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Conserved domains on  [gi|727186163|ref|WP_033648018|]
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MULTISPECIES: LysR family transcriptional regulator [Serratia]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 11426520)

LysR family transcriptional regulator negatively or positively regulates the transcription of specific genes; contains 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 proteins

CATH:  3.40.190.10
Gene Ontology:  GO:0003700|GO:0006355|GO:0003677
PubMed:  8257110|19047729
SCOP:  3000083|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];
8-302 4.30e-42

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 145.78  E-value: 4.30e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163   8 MKLHHLQMLVALGEQGNLTHVARMMNISQPALSKWLSQLEDEIGITLFERHSKGLRPSEGGKLLLQHAQRLINDLERSQS 87
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163  88 EIARFkQGGLVGSLKIGCSP-VATDCVSQAVLSLLQEMPTLHLNIEEKVMTPLLHDL--------IAGAVDVVVGrvggr 158
Cdd:COG0583   81 ELRAL-RGGPRGTLRIGAPPsLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALlegeldlaIRLGPPPDPG----- 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163 159 alqlpLNYQVLYTEPVCFVARPHHPLAKSATLTwhdlthwrwivwptgtpirlsidnaladngvmlpentvesASMNVST 238
Cdd:COG0583  155 -----LVARPLGEERLVLVASPDHPLARRAPLV----------------------------------------NSLEALL 189

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 727186163 239 NLLQSSDMISILSLRLAQRYASQGQLAILNLPKIEQKGSVGVFWRNSEPPFAALSRFLQLLTQA 302
Cdd:COG0583  190 AAVAAGLGIALLPRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREA 253
Periplasmic_Binding_Protein_Type_2 super family cl21456
Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent ...
 167-222 3.41e-06

Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent the ligand-binding domains found in solute binding proteins that serve as initial receptors in the transport, signal transduction and channel gating. The PBP2 proteins share the same architecture as periplasmic binding proteins type 1 (PBP1), but have a different topology. They are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The origin of PBP module can be traced across the distant phyla, including eukaryotes, archebacteria, and prokaryotes. The majority of PBP2 proteins are involved in the uptake of a variety of soluble substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the family includes ionotropic glutamate receptors and unorthodox sensor proteins involved in signal transduction. The substrate binding domain of the LysR transcriptional regulators and the oligopeptide-like transport systems also contain the type 2 periplasmic binding fold and thus they are significantly homologous to that of the PBP2; however, these two families are grouped into a separate hierarchy of the PBP2 superfamily due to the large number of protein sequences.


The actual alignment was detected with superfamily member cd08436:

Pssm-ID: 473866 [Multi-domain]  Cd Length: 194  Bit Score: 46.83  E-value: 3.41e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 727186163 167 QVLYTEPVCFVARPHHPLAKSATLTWHDLTHWRWIVWPTGTPIRLSIDNALADNGV 222
Cdd:cd08436   68 RELAREPLVAVVAPDHPLAGRRRVALADLADEPFVDFPPGTGARRQVDRAFAAAGV 123
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
8-302 4.30e-42

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 145.78  E-value: 4.30e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163   8 MKLHHLQMLVALGEQGNLTHVARMMNISQPALSKWLSQLEDEIGITLFERHSKGLRPSEGGKLLLQHAQRLINDLERSQS 87
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163  88 EIARFkQGGLVGSLKIGCSP-VATDCVSQAVLSLLQEMPTLHLNIEEKVMTPLLHDL--------IAGAVDVVVGrvggr 158
Cdd:COG0583   81 ELRAL-RGGPRGTLRIGAPPsLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALlegeldlaIRLGPPPDPG----- 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163 159 alqlpLNYQVLYTEPVCFVARPHHPLAKSATLTwhdlthwrwivwptgtpirlsidnaladngvmlpentvesASMNVST 238
Cdd:COG0583  155 -----LVARPLGEERLVLVASPDHPLARRAPLV----------------------------------------NSLEALL 189

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 727186163 239 NLLQSSDMISILSLRLAQRYASQGQLAILNLPKIEQKGSVGVFWRNSEPPFAALSRFLQLLTQA 302
Cdd:COG0583  190 AAVAAGLGIALLPRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREA 253
TF_pcaQ TIGR02424
pca operon transcription factor PcaQ; Members of this family are LysR-family transcription ...
 6-302 1.08e-39

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


Pssm-ID: 274127 [Multi-domain]  Cd Length: 300  Bit Score: 140.62  E-value: 1.08e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163    6 QKMKLHHLQMLVALGEQGNLTHVARMMNISQPALSKWLSQLEDEIGITLFERHSKGLRPSEGGKLLLQHAQRLINDLERS 85
Cdd:TIGR02424   1 TRIKFRHLQCFVEVARQGSVKRAAEALHITQPAVSKTLRELEEILGTPLFERDRRGIRLTRYGELFLRHAGASLAALRQG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163   86 QSEIARFKQGGLVgSLKIGCSP-VATDCVSQAVLSLLQEMPTLHLNI---EEKVMTPLLH----DLIAGAVDVVVGRVGg 157
Cdd:TIGR02424  81 VASLSQLGEGEGP-TVRIGALPtVAARLMPEVVKRFLARAPRLRVRImtgPNAYLLDQLRvgalDLVVGRLGAPETMQG- 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163  158 ralqlpLNYQVLYTEPVCFVARPHHPLAKSATLTWHDLTHWRWIVWPTGTPIRLSIDNALADNGVMLPENTVESASMNVS 237
Cdd:TIGR02424 159 ------LSFEHLYNEPVVFVVRAGHPLLAAPSLPVASLADYPVLLPPEGSAIRPLAERLFIACGIPPPPQRIETVSGSFG 232

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 727186163  238 TNLLQSSDMISILSLRLAQRYASQGQLAILNLPKIEQKGSVGVFWRNSEPPFAALSRFLQLLTQA 302
Cdd:TIGR02424 233 RRYVQESDAIWIISRGVVALDLADGTLVELPFDTRETGGPVGLCTRPDTQLSRAAQLFVDALRSA 297
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 100-299 2.29e-37

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: 131.63  E-value: 2.29e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163 100 SLKIGCSP-VATDCVSQAVLSLLQEMPTLHLNIEEK---VMTPLL----HDLIAGAVDVVVGRVGgralqlpLNYQVLYT 171
Cdd:cd08435    1 TVRVGAVPaAAPVLLPPAIARLLARHPRLTVRVVEGtsdELLEGLrageLDLAIGRLADDEQPPD-------LASEELAD 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163 172 EPVCFVARPHHPLAKSATLTWHDLTHWRWIVWPTGTPIRLSIDNALADNGVMLPENTVESASMNVSTNLLQSSDMISILS 251
Cdd:cd08435   74 EPLVVVARPGHPLARRARLTLADLADYPWVLPPPGTPLRQRLEQLFAAAGLPLPRNVVETASISALLALLARSDMLAVLP 153

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 727186163 252 LRLAQRYASQGQLAILNLPKIEQKGSVGVFWRNSEPPFAALSRFLQLL 299
Cdd:cd08435  154 RSVAEDELRAGVLRELPLPLPTSRRPIGITTRRGGPLSPAARALLDAL 201
PRK09791 PRK09791
LysR family transcriptional regulator;
5-269 1.95e-25

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 102.92  E-value: 1.95e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163   5 AQKMKLHHLQMLVALGEQGNLTHVARMMNISQPALSKWLSQLEDEIGITLFERHSKGLRPSEGGKLLLQHAQRLINDLER 84
Cdd:PRK09791   2 AFQVKIHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRA 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163  85 SQSEIaRFKQGGLVGSLKIGC-SPVATDCVSQAVLSLLQEMPTLHLNIEEKVMTPLLHDLIAGAVDVVVGRVGGRALQLP 163
Cdd:PRK09791  82 AQEDI-RQRQGQLAGQINIGMgASIARSLMPAVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDFTINTYYQGPYDHE 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163 164 LNYQVLYTEPVCFVARPHHPLAKSATLtwHDLTHWRWIV-WPTGTPIRLSIDnaLADNGVMLPENTVESASMNVSTNLLQ 242
Cdd:PRK09791 161 FTFEKLLEKQFAVFCRPGHPAIGARSL--KQLLDYSWTMpTPHGSYYKQLSE--LLDDQAQTPQVGVVCETFSACISLVA 236

                        250       260
                 ....*....|....*....|....*..
gi 727186163 243 SSDMISILSLRLAQRYASQGQLAILNL 269
Cdd:PRK09791 237 KSDFLSILPEEMGCDPLHGQGLVMLPV 263
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 99-302 3.73e-23

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


Pssm-ID: 460931 [Multi-domain]  Cd Length: 205  Bit Score: 94.28  E-value: 3.73e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163   99 GSLKIGCSP-VATDCVSQAVLSLLQEMPTLHLNIEEKVMTPLLHDL------IAGAVDVVVGRVggralqlpLNYQVLYT 171
Cdd:pfam03466   2 GRLRIGAPPtLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLlegeldLAIRRGPPDDPG--------LEARPLGE 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163  172 EPVCFVARPHHPLAKSATLTWHDLTHWRWIVWPTGTPIRLSIDNALADNGVmLPENTVESASMNVSTNLLQSSDMISILS 251
Cdd:pfam03466  74 EPLVLVAPPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGL-RPRVVLEVNSLEALLQLVAAGLGIALLP 152

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 727186163  252 LRLAQRYASQGQLAILNLPKIEQKGSVGVFWRNSEPPFAALSRFLQLLTQA 302
Cdd:pfam03466 153 RSAVARELADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREA 203
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 167-222 3.41e-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: 46.83  E-value: 3.41e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 727186163 167 QVLYTEPVCFVARPHHPLAKSATLTWHDLTHWRWIVWPTGTPIRLSIDNALADNGV 222
Cdd:cd08436   68 RELAREPLVAVVAPDHPLAGRRRVALADLADEPFVDFPPGTGARRQVDRAFAAAGV 123
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
8-302 4.30e-42

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 145.78  E-value: 4.30e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163   8 MKLHHLQMLVALGEQGNLTHVARMMNISQPALSKWLSQLEDEIGITLFERHSKGLRPSEGGKLLLQHAQRLINDLERSQS 87
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163  88 EIARFkQGGLVGSLKIGCSP-VATDCVSQAVLSLLQEMPTLHLNIEEKVMTPLLHDL--------IAGAVDVVVGrvggr 158
Cdd:COG0583   81 ELRAL-RGGPRGTLRIGAPPsLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALlegeldlaIRLGPPPDPG----- 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163 159 alqlpLNYQVLYTEPVCFVARPHHPLAKSATLTwhdlthwrwivwptgtpirlsidnaladngvmlpentvesASMNVST 238
Cdd:COG0583  155 -----LVARPLGEERLVLVASPDHPLARRAPLV----------------------------------------NSLEALL 189

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 727186163 239 NLLQSSDMISILSLRLAQRYASQGQLAILNLPKIEQKGSVGVFWRNSEPPFAALSRFLQLLTQA 302
Cdd:COG0583  190 AAVAAGLGIALLPRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREA 253
TF_pcaQ TIGR02424
pca operon transcription factor PcaQ; Members of this family are LysR-family transcription ...
 6-302 1.08e-39

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


Pssm-ID: 274127 [Multi-domain]  Cd Length: 300  Bit Score: 140.62  E-value: 1.08e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163    6 QKMKLHHLQMLVALGEQGNLTHVARMMNISQPALSKWLSQLEDEIGITLFERHSKGLRPSEGGKLLLQHAQRLINDLERS 85
Cdd:TIGR02424   1 TRIKFRHLQCFVEVARQGSVKRAAEALHITQPAVSKTLRELEEILGTPLFERDRRGIRLTRYGELFLRHAGASLAALRQG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163   86 QSEIARFKQGGLVgSLKIGCSP-VATDCVSQAVLSLLQEMPTLHLNI---EEKVMTPLLH----DLIAGAVDVVVGRVGg 157
Cdd:TIGR02424  81 VASLSQLGEGEGP-TVRIGALPtVAARLMPEVVKRFLARAPRLRVRImtgPNAYLLDQLRvgalDLVVGRLGAPETMQG- 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163  158 ralqlpLNYQVLYTEPVCFVARPHHPLAKSATLTWHDLTHWRWIVWPTGTPIRLSIDNALADNGVMLPENTVESASMNVS 237
Cdd:TIGR02424 159 ------LSFEHLYNEPVVFVVRAGHPLLAAPSLPVASLADYPVLLPPEGSAIRPLAERLFIACGIPPPPQRIETVSGSFG 232

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 727186163  238 TNLLQSSDMISILSLRLAQRYASQGQLAILNLPKIEQKGSVGVFWRNSEPPFAALSRFLQLLTQA 302
Cdd:TIGR02424 233 RRYVQESDAIWIISRGVVALDLADGTLVELPFDTRETGGPVGLCTRPDTQLSRAAQLFVDALRSA 297
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 100-299 2.29e-37

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: 131.63  E-value: 2.29e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163 100 SLKIGCSP-VATDCVSQAVLSLLQEMPTLHLNIEEK---VMTPLL----HDLIAGAVDVVVGRVGgralqlpLNYQVLYT 171
Cdd:cd08435    1 TVRVGAVPaAAPVLLPPAIARLLARHPRLTVRVVEGtsdELLEGLrageLDLAIGRLADDEQPPD-------LASEELAD 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163 172 EPVCFVARPHHPLAKSATLTWHDLTHWRWIVWPTGTPIRLSIDNALADNGVMLPENTVESASMNVSTNLLQSSDMISILS 251
Cdd:cd08435   74 EPLVVVARPGHPLARRARLTLADLADYPWVLPPPGTPLRQRLEQLFAAAGLPLPRNVVETASISALLALLARSDMLAVLP 153

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 727186163 252 LRLAQRYASQGQLAILNLPKIEQKGSVGVFWRNSEPPFAALSRFLQLL 299
Cdd:cd08435  154 RSVAEDELRAGVLRELPLPLPTSRRPIGITTRRGGPLSPAARALLDAL 201
PRK09791 PRK09791
LysR family transcriptional regulator;
5-269 1.95e-25

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 102.92  E-value: 1.95e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163   5 AQKMKLHHLQMLVALGEQGNLTHVARMMNISQPALSKWLSQLEDEIGITLFERHSKGLRPSEGGKLLLQHAQRLINDLER 84
Cdd:PRK09791   2 AFQVKIHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRA 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163  85 SQSEIaRFKQGGLVGSLKIGC-SPVATDCVSQAVLSLLQEMPTLHLNIEEKVMTPLLHDLIAGAVDVVVGRVGGRALQLP 163
Cdd:PRK09791  82 AQEDI-RQRQGQLAGQINIGMgASIARSLMPAVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDFTINTYYQGPYDHE 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163 164 LNYQVLYTEPVCFVARPHHPLAKSATLtwHDLTHWRWIV-WPTGTPIRLSIDnaLADNGVMLPENTVESASMNVSTNLLQ 242
Cdd:PRK09791 161 FTFEKLLEKQFAVFCRPGHPAIGARSL--KQLLDYSWTMpTPHGSYYKQLSE--LLDDQAQTPQVGVVCETFSACISLVA 236

                        250       260
                 ....*....|....*....|....*..
gi 727186163 243 SSDMISILSLRLAQRYASQGQLAILNL 269
Cdd:PRK09791 237 KSDFLSILPEEMGCDPLHGQGLVMLPV 263
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 99-302 3.73e-23

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


Pssm-ID: 460931 [Multi-domain]  Cd Length: 205  Bit Score: 94.28  E-value: 3.73e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163   99 GSLKIGCSP-VATDCVSQAVLSLLQEMPTLHLNIEEKVMTPLLHDL------IAGAVDVVVGRVggralqlpLNYQVLYT 171
Cdd:pfam03466   2 GRLRIGAPPtLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLlegeldLAIRRGPPDDPG--------LEARPLGE 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163  172 EPVCFVARPHHPLAKSATLTWHDLTHWRWIVWPTGTPIRLSIDNALADNGVmLPENTVESASMNVSTNLLQSSDMISILS 251
Cdd:pfam03466  74 EPLVLVAPPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGL-RPRVVLEVNSLEALLQLVAAGLGIALLP 152

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 727186163  252 LRLAQRYASQGQLAILNLPKIEQKGSVGVFWRNSEPPFAALSRFLQLLTQA 302
Cdd:pfam03466 153 RSAVARELADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREA 203
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 8-301 1.40e-18

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 83.85  E-value: 1.40e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163   8 MKLHHLQMLVALGEQGNLTHVARMMNISQPALSKWLSQLEDEIGITLFERHSKGLRPSEGGKLLLQHAQRLINDLERSQ- 86
Cdd:PRK11242   1 MLLRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRr 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163  87 -----SEIARfkqgglvGSLKIGCSPVATdcvSQAVLSLLQEM----PTLHLNIEE---KVMTPLLHD-----LIAGAVD 149
Cdd:PRK11242  81 aihdvADLSR-------GSLRLAMTPTFT---AYLIGPLIDAFharyPGITLTIREmsqERIEALLADdeldvGIAFAPV 150

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163 150 vvvgrvggralQLP-LNYQVLYTEPVCFVARPHHPLA-KSATLTWHDLTHWRWIVWPTGTPIRLSIDNALADNGVMlPEN 227
Cdd:PRK11242 151 -----------HSPeIEAQPLFTETLALVVGRHHPLAaRRKALTLDELADEPLVLLSAEFATREQIDRYFRRHGVT-PRV 218

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 727186163 228 TVESASMNVSTNLLQSSDMISILSLRLAQRyasQGQLAILNL-PKIEQKgSVGVFWRNSEPPFAALSRFLQLLTQ 301
Cdd:PRK11242 219 AIEANSISAVLEIVRRGRLATLLPAAIARE---HDGLCAIPLdPPLPQR-TAALLRRKGAYRSAAARAFIELALE 289
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
10-69 9.92e-17

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 72.80  E-value: 9.92e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163   10 LHHLQMLVALGEQGNLTHVARMMNISQPALSKWLSQLEDEIGITLFERHSKGLRPSEGGK 69
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
8-222 5.91e-16

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 76.55  E-value: 5.91e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163   8 MKLHHLQMLVALGEQG-NLTHVARMMNISQPALSKWLSQLEDEIGITLFERHSKGLRP-SEGGKLLLQHAQRLINDLE-- 83
Cdd:PRK12684   1 MNLHQLRFVREAVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRGlTEPGRIILASVERILQEVEnl 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163  84 -RSQSEIARFKQGGLVgslkigcspVATD------CVSQAVLSLLQEMPTLHLNIEE----KVMTPLLHDLIAGAVDVVV 152
Cdd:PRK12684  81 kRVGKEFAAQDQGNLT---------IATThtqaryALPAAIKEFKKRYPKVRLSILQgsptQIAEMVLHGQADLAIATEA 151

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163 153 GRVGGRALQLPlnyqvLYTEPVCFVARPHHPLAKSATLTWHDLTHWRWIVWPTGTPIRLSIDNALADNGV 222
Cdd:PRK12684 152 IADYKELVSLP-----CYQWNHCVVVPPDHPLLERKPLTLEDLAQYPLITYDFAFAGRSKINKAFALRGL 216
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 164-299 8.65e-16

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: 74.17  E-value: 8.65e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163 164 LNYQVLYTEPVCFVARPHHPLAKSATLTWHDLTHWRWIVWPTGTPIRLSIDNALADNGVmLPENTVESASMNVSTNLLQS 243
Cdd:cd05466   64 LESEPLFEEPLVLVVPPDHPLAKRKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGF-TPNIALEVDSLEAIKALVAA 142

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 727186163 244 SDMISILSLRLAQRYASqGQLAILNLPKIEQKGSVGVFWRNSEPPFAALSRFLQLL 299
Cdd:cd05466  143 GLGIALLPESAVEELAD-GGLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 8-221 1.39e-15

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 75.41  E-value: 1.39e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163   8 MKLHHLQMLVALGEQG-NLTHVARMMNISQPALSKWLSQLEDEIGITLFERHSKGL-RPSEGGKLLLQHAQRLINDLERS 85
Cdd:PRK12682   1 MNLQQLRFVREAVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLkGLTEPGKAVLDVIERILREVGNI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163  86 QsEIARFKQGGLVGSLKIGCS-PVATDCVSQAVLSLLQEMPTLHLNIEEKvmTPllhDLIAGAVDVVVGRVGGRALQLpL 164
Cdd:PRK12682  81 K-RIGDDFSNQDSGTLTIATThTQARYVLPRVVAAFRKRYPKVNLSLHQG--SP---DEIARMVISGEADIGIATESL-A 153

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 727186163 165 NYQVLYTEPV-----CFVARPHHPLAKSATLTWHDLTHWRWIVWPTGTPIRLSIDNALADNG 221
Cdd:PRK12682 154 DDPDLATLPCydwqhAVIVPPDHPLAQEERITLEDLAEYPLITYHPGFTGRSRIDRAFAAAG 215
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 10-222 1.53e-15

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 75.41  E-value: 1.53e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163  10 LHHLQMLVALGEQGNLTHVARMMNISQPALSKWLSQLEDEIGITLFERHSKGLRPSEGGKLLLQHAQRLINDLER---SQ 86
Cdd:PRK11013   6 LRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLFEEVQRSYYGLDRivsAA 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163  87 SEIARFKQgglvGSLKIGCSPVatdcVSQAVL-----SLLQEMPTLHLNI--EEkvmTPLL--------HDLiagavdvv 151
Cdd:PRK11013  86 ESLREFRQ----GQLSIACLPV----FSQSLLpglcqPFLARYPDVSLNIvpQE---SPLLeewlsaqrHDL-------- 146

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 727186163 152 vgrVGGRALQLPLNYQ---VLYTEPVCfVARPHHPLAKSATLTWHDLTHWRWIVWPTGTPIRLSIDNALADNGV 222
Cdd:PRK11013 147 ---GLTETLHTPAGTErteLLTLDEVC-VLPAGHPLAAKKVLTPDDFAGENFISLSRTDSYRQLLDQLFAEHGV 216
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 8-123 3.45e-13

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 68.56  E-value: 3.45e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163   8 MKLHHLQMLVALGEQGNLTHVARMMNISQPALSKWLSQLEDEIGITLFERHSKGLRPSEGGKLLLQHAQRLINDLERSQS 87
Cdd:PRK11233   1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQL 80

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 727186163  88 EIARFKQgGLVGSLKIGCSPvaTDCVSQAVLSLLQE 123
Cdd:PRK11233  81 AVHNVGQ-ALSGQVSIGLAP--GTAASSLTMPLLQA 113
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 8-222 1.02e-12

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 67.38  E-value: 1.02e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163   8 MKLHHLQMLVALGEQG-NLTHVARMMNISQPALSKWLSQLEDEIGITLFERHSK---GLrpSEGGKLLLQHAQRLINDLE 83
Cdd:PRK12683   1 MNFQQLRIIREAVRQNfNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKrltGL--TEPGKELLQIVERMLLDAE 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163  84 ---RSQSEIARFKQGGLVgslkigcspVATdCVSQA-------VLSLLQEMPTLHLNIEEKVMTPLLHDLIAGAVdvvvg 153
Cdd:PRK12683  79 nlrRLAEQFADRDSGHLT---------VAT-THTQAryalpkvVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEA----- 143

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163 154 rvggralQLPLNYQVLYTEPV-----------CFVARPHHPLAKSATLTWHDLTHWRWIVWPTGTPIRLSIDNALADNGV 222
Cdd:PRK12683 144 -------DIGIATEALDREPDlvsfpyyswhhVVVVPKGHPLTGRENLTLEAIAEYPIITYDQGFTGRSRIDQAFAEAGL 216
rbcR CHL00180
LysR transcriptional regulator; Provisional
 10-222 4.92e-12

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 65.04  E-value: 4.92e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163  10 LHHLQMLVALGEQGNLTHVARMMNISQPALSKWLSQLEDEIGITLFERHSKGLRPSEGGKLLLQHAQRLINDLERSQSEI 89
Cdd:CHL00180   7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRAL 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163  90 ARFKQGGlVGSLKIGCSPVATDCVSQAVLSLL-QEMPtlHLNIEEKVMTPllhDLIAGAVDVVVGRVGGRALQLPLN-YQ 167
Cdd:CHL00180  87 EDLKNLQ-RGTLIIGASQTTGTYLMPRLIGLFrQRYP--QINVQLQVHST---RRIAWNVANGQIDIAIVGGEVPTElKK 160

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163 168 VLYTEP-----VCFVARPHHPLAKSATLTWHDLTHWRWIVWPTGTPIRLSIDNALADNGV 222
Cdd:CHL00180 161 ILEITPyvedeLALIIPKSHPFAKLKKIQKEDLYRLNFITLDSNSTIRKVIDNILIQNGI 220
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 8-195 8.04e-12

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 64.41  E-value: 8.04e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163   8 MKLHHLQMLVALGEQGNLTHVARMMNISQPALSKWLSQLEDEIGITLFERHSKGLRPSEGGKLLLQHAQRLINDLERSQS 87
Cdd:PRK09906   1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163  88 EIARFKQGGLVgsLKIGCSPVATDCVSQAVLsllqemPTLHLNIEEkvmtpLLHDLIAGAVDVVVGRVGGRALQLPL--- 164
Cdd:PRK09906  81 RARKIVQEDRQ--LTIGFVPSAEVNLLPKVL------PMFRLRHPD-----TLIELVSLITTQQEEKLRRGELDVGFmrh 147

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 727186163 165 -------NYQVLYTEPVCFVARPHHPLAKSATLTWHDL 195
Cdd:PRK09906 148 pvysdeiDYLELLDEPLVVVLPVDHPLAHEKEITAAQL 185
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 8-143 6.90e-11

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 61.97  E-value: 6.90e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163   8 MKLHHLQMLVALGEQGNLTHVARMMNISQPALSKWLSQLEDEIGITLFERHSKGLRPSEGGKLLLQHAQRLINDLERSQs 87
Cdd:PRK11151   1 MNIRDLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVLK- 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 727186163  88 EIARFKQGGLVGSLKIGCSP-VATDCVSQAVLSLLQEMPTLHLNIEEKVMTPLLHDL 143
Cdd:PRK11151  80 EMASQQGETMSGPLHIGLIPtVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQL 136
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 164-299 1.37e-10

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: 59.46  E-value: 1.37e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163 164 LNYQVLYTEPVCFVARPHHPLAKSATLTWHDLTHWRWIVWPTGTPIRLSIDNALADNGVmLPENTVESASMNVSTNLLQS 243
Cdd:cd08440   64 LEFEPLLRDPFVLVCPKDHPLARRRSVTWAELAGYPLIALGRGSGVRALIDRALAAAGL-TLRPAYEVSHMSTALGMVAA 142

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 727186163 244 SDMISILSlRLAQRYASQGQLAILNL--PKIEQkgSVGVFWRNSEPPFAALSRFLQLL 299
Cdd:cd08440  143 GLGVAVLP-ALALPLADHPGLVARPLtePVVTR--TVGLIRRRGRSLSPAAQAFLDLL 197
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
8-231 3.40e-10

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 60.03  E-value: 3.40e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163   8 MKLHHLQMLVALGEQGNLTHVARMMNISQPALSKWLSQLEDEIGITLFERHSKGLRPSEGGKLLLQHAQRLINDLERSQS 87
Cdd:PRK15421   2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQ 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163  88 EIARFKQGGLvgSLKIGCSpvatDCV---SQAVLSLLQEMPTLHLNIEEKVM---TPLLH----DLIAGAVDvvvgrvgg 157
Cdd:PRK15421  82 ACNEPQQTRL--RIAIECH----SCIqwlTPALENFHKNWPQVEMDFKSGVTfdpQPALQqgelDLVMTSDI-------- 147

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163 158 ralqLP---LNYQVLYTEPVCFVARPHHPLAKSATLTWHDLTH---------------WRWIVWPTGT-PIRLSIDNAL- 217
Cdd:PRK15421 148 ----LPrsgLHYSPMFDYEVRLVLAPDHPLAAKTRITPEDLASetlliypvqrsrldvWRHFLQPAGVsPSLKSVDNTLl 223

                        250       260
                 ....*....|....*....|.
gi 727186163 218 ------ADNGV-MLPENTVES 231
Cdd:PRK15421 224 liqmvaARMGIaALPHWVVES 244
PBP2_TdcA cd08418
The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is ...
 116-299 7.10e-10

The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is involved in the degradation of L-serine and L-threonine, contains the type 2 periplasmic binding fold; TdcA, a member of the LysR family, activates the expression of the anaerobically-regulated tdcABCDEFG operon which is involved in the degradation of L-serine and L-threonine to acetate and propionate, respectively. The tdc operon is comprised of one regulatory gene tdcA and six structural genes, tdcB to tdcG. The expression of the tdc operon is affected by several transcription factors including the cAMP receptor protein (CRP), integration host factor (IHF), histone-like protein (HU), and the operon specific regulators TdcA and TcdR. TcdR is divergently transcribed from the operon and encodes a small protein that is required for efficient expression of the Escherichia coli tdc operon. 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: 176110 [Multi-domain]  Cd Length: 201  Bit Score: 57.75  E-value: 7.10e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163 116 AVLSLLQEM-PTLHLNIEEKVMTPLLHDLIAGAVDVVVGRVGGRALQLPLNYQVLYTEPVCFVARPHHPLAKSATLtwHD 194
Cdd:cd08418   17 AVINRFKEQfPDVQISIYEGQLSSLLPELRDGRLDFAIGTLPDEMYLKELISEPLFESDFVVVARKDHPLQGARSL--EE 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163 195 LTHWRWIV--WPTGTPIRLSidNALADNGVmLPENTVESASMNVSTNLLQSSDMISILSLRLAQRYASQGQLAILNLPKI 272
Cdd:cd08418   95 LLDASWVLpgTRMGYYNNLL--EALRRLGY-NPRVAVRTDSIVSIINLVEKADFLTILSRDMGRGPLDSFRLITIPVEEP 171

                        170       180
                 ....*....|....*....|....*..
gi 727186163 273 EQKGSVGVFWRNSEPPFAALSRFLQLL 299
Cdd:cd08418  172 LPSADYYLIYRKKSRLTPLAEQLVELF 198
PRK09986 PRK09986
LysR family transcriptional regulator;
7-100 9.47e-10

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 58.20  E-value: 9.47e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163   7 KMKLHHLQMLVALGEQGNLTHVARMMNISQPALSKWLSQLEDEIGITLFERHSKGLRPSEGGKLLLQHAQRLINDLERSQ 86
Cdd:PRK09986   6 RIDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSL 85

                         90       100
                 ....*....|....*....|.
gi 727186163  87 S---EIARFKQG----GLVGS 100
Cdd:PRK09986  86 ArveQIGRGEAGrieiGIVGT 106
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
9-145 1.09e-09

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 58.23  E-value: 1.09e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163   9 KLHHLQMLVALGEQGNLTHVARMMNISQPALSKWLSQLEDEIGITLFERHSKGLRPSEGGKLLLQHAQRLINDLERSQSE 88
Cdd:PRK10632   3 RLKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQ 82

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 727186163  89 IARFKQgGLVGSLKIGCSPVatdcVSQAVLS-----LLQEMPTLHLNIEEKVMTPllhDLIA 145
Cdd:PRK10632  83 LYAFNN-TPIGTLRIGCSST----MAQNVLAgltakMLKEYPGLSVNLVTGIPAP---DLIA 136
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 167-270 1.75e-09

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: 56.45  E-value: 1.75e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163 167 QVLYTEPVCFVARPHHPLAKsATLTWHDLTHWRWIVWPTGTPIRLSIDNALADNGvmLPEN-TVESASMNVSTNLLQSSD 245
Cdd:cd08417   67 QPLFEDRFVCVARKDHPLAG-GPLTLEDYLAAPHVLVSPRGRGHGLVDDALAELG--LSRRvALTVPHFLAAPALVAGTD 143

                         90       100
                 ....*....|....*....|....*
gi 727186163 246 MISILSLRLAQRYASQGQLAILNLP 270
Cdd:cd08417  144 LIATVPRRLAEALAERLGLRVLPLP 168
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
24-127 2.12e-08

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 54.29  E-value: 2.12e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163  24 NLTHVARMMNISQPALSKWLSQLEDEIGITLFERHSKGLRPSEGGKLLLQHAQRLINDLErsqSEIARFKQGGLVGSLKI 103
Cdd:PRK10082  27 NFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLE---SNLAELRGGSDYAQRKI 103

                         90       100
                 ....*....|....*....|....*
gi 727186163 104 GCSpvATDCVSQAVL-SLLQEMPTL 127
Cdd:PRK10082 104 KIA--AAHSLSLGLLpSIISQMPPL 126
PRK10341 PRK10341
transcriptional regulator TdcA;
9-89 2.18e-08

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 54.48  E-value: 2.18e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163   9 KLHHLQMLVALGEQGNLTHVARMMNISQPALSKWLSQLEDEIGITLFERHSKGLRPSEGGKLLLQHAQRLINDLERSQSE 88
Cdd:PRK10341   8 KTQHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNE 87


                 .
gi 727186163  89 I 89
Cdd:PRK10341  88 I 88
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
32-106 4.36e-07

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 50.20  E-value: 4.36e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 727186163  32 MNISQPALSKWLSQLEDEIGITLFERHSKGLRPSEGGKLLLQHAQRLINDLERSQSEIaRFKQGGLVGSLKIGCS 106
Cdd:PRK11716   1 MHVSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTL-DQQGPSLSGELSLFCS 74
cbl PRK12679
HTH-type transcriptional regulator Cbl;
24-81 6.24e-07

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 50.19  E-value: 6.24e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 727186163  24 NLTHVARMMNISQPALSKWLSQLEDEIGITLFERHSKGLRP-SEGGKLLLQHAQRLIND 81
Cdd:PRK12679  18 NLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRLLGmTEPGKALLVIAERILNE 76
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
 173-299 9.24e-07

The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO operon, which is involved in the carbon dioxide fixation, contains the type 2 periplasmic binding fold; CbbR, a LysR-type transcriptional regulator, is required to activate expression of RubisCO, one of two unique enzymes in the Calvin-Benson-Bassham (CBB) cycle pathway. All plants, cyanobacteria, and many autotrophic bacteria use the CBB cycle to fix carbon dioxide. Thus, this cycle plays an essential role in assimilating CO2 into organic carbon on earth. The key CBB cycle enzyme is ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO), which catalyzes the actual CO2 fixation reaction. The CO2 concentration affects the expression of RubisCO genes. It has also shown that NADPH enhances the DNA-binding ability of the CbbR. RubisCO is composed of eight large (CbbL) and eight small subunits (CbbS). 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: 176111  Cd Length: 197  Bit Score: 48.27  E-value: 9.24e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163 173 PVCFVARPHHPLAKSATLTWHDLTHWRWIVWPTGTPIRLSIDNALADNGVMLPentvesASMNVSTN--LLQS--SDM-I 247
Cdd:cd08419   72 PLVVIAPPDHPLAGQKRIPLERLAREPFLLREPGSGTRLAMERFFAEHGVTLR------VRMELGSNeaIKQAvmAGLgL 145

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 727186163 248 SILSLRLAQRYASQGQLAILN---LPKIEQKGSVgvfWRNSEPPFAALSRFLQLL 299
Cdd:cd08419  146 SVLSLHTLALELATGRLAVLDvegFPIRRQWYVV---HRKGKRLSPAAQAFLDFL 197
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 10-106 1.31e-06

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 48.92  E-value: 1.31e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163  10 LHHLQMLVALGEQGNLTHVARMMNISQPALSKWLSQLEDEIGITLFERHSKGLRPSEGGKLLLQHAQRLindLERSqSEI 89
Cdd:PRK10837   5 LRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALAL---LEQA-VEI 80

                         90
                 ....*....|....*..
gi 727186163  90 ARFKQGGLvGSLKIGCS 106
Cdd:PRK10837  81 EQLFREDN-GALRIYAS 96
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 164-299 1.48e-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: 47.87  E-value: 1.48e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163 164 LNYQVLYTEPVCFVARPHHPLAKSATLTWHDLTHWRWIVWPTGTPIRLSIDNALADNGVMLPEntvesasMNV-----ST 238
Cdd:cd08420   64 LIVEPFAEDELVLVVPPDHPLAGRKEVTAEELAAEPWILREPGSGTREVFERALAEAGLDGLD-------LNIvmelgST 136

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 727186163 239 ----NLLQSSDMISILSLRLAQRYASQGQLAILNLPKIEQKGSVGVFWRNSEPPFAALSRFLQLL 299
Cdd:cd08420  137 eaikEAVEAGLGISILSRLAVRKELELGRLVALPVEGLRLTRPFSLIYHKDKYLSPAAEAFLEFL 201
PRK09801 PRK09801
LysR family transcriptional regulator;
13-132 1.67e-06

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 48.88  E-value: 1.67e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163  13 LQMLVALGEQGNLTHVARMMNISQPALSKWLSQLEDEIGITLFERHSKGLRPSEGGKLLLQHAQRLINDLERSQSEIARF 92
Cdd:PRK09801  11 LQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVTQI 90

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 727186163  93 KQGGlVGSLKIGCS-PVATDCVSQAVLSLLQEMPTLHLNIE 132
Cdd:PRK09801  91 KTRP-EGMIRIGCSfGFGRSHIAPAITELMRNYPELQVHFE 130
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 167-222 3.41e-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: 46.83  E-value: 3.41e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 727186163 167 QVLYTEPVCFVARPHHPLAKSATLTWHDLTHWRWIVWPTGTPIRLSIDNALADNGV 222
Cdd:cd08436   68 RELAREPLVAVVAPDHPLAGRRRVALADLADEPFVDFPPGTGARRQVDRAFAAAGV 123
PRK12680 PRK12680
LysR family transcriptional regulator;
8-62 4.14e-06

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 47.69  E-value: 4.14e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 727186163   8 MKLHHLQMLVALGE-QGNLTHVARMMNISQPALSKWLSQLEDEIGITLFERHSKGL 62
Cdd:PRK12680   1 MTLTQLRYLVAIADaELNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSL 56
PBP2_LeuO cd08466
The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an ...
 167-270 1.49e-05

The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an activator of leucine synthesis operon, contains the type 2 periplasmic binding fold; LeuO, a LysR-type transcriptional regulator, was originally identified as an activator of the leucine synthesis operon (leuABCD). Subsequently, LeuO was found to be not a specific regulator of the leu gene but a global regulator of unrelated various genes. LeuO activates bglGFB (utilization of beta-D-glucoside) and represses cadCBA (lysine decarboxylation) and dsrA (encoding a regulatory small RNA for translational control of rpoS and hns). LeuO also regulates the yjjQ-bglJ operon which coding for a LuxR-type transcription factor. In Salmonella enterica serovar Typhi, LeuO is a positive regulator of ompS1 (encoding an outer membrane), ompS2 (encoding a pathogenicity determinant), and assT, while LeuO represses the expression of OmpX and Tpx. Both osmS1 and osmS2 influence virulence in the mouse model of Salmonella. In Vibrio cholerae, LeuO is involved in control of biofilm formation and in the stringent response. 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: 176155 [Multi-domain]  Cd Length: 200  Bit Score: 44.94  E-value: 1.49e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163 167 QVLYTEPVCFVARPHHPLAKSaTLTWHDLTHWRWIVWpTGTPIRLSIDNALADNGvmLPENTVESASMNVSTNLL--QSS 244
Cdd:cd08466   67 ELLFEDELVCVARKDHPRIQG-SLSLEQYLAEKHVVL-SLRRGNLSALDLLTEEV--LPQRNIAYEVSSLLSMLAvvSQT 142

                         90       100
                 ....*....|....*....|....*.
gi 727186163 245 DMISILSLRLAQRYASQGQLAILNLP 270
Cdd:cd08466  143 DLIAIAPRWLADQYAEQLNLQILPLP 168
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 7-108 1.49e-05

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 45.75  E-value: 1.49e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163   7 KMKLHHLQMLVALGEQGNLTHVARMMNISQPALSKWLSQLEDEIGITLFERHSKGLRPSEGGKLLLQHAQRLINDLERSQ 86
Cdd:PRK14997   1 KTDLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQ 80

                         90       100
                 ....*....|....*....|..
gi 727186163  87 SEIARFkQGGLVGSLKIGCsPV 108
Cdd:PRK14997  81 DAIAAL-QVEPRGIVKLTC-PV 100
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 173-299 2.02e-05

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


Pssm-ID: 176117 [Multi-domain]  Cd Length: 199  Bit Score: 44.61  E-value: 2.02e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163 173 PVCFVARPHHPLAKSATLTWHDLTHWRWIVWPTGTPIRLSIDNALADNGVMlPENTVESASMNVSTNLLQSSDMISILSL 252
Cdd:cd08426   73 PIGAVVPPGHPLARQPSVTLAQLAGYPLALPPPSFSLRQILDAAFARAGVQ-LEPVLISNSIETLKQLVAAGGGISLLTE 151

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 727186163 253 RLAQRYASQGQLAILNLP-KIEQKGSVGVFWRNSEPPFAALSRFLQLL 299
Cdd:cd08426  152 LAVRREIRRGQLVAVPLAdPHMNHRQLELQTRAGRQLPAAASAFLQLL 199
cysB PRK12681
HTH-type transcriptional regulator CysB;
8-62 2.68e-05

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 44.89  E-value: 2.68e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 727186163   8 MKLHHLQMLVALGEQG-NLTHVARMMNISQPALSKWLSQLEDEIGITLFERHSKGL 62
Cdd:PRK12681   1 MKLQQLRYIVEVVNHNlNVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHL 56
PBP2_DntR_NahR_LinR_like cd08459
The C-terminal substrate binding domain of LysR-type transcriptional regulators that are ...
 167-283 2.72e-05

The C-terminal substrate binding domain of LysR-type transcriptional regulators that are involved in the catabolism of dinitrotoluene, naphthalene and gamma-hexachlorohexane; contains the type 2 periplasmic binding fold; This CD includes LysR-like bacterial transcriptional regulators, DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. 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. DntR from Burkholderia species controls genes encoding enzymes for oxidative degradation of the nitro-aromatic compound 2,4-dinitrotoluene. The active form of DntR is homotetrameric, consisting of a dimer of dimers. NahR is a salicylate-dependent transcription activator of the nah and sal operons for naphthalene degradation. Salicylic acid is an intermediate of the oxidative degradation of the aromatic ring in soil bacteria. LinR positively regulates expression of the genes (linD and linE) encoding enzymes for gamma-hexachlorocyclohexane (a haloorganic insecticide) degradation. Expression of linD and linE are induced by their substrates, 2,5-dichlorohydroquinone (2,5-DCHQ) and chlorohydroquinone (CHQ). 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: 176148 [Multi-domain]  Cd Length: 201  Bit Score: 44.10  E-value: 2.72e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163 167 QVLYTEP-VCfVARPHHPLAKSaTLTWHDLTHWRWI-VWPTGTPIRLsIDNALADNGvmLPEN-TVESASMNVSTNLLQS 243
Cdd:cd08459   67 QRLFRERyVC-LVRKDHPRIGS-TLTLEQFLAARHVvVSASGTGHGL-VEQALREAG--IRRRiALRVPHFLALPLIVAQ 141

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 727186163 244 SDMISILSLRLAQRYASQGQLAILNLPKIEQKGSVGVFWR 283
Cdd:cd08459  142 TDLVATVPERLARLFARAGGLRIVPLPFPLPPFEVKLYWH 181
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
12-78 3.01e-05

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 44.76  E-value: 3.01e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 727186163  12 HLQMLVALGEQGNLTHVARMMNISQPALSKWLSQLEDEIGITLFERhSKGLRPSEGGKLLLQHAQRL 78
Cdd:PRK03635   6 QLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRLLRHARQV 71
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 100-299 5.59e-05

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


Pssm-ID: 176107 [Multi-domain]  Cd Length: 196  Bit Score: 43.32  E-value: 5.59e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163 100 SLKIGCSP-VATDCVSQAVLSLLQEMPTLHLNIE----EKVMTPLLH---DL-IAgavdvvvgrvggralQLPLNYQVLY 170
Cdd:cd08415    1 TLRIAALPaLALSLLPRAIARFRARHPDVRISLHtlssSTVVEAVLSgqaDLgLA---------------SLPLDHPGLE 65

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163 171 TEP------VCfVARPHHPLAKSATLTWHDLTHWRWIVWPTGTPIRLSIDNALADNGVMlPENTVESASMNVSTNLLQSS 244
Cdd:cd08415   66 SEPlasgraVC-VLPPGHPLARKDVVTPADLAGEPLISLGRGDPLRQRVDAAFERAGVE-PRIVIETQLSHTACALVAAG 143

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 727186163 245 DMISILSLRLAQRYASQGqLAILNL-PKIEQkgSVGVFWRNSEPPFAALSRFLQLL 299
Cdd:cd08415  144 LGVAIVDPLTAAGYAGAG-LVVRPFrPAIPF--EFALVRPAGRPLSRLAQAFIDLL 196
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 168-221 5.82e-05

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


Pssm-ID: 176115 [Multi-domain]  Cd Length: 200  Bit Score: 43.36  E-value: 5.82e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 727186163 168 VLYTEPVCFVARPHHPLAKSATLTWHDLTHWRWIVWPTGTPIRLSIDNALADNG 221
Cdd:cd08423   73 PLLDDPLDLVLPADHPLAGREEVALADLADEPWIAGCPGSPCHRWLVRACRAAG 126
leuO PRK09508
leucine transcriptional activator; Reviewed
 21-270 2.47e-04

leucine transcriptional activator; Reviewed


Pssm-ID: 181918 [Multi-domain]  Cd Length: 314  Bit Score: 41.93  E-value: 2.47e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163  21 EQgNLTHVARMMNISQPALSKWLSQLE----DEigitLFERHSKGLRPSEGGKLLL----QHAQRLINDLERSQSEIarf 92
Cdd:PRK09508  36 EQ-NITRAAHNLGMSQPAVSNAVARLKvmfnDE----LFVRYGRGIQPTARARQLFgpvrQALQLVQNELPGSGFEP--- 107

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163  93 KQGGLVGSLKIgCSPVATDCVSQAVLSLLQEMPTLHLNIEEkvmtpLLHDLIAGAvdvvvgrvggralqlpLNYQ----- 167
Cdd:PRK09508 108 ESSERVFNLCI-CSPLDIRLTSQIYNRIEQIAPNIHVVFKS-----SLNQNIEHQ----------------LRYQetefv 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163 168 --------------VLYTEPVCFVARPHHPlAKSATLTWHDLTHWRWIVwptgtpirLSIDN------ALADNGVMLPEN 227
Cdd:PRK09508 166 isyeefdrpeftsvPLFKDELVLVASKNHP-RIKGPITEEQLYNEQHAV--------VSLDRfasfsqPWYDTVDKQASI 236

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|...
gi 727186163 228 TVESASMNVSTNLLQSSDMISILSLRLAQRYASQGQLAILNLP 270
Cdd:PRK09508 237 AYQGTALSSVLNVVSQTHLVAIAPRWLAEEFAESLELQILPLP 279
PBP2_DntR_like_3 cd08461
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 164-282 2.61e-04

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


Pssm-ID: 176150 [Multi-domain]  Cd Length: 198  Bit Score: 41.11  E-value: 2.61e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163 164 LNYQVLYTEP-VCfVARPHHPLAKsatltwHDLTHWRW------IVWPTGTPIRLSIDNALADNGvmLPENTVESA-SMN 235
Cdd:cd08461   64 LRSRPLFEERyVC-VTRRGHPLLQ------GPLSLDQFcaldhiVVSPSGGGFAGSTDEALAALG--LTRNVVLSVpSFL 134

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 727186163 236 VSTNLLQSSDMISILSLRLAQryaSQGQLAILNLPKIEQKGSVGVFW 282
Cdd:cd08461  135 VVPEILAATDMVAFVPSRLVP---NLEGLQEVELPLEPPGFDVVMAW 178
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 164-299 3.15e-04

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: 41.00  E-value: 3.15e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163 164 LNYQVLYTEPVCFVARPHHPLAKSATLTWHDLTHWRWIVWPTGTPIRLSIDNALADNGVmLPENTVESASMNVSTNLLQS 243
Cdd:cd08438   64 FDSQPLCNEPLVAVLPRGHPLAGRKTVSLADLADEPFILFNEDFALHDRIIDACQQAGF-TPNIAARSSQWDFIAELVAA 142

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 727186163 244 SDMISILSLRLAQRYaSQGQLAILNLPKIEQKGSVGVFWRNSEPPFAALSRFLQLL 299
Cdd:cd08438  143 GLGVALLPRSIAQRL-DNAGVKVIPLTDPDLRWQLALIWRKGRYLSHAARAWLALL 197
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 11-132 4.32e-04

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 41.08  E-value: 4.32e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163  11 HHLQMLVALGEQGNLTHVARMMNISQPALSKWLSQLEDEIGITLFERHSKGLRPSEGGKLLLQHAQRLINDLE--RSQSE 88
Cdd:PRK11074   5 YSLEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQetRRQCQ 84

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 727186163  89 -IARfkqgGLVGSLKIGC-SPVATDCVSQAVLSLLQEMP--TLHLNIE 132
Cdd:PRK11074  85 qVAN----GWRGQLSIAVdNIVRPDRTRQLIVDFYRHFDdvELIIRQE 128
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 164-299 6.02e-04

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: 40.18  E-value: 6.02e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163 164 LNYQVLYTEPVCFVARPHHPLAKSATLTWHDLTHWRWIVWP--TGTPIRLSIDNALADNGVMlPENTVESASMNVSTNLL 241
Cdd:cd08414   64 LASRPLLREPLVVALPADHPLAARESVSLADLADEPFVLFPrePGPGLYDQILALCRRAGFT-PRIVQEASDLQTLLALV 142

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 727186163 242 QSSDMISILSlRLAQRYASQGqLAILNLPKIEQKGSVGVFWRnSEPPFAALSRFLQLL 299
Cdd:cd08414  143 AAGLGVALVP-ASVARLQRPG-VVYRPLADPPPRSELALAWR-RDNASPALRAFLELA 197
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
34-129 7.55e-04

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 40.39  E-value: 7.55e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163  34 ISQPALSKWLSQLEDEIGITLFERHSKGLRPSEGGKLLLQHAQRLINDLERSQSEIARFKQGGLvgsLKIGCSPVATDCV 113
Cdd:PRK03601  27 LTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYAETLMNTWQAAKKEVAHTSQHNE---LSIGASASLWECM 103

                         90
                 ....*....|....*..
gi 727186163 114 SQAVLS-LLQEMPTLHL 129
Cdd:PRK03601 104 LTPWLGrLYQNQEALQF 120
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
34-131 8.60e-04

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 40.37  E-value: 8.60e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163  34 ISQPALSKWLSQLEDEIGITLFERHSKGLRPSEGGKLLLQHAQRLINDLERsqsEIARFKQGGLVGSLKIGCSPVATDC- 112
Cdd:PRK10086  40 LTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLDTLNQ---EILDIKNQELSGTLTVYSRPSIAQCw 116

                         90
                 ....*....|....*....
gi 727186163 113 VSQAVLSLLQEMPTLHLNI 131
Cdd:PRK10086 117 LVPRLADFTRRYPSISLTI 135
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
13-284 6.67e-03

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 37.48  E-value: 6.67e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163  13 LQMLVALGEQGNLTHVARMMNISQPALSKWLSQLEDEIGITLFERHSKGLRPSEGGKLLLQHAQRLINDLERSQSEIARF 92
Cdd:PRK10094   7 LRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPSELQQV 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163  93 KQGgLVGSLKIGCSPVATDcvSQAVLSLL----QEMPTLHLNIEEKVMTPLLHDLIAGAVDVVVGRVGGRALQLPLNYQV 168
Cdd:PRK10094  87 NDG-VERQVNIVINNLLYN--PQAVAQLLawlnERYPFTQFHISRQIYMGVWDSLLYEGFSLAIGVTGTEALANTFSLDP 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163 169 LYTEPVCFVARPHHPLAK-SATLTwHDLTHWRWIVWPTGTPIRLSIDNALadngvMLP---ENTVESASMNVSTNLlqSS 244
Cdd:PRK10094 164 LGSVQWRFVMAADHPLANvEEPLT-EAQLRRFPAVNIEDSARTLTKRVAW-----RLPgqkEIIVPDMETKIAAHL--AG 235

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|
gi 727186163 245 DMISILSLRLAQRYASQGQLAILNLPKIEQKGSVGVFWRN 284
Cdd:PRK10094 236 VGIGFLPKSLCQSMIDNQQLVSRVIPTMRPPSPLSLAWRK 275
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 163-222 9.64e-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: 36.36  E-value: 9.64e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186163 163 PLNYQVLYTEPVCFVARPHHPLAKSATLTWHDLTHWRWIVWPTGTPIRLSIDNALADNGV 222
Cdd:cd08434   63 DIEWIPLFTEELVLVVPKDHPLAGRDSVDLAELADEPFVLLSPGFGLRPIVDELCAAAGF 122
 
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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