIPL 166
PBP2_LTTR_like_2 cd08427
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-255 2.18e-04

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


Pssm-ID: 176118 [Multi-domain]  Cd Length: 195  Bit Score: 41.41  E-value: 2.18e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230  92 IRLGVSETIVYTWLVEYIEKVQQEYPKVSVEIVVDLTPNLQEGVRTGDLDMAFLLGPTLAF--ECIEQALCDFELSFLAS 169
Cdd:cd08427    2 LRLGAIATVLTGLLPRALARLRRRHPDLEVHIVPGLSAELLARVDAGELDAAIVVEPPFPLpkDLVWTPLVREPLVLIAP 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230 170 PSFKGGvgqmSFKTLMShtilTYPKITYPYKELKAKM-----KEQGLDEPLSITSYSLATLLRLAEQGLGIAVVPtLTAL 244
Cdd:cd08427   82 AELAGD----DPRELLA----TQPFIRYDRSAWGGRLvdrflRRQGIRVREVMELDSLEAIAAMVAQGLGVAIVP-DIAV 152

                        170
                 ....*....|.
gi 480205230 245 KEITDGRLEIL 255
Cdd:cd08427  153 PLPAGPRVRVL 163
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 91-252 7.35e-04

The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate domain of LysR-type transcriptional regulators involved in controlling the expression of glutaryl-CoA dehydrogenase (GcdH), S-adenosyl-L-homocysteine hydrolase, cell division protein FtsW, tryptophan synthase, and beta-lactamase. 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: 176123 [Multi-domain]  Cd Length: 194  Bit Score: 39.87  E-value: 7.35e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230  91 TIRLGVSETIVYTWLVEYIEKVQQEYPKVSVEI-----VVDLtpnlqegvRTGDLDMA--FLLGPTLAFECIEqaLCDFE 163
Cdd:cd08432    1 VLTVSVTPSFAARWLIPRLARFQARHPDIDLRLstsdrLVDF--------AREGIDLAirYGDGDWPGLEAER--LMDEE 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230 164 LSFLASPSFKGGVGQMSFKTLMSHTILTYPKITYPYKELKAKMKEQGLDEPLSIT--SYSLAtlLRLAEQGLGIAVVPTL 241
Cdd:cd08432   71 LVPVCSPALLAGLPLLSPADLARHTLLHDATRPEAWQWWLWAAGVADVDARRGPRfdDSSLA--LQAAVAGLGVALAPRA 148

                        170
                 ....*....|.
gi 480205230 242 TALKEITDGRL 252
Cdd:cd08432  149 LVADDLAAGRL 159
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
6-68 9.34e-04

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 40.17  E-value: 9.34e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 480205230   6 LEAFYWVVTLNSFNKAAAKLQTTQPAVSQKITALENDLGFKVLDRSFRQLKPTHKGMTLFKYA 68
Cdd:PRK10094   7 LRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQA 69
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 91-145 4.06e-03

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: 37.52  E-value: 4.06e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 480205230  91 TIRLGVSETIVyTWLV-EYIEKVQQEYPKVSVEIVVDLTPNLQEGVRTGDLDMAFL 145
Cdd:cd08434    1 TVRLGFLHSLG-TSLVpDLIRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLALC 55
PBP2_AlsR cd08452
The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which ...
 94-239 4.07e-03

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: 37.87  E-value: 4.07e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230  94 LGVSETIVYTWLVEYIEKVQQEYPKVSVEIVVDLTPNLQEGVRTGDLDMAFLLGP----TLAFECIEQALCDFELSF--- 166
Cdd:cd08452    4 IGFVGAAIYEFLPPIVREYRKKFPSVKVELRELSSPDQVEELLKGRIDIGFLHPPiqhtALHIETVQSSPCVLALPKqhp 83

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 480205230 167 LASPSfkggvgQMSFKTLMSHTILTYPKITYP--YKELKAKMKEQGLDEPLSITSYSLATLLRLAEQGLGIAVVP 239
Cdd:cd08452   84 LASKE------EITIEDLRDEPIITVAREAWPtlYDEIIQLCEQAGFRPKIVQEATEYQTVIGLVSAGIGVTFVP 152
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 91-240 6.51e-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: 37.15  E-value: 6.51e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230  91 TIRLGVSETIVYTWLVEYIEKVQQEYPKVSVEIVVDLTPNLQEGVRTGDLDMAFLLGPTLAFECIEQALCDFELSFLASP 170
Cdd:cd08438    1 HLRLGLPPLGGSLLFAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVLPVDEEEFDSQPLCNEPLVAVLPR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480205230 171 sfkggvgqmsfktlmSHTILTYPKITypYKELKakmkeqglDEPLSI--TSYSLATLLR--------------------- 227
Cdd:cd08438   81 ---------------GHPLAGRKTVS--LADLA--------DEPFILfnEDFALHDRIIdacqqagftpniaarssqwdf 135

                        170
                 ....*....|....*.
gi 480205230 228 ---LAEQGLGIAVVPT 240
Cdd:cd08438  136 iaeLVAAGLGVALLPR 151
PBP2_YofA_SoxR_like cd08442
The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, ...
 91-148 9.52e-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: 36.43  E-value: 9.52e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 480205230  91 TIRLGVSETIVYTWLVEYIEKVQQEYPKVSVEIVVDLTPNLQEGVRTGDLDMAFLLGP 148
Cdd:cd08442    1 PLRLGSMETTAAVRLPPLLAAYHARYPKVDLSLSTGTTGALIQAVLEGRLDGAFVAGP 58
 
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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