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Conserved domains on  [gi|15596073|ref|NP_249567|]
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transcriptional regulator [Pseudomonas aeruginosa PAO1]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 10444056)

LysR family transcriptional regulator similar to Pseudomonas aeruginosa HTH-type transcriptional regulator PtxR, which regulates the toxA (exotoxin) and regA genes; substrate binding domain-containing protein is a type 2 periplasmic binding protein (PBP2), similar to the regulatory domain of Vibrio vulnificus virulence gene regulator AphB that has been implicated in acid resistance and pathogenesis

Gene Ontology:  GO:0001216|GO:0032993|GO:0006355
PubMed:  19047729|8257110

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 92-291 3.58e-66

The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; This CD includes the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA and its related homologs. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis further showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


:

Pssm-ID: 176114 [Multi-domain]  Cd Length: 197  Bit Score: 206.14  E-value: 3.58e-66
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073  92 GTLKVHAMTGIGQHYLIKAISQYCETYPEVGFDLTLANRITDILDEGYDISVVIApELPDSGFVSKCIGQTYSILCASPG 171
Cdd:cd08422   1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIG-ELPDSSLVARRLGPVRRVLVASPA 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073 172 YIAAHGFPKLPAELSAHRCLRLVNSvMSLDRWLFDGPDGQELACInQTHFQVNTADAMTEAVVSGMGIGALPVYAAVNGL 251
Cdd:cd08422  80 YLARHGTPQTPEDLARHRCLGYRLP-GRPLRWRFRRGGGEVEVRV-RGRLVVNDGEALRAAALAGLGIALLPDFLVAEDL 157

                       170       180       190       200
                ....*....|....*....|....*....|....*....|
gi 15596073 252 KDGSLVRVLPRYSLFHLNVYALYPSRQYLDAKIRTWVEFL 291
Cdd:cd08422 158 ASGRLVRVLPDWRPPPLPIYAVYPSRRHLPAKVRAFIDFL 197
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
7-63 1.64e-22

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


:

Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 88.60  E-value: 1.64e-22
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 15596073     7 MRAFVSVAETGSFTAAAQRLDLTTAYVSRAVAKLEAHLQTRLLHRTTRRIALTEAGQ 63
Cdd:pfam00126   4 LRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
 
Name Accession Description Interval E-value
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 92-291 3.58e-66

The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; This CD includes the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA and its related homologs. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis further showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176114 [Multi-domain]  Cd Length: 197  Bit Score: 206.14  E-value: 3.58e-66
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073  92 GTLKVHAMTGIGQHYLIKAISQYCETYPEVGFDLTLANRITDILDEGYDISVVIApELPDSGFVSKCIGQTYSILCASPG 171
Cdd:cd08422   1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIG-ELPDSSLVARRLGPVRRVLVASPA 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073 172 YIAAHGFPKLPAELSAHRCLRLVNSvMSLDRWLFDGPDGQELACInQTHFQVNTADAMTEAVVSGMGIGALPVYAAVNGL 251
Cdd:cd08422  80 YLARHGTPQTPEDLARHRCLGYRLP-GRPLRWRFRRGGGEVEVRV-RGRLVVNDGEALRAAALAGLGIALLPDFLVAEDL 157

                       170       180       190       200
                ....*....|....*....|....*....|....*....|
gi 15596073 252 KDGSLVRVLPRYSLFHLNVYALYPSRQYLDAKIRTWVEFL 291
Cdd:cd08422 158 ASGRLVRVLPDWRPPPLPIYAVYPSRRHLPAKVRAFIDFL 197
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-297 1.61e-57

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 185.84  E-value: 1.61e-57
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073   1 MDiLFNMRAFVSVAETGSFTAAAQRLDLTTAYVSRAVAKLEAHLQTRLLHRTTRRIALTEAGQRYLMRAQQILAYIEEAE 80
Cdd:COG0583   1 MD-LRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAE 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073  81 AEAGDAHARPSGTLKVHAMTGIGQHYLIKAISQYCETYPEVGFDLTLANR---ITDILDEGYDISVVIAPeLPDSGFVSK 157
Cdd:COG0583  80 AELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSdrlVDALLEGELDLAIRLGP-PPDPGLVAR 158

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073 158 CIGQTYSILCASPGYIAAHGFPklpaelsahrclrlvnsvmsldrwlfdgpdgqelacinqthfQVNTADAMTEAVVSGM 237
Cdd:COG0583 159 PLGEERLVLVASPDHPLARRAP------------------------------------------LVNSLEALLAAVAAGL 196

                       250       260       270       280       290       300
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073 238 GIGALPVYAAVNGLKDGSLVRVLPRYSLFHLNVYALYPSRQYLDAKIRTWVEFLREHMPA 297
Cdd:COG0583 197 GIALLPRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
PRK09801 PRK09801
LysR family transcriptional regulator;
6-292 2.15e-44

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 153.65  E-value: 2.15e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073    6 NMRAFVSVAETGSFTAAAQRLDLTTAYVSRAVAKLEAHLQTRLLHRTTRRIALTEAGQRYLMRAQQILAYIEEAEAEAGD 85
Cdd:PRK09801  10 DLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVTQ 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073   86 AHARPSGTLKVHAMTGIGQHYLIKAISQYCETYPEVGFDLTLANRITDILDEGYDISVVIAPELPDSgFVSKCIGQTYSI 165
Cdd:PRK09801  90 IKTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHFELFDRQIDLVQDNIDLDIRINDEIPDY-YIAHLLTKNKRI 168

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073  166 LCASPGYIAAHGFPKLPAELSAHRCLRLVNSVMSLDRWLFDgpDGQELACINQT-HFQVNTADAMTEAVVSGMGIGALPV 244
Cdd:PRK09801 169 LCAAPEYLQKYPQPQSLQELSRHDCLVTKERDMTHGIWELG--NGQEKKSVKVSgHLSSNSGEIVLQWALEGKGIMLRSE 246

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*...
gi 15596073  245 YAAVNGLKDGSLVRVLPRYSLfHLNVYALYPSRQYLDAKIRTWVEFLR 292
Cdd:PRK09801 247 WDVLPFLESGKLVQVLPEYAQ-SANIWAVYREPLYRSMKLRVCVEFLA 293
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 91-296 1.32e-30

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: 114.31  E-value: 1.32e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073    91 SGTLKVHAMTGIGQHYLIKAISQYCETYPEVGFDLTLAN--RITDILDEG-YDIsVVIAPELPDSGFVSKCIGQTYSILC 167
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNseELLDLLLEGeLDL-AIRRGPPDDPGLEARPLGEEPLVLV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073   168 ASPGYIAAHGFPKLPAELSAHRCLRLVNSvmSLDRWLFDGpDGQELACINQTHFQVNTADAMTEAVVSGMGIGALPVYAA 247
Cdd:pfam03466  80 APPDHPLARGEPVSLEDLADEPLILLPPG--SGLRDLLDR-ALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAV 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 15596073   248 VNGLKDGSLVRVLPRYSLFHLNVYALYPSRQYLDAKIRTWVEFLREHMP 296
Cdd:pfam03466 157 ARELADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREALA 205
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
7-63 1.64e-22

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 88.60  E-value: 1.64e-22
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 15596073     7 MRAFVSVAETGSFTAAAQRLDLTTAYVSRAVAKLEAHLQTRLLHRTTRRIALTEAGQ 63
Cdd:pfam00126   4 LRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-144 1.09e-16

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


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 78.81  E-value: 1.09e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073    1 MDiLFNMRAFVSVAETGSFTAAAQRLDLTTAYVSRAVAKLEAHLQTRLLHRTTRRIALTEAGQRYLMRAQQILAYIEEAE 80
Cdd:NF040786   1 MN-LKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLE 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15596073   81 AEAGDAHARPSGTLKVHAMTGIGQHYLIKAISQYCETYPEVGFDLtlanRITD-------ILDEGYDISVV 144
Cdd:NF040786  80 EEFDRYGKESKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKL----MISDsikvielLLEGEVDIGFT 146
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
7-73 1.10e-14

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 73.30  E-value: 1.10e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15596073    7 MRAFVSVAETGSFTAAAQRLDLTTAYVSRAVAKLEAHLQTRLLHRTTRRIALTEAGQRYLMRAQQIL 73
Cdd:PRK10094   7 LRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWL 73
MarR COG1846
DNA-binding transcriptional regulator, MarR family [Transcription];
23-73 7.77e-03

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


Pssm-ID: 441451 [Multi-domain]  Cd Length: 142  Bit Score: 36.10  E-value: 7.77e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 15596073  23 AQRLDLTTAYVSRAVAKLEAHlqtRLLHRTT-------RRIALTEAGQRYLMRAQQIL 73
Cdd:COG1846  59 AERLGLTKSTVSRLLDRLEEK---GLVEREPdpedrraVLVRLTEKGRALLEEARPAL 113
 
Name Accession Description Interval E-value
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 92-291 3.58e-66

The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; This CD includes the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA and its related homologs. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis further showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176114 [Multi-domain]  Cd Length: 197  Bit Score: 206.14  E-value: 3.58e-66
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073  92 GTLKVHAMTGIGQHYLIKAISQYCETYPEVGFDLTLANRITDILDEGYDISVVIApELPDSGFVSKCIGQTYSILCASPG 171
Cdd:cd08422   1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIG-ELPDSSLVARRLGPVRRVLVASPA 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073 172 YIAAHGFPKLPAELSAHRCLRLVNSvMSLDRWLFDGPDGQELACInQTHFQVNTADAMTEAVVSGMGIGALPVYAAVNGL 251
Cdd:cd08422  80 YLARHGTPQTPEDLARHRCLGYRLP-GRPLRWRFRRGGGEVEVRV-RGRLVVNDGEALRAAALAGLGIALLPDFLVAEDL 157

                       170       180       190       200
                ....*....|....*....|....*....|....*....|
gi 15596073 252 KDGSLVRVLPRYSLFHLNVYALYPSRQYLDAKIRTWVEFL 291
Cdd:cd08422 158 ASGRLVRVLPDWRPPPLPIYAVYPSRRHLPAKVRAFIDFL 197
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-297 1.61e-57

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 185.84  E-value: 1.61e-57
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073   1 MDiLFNMRAFVSVAETGSFTAAAQRLDLTTAYVSRAVAKLEAHLQTRLLHRTTRRIALTEAGQRYLMRAQQILAYIEEAE 80
Cdd:COG0583   1 MD-LRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAE 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073  81 AEAGDAHARPSGTLKVHAMTGIGQHYLIKAISQYCETYPEVGFDLTLANR---ITDILDEGYDISVVIAPeLPDSGFVSK 157
Cdd:COG0583  80 AELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSdrlVDALLEGELDLAIRLGP-PPDPGLVAR 158

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073 158 CIGQTYSILCASPGYIAAHGFPklpaelsahrclrlvnsvmsldrwlfdgpdgqelacinqthfQVNTADAMTEAVVSGM 237
Cdd:COG0583 159 PLGEERLVLVASPDHPLARRAP------------------------------------------LVNSLEALLAAVAAGL 196

                       250       260       270       280       290       300
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073 238 GIGALPVYAAVNGLKDGSLVRVLPRYSLFHLNVYALYPSRQYLDAKIRTWVEFLREHMPA 297
Cdd:COG0583 197 GIALLPRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
PRK09801 PRK09801
LysR family transcriptional regulator;
6-292 2.15e-44

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 153.65  E-value: 2.15e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073    6 NMRAFVSVAETGSFTAAAQRLDLTTAYVSRAVAKLEAHLQTRLLHRTTRRIALTEAGQRYLMRAQQILAYIEEAEAEAGD 85
Cdd:PRK09801  10 DLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVTQ 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073   86 AHARPSGTLKVHAMTGIGQHYLIKAISQYCETYPEVGFDLTLANRITDILDEGYDISVVIAPELPDSgFVSKCIGQTYSI 165
Cdd:PRK09801  90 IKTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHFELFDRQIDLVQDNIDLDIRINDEIPDY-YIAHLLTKNKRI 168

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073  166 LCASPGYIAAHGFPKLPAELSAHRCLRLVNSVMSLDRWLFDgpDGQELACINQT-HFQVNTADAMTEAVVSGMGIGALPV 244
Cdd:PRK09801 169 LCAAPEYLQKYPQPQSLQELSRHDCLVTKERDMTHGIWELG--NGQEKKSVKVSgHLSSNSGEIVLQWALEGKGIMLRSE 246

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*...
gi 15596073  245 YAAVNGLKDGSLVRVLPRYSLfHLNVYALYPSRQYLDAKIRTWVEFLR 292
Cdd:PRK09801 247 WDVLPFLESGKLVQVLPEYAQ-SANIWAVYREPLYRSMKLRVCVEFLA 293
PBP2_CrgA_like_2 cd08471
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-293 5.32e-44

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 2. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176160  Cd Length: 201  Bit Score: 149.21  E-value: 5.32e-44
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073  92 GTLKVHAMTGIGQHYLIKAISQYCETYPEVGFDLTLANRITDILDEGYDISVVIAPeLPDSGFVSKCIGQTYSILCASPG 171
Cdd:cd08471   1 GLLTVTAPVLFGRLHVLPIITDFLDAYPEVSVRLLLLDRVVNLLEEGVDVAVRIGH-LPDSSLVATRVGSVRRVVCASPA 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073 172 YIAAHGFPKLPAELSAHRCLRlVNSVMSLDRWLFdGPDGQELACINQTHFQVNTADAMTEAVVSGMGIGALPVYAAVNGL 251
Cdd:cd08471  80 YLARHGTPKHPDDLADHDCIA-FTGLSPAPEWRF-REGGKERSVRVRPRLTVNTVEAAIAAALAGLGLTRVLSYQVAEEL 157

                       170       180       190       200
                ....*....|....*....|....*....|....*....|..
gi 15596073 252 KDGSLVRVLPRYSLFHLNVYALYPSRQYLDAKIRTWVEFLRE 293
Cdd:cd08471 158 AAGRLQRVLEDFEPPPLPVHLVHPEGRLAPAKVRAFVDFAVP 199
PBP2_CrgA_like_8 cd08477
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-291 3.09e-43

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 8. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176166  Cd Length: 197  Bit Score: 146.99  E-value: 3.09e-43
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073  92 GTLKVHAMTGIGQHYLIKAISQYCETYPEVGFDLTLANRITDILDEGYDISVVIAPeLPDSGFVSKCIGQTYSILCASPG 171
Cdd:cd08477   1 GKLRISAPVTFGSHVLTPALAEYLARYPDVRVDLVLSDRLVDLVEEGFDAAFRIGE-LADSSLVARPLAPYRMVLCASPD 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073 172 YIAAHGFPKLPAELSAHRCLRLVNSVMsLDRWLFDGPDGQELACINQThFQVNTADAMTEAVVSGMGIGALPvYAAVNG- 250
Cdd:cd08477  80 YLARHGTPTTPEDLARHECLGFSYWRA-RNRWRLEGPGGEVKVPVSGR-LTVNSGQALRVAALAGLGIVLQP-EALLAEd 156

                       170       180       190       200
                ....*....|....*....|....*....|....*....|.
gi 15596073 251 LKDGSLVRVLPRYSLFHLNVYALYPSRQYLDAKIRTWVEFL 291
Cdd:cd08477 157 LASGRLVELLPDYLPPPRPMHLLYPPDRRPTPKLRSFIDFL 197
PBP2_CrgA_like_1 cd08470
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-295 3.14e-41

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding domain; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 1. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176159  Cd Length: 197  Bit Score: 142.06  E-value: 3.14e-41
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073  92 GTLKVHAMTGIGQHYLIKAISQYCETYPEVGFDLTLANRITDILDEGYDISVVIApELPDSGFVSKCIGQTYSILCASPG 171
Cdd:cd08470   1 GLLRITCPVAYGERFIAPLVNDFMQRYPKLEVDIELTNRVVDLVSEGFDLAIRLG-RLTDSSLMARRLASRRHYVCASPA 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073 172 YIAAHGFPKLPAELSAHRCLRlvnsvMSLDRWLFDgPDGQELACINQTHFQVNTADAMTEAVVSGMGIGALPVYAAVNGL 251
Cdd:cd08470  80 YLERHGTPHSLADLDRHNCLL-----GTSDHWRFQ-ENGRERSVRVQGRWRCNSGVALLDAALKGMGLAQLPDYYVDEHL 153

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....
gi 15596073 252 KDGSLVRVLPRYSLFHLNVYALYPSRQYLDAKIRTWVEFLREHM 295
Cdd:cd08470 154 AAGRLVPVLEDYRPPDEGIWALYPHNRHLSPKVRLLVDYLADAL 197
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
1-294 3.28e-40

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 142.59  E-value: 3.28e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073    1 MDILFNMRAFVSVAETGSFTAAAQRLDLTTAYVSRAVAKLEAHLQTRLLHRTTRRIALTEAGQRYLMRAQQILAYIEEAE 80
Cdd:PRK10632   1 MERLKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVH 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073   81 AEAGDAHARPSGTLKVHAMTGIGQHYLIKAISQYCETYPEVGFDLTLANRITDILDEGYDIsVVIAPELPDSGFVSKCIG 160
Cdd:PRK10632  81 EQLYAFNNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTGIPAPDLIADGLDV-VIRVGALQDSSLFSRRLG 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073  161 QTYSILCASPGYIAAHGFPKLPAELSAHRCLRLvnSVMSLDRWLFDGPDGQELACINQTHFQVNTADAMTEAVVSGMGIG 240
Cdd:PRK10632 160 AMPMVVCAAKSYLAQYGTPEKPADLSSHSWLEY--SVRPDNEFELIAPEGISTRLIPQGRFVTNDPQTLVRWLTAGAGIA 237

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....
gi 15596073  241 ALPVYAAVNGLKDGSLVRVLPRYSLFHLNVYALYPSRQYLDAKIRTWVEFLREH 294
Cdd:PRK10632 238 YVPLMWVIDEINRGELEILFPRYQSDPRPVYALYTEKDKLPLKVQVCINYLTDY 291
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 10-298 5.80e-40

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 141.67  E-value: 5.80e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073   10 FVSVAETGSFTAAAQRLDLTTAYVSRAVAKLEAHLQTRLLHRTTRRIALTEAGQRYLMRAQQILAYIEEAEAEAGDAHAR 89
Cdd:PRK14997  10 FVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDAIAALQVE 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073   90 PSGTLKVHAMTGIGQHYLIKAISQYCETYPEVGFDLTLANRITDILDEGYDISVVIAPE-LPDSGFVSKCIGQTYSILCA 168
Cdd:PRK14997  90 PRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLEATNRRVDVVGEGVDVAIRVRPRpFEDSDLVMRVLADRGHRLFA 169

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073  169 SPGYIAAHGFPKLPAELSAHRCLRLvNSVMSLDRWLFDGPDGQELacinQTHF--QVNTAD--AMTEAVVSGMGIGALPV 244
Cdd:PRK14997 170 SPDLIARMGIPSAPAELSHWPGLSL-ASGKHIHRWELYGPQGARA----EVHFtpRMITTDmlALREAAMAGVGLVQLPV 244

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 15596073  245 YAAVNGLKDGSLVRVL----PRYSLFHlnvyALYPSRQYLDAKIRTWVEFLREHMPAM 298
Cdd:PRK14997 245 LMVKEQLAAGELVAVLeewePRREVIH----AVFPSRRGLLPSVRALVDFLTEEYARM 298
PBP2_CrgA_like_7 cd08476
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-291 4.52e-38

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 7. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176165  Cd Length: 197  Bit Score: 133.91  E-value: 4.52e-38
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073  92 GTLKVHamTGIGQHYLIKAISQYCETYPEVGFDLTLANRITDILDEGYDIsVVIAPELPDSGFVSKCIGQTYSILCASPG 171
Cdd:cd08476   1 GRLRVS--LPLVGGLLLPVLAAFMQRYPEIELDLDFSDRLVDVIDEGFDA-VIRTGELPDSRLMSRRLGSFRMVLVASPD 77

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073 172 YIAAHGFPKLPAELSAHRCL--RLVNSvMSLDRWLFDGPDGQELACINQThFQVNTADAMTEAVVSGMGIGALPVYAAVN 249
Cdd:cd08476  78 YLARHGTPETPADLAEHACLryRFPTT-GKLEPWPLRGDGGDPELRLPTA-LVCNNIEALIEFALQGLGIACLPDFSVRE 155

                       170       180       190       200
                ....*....|....*....|....*....|....*....|..
gi 15596073 250 GLKDGSLVRVLPRYSLFHLNVYALYPSRQYLDAKIRTWVEFL 291
Cdd:cd08476 156 ALADGRLVTVLDDYVEERGQFRLLWPSSRHLSPKLRVFVDFM 197
PBP2_CrgA_like_9 cd08479
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-291 8.16e-37

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 9. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176168 [Multi-domain]  Cd Length: 198  Bit Score: 130.41  E-value: 8.16e-37
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073  92 GTLKVHAMTGIGQHYLIKAISQYCETYPEVGFDLTLANRITDILDEGYDISVVIApELPDSGFVSKCIGQTYSILCASPG 171
Cdd:cd08479   1 GLLRVNASFGFGRRHIAPALSDFAKRYPELEVQLELTDRPVDLVEEGFDLDIRVG-DLPDSSLIARKLAPNRRILCASPA 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073 172 YIAAHGFPKLPAELSAHRCLRLVNSVMSLDRWLFDGPDGQELACINqTHFQVNTADAMTEAVVSGMGIGALPVYAAVNGL 251
Cdd:cd08479  80 YLERHGAPASPEDLARHDCLVIRENDEDFGLWRLRNGDGEATVRVR-GALSSNDGEVVLQWALDGHGIILRSEWDVAPYL 158

                       170       180       190       200
                ....*....|....*....|....*....|....*....|
gi 15596073 252 KDGSLVRVLPRYSLFHLNVYALYPSRQYLDAKIRTWVEFL 291
Cdd:cd08479 159 RSGRLVRVLPDWQLPDADIWAVYPSRLSRSARVRVFVDFL 198
PBP2_CrgA_like_3 cd08472
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-293 1.02e-34

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 3. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176161  Cd Length: 202  Bit Score: 124.93  E-value: 1.02e-34
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073  92 GTLKVHAMTGIGQHYLIKAISQYCETYPEVGFDLTLANRITDILDEGYDiSVVIAPELPDSGFVSKCIGQTYSILCASPG 171
Cdd:cd08472   1 GRLRVDVPGSLARLLLIPALPDFLARYPDIELDLGVSDRPVDLIREGVD-CVIRVGELADSSLVARRLGELRMVTCASPA 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073 172 YIAAHGFPKLPAELSAHRCLRLVNSVM--SLDrWLFDgPDGQELACINQTHFQVNTADAMTEAVVSGMGIGALPVYAAVN 249
Cdd:cd08472  80 YLARHGTPRHPEDLERHRAVGYFSARTgrVLP-WEFQ-RDGEEREVKLPSRVSVNDSEAYLAAALAGLGIIQVPRFMVRP 157

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....
gi 15596073 250 GLKDGSLVRVLPRYSLFHLNVYALYPSRQYLDAKIRTWVEFLRE 293
Cdd:cd08472 158 HLASGRLVEVLPDWRPPPLPVSLLYPHRRHLSPRVRVFVDWVAE 201
PBP2_CrgA_like_6 cd08475
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-285 1.27e-33

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 6. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176164 [Multi-domain]  Cd Length: 199  Bit Score: 122.28  E-value: 1.27e-33
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073  92 GTLKVHAMTGIGQHYLIKAISQYCETYPEVGFDLTLANRITDILDEGYDISVVIApELPDS-GFVSKCIGQTYSILCASP 170
Cdd:cd08475   1 GRLRIDLPVAFGRLCVAPLLLELARRHPELELELSFSDRFVDLIEEGIDLAVRIG-ELADStGLVARRLGTQRMVLCASP 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073 171 GYIAAHGFPKLPAELSAHRCLRLVNSVMSLdRWLFDGPDGQELACINQTHFQVNTADAMTEAVVSGMGIGALPVYAAVNG 250
Cdd:cd08475  80 AYLARHGTPRTLEDLAEHQCIAYGRGGQPL-PWRLADEQGRLVRFRPAPRLQFDDGEAIADAALAGLGIAQLPTWLVADH 158

                       170       180       190
                ....*....|....*....|....*....|....*
gi 15596073 251 LKDGSLVRVLPRYSLFHLNVYALYPSRQYLDAKIR 285
Cdd:cd08475 159 LQRGELVEVLPELAPEGLPIHAVWPRTRHLPPKVR 193
PBP2_CrgA_like_10 cd08480
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-291 3.87e-33

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 10. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176169  Cd Length: 198  Bit Score: 120.90  E-value: 3.87e-33
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073  92 GTLKVHAMTGIGQHYLIKAISQYCETYPEVGFDLTLANRITDILDEGYDISVVIAPeLPDSGFVSKCIGQTYSILCASPG 171
Cdd:cd08480   1 GRLRVNASVPFGTHFLLPLLPAFLARYPEILVDLSLTDEVVDLLAERTDVAIRVGP-LPDSSLVARKLGESRRVIVASPS 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073 172 YIAAHGFPKLPAELSAHRCLRLvNSVMSLDRWLFDgPDGQELACINQTHFQVNTADAMTEAVVSGMGIGALPVYAAVNGL 251
Cdd:cd08480  80 YLARHGTPLTPQDLARHNCLGF-NFRRALPDWPFR-DGGRIVALPVSGNILVNDGEALRRLALAGAGLARLALFHVADDI 157

                       170       180       190       200
                ....*....|....*....|....*....|....*....|.
gi 15596073 252 KDGSLVRVLPRYSLFHLN-VYALYPSRQYLDAKIRTWVEFL 291
Cdd:cd08480 158 AAGRLVPVLEEYNPGDREpIHAVYVGGGRLPARVRAFLDFL 198
PBP2_CrgA_like_4 cd08473
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 90-291 1.61e-32

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 4. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176162 [Multi-domain]  Cd Length: 202  Bit Score: 119.20  E-value: 1.61e-32
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073  90 PSGTLKVHAMTGIGQHYLIKAISQYCETYPEVGFDLTLANRITDILDEGYDISVVIAPELP-DSGFVSKCIGQTYSILCA 168
Cdd:cd08473   1 PRGTVRVSCPPALAQELLAPLLPRFMAAYPQVRLQLEATNRRVDLIEEGIDVALRVRFPPLeDSSLVMRVLGQSRQRLVA 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073 169 SPGYIAAHGFPKLPAELSAHRCLRLvNSVMSLDRWLFDGPDGQELACINQTHFQVNTADAMTEAVVSGMGIGALPVYAAV 248
Cdd:cd08473  81 SPALLARLGRPRSPEDLAGLPTLSL-GDVDGRHSWRLEGPDGESITVRHRPRLVTDDLLTLRQAALAGVGIALLPDHLCR 159

                       170       180       190       200
                ....*....|....*....|....*....|....*....|...
gi 15596073 249 NGLKDGSLVRVLPRYSLFHLNVYALYPSRQYLDAKIRTWVEFL 291
Cdd:cd08473 160 EALRAGRLVRVLPDWTPPRGIVHAVFPSRRGLLPAVRALIDFL 202
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 90-291 1.04e-31

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 5. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176163 [Multi-domain]  Cd Length: 202  Bit Score: 117.18  E-value: 1.04e-31
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073  90 PSGTLKVHAMTGIGQHYLIKAISQYCETYPEVGFDLTLANRITDILDEGYDISVVIAPELPDsGFVSKCIGQTYSILC-A 168
Cdd:cd08474   1 PAGTLRINAPRVAARLLLAPLLARFLARYPDIRLELVVDDGLVDIVAEGFDAGIRLGESVEK-DMVAVPLGPPLRMAVvA 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073 169 SPGYIAAHGFPKLPAELSAHRCL--RLVNSVmSLDRWLFDGpDGQELACINQTHFQVNTADAMTEAVVSGMGIGALPVYA 246
Cdd:cd08474  80 SPAYLARHGTPEHPRDLLNHRCIryRFPTSG-ALYRWEFER-GGRELEVDVEGPLILNDSDLMLDAALDGLGIAYLFEDL 157

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*....
gi 15596073 247 AVNGLKDGSLVRVLPRYSL----FHLnvyaLYPSRQYLDAKIRTWVEFL 291
Cdd:cd08474 158 VAEHLASGRLVRVLEDWSPpfpgGYL----YYPSRRRVPPALRAFIDFL 202
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 91-296 1.32e-30

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: 114.31  E-value: 1.32e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073    91 SGTLKVHAMTGIGQHYLIKAISQYCETYPEVGFDLTLAN--RITDILDEG-YDIsVVIAPELPDSGFVSKCIGQTYSILC 167
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNseELLDLLLEGeLDL-AIRRGPPDDPGLEARPLGEEPLVLV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073   168 ASPGYIAAHGFPKLPAELSAHRCLRLVNSvmSLDRWLFDGpDGQELACINQTHFQVNTADAMTEAVVSGMGIGALPVYAA 247
Cdd:pfam03466  80 APPDHPLARGEPVSLEDLADEPLILLPPG--SGLRDLLDR-ALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAV 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 15596073   248 VNGLKDGSLVRVLPRYSLFHLNVYALYPSRQYLDAKIRTWVEFLREHMP 296
Cdd:pfam03466 157 ARELADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREALA 205
PBP2_CrgA cd08478
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains ...
 90-291 1.29e-22

The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains the type 2 periplasmic binding domain; This CD represents the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis further showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176167 [Multi-domain]  Cd Length: 199  Bit Score: 93.17  E-value: 1.29e-22
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073  90 PSGTLKVHAMTGIGQHYLIKAISQYCETYPEVGFDLTLANRITDILDEGYDISVVIAPeLPDSGFVSKCIGQTYSILCAS 169
Cdd:cd08478   1 PSGLLRVDAATPFVLHLLAPLIAKFRERYPDIELELVSNEGIIDLIERKTDVAIRIGE-LTDSTLHARPLGKSRLRILAS 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073 170 PGYIAAHGFPKLPAELSAHRCLRLvNSVMSLDRWLFDGPDGQELACinQTHFQVNTADAMTEAVVSGMGIGALPVYAAVN 249
Cdd:cd08478  80 PDYLARHGTPQSIEDLAQHQLLGF-TEPASLNTWPIKDADGNLLKI--QPTITASSGETLRQLALSGCGIACLSDFMTDK 156

                       170       180       190       200
                ....*....|....*....|....*....|....*....|...
gi 15596073 250 GLKDGSLVRVL-PRYSLFHLNVYALYPSRQYLDAKIRTWVEFL 291
Cdd:cd08478 157 DIAEGRLIPLFaEQTSDVRQPINAVYYRNTALSLRIRCFIDFL 199
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
7-63 1.64e-22

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 88.60  E-value: 1.64e-22
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 15596073     7 MRAFVSVAETGSFTAAAQRLDLTTAYVSRAVAKLEAHLQTRLLHRTTRRIALTEAGQ 63
Cdd:pfam00126   4 LRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-144 1.09e-16

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


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 78.81  E-value: 1.09e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073    1 MDiLFNMRAFVSVAETGSFTAAAQRLDLTTAYVSRAVAKLEAHLQTRLLHRTTRRIALTEAGQRYLMRAQQILAYIEEAE 80
Cdd:NF040786   1 MN-LKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLE 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15596073   81 AEAGDAHARPSGTLKVHAMTGIGQHYLIKAISQYCETYPEVGFDLtlanRITD-------ILDEGYDISVV 144
Cdd:NF040786  80 EEFDRYGKESKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKL----MISDsikvielLLEGEVDIGFT 146
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 8-261 1.41e-16

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 78.35  E-value: 1.41e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073    8 RAFVSVAETGSFTAAAQRLDLTTAYVSRAVAKLEAHLQTRLLHRTTRRIALTEAGQRYLMRAQQILAYIEEAEAEAGDAH 87
Cdd:PRK11139  12 RAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEATRKLRARS 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073   88 ARpsGTLKVHAMTGIGQHYLIKAISQYCETYPEVGFDLTLANRITDILDEgyDISVVIA------PELpdsgFVSKCIGQ 161
Cdd:PRK11139  92 AK--GALTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDRLEDFLRD--DVDVAIRygrgnwPGL----RVEKLLDE 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073  162 TYSILCaSPGYIAAHGFPKLPAELSAHRCLRlvnsVMSLDRWL--FDGPDGQELACINQTHFQvNTADAMtEAVVSGMGI 239
Cdd:PRK11139 164 YLLPVC-SPALLNGGKPLKTPEDLARHTLLH----DDSREDWRawFRAAGLDDLNVQQGPIFS-HSSMAL-QAAIHGQGV 236

                        250       260
                 ....*....|....*....|..
gi 15596073  240 GALPVYAAVNGLKDGSLVRVLP 261
Cdd:PRK11139 237 ALGNRVLAQPEIEAGRLVCPFD 258
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
8-265 4.43e-16

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 76.93  E-value: 4.43e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073    8 RAFVSVAETGSFTAAAQRLDLTTAYVSRAVAKLEAHLQTRLLHRtTRRIALTEAGQRYLMRAQQI-LAYIEEAEAEAGDA 86
Cdd:PRK13348   8 EALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQRLLRHLRQVaLLEADLLSTLPAER 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073   87 HARPSGTLKVHAMTGIGqhYLIKAISQYCETyPEVGFDLTL--ANRITDILDEGYDISVVIAPELPDSGFVSKCIGQTYS 164
Cdd:PRK13348  87 GSPPTLAIAVNADSLAT--WFLPALAAVLAG-ERILLELIVddQDHTFALLERGEVVGCVSTQPKPMRGCLAEPLGTMRY 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073  165 ILCASPGYIAAHgfpkLPAELSAHRCLR----LVNSVMSL-DRWL---FDGPDGQelaciNQTHFqVNTADAMTEAVVSG 236
Cdd:PRK13348 164 RCVASPAFAARY----FAQGLTRHSALKapavAFNRKDTLqDSFLeqlFGLPVGA-----YPRHY-VPSTHAHLAAIRHG 233

                        250       260
                 ....*....|....*....|....*....
gi 15596073  237 MGIGALPVYAAVNGLKDGSLVRVLPRYSL 265
Cdd:PRK13348 234 LGYGMVPELLIGPLLAAGRLVDLAPGHPV 262
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
7-73 1.10e-14

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 73.30  E-value: 1.10e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15596073    7 MRAFVSVAETGSFTAAAQRLDLTTAYVSRAVAKLEAHLQTRLLHRTTRRIALTEAGQRYLMRAQQIL 73
Cdd:PRK10094   7 LRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWL 73
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 93-291 2.99e-12

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: 64.54  E-value: 2.99e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073  93 TLKVHAMTGIGQHYLIKAISQYCETYPEVGFDLTLAN--RITDILDEG-YDISVVIAPeLPDSGFVSKCIGQTYSILCAS 169
Cdd:cd05466   1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGssELLEALLEGeLDLAIVALP-VDDPGLESEPLFEEPLVLVVP 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073 170 PGYIAAHGFPKLPAELSAHRCLrLVNSVMSLDRWLfdgpdgqELACIN-----QTHFQVNTADAMTEAVVSGMGIGALPV 244
Cdd:cd05466  80 PDHPLAKRKSVTLADLADEPLI-LFERGSGLRRLL-------DRAFAEagftpNIALEVDSLEAIKALVAAGLGIALLPE 151

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*..
gi 15596073 245 YaAVNGLKDGSLVRVLPRYSLFHLNVYALYPSRQYLDAKIRTWVEFL 291
Cdd:cd05466 152 S-AVEELADGGLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
4-193 2.17e-11

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 63.48  E-value: 2.17e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073    4 LFNMRAFVSVAETGSFTAAAQRLDLTTAYVSRAVAKLEAHLQTRLLHRTTRRIALTEAGQRYLMRAQQILayIEEAEAEA 83
Cdd:PRK10086  16 LSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSL--DTLNQEIL 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073   84 GDAHARPSGTLKVHAMTGIGQHYLIKAISQYCETYPEVGFDLTLANRITDIldEGYDISVVIA-PELPDSGFVSKCIGQT 162
Cdd:PRK10086  94 DIKNQELSGTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTILTGNENVNF--QRAGIDLAIYfDDAPSAQLTHHFLMDE 171

                        170       180       190
                 ....*....|....*....|....*....|.
gi 15596073  163 YSILCASPGYIAAHGFPKLPAELSahRCLRL 193
Cdd:PRK10086 172 EILPVCSPEYAERHALTGNPDNLR--HCTLL 200
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 10-262 5.98e-11

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 62.01  E-value: 5.98e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073   10 FVSVAETGSFTAAAQRLDLTTAYVSRAVAKLEAHLQTRLLHRTTRRIALTEAGQRYLMRAQQILayieEAEAEAGDAHAR 89
Cdd:PRK10837  11 FAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALL----EQAVEIEQLFRE 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073   90 PSGTLKVHAMTGIGQHYLIKAISQYCETYPEVGFDLTLANR---ITDILDEGYDISVVIAP-ELPDsgFVSKCIGQTYSI 165
Cdd:PRK10837  87 DNGALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNSqdvINAVLDFRVDIGLIEGPcHSPE--LISEPWLEDELV 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073  166 LCASPGYIAAHGFPKLPAELSAHRCLRLVNSVMS--LDRWLFDGPDGQELAcinqthFQVNTADAMTEAVVSGMGIGALP 243
Cdd:PRK10837 165 VFAAPDSPLARGPVTLEQLAAAPWILRERGSGTReiVDYLLLSHLPRFELA------MELGNSEAIKHAVRHGLGISCLS 238

                        250       260
                 ....*....|....*....|..
gi 15596073  244 VYAAVNGLKDGSLVRV---LPR 262
Cdd:PRK10837 239 RRVIADQLQAGTLVEVavpLPR 260
rbcR CHL00180
LysR transcriptional regulator; Provisional
 7-149 1.59e-10

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 60.80  E-value: 1.59e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073    7 MRAFVSVAETGSFTAAAQRLDLTTAYVSRAVAKLEAHLQTRLLHRTTRRIALTEAGQRYLMRAQQILAYIEEAEAEAGDA 86
Cdd:CHL00180  10 LRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRALEDL 89

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15596073   87 HARPSGTLKVHAMTGIGQHYLIKAISQYCETYPEVGFDLTL--ANRIT-DILDEGYDISVV---IAPEL 149
Cdd:CHL00180  90 KNLQRGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVhsTRRIAwNVANGQIDIAIVggeVPTEL 158
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 93-291 2.98e-10

The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate domain of LysR-type transcriptional regulators involved in controlling the expression of glutaryl-CoA dehydrogenase (GcdH), S-adenosyl-L-homocysteine hydrolase, cell division protein FtsW, tryptophan synthase, and beta-lactamase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176123 [Multi-domain]  Cd Length: 194  Bit Score: 58.75  E-value: 2.98e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073  93 TLKVHAMTGIGQHYLIKAISQYCETYPEVGFDLTLANRITDILDEGYDISVVIAPElPDSGFVSKCIGQTYSILCASPGY 172
Cdd:cd08432   1 VLTVSVTPSFAARWLIPRLARFQARHPDIDLRLSTSDRLVDFAREGIDLAIRYGDG-DWPGLEAERLMDEELVPVCSPAL 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073 173 IAAHGfPKLPAELSAHRCLRlvnSVMSLDRWLFDGPDGQELACINQTHFQVNTADAMTEAVVSGMGIGALPVYAAVNGLK 252
Cdd:cd08432  80 LAGLP-LLSPADLARHTLLH---DATRPEAWQWWLWAAGVADVDARRGPRFDDSSLALQAAVAGLGVALAPRALVADDLA 155

                       170       180       190
                ....*....|....*....|....*....|....*....
gi 15596073 253 DGSLVRVLPRYSLFHLNVYALYPSRQYLDAKIRTWVEFL 291
Cdd:cd08432 156 AGRLVRPFDLPLPSGGAYYLVYPPGRAESPAVAAFRDWL 194
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 93-291 4.88e-10

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: 58.27  E-value: 4.88e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073  93 TLKVHAMTGIGQHYLIKAISQYCETYPEVGFDLTLANR---ITDILDEGYDISVVIAPeLPDSGFVSKCIGQTYSILCAS 169
Cdd:cd08420   1 TLRIGASTTIGEYLLPRLLARFRKRYPEVRVSLTIGNTeeiAERVLDGEIDLGLVEGP-VDHPDLIVEPFAEDELVLVVP 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073 170 PGYIAAHGFPKLPAELSAHR--------CLRLVnsvmsLDRWLfdGPDGQELACINQThFQVNTADAMTEAVVSGMGIGA 241
Cdd:cd08420  80 PDHPLAGRKEVTAEELAAEPwilrepgsGTREV-----FERAL--AEAGLDGLDLNIV-MELGSTEAIKEAVEAGLGISI 151

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|
gi 15596073 242 LPVYAAVNGLKDGSLVRVLPRYSLFHLNVYALYPSRQYLDAKIRTWVEFL 291
Cdd:cd08420 152 LSRLAVRKELELGRLVALPVEGLRLTRPFSLIYHKDKYLSPAAEAFLEFL 201
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 4-73 8.51e-09

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 55.55  E-value: 8.51e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073    4 LFNMRAFVSVAETGSFTAAAQRLDLTTAYVSRAVAKLEAHLQTRLLHRTTRRIALTEAGQRYLMRAQQIL 73
Cdd:PRK09906   3 LRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAIL 72
PRK09791 PRK09791
LysR family transcriptional regulator;
4-121 4.05e-08

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 53.61  E-value: 4.05e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073    4 LFNMRAFVSVAETGSFTAAAQRLDLTTAYVSRAVAKLEAHLQTRLLHRTTRRIALTEAGQRYLMRAQQILAYIEEAEAEA 83
Cdd:PRK09791   7 IHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQEDI 86

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 15596073   84 GDAHARPSGTLKVHAMTGIGQHYLIKAISQYCETYPEV 121
Cdd:PRK09791  87 RQRQGQLAGQINIGMGASIARSLMPAVISRFHQQHPQV 124
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 13-73 1.31e-07

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 52.25  E-value: 1.31e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15596073   13 VAETGSFTAAAQRLDLTTAYVSRAVAKLEAHLQTRLLHRTTRRIALTEAGQRYLMRAQQIL 73
Cdd:PRK11074  13 VARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVI 73
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
8-274 1.99e-07

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 51.31  E-value: 1.99e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073    8 RAFVSVAETGSFTAAAQRLDLTTAYVSRAVAKLEAHLQTRLLHRtTRRIALTEAGQRYLMRAQQI-LAYIEEAEAEAGDA 86
Cdd:PRK03635   8 EALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRLLRHARQVrLLEAELLGELPALD 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073   87 HARPSGTLKVHA---MTgigqhYLIKAISQYCETYPeVGFDLTLAN--RITDILDEGYDISVVIAPELPDSGFVSKCIGQ 161
Cdd:PRK03635  87 GTPLTLSIAVNAdslAT-----WFLPALAPVLARSG-VLLDLVVEDqdHTAELLRRGEVVGAVTTEPQPVQGCRVDPLGA 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073  162 TYSILCASPGYIAAHgfpkLPAELSAHRcLRLVNSVM------SLDRWL---FDGPDGQELacinqTHFqVNTADAMTEA 232
Cdd:PRK03635 161 MRYLAVASPAFAARY----FPDGVTAEA-LAKAPAVVfnrkddLQDRFLrqaFGLPPGSVP-----CHY-VPSSEAFVRA 229

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|..
gi 15596073  233 VVSGMGIGALPVYAAVNGLKDGSLVRVLPRyslFHLNVyALY 274
Cdd:PRK03635 230 ALAGLGWGMIPELQIEPELASGELVDLTPG---RPLDV-PLY 267
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 4-73 2.46e-07

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 51.11  E-value: 2.46e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073    4 LFNMRAFVSVAETGSFTAAAQRLDLTTAYVSRAVAKLEAHLQTRLLHRTTRRIALTEAGQRYLMRAQQIL 73
Cdd:PRK11242   3 LRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRAL 72
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 7-73 1.23e-06

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 49.30  E-value: 1.23e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15596073    7 MRAFVSVAETGSFTAAAQRLDLTTAYVSRAVAKLEAHLQTRLLHRTTRRIALTEAGQRYLMRAQQIL 73
Cdd:PRK11233   6 LKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAIL 72
PRK10341 PRK10341
transcriptional regulator TdcA;
10-72 1.38e-06

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 49.09  E-value: 1.38e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15596073   10 FVSVAETGSFTAAAQRLDLTTAYVSRAVAKLEAHLQTRLLHRTTRRIALTEAGQRYLMRAQQI 72
Cdd:PRK10341  15 FQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESI 77
PRK09986 PRK09986
LysR family transcriptional regulator;
7-63 2.52e-06

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 48.18  E-value: 2.52e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 15596073    7 MRAFVSVAETGSFTAAAQRLDLTTAYVSRAVAKLEAHLQTRLLHRTTRRIALTEAGQ 63
Cdd:PRK09986  12 LRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGK 68
PBP2_HupR cd08431
The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which ...
 140-257 8.81e-05

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: 42.64  E-value: 8.81e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073 140 DISVVIAPELPDSGFVSKCIGQTYSILCASPG-YIAAHGFPKLPAELSAHRCLRLVNSVMSL---DRWLFDGpdgqelac 215
Cdd:cd08431  51 DLVIGATGELPPGGVKTRPLGEVEFVFAVAPNhPLAKLDGPLDASAIKQYPAIVVADTSRNLpprSSGLLEG-------- 122

                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 15596073 216 inQTHFQVNTADAMTEAVVSGMGIGALPVYAAVNGLKDGSLV 257
Cdd:cd08431 123 --QDRIRVPTMQAKIDAQVLGLGVGYLPRHLAKPELASGELV 162
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
34-152 1.24e-04

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 42.88  E-value: 1.24e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073   34 SRAVAKLEAHLQTRLLHRTTRRIALTEAGQRYLMRAQQILAYIEEAEAEAGDAHARPSGTLKVHAMTGIGQHYLIKAISQ 113
Cdd:PRK11716   9 SRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSLFCSVTAAYSHLPPILDR 88

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 15596073  114 YCETYPEVGFDLTL---ANRITDILDEGYDISVVIAPE-LPDS 152
Cdd:PRK11716  89 FRAEHPLVEIKLTTgdaADAVEKVQSGEADLAIAAKPEtLPAS 131
PRK15243 PRK15243
virulence genes transcriptional activator SpvR;
1-63 1.49e-04

virulence genes transcriptional activator SpvR;


Pssm-ID: 185155 [Multi-domain]  Cd Length: 297  Bit Score: 42.73  E-value: 1.49e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15596073    1 MDILFN--MRAFVSVAETGSFTAAAQRLDLTTAYVSRAVAKLEAHLQTRLLHRTTRRIALTEAGQ 63
Cdd:PRK15243   1 MDFLINkkLKIFITLMETGSFSIATSVLYITRTPLSRVISDLERELKQRLFIRKNGTLIPTEFAQ 65
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 7-73 4.06e-04

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 41.55  E-value: 4.06e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15596073    7 MRAFVSVAETGSFTAAAQRLDLTTAYVSRAVAKLEAHLQTRLLHRTTRRIALTEAGQRYLMRAQQIL 73
Cdd:PRK15092  16 LRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKIL 82
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 6-138 2.14e-03

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 39.24  E-value: 2.14e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073    6 NMRAF---VSVAETGSFTAAAQRLDLTTAYVSRAVAKLEAHLQTRLLHRTTRRIALTEAGQRYLMRAQQILAYIEEAEAE 82
Cdd:PRK11151   2 NIRDLeylVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVLKEM 81

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 15596073   83 AGDAHARPSGTLKVHAMTGIGQHYLIKAISQYCETYPEVGFDLTLA--NRITDILDEG 138
Cdd:PRK11151  82 ASQQGETMSGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAqtHQLLAQLDSG 139
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
6-257 5.24e-03

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 38.07  E-value: 5.24e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073    6 NMRAFVSVAETGSFTAAAQRLDLTTAYVSRAVAKLEAHLQTRLLHRTTRRIALTEAGQRYLMRAQQILAYIEEAEAE-AG 84
Cdd:PRK15421   6 HLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQAcNE 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073   85 DAHARPSGTLKVHAMTgigqHYLIKAISQYCETYPEVGFDLTLANRI--TDILDEGYDISVVIAPELPDSGFVSKCIGQT 162
Cdd:PRK15421  86 PQQTRLRIAIECHSCI----QWLTPALENFHKNWPQVEMDFKSGVTFdpQPALQQGELDLVMTSDILPRSGLHYSPMFDY 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596073  163 YSILCASPGYIAAHGFPKLPAELSAHRCLRLVNSVMSLDRWL-FDGPDGqelacINQTHFQVNTADAMTEAVVSGMGIGA 241
Cdd:PRK15421 162 EVRLVLAPDHPLAAKTRITPEDLASETLLIYPVQRSRLDVWRhFLQPAG-----VSPSLKSVDNTLLLIQMVAARMGIAA 236

                        250
                 ....*....|....*.
gi 15596073  242 LPVYAAVNGLKDGSLV 257
Cdd:PRK15421 237 LPHWVVESFERQGLVV 252
nhaR PRK11062
transcriptional activator NhaR; Provisional
 10-65 7.00e-03

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 37.68  E-value: 7.00e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 15596073   10 FVSVAETGSFTAAAQRLDLTTAYVSRAVAKLEAHLQTRLLHRTTRRIALTEAGQ---RY 65
Cdd:PRK11062  12 FWMVCKEGSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGElvfRY 70
MarR COG1846
DNA-binding transcriptional regulator, MarR family [Transcription];
23-73 7.77e-03

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


Pssm-ID: 441451 [Multi-domain]  Cd Length: 142  Bit Score: 36.10  E-value: 7.77e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 15596073  23 AQRLDLTTAYVSRAVAKLEAHlqtRLLHRTT-------RRIALTEAGQRYLMRAQQIL 73
Cdd:COG1846  59 AERLGLTKSTVSRLLDRLEEK---GLVEREPdpedrraVLVRLTEKGRALLEEARPAL 113
 
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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