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Conserved domains on  [gi|501039528|ref|WP_012091474|]
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MULTISPECIES: LysR family transcriptional regulator [Brucella/Ochrobactrum group]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 11426483)

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

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
4-291 1.52e-37

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 133.84  E-value: 1.52e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528   4 FTWDDLQYFLAVARTGQLSTAARQLRTSHVTVLRRIDRLEQALATKLFERNPRGYLLTPIGERLVNSAEVMEREAMKFQT 83
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528  84 EATGNLAALSGVVRLSTLEGFGNFFLADRLPVLAQSYPSLFVEVVTI---QQIMSLSRREAELSITLHMPRTGPYHSEKL 160
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGnsdRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528 161 TPYRLFIYGHRDY-LERHPPIrtredmarhpfigyiddmvftpgldymreilpgqrctyqSSSIHAQLIATQIGYGLCVL 239
Cdd:COG0583  161 GEERLVLVASPDHpLARRAPL---------------------------------------VNSLEALLAAVAAGLGIALL 201

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 501039528 240 PYFIASRHPE---LVPVLPREMHLVREYWMSCHIDVVAAPRIRVLSDFMIRAVRE 291
Cdd:COG0583  202 PRFLAADELAagrLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
4-291 1.52e-37

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 133.84  E-value: 1.52e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528   4 FTWDDLQYFLAVARTGQLSTAARQLRTSHVTVLRRIDRLEQALATKLFERNPRGYLLTPIGERLVNSAEVMEREAMKFQT 83
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528  84 EATGNLAALSGVVRLSTLEGFGNFFLADRLPVLAQSYPSLFVEVVTI---QQIMSLSRREAELSITLHMPRTGPYHSEKL 160
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGnsdRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528 161 TPYRLFIYGHRDY-LERHPPIrtredmarhpfigyiddmvftpgldymreilpgqrctyqSSSIHAQLIATQIGYGLCVL 239
Cdd:COG0583  161 GEERLVLVASPDHpLARRAPL---------------------------------------VNSLEALLAAVAAGLGIALL 201

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 501039528 240 PYFIASRHPE---LVPVLPREMHLVREYWMSCHIDVVAAPRIRVLSDFMIRAVRE 291
Cdd:COG0583  202 PRFLAADELAagrLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
6-65 2.07e-17

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 74.73  E-value: 2.07e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528    6 WDDLQYFLAVARTGQLSTAARQLRTSHVTVLRRIDRLEQALATKLFERNPRGYLLTPIGE 65
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 94-285 2.05e-16

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: 75.94  E-value: 2.05e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528  94 GVVRLSTLEGFGNFFLADRLPVLAQSYPSLFVEVVTIQQIMSLSRREAELSITLHMPRTGPYHSEKLTPYRLFIYGHRDY 173
Cdd:cd08422    1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVASPAY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528 174 LERHPPIRTREDMARHPFIGYiddmVFTPGLDYMREILPGQRCT------YQSSSIHAQLIATQIGYGLCVLPYFIASRH 247
Cdd:cd08422   81 LARHGTPQTPEDLARHRCLGY----RLPGRPLRWRFRRGGGEVEvrvrgrLVVNDGEALRAAALAGLGIALLPDFLVAED 156

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 501039528 248 ---PELVPVLP------REMHLV---REYwmschidvvAAPRIRVLSDFM 285
Cdd:cd08422  157 lasGRLVRVLPdwrpppLPIYAVypsRRH---------LPAKVRAFIDFL 197
PRK09801 PRK09801
LysR family transcriptional regulator;
8-189 9.15e-16

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 76.23  E-value: 9.15e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528   8 DLQYFLAVARTGQLSTAARQLRTSHVTVLRRIDRLEQALATKLFERNPRGYLLTPIGERLVNSAEVMEREAMKFQTEATG 87
Cdd:PRK09801  10 DLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVTQ 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528  88 NLAALSGVVRLSTLEGFGNFFLADRLPVLAQSYPSLFVEVVTIQQIMSLSRREAELSITLHMPRTGPYHSEKLTPYRLFI 167
Cdd:PRK09801  90 IKTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHFELFDRQIDLVQDNIDLDIRINDEIPDYYIAHLLTKNKRIL 169

                        170       180
                 ....*....|....*....|..
gi 501039528 168 YGHRDYLERHPPIRTREDMARH 189
Cdd:PRK09801 170 CAAPEYLQKYPQPQSLQELSRH 191
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
4-291 1.52e-37

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 133.84  E-value: 1.52e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528   4 FTWDDLQYFLAVARTGQLSTAARQLRTSHVTVLRRIDRLEQALATKLFERNPRGYLLTPIGERLVNSAEVMEREAMKFQT 83
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528  84 EATGNLAALSGVVRLSTLEGFGNFFLADRLPVLAQSYPSLFVEVVTI---QQIMSLSRREAELSITLHMPRTGPYHSEKL 160
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGnsdRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528 161 TPYRLFIYGHRDY-LERHPPIrtredmarhpfigyiddmvftpgldymreilpgqrctyqSSSIHAQLIATQIGYGLCVL 239
Cdd:COG0583  161 GEERLVLVASPDHpLARRAPL---------------------------------------VNSLEALLAAVAAGLGIALL 201

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 501039528 240 PYFIASRHPE---LVPVLPREMHLVREYWMSCHIDVVAAPRIRVLSDFMIRAVRE 291
Cdd:COG0583  202 PRFLAADELAagrLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
6-65 2.07e-17

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 74.73  E-value: 2.07e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528    6 WDDLQYFLAVARTGQLSTAARQLRTSHVTVLRRIDRLEQALATKLFERNPRGYLLTPIGE 65
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 94-285 2.05e-16

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: 75.94  E-value: 2.05e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528  94 GVVRLSTLEGFGNFFLADRLPVLAQSYPSLFVEVVTIQQIMSLSRREAELSITLHMPRTGPYHSEKLTPYRLFIYGHRDY 173
Cdd:cd08422    1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVASPAY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528 174 LERHPPIRTREDMARHPFIGYiddmVFTPGLDYMREILPGQRCT------YQSSSIHAQLIATQIGYGLCVLPYFIASRH 247
Cdd:cd08422   81 LARHGTPQTPEDLARHRCLGY----RLPGRPLRWRFRRGGGEVEvrvrgrLVVNDGEALRAAALAGLGIALLPDFLVAED 156

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 501039528 248 ---PELVPVLP------REMHLV---REYwmschidvvAAPRIRVLSDFM 285
Cdd:cd08422  157 lasGRLVRVLPdwrpppLPIYAVypsRRH---------LPAKVRAFIDFL 197
PRK09801 PRK09801
LysR family transcriptional regulator;
8-189 9.15e-16

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 76.23  E-value: 9.15e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528   8 DLQYFLAVARTGQLSTAARQLRTSHVTVLRRIDRLEQALATKLFERNPRGYLLTPIGERLVNSAEVMEREAMKFQTEATG 87
Cdd:PRK09801  10 DLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVTQ 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528  88 NLAALSGVVRLSTLEGFGNFFLADRLPVLAQSYPSLFVEVVTIQQIMSLSRREAELSITLHMPRTGPYHSEKLTPYRLFI 167
Cdd:PRK09801  90 IKTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHFELFDRQIDLVQDNIDLDIRINDEIPDYYIAHLLTKNKRIL 169

                        170       180
                 ....*....|....*....|..
gi 501039528 168 YGHRDYLERHPPIRTREDMARH 189
Cdd:PRK09801 170 CAAPEYLQKYPQPQSLQELSRH 191
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 93-290 7.33e-14

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: 68.85  E-value: 7.33e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528   93 SGVVRLSTLEGFGNFFLADRLPVLAQSYPSL---FVEVVTIQQIMSLSRREAELSITLHMPRTGPYHSEKLTPYRLFIYG 169
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVeleLTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528  170 HRDY-LERHPPIrTREDMARHPFIGYIDDMVFTPGLD-YMREILPGQRCTYQSSSIHAQLIATQIGYGLCVLPYFIASR- 246
Cdd:pfam03466  81 PPDHpLARGEPV-SLEDLADEPLILLPPGSGLRDLLDrALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARe 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 501039528  247 --HPELVPVLPREMHLVREYWMSCHIDVVAAPRIRVLSDFMIRAVR 290
Cdd:pfam03466 160 laDGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREALA 205
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 9-294 1.32e-12

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 66.79  E-value: 1.32e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528   9 LQYFLAVARTGQLSTAARQLRTSHVTVLRRIDRLEQALATKLFERNPRGYLLTPIGERLVNSAevmeREAMKFQTEATGN 88
Cdd:PRK11139  11 LRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDI----REIFDQLAEATRK 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528  89 LAALS--GVVRLSTLEGFGNFFLADRLPVLAQSYPSLFVEVVTIQQIMSLSRREAELSItlhmpRTGP-----YHSEKLT 161
Cdd:PRK11139  87 LRARSakGALTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDRLEDFLRDDVDVAI-----RYGRgnwpgLRVEKLL 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528 162 PYRLFIYGHRDYLERHPPIRTREDMARHPFIgYIDD------MVFTPGLDymrEILPGQRCTYQSSS------IHAQLIA 229
Cdd:PRK11139 162 DEYLLPVCSPALLNGGKPLKTPEDLARHTLL-HDDSredwraWFRAAGLD---DLNVQQGPIFSHSSmalqaaIHGQGVA 237

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 501039528 230 tqIGYGLCVLPYFIASRhpeLVPVLPREMHLVREYWMSCHIDVVAAPRIRVLSDFMIRAVRESSA 294
Cdd:PRK11139 238 --LGNRVLAQPEIEAGR---LVCPFDTVLPSPNAFYLVCPDSQAELPKVAAFRQWLLAEAAQEQE 297
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 96-285 4.40e-11

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: 61.08  E-value: 4.40e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528  96 VRLSTLEGFGNFFLADRLPVLAQSYPSL---FVEVVTIQQIMSLSRREAELSITLHMPRTGPYHSEKLTPYRLFIYGHRD 172
Cdd:cd05466    2 LRIGASPSIAAYLLPPLLAAFRQRYPGVelsLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPPD 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528 173 YLERHPPIRTREDMARHPFIGYIDDMVFTPGLDYM-REILPGQRCTYQSSSIHAQLIATQIGYGLCVLPYFIA--SRHPE 249
Cdd:cd05466   82 HPLAKRKSVTLADLADEPLILFERGSGLRRLLDRAfAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVeeLADGG 161

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 501039528 250 LVPVLPREMHLVREYWMSCHIDVVAAPRIRVLSDFM 285
Cdd:cd05466  162 LVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
9-177 5.49e-10

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 59.25  E-value: 5.49e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528   9 LQYFLAVARTGQLSTAARQLRTSHVTVLRRIDRLEQALATKLFERNPRGYLLTPIGER----LVNSAEVMEREAMKFQTe 84
Cdd:PRK10086  19 LHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRvfwaLKSSLDTLNQEILDIKN- 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528  85 atgnlAALSGVVRLSTLEGFGNFFLADRLPVLAQSYPSLFVEVVTIQQIMSLSRREAELSITLHMPRTGPYHSEKLTPYR 164
Cdd:PRK10086  98 -----QELSGTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTILTGNENVNFQRAGIDLAIYFDDAPSAQLTHHFLMDEE 172

                        170
                 ....*....|...
gi 501039528 165 LFIYGHRDYLERH 177
Cdd:PRK10086 173 ILPVCSPEYAERH 185
PBP2_CrgA_like_8 cd08477
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-284 1.04e-08

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: 54.16  E-value: 1.04e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528  94 GVVRLSTLEGFGNFFLADRLPVLAQSYPSLFVEVVTIQQIMSLSRREAELSItlhmpRTGPYHSE-----KLTPYRLFIY 168
Cdd:cd08477    1 GKLRISAPVTFGSHVLTPALAEYLARYPDVRVDLVLSDRLVDLVEEGFDAAF-----RIGELADSslvarPLAPYRMVLC 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528 169 GHRDYLERHPPIRTREDMARHPFIGYiddmVFTPGLDYMREILPG------QRCTYQSSSIHAQLIATQIGYGLCVLPYF 242
Cdd:cd08477   76 ASPDYLARHGTPTTPEDLARHECLGF----SYWRARNRWRLEGPGgevkvpVSGRLTVNSGQALRVAALAGLGIVLQPEA 151

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|.
gi 501039528 243 IASRHPE---LVPVLP------REMHLVreYwmscHIDVVAAPRIRVLSDF 284
Cdd:cd08477  152 LLAEDLAsgrLVELLPdylpppRPMHLL--Y----PPDRRPTPKLRSFIDF 196
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
9-71 1.37e-07

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 52.12  E-value: 1.37e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 501039528   9 LQYFLAVARTGQLSTAARQLRTSHVTVLRRIDRLEQALATKLFERNPRGYLLTPIGERLVNSA 71
Cdd:PRK10094   7 LRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQA 69
PRK09791 PRK09791
LysR family transcriptional regulator;
9-158 2.76e-07

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 50.92  E-value: 2.76e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528   9 LQYFLAVARTGQLSTAARQLRTSHVTVLRRIDRLEQALATKLFERNPRGYLLTPIGERLVNSAEVMEREAMKFQTEATGN 88
Cdd:PRK09791  10 IRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQEDIRQR 89

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 501039528  89 LAALSGVVRLSTLEGFGNFFLADRLPVLAQSYPSLFVEVVTIQQI-MSLSRREAELSITLHMPRTGPYHSE 158
Cdd:PRK09791  90 QGQLAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRIMEGQLVsMINELRQGELDFTINTYYQGPYDHE 160
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
9-292 4.47e-07

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 50.35  E-value: 4.47e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528   9 LQYFLAVARTGQLSTAARQLrtsHVT---VLRRIDRLEQALATKLF--ERNPRGyllTPIGERL---VNSAEVMEREAMK 80
Cdd:PRK13348   7 LEALAAVVETGSFERAARRL---HVTpsaVSQRIKALEESLGQPLLvrGRPCRP---TPAGQRLlrhLRQVALLEADLLS 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528  81 FQTEATGNLAALSGVVRLSTLegfGNFFLADRLPVLAQsyPSLFVEVVTIQQIMSLSR-REAELS---ITLHMPRTG--- 153
Cdd:PRK13348  81 TLPAERGSPPTLAIAVNADSL---ATWFLPALAAVLAG--ERILLELIVDDQDHTFALlERGEVVgcvSTQPKPMRGcla 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528 154 ------------------PYHSEKLTPYRL-----FIYGHRD-----YLERHPPIRTREdmarhpfigyiddmvftpgld 205
Cdd:PRK13348 156 eplgtmryrcvaspafaaRYFAQGLTRHSAlkapaVAFNRKDtlqdsFLEQLFGLPVGA--------------------- 214

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528 206 YMREILPgqrctyqssSIHAQLIATQIGYGLCVLPYFIASRHPE---LVPVLPREMHLVREYWmscHIDVVAAPRIRVLS 282
Cdd:PRK13348 215 YPRHYVP---------STHAHLAAIRHGLGYGMVPELLIGPLLAagrLVDLAPGHPVDVALYW---HHWEVESPTMEALS 282

                        330
                 ....*....|
gi 501039528 283 DFMIRAVRES 292
Cdd:PRK13348 283 QRVVEAARRL 292
PRK10341 PRK10341
transcriptional regulator TdcA;
9-153 5.70e-07

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 50.25  E-value: 5.70e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528   9 LQYFLAVARTGQLSTAARQLRTSHVTVLRRIDRLEQALATKLFERNPRGYLLTPIGERLVNSAEVMEREAMKFQTEAtgN 88
Cdd:PRK10341  12 LVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEI--N 89

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 501039528  89 LAALSGVVRLS----TLEGFGnfFLADRLPVLAQSYPSlfvevvtiqqiMSLSRREAELSITLHMPRTG 153
Cdd:PRK10341  90 GMSSEAVVDVSfgfpSLIGFT--FMSDMINKFKEVFPK-----------AQVSMYEAQLSSFLPAIRDG 145
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 14-99 9.44e-07

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 49.56  E-value: 9.44e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528  14 AVARTGQLSTAARQLRTSHVTVLRRIDRLEQALATKLFERNPRGYLLTPIGERLVNSAEVMER--EAMKFQTEATGN--- 88
Cdd:PRK11074  12 AVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKkmQETRRQCQQVANgwr 91

                         90
                 ....*....|....
gi 501039528  89 --LA-ALSGVVRLS 99
Cdd:PRK11074  92 gqLSiAVDNIVRPD 105
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 7-156 1.10e-06

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 49.26  E-value: 1.10e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528   7 DDLQYFLAVARTGQLSTAARQLRTSHVTVLRRIDRLEQALATKLFERNPRGYLLTPIGERLVNSAevmeREAMKFQTEAT 86
Cdd:PRK15092  14 DLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYA----RKILRFNDEAC 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528  87 GNL--AALSGVVRLSTLEGFGNFFLADRLPVLAQSYPSLFVEVVT--IQQIMS-LSRREAELSITLHMP--------RTG 153
Cdd:PRK15092  90 SSLmySNLQGVLTIGASDDTADTILPFLLNRVSSVYPKLALDVRVkrNAFMMEmLESQEVDLAVTTHRPssfpalnlRTS 169


                 ...
gi 501039528 154 PYH 156
Cdd:PRK15092 170 PTL 172
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 8-123 3.41e-06

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 47.72  E-value: 3.41e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528   8 DLQYFLAVARTGQLSTAARQLRTSHVTVLRRIDRLEQALATKLFERNPRGYLLTPIGERLVNSAEVMEREAMKFQTEATG 87
Cdd:PRK11151   5 DLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVLKEMASQ 84

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 501039528  88 NLAALSGVVRLSTLEGFGNFFLADRLPVLAQSYPSL 123
Cdd:PRK11151  85 QGETMSGPLHIGLIPTVGPYLLPHIIPMLHQTFPKL 120
PBP2_CrgA_like_1 cd08470
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-254 3.84e-06

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: 46.53  E-value: 3.84e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528  94 GVVRLSTLEGFGNFFLADRLPVLAQSYPSLFVEVVTIQQIMSLSRREAELSITLHMPRTGPYHSEKLTPYRLFIYGHRDY 173
Cdd:cd08470    1 GLLRITCPVAYGERFIAPLVNDFMQRYPKLEVDIELTNRVVDLVSEGFDLAIRLGRLTDSSLMARRLASRRHYVCASPAY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528 174 LERHPPIRTREDMARHP-FIGYIDDMVFTPGlDYMREILPGQRctYQSSSIHAQLIATQIGYGLCVLPYFIASRHPE--- 249
Cdd:cd08470   81 LERHGTPHSLADLDRHNcLLGTSDHWRFQEN-GRERSVRVQGR--WRCNSGVALLDAALKGMGLAQLPDYYVDEHLAagr 157


                 ....*
gi 501039528 250 LVPVL 254
Cdd:cd08470  158 LVPVL 162
rbcR CHL00180
LysR transcriptional regulator; Provisional
 4-72 6.60e-06

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 46.94  E-value: 6.60e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 501039528   4 FTWDDLQYFLAVARTGQLSTAARQLRTSHVTVLRRIDRLEQALATKLFERNPRGYLLTPIGERLVNSAE 72
Cdd:CHL00180   5 FTLDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGN 73
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 1-53 1.16e-05

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 46.14  E-value: 1.16e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 501039528   1 MRQFTWDDLQYFLAVARTGQLSTAARQLRTSHVTVLRRIDRLEQALATKLFER 53
Cdd:PRK11013   1 MAAVSLRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFER 53
PBP2_CrgA_like_3 cd08472
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-255 1.25e-05

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 45.20  E-value: 1.25e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528  94 GVVRLSTLEGFGNFFLADRLPVLAQSYPSlfvevvtIQQIMSLSRREAEL-------SITLHMPRTGPYHSEKLTPYRLF 166
Cdd:cd08472    1 GRLRVDVPGSLARLLLIPALPDFLARYPD-------IELDLGVSDRPVDLiregvdcVIRVGELADSSLVARRLGELRMV 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528 167 IYGHRDYLERHPPIRTREDMARHPFIGYiddmvFTPG------LDYMREilpGQRCTYQSSSI------HAQLIATQIGY 234
Cdd:cd08472   74 TCASPAYLARHGTPRHPEDLERHRAVGY-----FSARtgrvlpWEFQRD---GEEREVKLPSRvsvndsEAYLAAALAGL 145

                        170       180
                 ....*....|....*....|....
gi 501039528 235 GLCVLPYFIASRH---PELVPVLP 255
Cdd:cd08472  146 GIIQVPRFMVRPHlasGRLVEVLP 169
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
9-89 3.68e-05

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 44.58  E-value: 3.68e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528   9 LQYFLAVARTG-QLSTAARQLRTSHVTVLRRIDRLEQALATKLFERN-PRGYLLTPIGERLVNSAEVMEREA-------M 79
Cdd:PRK12684   6 LRFVREAVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHgKRLRGLTEPGRIILASVERILQEVenlkrvgK 85

                         90
                 ....*....|
gi 501039528  80 KFQTEATGNL 89
Cdd:PRK12684  86 EFAAQDQGNL 95
cbl PRK12679
HTH-type transcriptional regulator Cbl;
21-194 3.75e-05

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 44.42  E-value: 3.75e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528  21 LSTAARQLRTSHVTVLRRIDRLEQALATKLFER---------NPRGYLLTpIGERLVNSAEVMEREAMKFQTEAtgnlaa 91
Cdd:PRK12679  19 LTEVANMLFTSQSGVSRHIRELEDELGIEIFIRrgkrllgmtEPGKALLV-IAERILNEASNVRRLADLFTNDT------ 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528  92 lSGVVRLSTLEGFGNFFLADRLPVLAQSYPSLFVEVV--TIQQIMS-LSRREAELSITLHMPRTGPyhseKLTPYRLFIY 168
Cdd:PRK12679  92 -SGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIqgTPQEIATlLQNGEADIGIASERLSNDP----QLVAFPWFRW 166

                        170       180       190
                 ....*....|....*....|....*....|..
gi 501039528 169 GH-----RDY-LERHPPIrTREDMARHPFIGY 194
Cdd:PRK12679 167 HHsllvpHDHpLTQITPL-TLESIAKWPLITY 197
PBP2_CrgA_like_7 cd08476
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 157-285 3.92e-05

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 43.77  E-value: 3.92e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528 157 SEKLTPYRLFIYGHRDYLERHPPIRTREDMARHPFIGYiddmVF-TPG------LDYMREILPGQ-RCTYQSSSIHAQLI 228
Cdd:cd08476   62 SRRLGSFRMVLVASPDYLARHGTPETPADLAEHACLRY----RFpTTGklepwpLRGDGGDPELRlPTALVCNNIEALIE 137

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 501039528 229 ATQIGYGLCVLPYFIASRHPE---LVPVLPREMHLVREYWM----SCHIdvvaAPRIRVLSDFM 285
Cdd:cd08476  138 FALQGLGIACLPDFSVREALAdgrLVTVLDDYVEERGQFRLlwpsSRHL----SPKLRVFVDFM 197
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
9-72 4.86e-05

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 44.24  E-value: 4.86e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 501039528   9 LQYFLAVARTGQLSTAARQLRTSHVTVLRRIDRLEQALATKLFERNPRGYLLTPIGERLVNSAE 72
Cdd:PRK03601   6 LKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYAE 69
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 7-99 5.35e-05

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 44.21  E-value: 5.35e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528   7 DDLQYFLAVARTGQLSTAARQLRTSHVTVLRRIDRLEQALATKLFERNPRGYLLTPIGERLVNSAEVMEREAMKFQTEAT 86
Cdd:PRK14997   5 NDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDAIA 84

                         90
                 ....*....|...
gi 501039528  87 GNLAALSGVVRLS 99
Cdd:PRK14997  85 ALQVEPRGIVKLT 97
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 9-253 7.37e-05

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 43.41  E-value: 7.37e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528   9 LQYFLAVARTGQLSTAARQLRTSHVTVLRRIDRLEQALATKLFERNPRGYLLTPIGERLVNSAE--VMEREAMKfqtEAT 86
Cdd:PRK11242   6 IRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARraLQDLEAGR---RAI 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528  87 GNLAALS-GVVRLSTLEGFGNFFLADRLPVLAQSYPSLfveVVTIQQiMSLSRREAELS-------ITLHMPRTGPYHSE 158
Cdd:PRK11242  83 HDVADLSrGSLRLAMTPTFTAYLIGPLIDAFHARYPGI---TLTIRE-MSQERIEALLAddeldvgIAFAPVHSPEIEAQ 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528 159 KLTPYRL-FIYGHRDYLERHPPIRTREDMARHPFI---------GYIDdmvftpglDYMRE--ILPgqRCTYQSSSIHAQ 226
Cdd:PRK11242 159 PLFTETLaLVVGRHHPLAARRKALTLDELADEPLVllsaefatrEQID--------RYFRRhgVTP--RVAIEANSISAV 228

                        250       260
                 ....*....|....*....|....*..
gi 501039528 227 LIATQIGYGLCVLPYFIASRHPELVPV 253
Cdd:PRK11242 229 LEIVRRGRLATLLPAAIAREHDGLCAI 255
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 9-148 1.02e-04

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 43.22  E-value: 1.02e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528   9 LQYFLAVARTGQLSTAARQLRTSHVTVLRRIDRLEQALATKLFERNPRGYLLTPIGE------RLV----NSAEVMEREA 78
Cdd:PRK09906   6 LRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEvflqdaRAIleqaEKAKLRARKI 85

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 501039528  79 MKFQTEATgnlaalSGVVRLSTLEgfgnfFLADRLPVLAQSYPSLFVEVVTI---QQIMSLSRREAELSITLH 148
Cdd:PRK09906  86 VQEDRQLT------IGFVPSAEVN-----LLPKVLPMFRLRHPDTLIELVSLittQQEEKLRRGELDVGFMRH 147
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 9-78 2.17e-04

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 42.29  E-value: 2.17e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 501039528   9 LQYFLAVARTG-QLSTAARQLRTSHVTVLRRIDRLEQALATKLFERNPRGYL-LTPIGERLVNSAEVMEREA 78
Cdd:PRK12682   6 LRFVREAVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKgLTEPGKAVLDVIERILREV 77
PBP2_CrgA_like_9 cd08479
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-192 2.23e-04

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: 41.43  E-value: 2.23e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528  94 GVVRLSTLEGFGNFFLADRLPVLAQSYPSLFVEVVTIQQIMSLSRREAELSITLHMPRTGPYHSEKLTPYRLFIYGHRDY 173
Cdd:cd08479    1 GLLRVNASFGFGRRHIAPALSDFAKRYPELEVQLELTDRPVDLVEEGFDLDIRVGDLPDSSLIARKLAPNRRILCASPAY 80

                         90
                 ....*....|....*....
gi 501039528 174 LERHPPIRTREDMARHPFI 192
Cdd:cd08479   81 LERHGAPASPEDLARHDCL 99
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 95-283 3.78e-04

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


Pssm-ID: 176123 [Multi-domain]  Cd Length: 194  Bit Score: 40.64  E-value: 3.78e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528  95 VVRLSTLEGFGNFFLADRLPVLAQSYPSLFVEVVTIQQIMSLSRREAELSItlhmpR--TGPY---HSEKLTPYRLFIYG 169
Cdd:cd08432    1 VLTVSVTPSFAARWLIPRLARFQARHPDIDLRLSTSDRLVDFAREGIDLAI-----RygDGDWpglEAERLMDEELVPVC 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528 170 HRDYLERHPPiRTREDMARHPFI---GYIDDMVFTPGLDYMREILPGQRCTYQSSS--IHAqliATQiGYGLCVLPYFIA 244
Cdd:cd08432   76 SPALLAGLPL-LSPADLARHTLLhdaTRPEAWQWWLWAAGVADVDARRGPRFDDSSlaLQA---AVA-GLGVALAPRALV 150

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 501039528 245 SRHPE---LVPVLPREMHLVREYWMSCHIDVVAAPRIRVLSD 283
Cdd:cd08432  151 ADDLAagrLVRPFDLPLPSGGAYYLVYPPGRAESPAVAAFRD 192
PBP2_CrgA_like_10 cd08480
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-194 3.93e-04

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: 40.78  E-value: 3.93e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528  94 GVVRLSTLEGFGNFFLADRLPVLAQSYPSLFVEVVTIQQIMSLSRREAELSItlhmpRTGPYHSEKLTPYRL-----FIY 168
Cdd:cd08480    1 GRLRVNASVPFGTHFLLPLLPAFLARYPEILVDLSLTDEVVDLLAERTDVAI-----RVGPLPDSSLVARKLgesrrVIV 75

                         90       100
                 ....*....|....*....|....*.
gi 501039528 169 GHRDYLERHPPIRTREDMARHPFIGY 194
Cdd:cd08480   76 ASPSYLARHGTPLTPQDLARHNCLGF 101
PRK09986 PRK09986
LysR family transcriptional regulator;
9-72 4.85e-04

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 41.25  E-value: 4.85e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 501039528   9 LQYFLAVARTGQLSTAARQLRTSHVTVLRRIDRLEQALATKLFERNPRGYLLTPIGE-------RLVNSAE 72
Cdd:PRK09986  12 LRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKilmeesrRLLDNAE 82
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
32-98 4.90e-04

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 40.96  E-value: 4.90e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528  32 HV---TVLRRIDRLEQALATKLFERNPRGYLLTPIGERLVNSAEVMEREAMKFQTEATGNLAALSGVVRL 98
Cdd:PRK11716   2 HVspsTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSL 71
PRK12680 PRK12680
LysR family transcriptional regulator;
5-238 1.09e-03

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 39.99  E-value: 1.09e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528   5 TWDDLQYFLAVARTG-QLSTAARQLRTSHVTVLRRIDRLEQALATKLFERNPRGY-LLTPIGERLVNSAEVMEREAMKFQ 82
Cdd:PRK12680   2 TLTQLRYLVAIADAElNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLeSVTPAGVEVIERARAVLSEANNIR 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528  83 TEATGNLAALSGVVRLSTLEGFGNFFLADRLPVLAQSYPSLFVEvvtIQQIMS------LSRREAELSItLHMPRTGPYH 156
Cdd:PRK12680  82 TYAANQRRESQGQLTLTTTHTQARFVLPPAVAQIKQAYPQVSVH---LQQAAEsaaldlLGQGDADIAI-VSTAGGEPSA 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528 157 SEKLTPYR-----LFIYGHR-DYLERHPPIRTredMARHPFIGYidDMVFTPGLDYMREILP-GQRCTYQSSSIHAQLIA 229
Cdd:PRK12680 158 GIAVPLYRwrrlvVVPRGHAlDTPRRAPDMAA---LAEHPLISY--ESSTRPGSSLQRAFAQlGLEPSIALTALDADLIK 232


                 ....*....
gi 501039528 230 TQIGYGLCV 238
Cdd:PRK12680 233 TYVRAGLGV 241
PBP2_CrgA cd08478
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains ...
 93-285 1.20e-03

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: 39.24  E-value: 1.20e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528  93 SGVVRLSTLEGFGNFFLADRLPVLAQSYPSLFVEVVTIQQIMSLSRREAELSItlhmpRTGP-----YHSEKLTPYRLFI 167
Cdd:cd08478    2 SGLLRVDAATPFVLHLLAPLIAKFRERYPDIELELVSNEGIIDLIERKTDVAI-----RIGEltdstLHARPLGKSRLRI 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528 168 YGHRDYLERHPPIRTREDMARHPFIG-----YIDDMVFTPGLDYMREILPgqRCTYQSSSIHAQLIATqiGYGLCVLPYF 242
Cdd:cd08478   77 LASPDYLARHGTPQSIEDLAQHQLLGftepaSLNTWPIKDADGNLLKIQP--TITASSGETLRQLALS--GCGIACLSDF 152

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 501039528 243 IASR---HPELVPVLPREM-HLVREYWMSCHIDVVAAPRIRVLSDFM 285
Cdd:cd08478  153 MTDKdiaEGRLIPLFAEQTsDVRQPINAVYYRNTALSLRIRCFIDFL 199
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
12-129 3.29e-03

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 38.59  E-value: 3.29e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528  12 FLAVARTGQLSTAARQLRTSHVTVLRRIDRLEQALATKLFERNPRGYLLTPIGERLVNSAEVMEREAMKF--QTEATGNl 89
Cdd:PRK10632  10 FAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVheQLYAFNN- 88

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 501039528  90 aALSGVVRLSTLEGFGNFFLADRLPVLAQSYPSLFVEVVT 129
Cdd:PRK10632  89 -TPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVT 127
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 14-201 4.50e-03

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 38.10  E-value: 4.50e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528  14 AVARTGQLSTAARQLRTSHVTVLRRIDRLEQALATKLFERnpRGYLLT----------PIGERLVNSAEVMEREAMKFQT 83
Cdd:PRK12683  12 AVRQNFNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIR--RGKRLTgltepgkellQIVERMLLDAENLRRLAEQFAD 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528  84 EATGNLA----------ALSGVVRlstleGFGNFFLADRLpVLAQSYPslfvevvtiQQIMSLSRR-EAELSITlhmprt 152
Cdd:PRK12683  90 RDSGHLTvatthtqaryALPKVVR-----QFKEVFPKVHL-ALRQGSP---------QEIAEMLLNgEADIGIA------ 148

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 501039528 153 gpyhSEKLT--------PYRLFIY------GHRdyLERHPPIrTREDMARHPFIGYidDMVFT 201
Cdd:PRK12683 149 ----TEALDrepdlvsfPYYSWHHvvvvpkGHP--LTGRENL-TLEAIAEYPIITY--DQGFT 202
PBP2_CrgA_like_6 cd08475
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 172-261 5.27e-03

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: 37.15  E-value: 5.27e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039528 172 DYLERHPPIRTREDMARHPFIGYIDDMVFTPGL-----DYMREILPGQRctYQSSSIHAQLIATQIGYGLCVLPYFIASR 246
Cdd:cd08475   80 AYLARHGTPRTLEDLAEHQCIAYGRGGQPLPWRladeqGRLVRFRPAPR--LQFDDGEAIADAALAGLGIAQLPTWLVAD 157

                         90       100
                 ....*....|....*....|....
gi 501039528 247 H---PELVPVLPR------EMHLV 261
Cdd:cd08475  158 HlqrGELVEVLPElapeglPIHAV 181
nhaR PRK11062
transcriptional activator NhaR; Provisional
 1-74 7.87e-03

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 37.30  E-value: 7.87e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 501039528   1 MRQFTWDDLQYFLAVARTGQLSTAARQLRTSHVTVLRRIDRLEQALATKLFERNPRGYLLTPIGERLVNSAEVM 74
Cdd:PRK11062   1 MSHINYNHLYYFWMVCKEGSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGELVFRYADKM 74
 
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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