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Conserved domains on  [gi|489198531|ref|WP_003107805|]
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MULTISPECIES: LysR family transcriptional regulator [Pseudomonas]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 20370986)

LysR family transcriptional regulator negatively or positively regulates the transcription of specific genes; contains an N-terminal HTH (helix-turn-helix) DNA-binding domain and a C-terminal substrate binding domain, which is structurally homologous to the type 2 periplasmic binding proteins

CATH:  3.40.190.10
Gene Ontology:  GO:0003700|GO:0006355|GO:0003677
PubMed:  8257110|19047729
SCOP:  4000316|3000083

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 ...
91-289 1.36e-60

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: 191.11  E-value: 1.36e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531  91 GPLKITTPQALGRIVIMPVLRELTRRYPQLQIEAAMTDRLVDLTEEGFDAAVRLGRVGDVRLIARPLAALRWVTVASPEY 170
Cdd:cd08422    1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVASPAY 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531 171 LRSHGTPERLEQLAGHNCptVRDLHTGKLLEWQFQRDGQPLSLAVRGDLVLDVADALVDAALVGQGIVQVMGFMAEEAIR 250
Cdd:cd08422   81 LARHGTPQTPEDLARHRC--LGYRLPGRPLRWRFRRGGGEVEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAEDLA 158
                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 489198531 251 RRRLVRILQPFEPPLCPVSLIYPPSRQCSLKIGALYEEL 289
Cdd:cd08422  159 SGRLVRVLPDWRPPPLPIYAVYPSRRHLPAKVRAFIDFL 197
LysR_Sec_metab super family cl49002
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
1-150 8.85e-23

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.


The actual alignment was detected with superfamily member NF040786:

Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 95.38  E-value: 8.85e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531   1 MDLNAVKLLARVAETRSFTQAAVSLGLTQSGLSRAIGRLEAELGVRLLHRTTRSVSLTPDGQLFYERCAPLLAELEEVEK 80
Cdd:NF040786   1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489198531  81 LLVDRQCAPSGPLKI---TTPqalGRIVIMPVLRELTRRYPQLQIEAAMTD--RLVDLTEEGfdaAVRLGRVGDV 150
Cdd:NF040786  81 EFDRYGKESKGVLRIgasTIP---GQYLLPELLKKFKEKYPNVRFKLMISDsiKVIELLLEG---EVDIGFTGTK 149
 
Name Accession Description Interval E-value
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
91-289 1.36e-60

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: 191.11  E-value: 1.36e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531  91 GPLKITTPQALGRIVIMPVLRELTRRYPQLQIEAAMTDRLVDLTEEGFDAAVRLGRVGDVRLIARPLAALRWVTVASPEY 170
Cdd:cd08422    1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVASPAY 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531 171 LRSHGTPERLEQLAGHNCptVRDLHTGKLLEWQFQRDGQPLSLAVRGDLVLDVADALVDAALVGQGIVQVMGFMAEEAIR 250
Cdd:cd08422   81 LARHGTPQTPEDLARHRC--LGYRLPGRPLRWRFRRGGGEVEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAEDLA 158
                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 489198531 251 RRRLVRILQPFEPPLCPVSLIYPPSRQCSLKIGALYEEL 289
Cdd:cd08422  159 SGRLVRVLPDWRPPPLPIYAVYPSRRHLPAKVRAFIDFL 197
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-292 3.63e-54

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 176.60  E-value: 3.63e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531   1 MDLNAVKLLARVAETRSFTQAAVSLGLTQSGLSRAIGRLEAELGVRLLHRTTRSVSLTPDGQLFYERCAPLLAELEEVEK 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531  81 LLVDRQCAPSGPLKITTPQALGRIVIMPVLRELTRRYPQLQIE--AAMTDRLVD-LTEEGFDAAVRLGRVGDVRLIARPL 157
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLElrEGNSDRLVDaLLEGELDLAIRLGPPPDPGLVARPL 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531 158 AALRWVTVASPEYLrshgtperleqLAGHNcPTVRDLhtgkllewqfqrdgqplslavrgdlvldvaDALVDAALVGQGI 237
Cdd:COG0583  161 GEERLVLVASPDHP-----------LARRA-PLVNSL------------------------------EALLAAVAAGLGI 198
                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 489198531 238 VQVMGFMAEEAIRRRRLVRILQPFEPPLCPVSLIYPPSRQCSLKIGALYEELKSA 292
Cdd:COG0583  199 ALLPRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREA 253
PRK09801 PRK09801
LysR family transcriptional regulator;
6-238 1.00e-32

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 122.45  E-value: 1.00e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531   6 VKLLARVAETRSFTQAAVSLGLTQSGLSRAIGRLEAELGVRLLHRTTRSVSLTPDGQLFYERCAPLLAELEEVEKLLVDR 85
Cdd:PRK09801  11 LQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVTQI 90
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531  86 QCAPSGPLKITTPQALGRIVIMPVLRELTRRYPQLQIEAAMTDRLVDLTEEGFDAAVRLGRVGDVRLIARPLAALRWVTV 165
Cdd:PRK09801  91 KTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHFELFDRQIDLVQDNIDLDIRINDEIPDYYIAHLLTKNKRILC 170
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489198531 166 ASPEYLRSHGTPERLEQLAGHNCPTV--RDLHTGKlleWQFQRDGQPLSLAVRGDLVLDVADALVDAALVGQGIV 238
Cdd:PRK09801 171 AAPEYLQKYPQPQSLQELSRHDCLVTkeRDMTHGI---WELGNGQEKKSVKVSGHLSSNSGEIVLQWALEGKGIM 242
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
1-150 8.85e-23

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: 95.38  E-value: 8.85e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531   1 MDLNAVKLLARVAETRSFTQAAVSLGLTQSGLSRAIGRLEAELGVRLLHRTTRSVSLTPDGQLFYERCAPLLAELEEVEK 80
Cdd:NF040786   1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489198531  81 LLVDRQCAPSGPLKI---TTPqalGRIVIMPVLRELTRRYPQLQIEAAMTD--RLVDLTEEGfdaAVRLGRVGDV 150
Cdd:NF040786  81 EFDRYGKESKGVLRIgasTIP---GQYLLPELLKKFKEKYPNVRFKLMISDsiKVIELLLEG---EVDIGFTGTK 149
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
90-292 4.91e-22

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: 91.20  E-value: 4.91e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531   90 SGPLKITTPQALGRIVIMPVLRELTRRYPQLQIE--AAMTDRLVDLTEEG-FDAAVRLGRVGDVRLIARPLAALRWVTVA 166
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELEltEGNSEELLDLLLEGeLDLAIRRGPPDDPGLEARPLGEEPLVLVA 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531  167 SPEYLRSHGTPERLEQLAGHNCPTVRDLHTgklLEWQFQRDGQPLSLAVRGDLVLDVADALVDAALVGQGIVQVMGFMAE 246
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLPPGSG---LRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVA 157
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 489198531  247 EAIRRRRLVRILQPFEPPLCPVSLIYPPSRQCSLKIGALYEELKSA 292
Cdd:pfam03466 158 RELADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREA 203
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-62 3.52e-21

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 84.74  E-value: 3.52e-21
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531    3 LNAVKLLARVAETRSFTQAAVSLGLTQSGLSRAIGRLEAELGVRLLHRTTRSVSLTPDGQ 62
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
rbcR CHL00180
LysR transcriptional regulator; Provisional
3-123 3.69e-15

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 74.29  E-value: 3.69e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531   3 LNAVKLLARVAETRSFTQAAVSLGLTQSGLSRAIGRLEAELGVRLLHRTTRSVSLTPDGQLFYERCAPLLAELEEVEKLL 82
Cdd:CHL00180   7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRAL 86
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 489198531  83 VDRQCAPSGPLKITTPQALGRiVIMPVLRELTR-RYPQLQIE 123
Cdd:CHL00180  87 EDLKNLQRGTLIIGASQTTGT-YLMPRLIGLFRqRYPQINVQ 127
COG4742 COG4742
Predicted transcriptional regulator, contains HTH domain [Transcription];
6-81 5.32e-03

Predicted transcriptional regulator, contains HTH domain [Transcription];


Pssm-ID: 443776 [Multi-domain]  Cd Length: 267  Bit Score: 37.57  E-value: 5.32e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489198531   6 VKLLARVAET-RSFTQAAVSLGLTQSGLSRAIGRLEAElgvRLLHRTTRSVSLTPDGQLFYERCAPLLAELEEVEKL 81
Cdd:COG4742   19 KNILLLLAEGpKTRSELAESLDVSRSTILRQLKELEER---GLIERDDGEYELTTLGRLVVEEMEPLLDTLEVLEEN 92
 
Name Accession Description Interval E-value
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
91-289 1.36e-60

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: 191.11  E-value: 1.36e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531  91 GPLKITTPQALGRIVIMPVLRELTRRYPQLQIEAAMTDRLVDLTEEGFDAAVRLGRVGDVRLIARPLAALRWVTVASPEY 170
Cdd:cd08422    1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVASPAY 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531 171 LRSHGTPERLEQLAGHNCptVRDLHTGKLLEWQFQRDGQPLSLAVRGDLVLDVADALVDAALVGQGIVQVMGFMAEEAIR 250
Cdd:cd08422   81 LARHGTPQTPEDLARHRC--LGYRLPGRPLRWRFRRGGGEVEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAEDLA 158
                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 489198531 251 RRRLVRILQPFEPPLCPVSLIYPPSRQCSLKIGALYEEL 289
Cdd:cd08422  159 SGRLVRVLPDWRPPPLPIYAVYPSRRHLPAKVRAFIDFL 197
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-292 3.63e-54

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 176.60  E-value: 3.63e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531   1 MDLNAVKLLARVAETRSFTQAAVSLGLTQSGLSRAIGRLEAELGVRLLHRTTRSVSLTPDGQLFYERCAPLLAELEEVEK 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531  81 LLVDRQCAPSGPLKITTPQALGRIVIMPVLRELTRRYPQLQIE--AAMTDRLVD-LTEEGFDAAVRLGRVGDVRLIARPL 157
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLElrEGNSDRLVDaLLEGELDLAIRLGPPPDPGLVARPL 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531 158 AALRWVTVASPEYLrshgtperleqLAGHNcPTVRDLhtgkllewqfqrdgqplslavrgdlvldvaDALVDAALVGQGI 237
Cdd:COG0583  161 GEERLVLVASPDHP-----------LARRA-PLVNSL------------------------------EALLAAVAAGLGI 198
                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 489198531 238 VQVMGFMAEEAIRRRRLVRILQPFEPPLCPVSLIYPPSRQCSLKIGALYEELKSA 292
Cdd:COG0583  199 ALLPRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREA 253
PBP2_CrgA_like_3 cd08472
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
91-281 1.82e-53

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: 173.08  E-value: 1.82e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531  91 GPLKITTPQALGRIVIMPVLRELTRRYPQLQIEAAMTDRLVDLTEEGFDAAVRLGRVGDVRLIARPLAALRWVTVASPEY 170
Cdd:cd08472    1 GRLRVDVPGSLARLLLIPALPDFLARYPDIELDLGVSDRPVDLIREGVDCVIRVGELADSSLVARRLGELRMVTCASPAY 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531 171 LRSHGTPERLEQLAGHNCPTVRDLHTGKLLEWQFQRDGQPLSLAVRGDLVLDVADALVDAALVGQGIVQVMGFMAEEAIR 250
Cdd:cd08472   81 LARHGTPRHPEDLERHRAVGYFSARTGRVLPWEFQRDGEEREVKLPSRVSVNDSEAYLAAALAGLGIIQVPRFMVRPHLA 160
                        170       180       190
                 ....*....|....*....|....*....|.
gi 489198531 251 RRRLVRILQPFEPPLCPVSLIYPPSRQCSLK 281
Cdd:cd08472  161 SGRLVEVLPDWRPPPLPVSLLYPHRRHLSPR 191
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
89-289 1.16e-52

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: 171.11  E-value: 1.16e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531  89 PSGPLKITTPQALGRIVIMPVLRELTRRYPQLQIEAAMTDRLVDLTEEGFDAAVRLGRVGDVRLIARPLA-ALRWVTVAS 167
Cdd:cd08474    1 PAGTLRINAPRVAARLLLAPLLARFLARYPDIRLELVVDDGLVDIVAEGFDAGIRLGESVEKDMVAVPLGpPLRMAVVAS 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531 168 PEYLRSHGTPERLEQLAGHNCPTVRDLHTGKLLEWQFQRDGQPLSLAVRGDLVLDVADALVDAALVGQGIVQVMGFMAEE 247
Cdd:cd08474   81 PAYLARHGTPEHPRDLLNHRCIRYRFPTSGALYRWEFERGGRELEVDVEGPLILNDSDLMLDAALDGLGIAYLFEDLVAE 160
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 489198531 248 AIRRRRLVRILQPFEPPLCPVSLIYPPSRQCSLKIGALYEEL 289
Cdd:cd08474  161 HLASGRLVRVLEDWSPPFPGGYLYYPSRRRVPPALRAFIDFL 202
PBP2_CrgA_like_2 cd08471
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
91-282 1.29e-46

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: 155.38  E-value: 1.29e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531  91 GPLKITTPQALGRIVIMPVLRELTRRYPQLQIEAAMTDRLVDLTEEGFDAAVRLGRVGDVRLIARPLAALRWVTVASPEY 170
Cdd:cd08471    1 GLLTVTAPVLFGRLHVLPIITDFLDAYPEVSVRLLLLDRVVNLLEEGVDVAVRIGHLPDSSLVATRVGSVRRVVCASPAY 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531 171 LRSHGTPERLEQLAGHNCPTVRDLhtGKLLEWQFQRDGQPLSLAVRGDLVLDVADALVDAALVGQGIVQVMGFMAEEAIR 250
Cdd:cd08471   81 LARHGTPKHPDDLADHDCIAFTGL--SPAPEWRFREGGKERSVRVRPRLTVNTVEAAIAAALAGLGLTRVLSYQVAEELA 158
                        170       180       190
                 ....*....|....*....|....*....|..
gi 489198531 251 RRRLVRILQPFEPPLCPVSLIYPPSRQCSLKI 282
Cdd:cd08471  159 AGRLQRVLEDFEPPPLPVHLVHPEGRLAPAKV 190
PBP2_CrgA_like_1 cd08470
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
91-292 4.96e-46

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: 154.00  E-value: 4.96e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531  91 GPLKITTPQALGRIVIMPVLRELTRRYPQLQIEAAMTDRLVDLTEEGFDAAVRLGRVGDVRLIARPLAALRWVTVASPEY 170
Cdd:cd08470    1 GLLRITCPVAYGERFIAPLVNDFMQRYPKLEVDIELTNRVVDLVSEGFDLAIRLGRLTDSSLMARRLASRRHYVCASPAY 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531 171 LRSHGTPERLEQLAGHNCptvrdlHTGKLLEWQFQRDGQPLSLAVRGDLVLDVADALVDAALVGQGIVQVMGFMAEEAIR 250
Cdd:cd08470   81 LERHGTPHSLADLDRHNC------LLGTSDHWRFQENGRERSVRVQGRWRCNSGVALLDAALKGMGLAQLPDYYVDEHLA 154
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 489198531 251 RRRLVRILQPFEPPLCPVSLIYPPSRQCSLKIGALYEELKSA 292
Cdd:cd08470  155 AGRLVPVLEDYRPPDEGIWALYPHNRHLSPKVRLLVDYLADA 196
PBP2_CrgA_like_6 cd08475
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
91-289 6.22e-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 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: 148.47  E-value: 6.22e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531  91 GPLKITTPQALGRIVIMPVLRELTRRYPQLQIEAAMTDRLVDLTEEGFDAAVRLGRVGD-VRLIARPLAALRWVTVASPE 169
Cdd:cd08475    1 GRLRIDLPVAFGRLCVAPLLLELARRHPELELELSFSDRFVDLIEEGIDLAVRIGELADsTGLVARRLGTQRMVLCASPA 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531 170 YLRSHGTPERLEQLAGHNCptVRDLHTGKLLEWQFQR-DGQPLSLAVRGDLVLDVADALVDAALVGQGIVQVMGFMAEEA 248
Cdd:cd08475   81 YLARHGTPRTLEDLAEHQC--IAYGRGGQPLPWRLADeQGRLVRFRPAPRLQFDDGEAIADAALAGLGIAQLPTWLVADH 158
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 489198531 249 IRRRRLVRILQPFEPPLCPVSLIYPPSRQCSLKIGALYEEL 289
Cdd:cd08475  159 LQRGELVEVLPELAPEGLPIHAVWPRTRHLPPKVRAAVDAL 199
PBP2_CrgA_like_8 cd08477
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
91-282 1.92e-42

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: 144.68  E-value: 1.92e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531  91 GPLKITTPQALGRIVIMPVLRELTRRYPQLQIEAAMTDRLVDLTEEGFDAAVRLGRVGDVRLIARPLAALRWVTVASPEY 170
Cdd:cd08477    1 GKLRISAPVTFGSHVLTPALAEYLARYPDVRVDLVLSDRLVDLVEEGFDAAFRIGELADSSLVARPLAPYRMVLCASPDY 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531 171 LRSHGTPERLEQLAGHNCptVRDLHTGKLLEWQFQRDGQPLSLAVRGDLVLDVADALVDAALVGQGIVqvmgFMAEEAIR 250
Cdd:cd08477   81 LARHGTPTTPEDLARHEC--LGFSYWRARNRWRLEGPGGEVKVPVSGRLTVNSGQALRVAALAGLGIV----LQPEALLA 154
                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 489198531 251 RRRLVRILQP----FEPPLCPVSLIYPPSRQCSLKI 282
Cdd:cd08477  155 EDLASGRLVEllpdYLPPPRPMHLLYPPDRRPTPKL 190
PBP2_CrgA_like_7 cd08476
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
91-282 1.95e-40

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: 139.30  E-value: 1.95e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531  91 GPLKITTPqaLGRIVIMPVLRELTRRYPQLQIEAAMTDRLVDLTEEGFDAAVRLGRVGDVRLIARPLAALRWVTVASPEY 170
Cdd:cd08476    1 GRLRVSLP--LVGGLLLPVLAAFMQRYPEIELDLDFSDRLVDVIDEGFDAVIRTGELPDSRLMSRRLGSFRMVLVASPDY 78
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531 171 LRSHGTPERLEQLAGHNCPTVRDLHTGKLLEWQFQRDGQPLSLAVRGDLVLDVADALVDAALVGQGIVQVMGFMAEEAIR 250
Cdd:cd08476   79 LARHGTPETPADLAEHACLRYRFPTTGKLEPWPLRGDGGDPELRLPTALVCNNIEALIEFALQGLGIACLPDFSVREALA 158
                        170       180       190
                 ....*....|....*....|....*....|..
gi 489198531 251 RRRLVRILQPFEPPLCPVSLIYPPSRQCSLKI 282
Cdd:cd08476  159 DGRLVTVLDDYVEERGQFRLLWPSSRHLSPKL 190
PBP2_CrgA_like_9 cd08479
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
91-238 1.93e-35

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: 126.56  E-value: 1.93e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531  91 GPLKITTPQALGRIVIMPVLRELTRRYPQLQIEAAMTDRLVDLTEEGFDAAVRLGRVGDVRLIARPLAALRWVTVASPEY 170
Cdd:cd08479    1 GLLRVNASFGFGRRHIAPALSDFAKRYPELEVQLELTDRPVDLVEEGFDLDIRVGDLPDSSLIARKLAPNRRILCASPAY 80
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489198531 171 LRSHGTPERLEQLAGHNCPTVRDLHTGKLLeWQFQRDGQPLSLAVRGDLVLDVADALVDAALVGQGIV 238
Cdd:cd08479   81 LERHGAPASPEDLARHDCLVIRENDEDFGL-WRLRNGDGEATVRVRGALSSNDGEVVLQWALDGHGII 147
PRK09801 PRK09801
LysR family transcriptional regulator;
6-238 1.00e-32

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 122.45  E-value: 1.00e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531   6 VKLLARVAETRSFTQAAVSLGLTQSGLSRAIGRLEAELGVRLLHRTTRSVSLTPDGQLFYERCAPLLAELEEVEKLLVDR 85
Cdd:PRK09801  11 LQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVTQI 90
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531  86 QCAPSGPLKITTPQALGRIVIMPVLRELTRRYPQLQIEAAMTDRLVDLTEEGFDAAVRLGRVGDVRLIARPLAALRWVTV 165
Cdd:PRK09801  91 KTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHFELFDRQIDLVQDNIDLDIRINDEIPDYYIAHLLTKNKRILC 170
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489198531 166 ASPEYLRSHGTPERLEQLAGHNCPTV--RDLHTGKlleWQFQRDGQPLSLAVRGDLVLDVADALVDAALVGQGIV 238
Cdd:PRK09801 171 AAPEYLQKYPQPQSLQELSRHDCLVTkeRDMTHGI---WELGNGQEKKSVKVSGHLSSNSGEIVLQWALEGKGIM 242
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
1-276 2.63e-32

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 121.25  E-value: 2.63e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531   1 MDLNAVKLLARVAETRSFTQAAVSLGLTQSGLSRAIGRLEAELGVRLLHRTTRSVSLTPDGQLFYERCAPLLAELEEVEK 80
Cdd:PRK14997   2 TDLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQD 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531  81 LLVDRQCAPSGPLKITTPQALGRIVIMPVLRELTRRYPQLQIEAAMTDRLVDLTEEGFDAAVRL--GRVGDVRLIARPLA 158
Cdd:PRK14997  82 AIAALQVEPRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLEATNRRVDVVGEGVDVAIRVrpRPFEDSDLVMRVLA 161
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531 159 ALRWVTVASPEYLRSHGTPERLEQLagHNCPTVrDLHTGK-LLEWQ-FQRDGQPLSLAVRGDLVLDVADALVDAALVGQG 236
Cdd:PRK14997 162 DRGHRLFASPDLIARMGIPSAPAEL--SHWPGL-SLASGKhIHRWElYGPQGARAEVHFTPRMITTDMLALREAAMAGVG 238
                        250       260       270       280
                 ....*....|....*....|....*....|....*....|
gi 489198531 237 IVQVMGFMAEEAIRRRRLVRILQPFEPPLCPVSLIYPPSR 276
Cdd:PRK14997 239 LVQLPVLMVKEQLAAGELVAVLEEWEPRREVIHAVFPSRR 278
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
3-186 1.34e-30

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 116.78  E-value: 1.34e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531   3 LNAVKLLARVAETRSFTQAAVSLGLTQSGLSRAIGRLEAELGVRLLHRTTRSVSLTPDGQLFYERCAPLLAELEEVEKLL 82
Cdd:PRK10632   4 LKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQL 83
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531  83 VDRQCAPSGPLKITTPQALGRIVIMPVLRELTRRYPQLQIEAAMTDRLVDLTEEGFDAAVRLGRVGDVRLIARPLAALRW 162
Cdd:PRK10632  84 YAFNNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTGIPAPDLIADGLDVVIRVGALQDSSLFSRRLGAMPM 163
                        170       180
                 ....*....|....*....|....
gi 489198531 163 VTVASPEYLRSHGTPERLEQLAGH 186
Cdd:PRK10632 164 VVCAAKSYLAQYGTPEKPADLSSH 187
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
3-238 7.26e-28

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 109.16  E-value: 7.26e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531   3 LNAVKLLARVAETRSFTQAAVSLGLTQSGLSRAIGRLEAELGVRLLHRTTRSVSLTPDGQLFYERCAPLLAELEEV-EKL 81
Cdd:PRK11139   8 LNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEAtRKL 87
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531  82 L-VDRQCApsgpLKITTPQALGRIVIMPVLRELTRRYPQLQIEAAMTDRLVDLTEEGFDAAVRLGRVGDVRLIARPLAAL 160
Cdd:PRK11139  88 RaRSAKGA----LTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDRLEDFLRDDVDVAIRYGRGNWPGLRVEKLLDE 163
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531 161 RWVTVASPEYLRSHGTPERLEQLAGHNCptvrdLHTGKLLEWQ--FQRDGQPlSLAVRGDLVLDVADALVDAALVGQGIV 238
Cdd:PRK11139 164 YLLPVCSPALLNGGKPLKTPEDLARHTL-----LHDDSREDWRawFRAAGLD-DLNVQQGPIFSHSSMALQAAIHGQGVA 237
PBP2_CrgA_like_10 cd08480
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
91-243 4.71e-26

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: 102.03  E-value: 4.71e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531  91 GPLKITTPQALGRIVIMPVLRELTRRYPQLQIEAAMTDRLVDLTEEGFDAAVRLGRVGDVRLIARPLAALRWVTVASPEY 170
Cdd:cd08480    1 GRLRVNASVPFGTHFLLPLLPAFLARYPEILVDLSLTDEVVDLLAERTDVAIRVGPLPDSSLVARKLGESRRVIVASPSY 80
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489198531 171 LRSHGTPERLEQLAGHNCPT---VRDLHtgkllEWQFQRDGQPLSLAVRGDLVLDVADALVDAALVGQGIVQVMGF 243
Cdd:cd08480   81 LARHGTPLTPQDLARHNCLGfnfRRALP-----DWPFRDGGRIVALPVSGNILVNDGEALRRLALAGAGLARLALF 151
PBP2_CrgA cd08478
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains ...
89-244 6.18e-23

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: 93.56  E-value: 6.18e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531  89 PSGPLKI--TTPQALGriVIMPVLRELTRRYPQLQIEAAMTDRLVDLTEEGFDAAVRLGRVGDVRLIARPLAALRWVTVA 166
Cdd:cd08478    1 PSGLLRVdaATPFVLH--LLAPLIAKFRERYPDIELELVSNEGIIDLIERKTDVAIRIGELTDSTLHARPLGKSRLRILA 78
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531 167 SPEYLRSHGTPERLEQLAGHNC-----PTvrdlhtgKLLEWQFqRDGQPLSLAVRGDLVLDVADALVDAALVGQGIVQVM 241
Cdd:cd08478   79 SPDYLARHGTPQSIEDLAQHQLlgftePA-------SLNTWPI-KDADGNLLKIQPTITASSGETLRQLALSGCGIACLS 150

                 ...
gi 489198531 242 GFM 244
Cdd:cd08478  151 DFM 153
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
1-150 8.85e-23

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: 95.38  E-value: 8.85e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531   1 MDLNAVKLLARVAETRSFTQAAVSLGLTQSGLSRAIGRLEAELGVRLLHRTTRSVSLTPDGQLFYERCAPLLAELEEVEK 80
Cdd:NF040786   1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489198531  81 LLVDRQCAPSGPLKI---TTPqalGRIVIMPVLRELTRRYPQLQIEAAMTD--RLVDLTEEGfdaAVRLGRVGDV 150
Cdd:NF040786  81 EFDRYGKESKGVLRIgasTIP---GQYLLPELLKKFKEKYPNVRFKLMISDsiKVIELLLEG---EVDIGFTGTK 149
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
90-292 4.91e-22

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: 91.20  E-value: 4.91e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531   90 SGPLKITTPQALGRIVIMPVLRELTRRYPQLQIE--AAMTDRLVDLTEEG-FDAAVRLGRVGDVRLIARPLAALRWVTVA 166
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELEltEGNSEELLDLLLEGeLDLAIRRGPPDDPGLEARPLGEEPLVLVA 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531  167 SPEYLRSHGTPERLEQLAGHNCPTVRDLHTgklLEWQFQRDGQPLSLAVRGDLVLDVADALVDAALVGQGIVQVMGFMAE 246
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLPPGSG---LRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVA 157
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 489198531  247 EAIRRRRLVRILQPFEPPLCPVSLIYPPSRQCSLKIGALYEELKSA 292
Cdd:pfam03466 158 RELADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREA 203
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
12-242 6.74e-22

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 93.14  E-value: 6.74e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531  12 VAETRSFTQAAVSLGLTQSGLSRAIGRLEAELGVRLLHRTTRSVSLTPDGQLFYercAPLLAELEEVEKLLVDRQCA-PS 90
Cdd:PRK10086  25 AARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVF---WALKSSLDTLNQEILDIKNQeLS 101
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531  91 GPLKITTPQALGRIVIMPVLRELTRRYPQLQIEAAMTDRLVDLTEEGFDAAVRLGRVGDVRLIARPLAALRWVTVASPEY 170
Cdd:PRK10086 102 GTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTILTGNENVNFQRAGIDLAIYFDDAPSAQLTHHFLMDEEILPVCSPEY 181
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531 171 LRSH---GTPERLEQlaghnCPTVRDL----HTGKLLEWQF--QRDGQPLSLAVRGdLVLDVADALVDAALVGQGIvqVM 241
Cdd:PRK10086 182 AERHaltGNPDNLRH-----CTLLHDRqawsNDSGTDEWHSwaQHFGVNLLPPSSG-IGFDRSDLAVIAAMNHIGV--AM 253

                 .
gi 489198531 242 G 242
Cdd:PRK10086 254 G 254
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-62 3.52e-21

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 84.74  E-value: 3.52e-21
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531    3 LNAVKLLARVAETRSFTQAAVSLGLTQSGLSRAIGRLEAELGVRLLHRTTRSVSLTPDGQ 62
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PBP2_CrgA_like_4 cd08473
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
89-248 1.06e-20

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: 87.61  E-value: 1.06e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531  89 PSGPLKITTPQALGRIVIMPVLRELTRRYPQLQIEAAMTDRLVDLTEEGFDAA--VRLGRVGDVRLIARPLAALRWVTVA 166
Cdd:cd08473    1 PRGTVRVSCPPALAQELLAPLLPRFMAAYPQVRLQLEATNRRVDLIEEGIDVAlrVRFPPLEDSSLVMRVLGQSRQRLVA 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531 167 SPEYLRSHGTPERLEQLAGHncPTVRDLHTGKLLEWQ-FQRDGQPLSLAVRGDLVLDVADALVDAALVGQGIVQVMGFMA 245
Cdd:cd08473   81 SPALLARLGRPRSPEDLAGL--PTLSLGDVDGRHSWRlEGPDGESITVRHRPRLVTDDLLTLRQAALAGVGIALLPDHLC 158

                 ...
gi 489198531 246 EEA 248
Cdd:cd08473  159 REA 161
rbcR CHL00180
LysR transcriptional regulator; Provisional
3-123 3.69e-15

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 74.29  E-value: 3.69e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531   3 LNAVKLLARVAETRSFTQAAVSLGLTQSGLSRAIGRLEAELGVRLLHRTTRSVSLTPDGQLFYERCAPLLAELEEVEKLL 82
Cdd:CHL00180   7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRAL 86
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 489198531  83 VDRQCAPSGPLKITTPQALGRiVIMPVLRELTR-RYPQLQIE 123
Cdd:CHL00180  87 EDLKNLQRGTLIIGASQTTGT-YLMPRLIGLFRqRYPQINVQ 127
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
92-285 5.10e-15

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: 71.84  E-value: 5.10e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531  92 PLKITTPQALGRIVIMPVLRELTRRYPQLQIEAAMTDRLVDLTEEGFDAAVRLGRVGDVRLIARPLAALRWVTVASPEYL 171
Cdd:cd08432    1 VLTVSVTPSFAARWLIPRLARFQARHPDIDLRLSTSDRLVDFAREGIDLAIRYGDGDWPGLEAERLMDEELVPVCSPALL 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531 172 RSHGtPERLEQLAGHncPTVRDLHTGKLLEWQFQRDGQPLSLAVRGdLVLDVADALVDAALVGQGIVQVMGFMAEEAirr 251
Cdd:cd08432   81 AGLP-LLSPADLARH--TLLHDATRPEAWQWWLWAAGVADVDARRG-PRFDDSSLALQAAVAGLGVALAPRALVADD--- 153
                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 489198531 252 RRLVRILQPFEPPLCPVS---LIYPPSRQCSLKIGAL 285
Cdd:cd08432  154 LAAGRLVRPFDLPLPSGGayyLVYPPGRAESPAVAAF 190
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
1-183 1.36e-14

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 72.53  E-value: 1.36e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531   1 MDLNAVKLLARVAETRSFTQAAVSLGLTQSGLSRAIGRLEAELGVRLLHRTTRSVSLTPDGQLFYERCAPLLAELEEVEK 80
Cdd:PRK10094   2 FDPETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPS 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531  81 LL------VDRQCAPSGPLKITTPQALGRIvimpvLRELTRRYP--QLQIEAAMTDRLVD-LTEEGFDAAVrlGRVGDVR 151
Cdd:PRK10094  82 ELqqvndgVERQVNIVINNLLYNPQAVAQL-----LAWLNERYPftQFHISRQIYMGVWDsLLYEGFSLAI--GVTGTEA 154
                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 489198531 152 LIAR----PLAALRWVTVASPEY-LRSHGTPERLEQL 183
Cdd:PRK10094 155 LANTfsldPLGSVQWRFVMAADHpLANVEEPLTEAQL 191
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
8-133 1.05e-12

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 66.90  E-value: 1.05e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531   8 LLArVAETRSFTQAAVSLGLTQSGLSRAIGRLEAELGVRLLHRTTRSVSLTPDGQLFYERCAPLLAELEEVEKLLVDRQC 87
Cdd:PRK11242   9 FLA-VAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRRAIHDVAD 87
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 489198531  88 APSGPLKITTPQALGRIVIMPVLRELTRRYP----------QLQIEAAMTDRLVDL 133
Cdd:PRK11242  88 LSRGSLRLAMTPTFTAYLIGPLIDAFHARYPgitltiremsQERIEALLADDELDV 143
PRK12680 PRK12680
LysR family transcriptional regulator;
1-142 7.16e-12

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 65.03  E-value: 7.16e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531   1 MDLNAVKLLARVAETR-SFTQAAVSLGLTQSGLSRAIGRLEAELGVRLLHRTTRSV-SLTPDGQLFYERCAPLLAELEEV 78
Cdd:PRK12680   1 MTLTQLRYLVAIADAElNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLeSVTPAGVEVIERARAVLSEANNI 80
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489198531  79 EKLLVDRQCAPSGPLKITTPQALGRIVIMPVLRELTRRYPQLQI---EAAMTDRLVDLTEEGFDAAV 142
Cdd:PRK12680  81 RTYAANQRRESQGQLTLTTTHTQARFVLPPAVAQIKQAYPQVSVhlqQAAESAALDLLGQGDADIAI 147
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
1-137 2.08e-10

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 60.43  E-value: 2.08e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531   1 MDLNAVKLLARVAETRSFTQAAVSLGLTQSGLSRAIGRLEAELGVRLLHRTTRSVSLTPDGQLFYERCAPLLAELEEVEK 80
Cdd:PRK11151   1 MNIRDLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVLKE 80
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489198531  81 LLVDRQCAPSGPLKITTPQALGRIV---IMPVLRELtrrYPQLQ--IEAAMTDRLVDLTEEG 137
Cdd:PRK11151  81 MASQQGETMSGPLHIGLIPTVGPYLlphIIPMLHQT---FPKLEmyLHEAQTHQLLAQLDSG 139
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
3-123 3.98e-10

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 59.32  E-value: 3.98e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531   3 LNAVKLLARVAETRSFTQAAVSLGLTQSGLSRAIGRLEAELGVRLLHRTTRSVSLTPDGQLFYERCAPLLAELEEVEKLL 82
Cdd:PRK10837   5 LRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQAVEIEQLF 84
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 489198531  83 VdrqcAPSGPLKITTPQALGRIVIMPVLRELTRRYPQLQIE 123
Cdd:PRK10837  85 R----EDNGALRIYASSTIGNYILPAMIARYRRDYPQLPLE 121
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
9-174 4.99e-10

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 59.21  E-value: 4.99e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531   9 LARVAETRSFTQAAVSLGLTQSGLSRAIGRLEAELGVRLLHRtTRSVSLTPDGQLfyercapLLAELEEVEKLLVD--RQ 86
Cdd:PRK13348  10 LAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQR-------LLRHLRQVALLEADllST 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531  87 CAPSGPLKITTPQALGRIVI----MPVLRELTRRypqlqiEAAMTDRLVDLTEEGFDAAVRLGRVGDVR--------LIA 154
Cdd:PRK13348  82 LPAERGSPPTLAIAVNADSLatwfLPALAAVLAG------ERILLELIVDDQDHTFALLERGEVVGCVStqpkpmrgCLA 155
                        170       180
                 ....*....|....*....|
gi 489198531 155 RPLAALRWVTVASPEYLRSH 174
Cdd:PRK13348 156 EPLGTMRYRCVASPAFAARY 175
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
1-81 5.41e-10

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 59.01  E-value: 5.41e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531   1 MDLNAVKLLARVAETRSFTQAAVSLGLTQSGLSRAIGRLEAELGVRLLHRTTRSVSLTPDGQLFYERCAPLLAELEEVEK 80
Cdd:PRK09906   1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKL 80

                 .
gi 489198531  81 L 81
Cdd:PRK09906  81 R 81
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
19-122 1.57e-09

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 57.69  E-value: 1.57e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531  19 TQAAVSLGLTQSGLSRAIGRLEAELGVRLLHRT-TRSVSLTPDGQLFYERCAPLLAELEEVEKLLVDRQCAPSGPLKITT 97
Cdd:PRK12682  20 TEAAKALHTSQPGVSKAIIELEEELGIEIFIRHgKRLKGLTEPGKAVLDVIERILREVGNIKRIGDDFSNQDSGTLTIAT 99
                         90       100
                 ....*....|....*....|....*
gi 489198531  98 PQALGRIVIMPVLRELTRRYPQLQI 122
Cdd:PRK12682 100 THTQARYVLPRVVAAFRKRYPKVNL 124
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
93-289 1.92e-09

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: 56.07  E-value: 1.92e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531  93 LKITTPQALGRIVIMPVLRELTRRYP--QLQIEAAMTDRLVDLTEEG-FDAAVRLGRVGDVRLIARPLAALRWVTVASPE 169
Cdd:cd05466    2 LRIGASPSIAAYLLPPLLAAFRQRYPgvELSLVEGGSSELLEALLEGeLDLAIVALPVDDPGLESEPLFEEPLVLVVPPD 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531 170 YLRSHGTPERLEQLAGHN-CPTVRDLHTGKLLEWQFQRDGQPLSLAVRGDLVldvaDALVDAALVGQGIvqvmGFMAEEA 248
Cdd:cd05466   82 HPLAKRKSVTLADLADEPlILFERGSGLRRLLDRAFAEAGFTPNIALEVDSL----EAIKALVAAGLGI----ALLPESA 153
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 489198531 249 IRRRRLVRILQ-PFEPPLC--PVSLIYPPSRQCSLKIGALYEEL 289
Cdd:cd05466  154 VEELADGGLVVlPLEDPPLsrTIGLVWRKGRYLSPAARAFLELL 197
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
12-170 6.64e-09

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 55.72  E-value: 6.64e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531  12 VAETRSFTQAAVSLGLTQSGLSRAIGRLEAELGVRLLHRTTRSVSLTPDGQLFYERCAPLLAELEEVEkllvdRQCAP-- 89
Cdd:PRK11074  13 VARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETR-----RQCQQva 87
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531  90 ---SGPLKIttpqALGRIV----IMPVLRELTRRYP--QLQI---------EAAMTDRlVDLTeEGFDAAVRLGrvGDVR 151
Cdd:PRK11074  88 ngwRGQLSI----AVDNIVrpdrTRQLIVDFYRHFDdvELIIrqevfngvwDALADGR-VDIA-IGATRAIPVG--GRFA 159
                        170
                 ....*....|....*....
gi 489198531 152 LiaRPLAALRWVTVASPEY 170
Cdd:PRK11074 160 F--RDMGMLSWACVVSSDH 176
PRK09791 PRK09791
LysR family transcriptional regulator;
3-122 1.10e-08

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 55.15  E-value: 1.10e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531   3 LNAVKLLARVAETRSFTQAAVSLGLTQSGLSRAIGRLEAELGVRLLHRTTRSVSLTPDGQLFYERCAPLLAELEEVEKLL 82
Cdd:PRK09791   7 IHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQEDI 86
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 489198531  83 VDRQCAPSGPLKITTPQALGRIVIMPVLRELTRRYPQLQI 122
Cdd:PRK09791  87 RQRQGQLAGQINIGMGASIARSLMPAVISRFHQQHPQVKV 126
PRK10341 PRK10341
transcriptional regulator TdcA;
12-183 1.46e-08

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 54.87  E-value: 1.46e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531  12 VAETRSFTQAAVSLGLTQSGLSRAIGRLEAELGVRLLHRTTRSVSLTPDGQLFYERCAPLLAELEEVEKLLVDRQCAPSG 91
Cdd:PRK10341  18 VIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEINGMSSEAVV 97
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531  92 PLKITTPQALGRIVIMPVLRELTRRYPQLQI---EAAMTDRLVDLTEEGFDAAVrlGRVGDVRLI----ARPLAALRWVT 164
Cdd:PRK10341  98 DVSFGFPSLIGFTFMSDMINKFKEVFPKAQVsmyEAQLSSFLPAIRDGRLDFAI--GTLSNEMKLqdlhVEPLFESEFVL 175
                        170
                 ....*....|....*....
gi 489198531 165 VASPeyLRSHGTPERLEQL 183
Cdd:PRK10341 176 VASK--SRTCTGTTTLESL 192
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
16-137 3.49e-08

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 53.90  E-value: 3.49e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531  16 RSFTQAAVSLGLTQSGLSRAIGRLEAELGVRLLHRTTRSVSLTPDGQLFYERCAPLLAELEEVEKLLVDRQCAPSGPLKI 95
Cdd:PRK10082  26 RNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESNLAELRGGSDYAQRKIKI 105
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 489198531  96 TTPQALGriviMPVLRELTRRYPQL---QIEAAMTDRLVDLTEEG 137
Cdd:PRK10082 106 AAAHSLS----LGLLPSIISQMPPLftwAIEAIDVDEAVDKLREG 146
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
19-119 9.70e-08

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 52.29  E-value: 9.70e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531  19 TQAAVSLGLTQSGLSRAIGRLEAELGVRLLHRT-TRSVSLTPDGQLFYERCAPLLAELEEVEKLLVDRQCAPSGPLKITT 97
Cdd:PRK12684  20 TEAAKALYTSQPGVSKAIIELEDELGVEIFTRHgKRLRGLTEPGRIILASVERILQEVENLKRVGKEFAAQDQGNLTIAT 99
                         90       100
                 ....*....|....*....|..
gi 489198531  98 PQALGRIVIMPVLRELTRRYPQ 119
Cdd:PRK12684 100 THTQARYALPAAIKEFKKRYPK 121
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
19-246 1.08e-07

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 52.35  E-value: 1.08e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531  19 TQAAVSLGLTQSGLSRAIGRLEAELGVRLLHRT-TRSVSLTPDGQLFYERCAPLLAELEEVEKLLVDRQCAPSGPLKITT 97
Cdd:PRK12683  20 TEVANALYTSQSGVSKQIKDLEDELGVEIFIRRgKRLTGLTEPGKELLQIVERMLLDAENLRRLAEQFADRDSGHLTVAT 99
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531  98 PQALGRIVIMPVLRELTRRYPQLQIE--AAMTDRLVDLTEEG-FDAAV---RLGRVGDvrLIARPLAALRWVTVASPEYL 171
Cdd:PRK12683 100 THTQARYALPKVVRQFKEVFPKVHLAlrQGSPQEIAEMLLNGeADIGIateALDREPD--LVSFPYYSWHHVVVVPKGHP 177
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531 172 RSHGTPERLEQLAGHNCPTVRDLHTGKL-LEWQFQRDG-QPlslavrgDLVLDVADALVDAALV----GQGIVQVMGFMA 245
Cdd:PRK12683 178 LTGRENLTLEAIAEYPIITYDQGFTGRSrIDQAFAEAGlVP-------DIVLTALDADVIKTYVelgmGVGIVAAMAYDP 250

                 .
gi 489198531 246 E 246
Cdd:PRK12683 251 Q 251
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
1-118 1.12e-07

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 52.38  E-value: 1.12e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531   1 MDLNAVKLLARVAETRSFTQAAVSLGLTQSGLSRAIGRLEAELGVRLLHRTTRSVSLTPDGQLFYERCAPLLAELEEVeK 80
Cdd:PRK11233   1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQA-Q 79
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 489198531  81 LLVDRQC-APSGPLKI-TTPQALGRIVIMPVLRELTRRYP 118
Cdd:PRK11233  80 LAVHNVGqALSGQVSIgLAPGTAASSLTMPLLQAVRAEFP 119
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
30-64 2.25e-07

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 50.97  E-value: 2.25e-07
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 489198531  30 SGLSRAIGRLEAELGVRLLHRTTRSVSLTPDGQLF 64
Cdd:PRK11716   6 STLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEEL 40
PBP2_HvrB cd08483
The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an ...
92-237 5.12e-07

The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an activator of S-adenosyl-L-homocysteine hydrolase expression, contains the type 2 periplasmic binding fold; The transcriptional regulator HvrB of the LysR family is required for the light-dependent activation of both ahcY, which encoding the enzyme S-adenosyl-L-homocysteine hydrolase (AdoHcyase) that responsible for the reversible hydrolysis of AdoHcy to adenosine and homocysteine, and orf5, a gene of unknown. The topology of this C-terminal domain of HvrB 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: 176172 [Multi-domain]  Cd Length: 190  Bit Score: 49.27  E-value: 5.12e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531  92 PLKITTPQALGRIVIMPVLRELTRRYPQLQIEAAMTDRLVDLTEEGFDAAVRLGRVGDVRLIARPLAALRWVTVASPEYL 171
Cdd:cd08483    1 PLTVTLTPSFASNWLMPRLGSFWAKHPEIELSLLPSADLVDLRPDGIDVAIRYGNGDWPGLESEPLTAAPFVVVAAPGLL 80
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489198531 172 RSHgTPERLEQLAGHncPTVRDLHTGKLLEWQFQRDgqpLSLAVRGDLVLDVADALVDAALVGQGI 237
Cdd:cd08483   81 GDR-KVDSLADLAGL--PWLQERGTNEQRVWLASMG---VVPDLERGVTFLPGQLVLEAARAGLGL 140
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
1-129 7.17e-07

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 49.63  E-value: 7.17e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531   1 MDLNAVKLLARVAETRSFTQAAVSLGLTQSGLSRAIGRLEAELGVRLLHRTTRSVSLTPDGqlfyERCAPLlaeleeVEK 80
Cdd:PRK03601   1 MDTELLKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAG----ERLLPY------AET 70
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 489198531  81 LLVDRQCAPS--------GPLKITTPQALGRIVIMPVLRELTRRYPQLQIEAAMTDR 129
Cdd:PRK03601  71 LMNTWQAAKKevahtsqhNELSIGASASLWECMLTPWLGRLYQNQEALQFEARIAQR 127
PRK09986 PRK09986
LysR family transcriptional regulator;
1-78 8.66e-07

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 49.34  E-value: 8.66e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489198531   1 MDLNAVKLLARVAETRSFTQAAVSLGLTQSGLSRAIGRLEAELGVRLLHRTTRSVSLTPDGQLFYERCAPLLAELEEV 78
Cdd:PRK09986   7 IDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQS 84
PBP2_BlaA cd08487
The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which ...
106-244 8.57e-06

The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which involved in control of the beta-lactamase gene expression; contains the type 2 periplasmic binding fold; This CD represents the C-terminal substrate binding domain of LysR-type transcriptional regulator, BlaA, that involved in control of the expression of beta-lactamase genes, blaA and blaB. Beta-lactamases are responsible for bacterial resistance to beta-lactam antibiotics such as penicillins. The blaA gene is located just upstream of blaB in the opposite direction and regulates the expression of the blaB. BlaA also negatively auto-regulates the expression of its own gene, blaA. BlaA (a constitutive class A penicllinase) belongs to the LysR family of transcriptional regulators, whereas BlaB (an inducible class C cephalosporinase or AmpC) can be referred to as a penicillin binding protein but it does not act as a beta-lactamase. 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: 176176 [Multi-domain]  Cd Length: 189  Bit Score: 45.61  E-value: 8.57e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531 106 IMPVLRELTRRYPQLQIEAAMTDRLVDLTEEGFDAAVRLGR-----VGDVRLIARPLAALrwvtvASPEYLRSHGTPERL 180
Cdd:cd08487   15 LLPRLAEFRQLHPFIELRLRTNNNVVDLATEGLDFAIRFGEglwpaTHNERLLDAPLSVL-----CSPEIAKRLSHPADL 89
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489198531 181 EqlaghNCPTVRDLHTGKLLEWqFQRDGQPlSLAVRGDlVLDVADALVDAALVGQGIVQVMGFM 244
Cdd:cd08487   90 I-----NETLLRSYRTDEWLQW-FEAANMP-PIKIRGP-VFDSSRLMVEAAMQGAGVALAPAKM 145
cbl PRK12679
HTH-type transcriptional regulator Cbl;
1-123 9.02e-06

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 46.34  E-value: 9.02e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531   1 MDLNAVKLLaRVAETRSF--TQAAVSLGLTQSGLSRAIGRLEAELGVRL-LHRTTRSVSLTPDGQLFYERCAPLLAELEE 77
Cdd:PRK12679   1 MNFQQLKII-REAARQDYnlTEVANMLFTSQSGVSRHIRELEDELGIEIfIRRGKRLLGMTEPGKALLVIAERILNEASN 79
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 489198531  78 VEKLLVDRQCAPSGPLKITTPQALGRIVIMPVLRELTRRYPQLQIE 123
Cdd:PRK12679  80 VRRLADLFTNDTSGVLTIATTHTQARYSLPEVIKAFRELFPEVRLE 125
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
1-174 1.28e-05

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 45.92  E-value: 1.28e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531   1 MDLNAVKLLARVAETRSFTQAAVSLGLTQSGLSRAIGRLEAELGVRLLHRtTRSVSLTPDGQL---FYERCAPLLAElee 77
Cdd:PRK03635   2 LDYKQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRllrHARQVRLLEAE--- 77
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531  78 vekLLVDRQCAPSGPLKIttpqalgRIVI---------MPVLRELtrrypqlqieAAMTDRLVDLTEEGFDAAVRLGRVG 148
Cdd:PRK03635  78 ---LLGELPALDGTPLTL-------SIAVnadslatwfLPALAPV----------LARSGVLLDLVVEDQDHTAELLRRG 137
                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 489198531 149 DV--------RLIA----RPLAALRWVTVASPEYLRSH 174
Cdd:PRK03635 138 EVvgavttepQPVQgcrvDPLGAMRYLAVASPAFAARY 175
PBP2_LTTR_beta_lactamase cd08484
The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase ...
106-237 3.71e-05

The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase genes, contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators, BlaA and AmpR, that are involved in control of the expression of beta-lactamase genes. Beta-lactamases are responsible for bacterial resistance to beta-lactam antibiotics such as penicillins. BlaA (a constitutive class A penicillinase) belongs to the LysR family of transcriptional regulators, while BlaB (an inducible class C cephalosporinase or AmpC) can be referred to as a penicillin-binding protein, but it does not act as a beta-lactamase. AmpR regulates the expression of beta-lactamases in many enterobacterial strains and many other gram-negative bacilli. In contrast to BlaA, AmpR acts an activator only in the presence of the beta-lactam inducer. In the absence of the inducer, AmpR acts as a repressor. 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: 176173 [Multi-domain]  Cd Length: 189  Bit Score: 43.51  E-value: 3.71e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531 106 IMPVLRELTRRYPQLQIEAAMTDRLVDLTEEGFDAAVRLGRVG-----DVRLIARPLAALrwvtvASPEYLRSHGTPerl 180
Cdd:cd08484   15 LLPRLAEFRQLHPFIDLRLSTNNNRVDIAAEGLDFAIRFGEGAwpgtdATRLFEAPLSPL-----CTPELARRLSEP--- 86
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 489198531 181 EQLAGHncPTVRDLHTGKLLEWqFQRDGQPlSLAVRGdLVLDVADALVDAALVGQGI 237
Cdd:cd08484   87 ADLANE--TLLRSYRADEWPQW-FEAAGVP-PPPING-PVFDSSLLMVEAALQGAGV 138
PBP2_AmpR cd08488
The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in ...
106-265 5.07e-05

The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in control of the expression of beta-lactamase gene ampC, contains the type 2 periplasmic binding fold; AmpR acts as a transcriptional activator by binding to a DNA region immediately upstream of the ampC promoter. In the absence of a beta-lactam inducer, AmpR represses the synthesis of beta-lactamase, whereas expression is induced in the presence of a beta-lactam inducer. The AmpD, AmpG, and AmpR proteins are involved in the induction of AmpC-type beta-lactamase (class C) which produced by enterobacterial strains and many other gram-negative bacilli. The activation of ampC by AmpR requires ampG for induction or high-level expression of AmpC. It is probable that the AmpD and AmpG work together to modulate the ability of AmpR to activate ampC expression. 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: 176177 [Multi-domain]  Cd Length: 191  Bit Score: 43.29  E-value: 5.07e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531 106 IMPVLRELTRRYPQLQIEAAMTDRLVDLTEEGFDAAVRLGR-----VGDVRLIARPLAALrwvtvASPEYLRSHGTPerl 180
Cdd:cd08488   15 LLPRLADFQNRHPFIDLRLSTNNNRVDIAAEGLDYAIRFGSgawhgIDATRLFEAPLSPL-----CTPELARQLREP--- 86
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531 181 EQLAGHNcpTVRDLHTGKLLEWqFQRDGQPLSLAVRGDLVLDVADALVDAALVGQGIVQVMGFMAEEAirrRRLVRILQP 260
Cdd:cd08488   87 ADLARHT--LLRSYRADEWPQW-FEAAGVGHPCGLPNSIMFDSSLGMMEAALQGLGVALAPPSMFSRQ---LASGALVQP 160

                 ....*
gi 489198531 261 FEPPL 265
Cdd:cd08488  161 FATTL 165
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
1-173 1.35e-04

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 42.70  E-value: 1.35e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531   1 MDLNAVKLLARVAETRSFTQAAVSLGLTQSGLSRAIGRLEAELGVRLLHRTTRSVSLTPDGQLFYERCAPLLAELEEVEK 80
Cdd:PRK15421   2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQ 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531  81 LLVDRQcapsgplkittpQALGRIVI---------MPVLRELTRRYPQLQIE--AAMT-DRLVDLTEEGFDAAVR---LG 145
Cdd:PRK15421  82 ACNEPQ------------QTRLRIAIechsciqwlTPALENFHKNWPQVEMDfkSGVTfDPQPALQQGELDLVMTsdiLP 149
                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 489198531 146 RVG---------DVRLIARPLAALRWVTVASPEYLRS 173
Cdd:PRK15421 150 RSGlhyspmfdyEVRLVLAPDHPLAAKTRITPEDLAS 186
cysB PRK12681
HTH-type transcriptional regulator CysB;
19-144 1.59e-04

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 42.58  E-value: 1.59e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531  19 TQAAVSLGLTQSGLSRAIGRLEAELGVRLLHRTTRSVS-LTPDGQLFYERCAPLLAELEEVEKLLVDRQCAPSGPLKITT 97
Cdd:PRK12681  20 SATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTqVTPAGEEIIRIAREILSKVESIKSVAGEHTWPDKGSLYIAT 99
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489198531  98 PQALGRIVIMPVLRELTRRYPQL----------QIEAAMTDRLVDL---TE--EGFDAAVRL 144
Cdd:PRK12681 100 THTQARYALPPVIKGFIERYPRVslhmhqgsptQIAEAAAKGNADFaiaTEalHLYDDLIML 161
COG4742 COG4742
Predicted transcriptional regulator, contains HTH domain [Transcription];
6-81 5.32e-03

Predicted transcriptional regulator, contains HTH domain [Transcription];


Pssm-ID: 443776 [Multi-domain]  Cd Length: 267  Bit Score: 37.57  E-value: 5.32e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489198531   6 VKLLARVAET-RSFTQAAVSLGLTQSGLSRAIGRLEAElgvRLLHRTTRSVSLTPDGQLFYERCAPLLAELEEVEKL 81
Cdd:COG4742   19 KNILLLLAEGpKTRSELAESLDVSRSTILRQLKELEER---GLIERDDGEYELTTLGRLVVEEMEPLLDTLEVLEEN 92
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
98-237 5.58e-03

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


Pssm-ID: 176124  Cd Length: 198  Bit Score: 37.19  E-value: 5.58e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489198531  98 PQALGRIVIMPVLRELTRRYP--QLQIEAAMTDRLVDLTEEG-FDAAVRLGRVGDVRLIARPLAALRWVTVASPEYLRSH 174
Cdd:cd08433    7 PPSAASVLAVPLLRAVRRRYPgiRLRIVEGLSGHLLEWLLNGrLDLALLYGPPPIPGLSTEPLLEEDLFLVGPADAPLPR 86
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489198531 175 GTPERLEQLAGHNCPTVRDLHTG-KLLEWQFQRDGQPLslavrgDLVLDVADALVDAALVGQGI 237
Cdd:cd08433   87 GAPVPLAELARLPLILPSRGHGLrRLVDEAAARAGLTL------NVVVEIDSVATLKALVAAGL 144
 
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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