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Conserved domains on  [gi|1632151917|gb|QCH93253|]
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LysR family transcriptional regulator [Escherichia coli O145:NM]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Periplasmic_Binding_Protein_Type_2 super family cl21456
Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent ...
 94-289 1.21e-63

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 cd08431:

Pssm-ID: 473866 [Multi-domain]  Cd Length: 195  Bit Score: 199.42  E-value: 1.21e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917  94 ELVIGVDDTFPFSLLAPLIEAFYQHHSVTRLKFINGVLGGSWDALTQGRADIIVGAMHEPPSSsEFGFSRLGDLEQVFAV 173
Cdd:cd08431     1 ELRIAIDTVLPLQPLYPLIAEFYQLNKATRIRLSEEVLGGTWDALASGRADLVIGATGELPPG-GVKTRPLGEVEFVFAV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917 174 APHHPLALEEEPLNRRIIKRYRAIVVGDTAQAGASTASQLLDEQEAITVFDFKTKLELQISGLGCGYLPRYLAQRFLDSG 253
Cdd:cd08431    80 APNHPLAKLDGPLDASAIKQYPAIVVADTSRNLPPRSSGLLEGQDRIRVPTMQAKIDAQVLGLGVGYLPRHLAKPELASG 159

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1632151917 254 ALIEKKVVAQTLFEPVWIGWNEQTAGLASGWWRDEI 289
Cdd:cd08431   160 ELVEKALEDPRPPQELFLAWRKDQRGKALAWFVQRL 195
rbcR super family cl31781
LysR transcriptional regulator; Provisional
 5-148 3.32e-17

LysR transcriptional regulator; Provisional


The actual alignment was detected with superfamily member CHL00180:

Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 80.06  E-value: 3.32e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917   5 LDVLMILDALEKEGSFAAASAKLYKTPSALSYTVHKLESDLNIQLLDRSGHRAKFTRTGKMLLEKGREVLHTVRELEKQA 84
Cdd:CHL00180    7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRAL 86

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1632151917  85 IKLHEGWENELVIGVDDTFPFSLLAPLIEAFYQHHSVTRLKF-INGVLGGSWDALtQGRADI-IVG 148
Cdd:CHL00180   87 EDLKNLQRGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLqVHSTRRIAWNVA-NGQIDIaIVG 151
 
Name Accession Description Interval E-value
PBP2_HupR cd08431
The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which ...
 94-289 1.21e-63

The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which regulates expression of the heme uptake receptor HupA; contains the type 2 periplasmic binding fold; HupR, a member of the LysR family, activates hupA transcription under low-iron conditions in the presence of hemin. The expression of many iron-uptake genes, such as hupA, is regulated at the transcriptional level by iron and an iron-binding repressor protein called Fur (ferric uptake regulation). Under iron-abundant conditions with heme, the active Fur repressor protein represses transcription of the iron-uptake gene hupA, and prevents transcriptional activation via HupR. Under low-iron conditions with heme, the Fur repressor is inactive and transcription of the hupA is allowed. 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: 176122 [Multi-domain]  Cd Length: 195  Bit Score: 199.42  E-value: 1.21e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917  94 ELVIGVDDTFPFSLLAPLIEAFYQHHSVTRLKFINGVLGGSWDALTQGRADIIVGAMHEPPSSsEFGFSRLGDLEQVFAV 173
Cdd:cd08431     1 ELRIAIDTVLPLQPLYPLIAEFYQLNKATRIRLSEEVLGGTWDALASGRADLVIGATGELPPG-GVKTRPLGEVEFVFAV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917 174 APHHPLALEEEPLNRRIIKRYRAIVVGDTAQAGASTASQLLDEQEAITVFDFKTKLELQISGLGCGYLPRYLAQRFLDSG 253
Cdd:cd08431    80 APNHPLAKLDGPLDASAIKQYPAIVVADTSRNLPPRSSGLLEGQDRIRVPTMQAKIDAQVLGLGVGYLPRHLAKPELASG 159

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1632151917 254 ALIEKKVVAQTLFEPVWIGWNEQTAGLASGWWRDEI 289
Cdd:cd08431   160 ELVEKALEDPRPPQELFLAWRKDQRGKALAWFVQRL 195
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 8-284 1.54e-54

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 179.37  E-value: 1.54e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917   8 LMILDALEKEGSFAAASAKLYKTPSALSYTVHKLESDLNIQLLDRSGHRAKFTRTGKMLLEKGREVLHTVRELEKQAIKL 87
Cdd:PRK11074    7 LEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRRQCQQV 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917  88 HEGWENELVIGVDDTFPFSLLAPLIEAFYQHHSVTRLKFINGVLGGSWDALTQGRADIIVGAMHEPPSSSEFGFSRLGDL 167
Cdd:PRK11074   87 ANGWRGQLSIAVDNIVRPDRTRQLIVDFYRHFDDVELIIRQEVFNGVWDALADGRVDIAIGATRAIPVGGRFAFRDMGML 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917 168 EQVFAVAPHHPLALEEEPLNRRIIKRYRAIVVGDTAQAGASTASQLLDEQEAITVFDFKTKLELQISGLGCGYLPRYLAQ 247
Cdd:PRK11074  167 SWACVVSSDHPLASMDGPLSDDELRPYPSLCLEDTSRTLPKRITWLLDNQRRLVVPDWESAINCLSAGLCVGMVPTHFAK 246

                         250       260       270
                  ....*....|....*....|....*....|....*..
gi 1632151917 248 RFLDSGALIEKKVVAQTLFEPVWIGWNEQTAGLASGW 284
Cdd:PRK11074  247 PLINSGKLVELTLENPFPDSPCCLTWQQNDMSPALAW 283
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
5-291 3.39e-44

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 151.17  E-value: 3.39e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917   5 LDVLMILDALEKEGSFAAASAKLYKTPSALSYTVHKLESDLNIQLLDRSGHRAKFTRTGKMLLEKGREVLHTVRELEKQA 84
Cdd:COG0583     3 LRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAEL 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917  85 IKLHEGWENELVIGVDDTFPFSLLAPLIEAFYQHHSVTRLKFINGVLGGSWDALTQGRADIIVGamHEPPSSSEFGFSRL 164
Cdd:COG0583    83 RALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIR--LGPPPDPGLVARPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917 165 GDLEQVFAVAPHHPLALeeeplnrriikryRAIVVGDTAqagastasqlldeqeaitvfdfkTKLELQISGLGCGYLPRY 244
Cdd:COG0583   161 GEERLVLVASPDHPLAR-------------RAPLVNSLE-----------------------ALLAAVAAGLGIALLPRF 204

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*...
gi 1632151917 245 LAQRFLDSGALIEKKVVAQTLFEPVWIGWNEQTA-GLASGWWRDEILA 291
Cdd:COG0583   205 LAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHlSPAVRAFLDFLRE 252
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 94-294 6.59e-24

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: 96.59  E-value: 6.59e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917  94 ELVIGVDDTFPFSLLAPLIEAFYQHHSVTRLKFINGVLGGSWDALTQGRADIIVgaMHEPPSSSEFGFSRLGDLEQVFAV 173
Cdd:pfam03466   3 RLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAI--RRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917 174 APHHPLAlEEEPLNRRIIKRYRAIVV----GDTAQAGASTASQLLDEQEAITVFDFKTKLELQISGLGCGYLPRYLAQRF 249
Cdd:pfam03466  81 PPDHPLA-RGEPVSLEDLADEPLILLppgsGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARE 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1632151917 250 LDSGALIEKKVVAQTLFEPVWIGWN-EQTAGLASGWWRDEILANSA 294
Cdd:pfam03466 160 LADGRLVALPLPEPPLPRELYLVWRkGRPLSPAVRAFIEFLREALA 205
rbcR CHL00180
LysR transcriptional regulator; Provisional
 5-148 3.32e-17

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 80.06  E-value: 3.32e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917   5 LDVLMILDALEKEGSFAAASAKLYKTPSALSYTVHKLESDLNIQLLDRSGHRAKFTRTGKMLLEKGREVLHTVRELEKQA 84
Cdd:CHL00180    7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRAL 86

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1632151917  85 IKLHEGWENELVIGVDDTFPFSLLAPLIEAFYQHHSVTRLKF-INGVLGGSWDALtQGRADI-IVG 148
Cdd:CHL00180   87 EDLKNLQRGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLqVHSTRRIAWNVA-NGQIDIaIVG 151
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 17-260 3.86e-15

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


Pssm-ID: 468965 [Multi-domain]  Cd Length: 301  Bit Score: 74.39  E-value: 3.86e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917  17 EGSFAAASAKLYKTPSALSYTVHKLESDLNIQLLDRSGHRAKFTRTGKMLLEKGREVLHTVRELEKQAIKLHEgwENELV 96
Cdd:NF041036   15 EGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRILDIEDSLMDELKSFKG--RQRLS 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917  97 IGVDDTFPFSLLAPLIEAFYQHH-SVTRLKF--------INGVLGGSWD-ALTQGRADIIVGAMHEPPsssefgfsrLGD 166
Cdd:NF041036   93 ICCTPTFGMAHLPGVLNRFMLRNaDVVDLKFlfhspaqaLEGIQNKEFDlAIIEHCADLDLGRFHTYP---------LPQ 163

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917 167 LEQVFAVAPH-----HPLALeEEPLNRRIIKRYRAIVVGDTAQAG-ASTASQLLDEQEAITVFDFKTKLELQISGLGCGY 240
Cdd:NF041036  164 DELVFVSAPSlglptPNVTL-ERLLELCLITRRDGCSSRDLLRRNlAEQGRDLDDFRRVVVSDDLRLTIQTVLDGGGISF 242

                         250       260
                  ....*....|....*....|
gi 1632151917 241 LPRYLAQRFLDSGALIEKKV 260
Cdd:NF041036  243 VSRSLVCEYLKNGQLREHYV 262
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
5-64 1.35e-12

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 61.63  E-value: 1.35e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917   5 LDVLMILDALEKEGSFAAASAKLYKTPSALSYTVHKLESDLNIQLLDRSGHRAKFTRTGK 64
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
 
Name Accession Description Interval E-value
PBP2_HupR cd08431
The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which ...
 94-289 1.21e-63

The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which regulates expression of the heme uptake receptor HupA; contains the type 2 periplasmic binding fold; HupR, a member of the LysR family, activates hupA transcription under low-iron conditions in the presence of hemin. The expression of many iron-uptake genes, such as hupA, is regulated at the transcriptional level by iron and an iron-binding repressor protein called Fur (ferric uptake regulation). Under iron-abundant conditions with heme, the active Fur repressor protein represses transcription of the iron-uptake gene hupA, and prevents transcriptional activation via HupR. Under low-iron conditions with heme, the Fur repressor is inactive and transcription of the hupA is allowed. 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: 176122 [Multi-domain]  Cd Length: 195  Bit Score: 199.42  E-value: 1.21e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917  94 ELVIGVDDTFPFSLLAPLIEAFYQHHSVTRLKFINGVLGGSWDALTQGRADIIVGAMHEPPSSsEFGFSRLGDLEQVFAV 173
Cdd:cd08431     1 ELRIAIDTVLPLQPLYPLIAEFYQLNKATRIRLSEEVLGGTWDALASGRADLVIGATGELPPG-GVKTRPLGEVEFVFAV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917 174 APHHPLALEEEPLNRRIIKRYRAIVVGDTAQAGASTASQLLDEQEAITVFDFKTKLELQISGLGCGYLPRYLAQRFLDSG 253
Cdd:cd08431    80 APNHPLAKLDGPLDASAIKQYPAIVVADTSRNLPPRSSGLLEGQDRIRVPTMQAKIDAQVLGLGVGYLPRHLAKPELASG 159

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1632151917 254 ALIEKKVVAQTLFEPVWIGWNEQTAGLASGWWRDEI 289
Cdd:cd08431   160 ELVEKALEDPRPPQELFLAWRKDQRGKALAWFVQRL 195
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 8-284 1.54e-54

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 179.37  E-value: 1.54e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917   8 LMILDALEKEGSFAAASAKLYKTPSALSYTVHKLESDLNIQLLDRSGHRAKFTRTGKMLLEKGREVLHTVRELEKQAIKL 87
Cdd:PRK11074    7 LEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRRQCQQV 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917  88 HEGWENELVIGVDDTFPFSLLAPLIEAFYQHHSVTRLKFINGVLGGSWDALTQGRADIIVGAMHEPPSSSEFGFSRLGDL 167
Cdd:PRK11074   87 ANGWRGQLSIAVDNIVRPDRTRQLIVDFYRHFDDVELIIRQEVFNGVWDALADGRVDIAIGATRAIPVGGRFAFRDMGML 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917 168 EQVFAVAPHHPLALEEEPLNRRIIKRYRAIVVGDTAQAGASTASQLLDEQEAITVFDFKTKLELQISGLGCGYLPRYLAQ 247
Cdd:PRK11074  167 SWACVVSSDHPLASMDGPLSDDELRPYPSLCLEDTSRTLPKRITWLLDNQRRLVVPDWESAINCLSAGLCVGMVPTHFAK 246

                         250       260       270
                  ....*....|....*....|....*....|....*..
gi 1632151917 248 RFLDSGALIEKKVVAQTLFEPVWIGWNEQTAGLASGW 284
Cdd:PRK11074  247 PLINSGKLVELTLENPFPDSPCCLTWQQNDMSPALAW 283
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
5-291 3.39e-44

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 151.17  E-value: 3.39e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917   5 LDVLMILDALEKEGSFAAASAKLYKTPSALSYTVHKLESDLNIQLLDRSGHRAKFTRTGKMLLEKGREVLHTVRELEKQA 84
Cdd:COG0583     3 LRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAEL 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917  85 IKLHEGWENELVIGVDDTFPFSLLAPLIEAFYQHHSVTRLKFINGVLGGSWDALTQGRADIIVGamHEPPSSSEFGFSRL 164
Cdd:COG0583    83 RALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIR--LGPPPDPGLVARPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917 165 GDLEQVFAVAPHHPLALeeeplnrriikryRAIVVGDTAqagastasqlldeqeaitvfdfkTKLELQISGLGCGYLPRY 244
Cdd:COG0583   161 GEERLVLVASPDHPLAR-------------RAPLVNSLE-----------------------ALLAAVAAGLGIALLPRF 204

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*...
gi 1632151917 245 LAQRFLDSGALIEKKVVAQTLFEPVWIGWNEQTA-GLASGWWRDEILA 291
Cdd:COG0583   205 LAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHlSPAVRAFLDFLRE 252
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
18-281 9.10e-42

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 146.49  E-value: 9.10e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917  18 GSFAAASAKLYKTPSALSYTVHKLESDLNIQLLDRSGHRAKFTRTGKMLLEKGREVLHTVRELEKQAIKLHEGWENELVI 97
Cdd:PRK10094   17 GSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPSELQQVNDGVERQVNI 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917  98 GVDD-TFPFSLLAPLIEAFYQHHSVTRLKFINGVLGGSWDALTQGRADIIVGAMHEPPSSSEFGFSRLGDLEQVFAVAPH 176
Cdd:PRK10094   97 VINNlLYNPQAVAQLLAWLNERYPFTQFHISRQIYMGVWDSLLYEGFSLAIGVTGTEALANTFSLDPLGSVQWRFVMAAD 176

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917 177 HPLALEEEPLNRRIIKRYRAIVVGDTAQAGASTASQLLDEQEAITVFDFKTKLELQISGLGCGYLPRYLAQRFLDSGALI 256
Cdd:PRK10094  177 HPLANVEEPLTEAQLRRFPAVNIEDSARTLTKRVAWRLPGQKEIIVPDMETKIAAHLAGVGIGFLPKSLCQSMIDNQQLV 256

                         250       260
                  ....*....|....*....|....*
gi 1632151917 257 EKKVVAQTLFEPVWIGWNEQTAGLA 281
Cdd:PRK10094  257 SRVIPTMRPPSPLSLAWRKFGSGKA 281
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 94-294 6.59e-24

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: 96.59  E-value: 6.59e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917  94 ELVIGVDDTFPFSLLAPLIEAFYQHHSVTRLKFINGVLGGSWDALTQGRADIIVgaMHEPPSSSEFGFSRLGDLEQVFAV 173
Cdd:pfam03466   3 RLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAI--RRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917 174 APHHPLAlEEEPLNRRIIKRYRAIVV----GDTAQAGASTASQLLDEQEAITVFDFKTKLELQISGLGCGYLPRYLAQRF 249
Cdd:pfam03466  81 PPDHPLA-RGEPVSLEDLADEPLILLppgsGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARE 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1632151917 250 LDSGALIEKKVVAQTLFEPVWIGWN-EQTAGLASGWWRDEILANSA 294
Cdd:pfam03466 160 LADGRLVALPLPEPPLPRELYLVWRkGRPLSPAVRAFIEFLREALA 205
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
8-270 5.14e-19

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 85.45  E-value: 5.14e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917   8 LMILDALEKEGSFAAASAKLYKTPSALSYTVHKLESDLNIQLLDRSGHRAKFTRTGKMLLEKGREVLHTV-RELEkqaiK 86
Cdd:PRK15421    7 LKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQIsQALQ----A 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917  87 LHEGWENELVIGVDDTFPFSLLAPLIEAFYQHHSVTRLKFINGVLGGSWDALTQGRADIIVGAMHEPPSSseFGFSRLGD 166
Cdd:PRK15421   83 CNEPQQTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSG--LHYSPMFD 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917 167 LEQVFAVAPHHPLA---------LEEEPLNRRIIKRYRAIVVGDTAQ-AGASTASQLLDeqeaitvfdfKTKLELQI--S 234
Cdd:PRK15421  161 YEVRLVLAPDHPLAaktritpedLASETLLIYPVQRSRLDVWRHFLQpAGVSPSLKSVD----------NTLLLIQMvaA 230

                         250       260       270
                  ....*....|....*....|....*....|....*.
gi 1632151917 235 GLGCGYLPRYLAQRFLDSGAliekkVVAQTLFEPVW 270
Cdd:PRK15421  231 RMGIAALPHWVVESFERQGL-----VVTKTLGEGLW 261
rbcR CHL00180
LysR transcriptional regulator; Provisional
 5-148 3.32e-17

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 80.06  E-value: 3.32e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917   5 LDVLMILDALEKEGSFAAASAKLYKTPSALSYTVHKLESDLNIQLLDRSGHRAKFTRTGKMLLEKGREVLHTVRELEKQA 84
Cdd:CHL00180    7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRAL 86

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1632151917  85 IKLHEGWENELVIGVDDTFPFSLLAPLIEAFYQHHSVTRLKF-INGVLGGSWDALtQGRADI-IVG 148
Cdd:CHL00180   87 EDLKNLQRGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLqVHSTRRIAWNVA-NGQIDIaIVG 151
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 17-260 3.86e-15

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


Pssm-ID: 468965 [Multi-domain]  Cd Length: 301  Bit Score: 74.39  E-value: 3.86e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917  17 EGSFAAASAKLYKTPSALSYTVHKLESDLNIQLLDRSGHRAKFTRTGKMLLEKGREVLHTVRELEKQAIKLHEgwENELV 96
Cdd:NF041036   15 EGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRILDIEDSLMDELKSFKG--RQRLS 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917  97 IGVDDTFPFSLLAPLIEAFYQHH-SVTRLKF--------INGVLGGSWD-ALTQGRADIIVGAMHEPPsssefgfsrLGD 166
Cdd:NF041036   93 ICCTPTFGMAHLPGVLNRFMLRNaDVVDLKFlfhspaqaLEGIQNKEFDlAIIEHCADLDLGRFHTYP---------LPQ 163

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917 167 LEQVFAVAPH-----HPLALeEEPLNRRIIKRYRAIVVGDTAQAG-ASTASQLLDEQEAITVFDFKTKLELQISGLGCGY 240
Cdd:NF041036  164 DELVFVSAPSlglptPNVTL-ERLLELCLITRRDGCSSRDLLRRNlAEQGRDLDDFRRVVVSDDLRLTIQTVLDGGGISF 242

                         250       260
                  ....*....|....*....|
gi 1632151917 241 LPRYLAQRFLDSGALIEKKV 260
Cdd:NF041036  243 VSRSLVCEYLKNGQLREHYV 262
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 94-273 8.64e-13

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: 65.70  E-value: 8.64e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917  94 ELVIGVDDTFPFSLLAPLIEAFYQHHSVTRLKFINGVLGGSWDALTQGRADIIVGAMhePPSSSEFGFSRLGDLEQVFAV 173
Cdd:cd05466     1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVAL--PVDDPGLESEPLFEEPLVLVV 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917 174 APHHPLA---------LEEEPLnrrII----KRYRAIVVGDTAQAGASTASQL-LDEQEAItvfdfktkLELQISGLGCG 239
Cdd:cd05466    79 PPDHPLAkrksvtladLADEPL---ILfergSGLRRLLDRAFAEAGFTPNIALeVDSLEAI--------KALVAAGLGIA 147

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1632151917 240 YLPRYLAQRFLDSGaLIEKKVVAQTLFEPVWIGW 273
Cdd:cd05466   148 LLPESAVEELADGG-LVVLPLEDPPLSRTIGLVW 180
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
5-64 1.35e-12

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 61.63  E-value: 1.35e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917   5 LDVLMILDALEKEGSFAAASAKLYKTPSALSYTVHKLESDLNIQLLDRSGHRAKFTRTGK 64
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 13-246 2.66e-10

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 60.17  E-value: 2.66e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917  13 ALEKEGSFAAASAKLYKTPSALSYTVHKLESDLNIQLLDRSGHRAKFTRTGKMLLEKGREVLHTVRELEKQAIKLHEGwE 92
Cdd:PRK09906   11 AVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKLRARKIVQE-D 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917  93 NELVIGVDDTFPFSLLAPLIEAFYQHHSVTRLKFINGVLGGSWDALTQGraDIIVGAMHEPPSSSEFGFSRLGDLEQVFA 172
Cdd:PRK09906   90 RQLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRG--ELDVGFMRHPVYSDEIDYLELLDEPLVVV 167

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917 173 VAPHHPLALEEE-PLNRRIIKRYraiVVGDTAQAG----------ASTASQLLDEQEAITVFdfkTKLELQISGLGCGYL 241
Cdd:PRK09906  168 LPVDHPLAHEKEiTAAQLDGVNF---ISTDPAYSGslapiikawfAQHNSQPNIVQVATNIL---VTMNLVGMGLGCTII 241


                  ....*
gi 1632151917 242 PRYLA 246
Cdd:PRK09906  242 PGYMN 246
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 13-194 3.96e-10

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 59.58  E-value: 3.96e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917  13 ALEKEGSFAAASAKLYKTPSALSYTVHKLESDLNIQLLDRSGHRAKFTRTGKMLLEKGREVLHtvrELEKQAIKLHEGWE 92
Cdd:PRK11242   11 AVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQ---DLEAGRRAIHDVAD 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917  93 ---NELVIGVDDTFPFSLLAPLIEAFYQHHSVTRLkfingvlggSWDALTQGR------ADII-VGAMHEPPSSSEFGFS 162
Cdd:PRK11242   88 lsrGSLRLAMTPTFTAYLIGPLIDAFHARYPGITL---------TIREMSQERieallaDDELdVGIAFAPVHSPEIEAQ 158

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 1632151917 163 RLGDLEQVFAVAPHHPLA----------LEEEPL--------NRRIIKRY 194
Cdd:PRK11242  159 PLFTETLALVVGRHHPLAarrkaltldeLADEPLvllsaefaTREQIDRY 208
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
18-111 1.06e-09

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 58.62  E-value: 1.06e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917  18 GSFAAASAKLYKTPSALSYTVHKLESDLNIQLLDRSGHRAKFTRTGKMLLEKGREVLHTVRELEKQAIKLHEGWENELVI 97
Cdd:PRK10632   17 GSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQLYAFNNTPIGTLRI 96

                          90
                  ....*....|....
gi 1632151917  98 GVDDTFPFSLLAPL 111
Cdd:PRK10632   97 GCSSTMAQNVLAGL 110
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 16-270 1.85e-08

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 54.69  E-value: 1.85e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917  16 KEGSFAAASAKLYKTPSALSYTVHKLESDLNIQLLDRSGHRAKFTRTGKMLLEKGREVLHTVRELEkQAIKLHEGwenEL 95
Cdd:PRK10837   16 KSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQAVEIE-QLFREDNG---AL 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917  96 VIGVDDTFPFSLLAPLIEAFYQHHSVTRLKFingVLGGSWD---ALTQGRADI--IVGAMHEPPSSSEfgfSRLGDLEQV 170
Cdd:PRK10837   92 RIYASSTIGNYILPAMIARYRRDYPQLPLEL---SVGNSQDvinAVLDFRVDIglIEGPCHSPELISE---PWLEDELVV 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917 171 FAvAPHHPLALEEEPLNRRI----IKRyraivvgdtaQAGASTaSQLLDEQEAITVFDFKTKLELQIS---------GLG 237
Cdd:PRK10837  166 FA-APDSPLARGPVTLEQLAaapwILR----------ERGSGT-REIVDYLLLSHLPRFELAMELGNSeaikhavrhGLG 233

                         250       260       270
                  ....*....|....*....|....*....|...
gi 1632151917 238 CGYLPRYLAQRFLDSGALIEKKVVAQTLFEPVW 270
Cdd:PRK10837  234 ISCLSRRVIADQLQAGTLVEVAVPLPRLMRTLY 266
PRK09801 PRK09801
LysR family transcriptional regulator;
3-126 3.63e-08

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 53.89  E-value: 3.63e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917   3 PLLDVLMILDALEKEGSFAAASAKLYKTPSALSYTVHKLESDLNIQLLDRSGHRAKFTRTGKMLLEKGREVLHTVRELEK 82
Cdd:PRK09801    6 PLAKDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVD 85

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1632151917  83 QAIKLHEGWENELVIGVDDTFPFSLLAPLIEAFYQHHSVTRLKF 126
Cdd:PRK09801   86 DVTQIKTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHF 129
PRK09791 PRK09791
LysR family transcriptional regulator;
16-180 2.71e-07

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 51.30  E-value: 2.71e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917  16 KEGSFAAASAKLYKTPSALSYTVHKLESDLNIQLLDRSGHRAKFTRTGKMLLEKGREVLHTVR---ELEKQAIKLHEGWE 92
Cdd:PRK09791   18 RQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRaaqEDIRQRQGQLAGQI 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917  93 NelvIGVDDTFPFSLLAPLIEAFYQHHSVTRLKFINGVLGGSWDALTQGRADIIVGAMHEPPSSSEFGFSRLGDLEQVFA 172
Cdd:PRK09791   98 N---IGMGASIARSLMPAVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDFTINTYYQGPYDHEFTFEKLLEKQFAVF 174


                  ....*...
gi 1632151917 173 VAPHHPLA 180
Cdd:PRK09791  175 CRPGHPAI 182
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 106-185 1.36e-06

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: 48.04  E-value: 1.36e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917 106 SLLAPLIEAFYQHHSVTRLKfingVLGGSWDALT----QGRADIIVGAMHEPPSSSEFGFSRLGDLEQVFAVAPHHPLAL 181
Cdd:cd08435    13 VLLPPAIARLLARHPRLTVR----VVEGTSDELLeglrAGELDLAIGRLADDEQPPDLASEELADEPLVVVARPGHPLAR 88


                  ....
gi 1632151917 182 EEEP 185
Cdd:cd08435    89 RARL 92
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
19-129 9.59e-06

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 46.53  E-value: 9.59e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917  19 SFAAASAKLYKTPSALSYTVHKLESDLNIQLLDRSGHRAKFTRTGKML---LEKGREVL-HTVRELEKQAIklhegwENE 94
Cdd:PRK10086   30 SFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVfwaLKSSLDTLnQEILDIKNQEL------SGT 103

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1632151917  95 LVIGVDDTFPFSLLAPLIEAFYQHHSVTRLKFING 129
Cdd:PRK10086  104 LTVYSRPSIAQCWLVPRLADFTRRYPSISLTILTG 138
PRK09986 PRK09986
LysR family transcriptional regulator;
13-180 2.43e-05

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 45.10  E-value: 2.43e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917  13 ALEKEGSFAAASAKLYKTPSALSYTVHKLESDLNIQLLDRSGHRAKFTRTGKMLLEKGREVLHTVRELEKQAIKLHEGWE 92
Cdd:PRK09986   17 AVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLARVEQIGRGEA 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917  93 NELVIGVDDTFPFSLLAPLIEAFYQHHSVTRLKFINGVLGGSWDALTQGRADIIVGAMHEPPSSSEFGFSRLGdlEQVFA 172
Cdd:PRK09986   97 GRIEIGIVGTALWGRLRPAMRHFLKENPNVEWLLRELSPSMQMAALERRELDAGIWRMADLEPNPGFTSRRLH--ESAFA 174

                         170
                  ....*....|
gi 1632151917 173 VAPH--HPLA 180
Cdd:PRK09986  175 VAVPeeHPLA 184
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
30-185 1.33e-04

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 42.88  E-value: 1.33e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917  30 TPSALSYTVHKLESDLNIQLLDRSGHRAKFTRTGKMLLEKGREVLHTVRELeKQAIKLHEG-WENELVIGVDDTFPFSLL 108
Cdd:PRK11716    4 SPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQL-RHTLDQQGPsLSGELSLFCSVTAAYSHL 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917 109 APLIEAFYQHHSVTRLKFINGvlggswDA------LTQGRADIIVGAMHEPPSSSeFGFSRLGDLEQVFaVAPHHP---- 178
Cdd:PRK11716   83 PPILDRFRAEHPLVEIKLTTG------DAadavekVQSGEADLAIAAKPETLPAS-VAFSPIDEIPLVL-IAPALPcpvr 154


                  ....*...
gi 1632151917 179 -LALEEEP 185
Cdd:PRK11716  155 qQLSQEKP 162
PBP2_MetR cd08441
The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which ...
 105-180 1.51e-04

The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which regulates the expression of methionine biosynthetic genes, contains type 2 periplasmic binding fold; MetR, a member of the LysR family, is a positive regulator for the metA, metE, metF, and metH genes. The sulfur-containing amino acid methionine is the universal initiator of protein synthesis in all known organisms and its derivative S-adenosylmethionine (SAM) and autoinducer-2 (AI-2) are involved in various cellular processes. SAM plays a central role as methyl donor in methylation reactions, which are essential for the biosynthesis of phospholipids, proteins, DNA and RNA. The interspecies signaling molecule AI-2 is involved in cell-cell communication process (quorum sensing) and gene regulation in bacteria. Although methionine biosynthetic enzymes and metabolic pathways are well conserved in bacteria, the regulation of methionine biosynthesis involves various regulatory mechanisms. In Escherichia coli and Salmonella enterica serovar Typhimurium, MetJ and MetR regulate the expression of methionine biosynthetic genes. The MetJ repressor negatively regulates the E. coli met genes, except for metH. Several of these genes are also under the positive control of MetR with homocysteine as a co-inducer. In Bacillus subtilis, the met genes are controlled by S-box termination-antitermination system. 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: 176132  Cd Length: 198  Bit Score: 41.78  E-value: 1.51e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1632151917 105 FSLLAPLIEAFYQHHSVTRLKFINGVLGGSWDALTQGRADIIVGAmhEPPSSSEFGFSRLGDLEQVFAVAPHHPLA 180
Cdd:cd08441    12 FDWLMPVLDQFRERWPDVELDLSSGFHFDPLPALLRGELDLVITS--DPLPLPGIAYEPLFDYEVVLVVAPDHPLA 85
PBP2_TdcA cd08418
The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is ...
 97-180 1.60e-04

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: 41.96  E-value: 1.60e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917  97 IGVDDTFPFSLLAPLIEAFYQHHSVTRLKFINGVLGGSWDALTQGRADIIVGAMHEPPSSSEFGFSRLGDLEQVFAVAPH 176
Cdd:cd08418     4 IGVSSLIAHTLMPAVINRFKEQFPDVQISIYEGQLSSLLPELRDGRLDFAIGTLPDEMYLKELISEPLFESDFVVVARKD 83


                  ....
gi 1632151917 177 HPLA 180
Cdd:cd08418    84 HPLQ 87
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 34-184 1.80e-04

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 42.32  E-value: 1.80e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917  34 LSYTVHKLESDLNIQLLDRSGHRAKFTRTGKMLLEKGREVLHTVRELEKQAIKLHEGWENELVIGVDDTF-PFslLAPLI 112
Cdd:PRK11151   32 LSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVLKEMASQQGETMSGPLHIGLIPTVgPY--LLPHI 109

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917 113 -----EAF-----YQHHSVTrlkfiNGVLggswDALTQGRADIIVGAMhePPSSSEFGFSRLGDLEQVFAVAPHHPLALE 182
Cdd:PRK11151  110 ipmlhQTFpklemYLHEAQT-----HQLL----AQLDSGKLDCAILAL--VKESEAFIEVPLFDEPMLLAVYEDHPWANR 178


                  ..
gi 1632151917 183 EE 184
Cdd:PRK11151  179 DR 180
PRK12680 PRK12680
LysR family transcriptional regulator;
10-241 2.55e-04

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 42.30  E-value: 2.55e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917  10 ILDAlekEGSFAAASAKLYKTPSALSYTVHKLESDLNIQLLDRSGHRAK-FTRTGKMLLEKGREVLHTVRELEKQAIKLH 88
Cdd:PRK12680   12 IADA---ELNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLEsVTPAGVEVIERARAVLSEANNIRTYAANQR 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917  89 EGWENELVIGVDDTFPFSLLAPLIEAFYQHHSVTRLKFINGVLGGSWDALTQGRADIIV--GAMHEPPSSSEFGFSRlgd 166
Cdd:PRK12680   89 RESQGQLTLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIvsTAGGEPSAGIAVPLYR--- 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917 167 LEQVFAVAPHHPLALEEEPLNRRIIKRYRAIVVGDTAQAGAST----ASQLLDEQEAITVFD---FKTKLElqiSGLGCG 239
Cdd:PRK12680  166 WRRLVVVPRGHALDTPRRAPDMAALAEHPLISYESSTRPGSSLqrafAQLGLEPSIALTALDadlIKTYVR---AGLGVG 242


                  ..
gi 1632151917 240 YL 241
Cdd:PRK12680  243 LL 244
PRK10341 PRK10341
transcriptional regulator TdcA;
8-159 1.23e-03

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 39.85  E-value: 1.23e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917   8 LMILDALEKEGSFAAASAKLYKTPSALSYTVHKLESDLNIQLLDRSGHRAKFTRTGKMLLEKgreVLHTVRELeKQAIKL 87
Cdd:PRK10341   12 LVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSR---SESITREM-KNMVNE 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917  88 HEGWENELVIGVDDTFP----FSLLAPLIEAFYQHHSVTRLKFINGVLGGSWDALTQGRADIIVGAMH----------EP 153
Cdd:PRK10341   88 INGMSSEAVVDVSFGFPsligFTFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIGTLSnemklqdlhvEP 167


                  ....*.
gi 1632151917 154 PSSSEF 159
Cdd:PRK10341  168 LFESEF 173
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 95-249 1.82e-03

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


Pssm-ID: 176127 [Multi-domain]  Cd Length: 194  Bit Score: 38.74  E-value: 1.82e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917  95 LVIGVDDTFPFSLLAPLIEAFYQHHSVTRLKFINGVLGGSWDALTQGRADI-IVGAMHEPPSssEFGFSRLGDLEQVFAV 173
Cdd:cd08436     2 LAIGTITSLAAVDLPELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLaFVGLPERRPP--GLASRELAREPLVAVV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917 174 APHHPLA---------LEEEPL--------NRRIIkryraivvgDTAQAGASTASQLldeqeAITVFDFKTKLELQISGL 236
Cdd:cd08436    80 APDHPLAgrrrvaladLADEPFvdfppgtgARRQV---------DRAFAAAGVRRRV-----AFEVSDVDLLLDLVARGL 145

                         170
                  ....*....|...
gi 1632151917 237 GCGYLPRYLAQRF 249
Cdd:cd08436   146 GVALLPASVAARL 158
cbl PRK12679
HTH-type transcriptional regulator Cbl;
9-272 1.87e-03

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 39.41  E-value: 1.87e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917   9 MILDALEKEGSFAAASAKLYKTPSALSYTVHKLESDLNIQLLDRSGHR-AKFTRTGKMLLEKGREVLHTVRELEKQAIKL 87
Cdd:PRK12679    8 IIREAARQDYNLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRlLGMTEPGKALLVIAERILNEASNVRRLADLF 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917  88 HEGWENELVIGVDDTFPFSLLAPLIEAFYQHHSVTRLKFINGVLGGSWDALTQGRADIIVGA--MHEPPSSSEFGFSRlg 165
Cdd:PRK12679   88 TNDTSGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASerLSNDPQLVAFPWFR-- 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917 166 dLEQVFAVAPHHPLAlEEEPLNRRIIKR-----YRAIVVG----DTAQAGAS-TASQLLDEQEAITVfdfKTKLELqisG 235
Cdd:PRK12679  166 -WHHSLLVPHDHPLT-QITPLTLESIAKwplitYRQGITGrsriDDAFARKGlLADIVLSAQDSDVI---KTYVAL---G 237

                         250       260       270
                  ....*....|....*....|....*....|....*....
gi 1632151917 236 LGCGYLPRYLAQRFLDSGALiekKVVAQTLFEP--VWIG 272
Cdd:PRK12679  238 LGIGLVAEQSSGEQEESNLI---RLDTRHLFDAntVWLG 273
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 94-186 2.31e-03

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


Pssm-ID: 176104 [Multi-domain]  Cd Length: 198  Bit Score: 38.29  E-value: 2.31e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917  94 ELVIGVDDTFPFSLLAPLIEAFYQHHSVTRLKFINGVLGGSWDALTQGRADIIVGAMHEPPssSEFGFSRLGDLEQVFAV 173
Cdd:cd08412     1 TLRIGCFSTLAPYYLPGLLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALTYDLDLP--EDIAFEPLARLPPYVWL 78

                          90       100
                  ....*....|....*....|..
gi 1632151917 174 APHHPLA---------LEEEPL 186
Cdd:cd08412    79 PADHPLAgkdevsladLAAEPL 100
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 19-119 2.76e-03

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 38.67  E-value: 2.76e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917  19 SFAAASAKLYKTPSALSYTVHKLESDLNIQLLDRSGHRAKFTRTGKMLLEKGREVLHTVRELEKQAikLHEGWENELVIG 98
Cdd:PRK11139   22 SFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEATRKL--RARSAKGALTVS 99

                          90       100
                  ....*....|....*....|.
gi 1632151917  99 VDDTFPFSLLAPLIEAFYQHH 119
Cdd:PRK11139  100 LLPSFAIQWLVPRLSSFNEAH 120
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
11-54 2.87e-03

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 38.80  E-value: 2.87e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1632151917  11 LDALEKEGSFAAASAKLYKTPSALSYTVHKLESDLNIQLLDRSG 54
Cdd:PRK13348   10 LAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRGR 53
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 94-180 3.17e-03

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: 37.96  E-value: 3.17e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917  94 ELVIGVDDTFPFSLLAPLIEAFYQHHSVTRLKFINGVLGGSWDALTQGRADIIVGAMHEPPSssEFGFSRLGDLEQVFAV 173
Cdd:cd08417     1 TFRIAASDYLEALLLPPLLARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELPP--GLRSQPLFEDRFVCVA 78


                  ....*..
gi 1632151917 174 APHHPLA 180
Cdd:cd08417    79 RKDHPLA 85
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 103-180 5.78e-03

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


Pssm-ID: 176125 [Multi-domain]  Cd Length: 195  Bit Score: 37.13  E-value: 5.78e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632151917 103 FPFSL---LAP-LIEAFYQHHSVTRLKFINGVLGGSWDALTQGRADIIVGAmhEPPSSSEFGFSRLGDLEQVFAVAPHHP 178
Cdd:cd08434     6 FLHSLgtsLVPdLIRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLALCS--PVPDEPDIEWIPLFTEELVLVVPKDHP 83


                  ..
gi 1632151917 179 LA 180
Cdd:cd08434    84 LA 85
 
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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