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Conserved domains on  [gi|1327307407|gb|PMO68807|]
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LysR family transcriptional regulator [Vibrio splendidus]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 10444056)

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

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 91-294 1.08e-79

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: 240.03  E-value: 1.08e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407  91 GHIKMSVPTISGDLILADAVAEFCNMHPGLTVDMSLNNRFVDLVDDGLDLVIRTGYLEDSSLIARHILDSQWVVCASPSY 170
Cdd:cd08422     1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVASPAY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407 171 IAKNGKPMQPKDLVEHNCLQYAYQtTGASEWQFLHskdgftDNDKYIVRVSGSFSTDNATALRKAALGGHGVAYVPRCLV 250
Cdd:cd08422    81 LARHGTPQTPEDLARHRCLGYRLP-GRPLRWRFRR------GGGEVEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLV 153

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1327307407 251 YHDIRNGQLVDIFPDLVGKKLGIYAVYPFTRQPPNKIKLLIEHI 294
Cdd:cd08422   154 AEDLASGRLVRVLPDWRPPPLPIYAVYPSRRHLPAKVRAFIDFL 197
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
4-62 2.41e-21

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


:

Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 85.13  E-value: 2.41e-21
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1327307407   4 DDLILFSQVVELGSFSKVAEQNNLTNSVVSKRIARLEEEIGVQLLYRTTRKLTLTEAGK 62
Cdd:pfam00126   2 RQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
 
Name Accession Description Interval E-value
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 91-294 1.08e-79

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: 240.03  E-value: 1.08e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407  91 GHIKMSVPTISGDLILADAVAEFCNMHPGLTVDMSLNNRFVDLVDDGLDLVIRTGYLEDSSLIARHILDSQWVVCASPSY 170
Cdd:cd08422     1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVASPAY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407 171 IAKNGKPMQPKDLVEHNCLQYAYQtTGASEWQFLHskdgftDNDKYIVRVSGSFSTDNATALRKAALGGHGVAYVPRCLV 250
Cdd:cd08422    81 LARHGTPQTPEDLARHRCLGYRLP-GRPLRWRFRR------GGGEVEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLV 153

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1327307407 251 YHDIRNGQLVDIFPDLVGKKLGIYAVYPFTRQPPNKIKLLIEHI 294
Cdd:cd08422   154 AEDLASGRLVRVLPDWRPPPLPIYAVYPSRRHLPAKVRAFIDFL 197
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-297 3.02e-61

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 195.09  E-value: 3.02e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407   1 MRADDLILFSQVVELGSFSKVAEQNNLTNSVVSKRIARLEEEIGVQLLYRTTRKLTLTEAGKAMLHGAKNVKQAAQEAMD 80
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407  81 AVSGFGENVSGHIKMSVPTISGDLILADAVAEFCNMHPGLTVDMSLNN--RFVD-LVDDGLDLVIRTGYLEDSSLIARHI 157
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNsdRLVDaLLEGELDLAIRLGPPPDPGLVARPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407 158 LDSQWVVCASPSYIAKNGKPMqpkdlvehnclqyayqttgasewqflhskdgftdndkyivrvsgsfsTDNATALRKAAL 237
Cdd:COG0583   161 GEERLVLVASPDHPLARRAPL-----------------------------------------------VNSLEALLAAVA 193

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407 238 GGHGVAYVPRCLVYHDIRNGQLVDIFPDLVGKKLGIYAVYPFTRQPPNKIKLLIEHIRTR 297
Cdd:COG0583   194 AGLGIALLPRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREA 253
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
8-305 9.27e-50

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 167.24  E-value: 9.27e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407   8 LFSQVVELGSFSKVAEQNNLTNSVVSKRIARLEEEIGVQLLYRTTRKLTLTEAGKAMLHGAKNVKQAAQEAMDAVSGFGE 87
Cdd:PRK10632    9 VFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQLYAFNN 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407  88 NVSGHIKMSVPTISGDLILADAVAEFCNMHPGLTVDMSLNNRFVDLVDDGLDLVIRTGYLEDSSLIARHILDSQWVVCAS 167
Cdd:PRK10632   89 TPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTGIPAPDLIADGLDVVIRVGALQDSSLFSRRLGAMPMVVCAA 168

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407 168 PSYIAKNGKPMQPKDLVEHNCLQYAYQTtgASEWQfLHSKDGFTdndkyiVRVS--GSFSTDNATALRKAALGGHGVAYV 245
Cdd:PRK10632  169 KSYLAQYGTPEKPADLSSHSWLEYSVRP--DNEFE-LIAPEGIS------TRLIpqGRFVTNDPQTLVRWLTAGAGIAYV 239

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407 246 PRCLVYHDIRNGQLVDIFPDLVGKKLGIYAVYPFTRQPPNKIKLLIEhirtrYLTisHYF 305
Cdd:PRK10632  240 PLMWVIDEINRGELEILFPRYQSDPRPVYALYTEKDKLPLKVQVCIN-----YLT--DYF 292
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 90-297 3.92e-38

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: 133.95  E-value: 3.92e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407  90 SGHIKMSVPTISGDLILADAVAEFCNMHPGLTVDMSLNN--RFVDLVDDG-LDLVIRTGYLEDSSLIARHILDSQWVVCA 166
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNseELLDLLLEGeLDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407 167 SPSYIAKNGKPMQPKDLVEHNCLQYAYQTTGASEWQFLHSKDGFtdndkyivRVSGSFSTDNATALRKAALGGHGVAYVP 246
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGL--------RPRVVLEVNSLEALLQLVAAGLGIALLP 152

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1327307407 247 RCLVYHDIRNGQLVDI-FPDLVGkKLGIYAVYPFTRQPPNKIKLLIEHIRTR 297
Cdd:pfam03466 153 RSAVARELADGRLVALpLPEPPL-PRELYLVWRKGRPLSPAVRAFIEFLREA 203
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
4-62 2.41e-21

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 85.13  E-value: 2.41e-21
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1327307407   4 DDLILFSQVVELGSFSKVAEQNNLTNSVVSKRIARLEEEIGVQLLYRTTRKLTLTEAGK 62
Cdd:pfam00126   2 RQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
9-69 5.55e-13

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 67.91  E-value: 5.55e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1327307407   9 FSQVVELGSFSKVAEQNNLTNSVVSKRIARLEEEIGVQLLYRTTRKLTLTEAGKAMLHGAK 69
Cdd:PRK10094   10 FIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQAR 70
MarR COG1846
DNA-binding transcriptional regulator, MarR family [Transcription];
17-83 7.62e-03

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


Pssm-ID: 441451 [Multi-domain]  Cd Length: 142  Bit Score: 36.10  E-value: 7.62e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1327307407  17 SFSKVAEQNNLTNSVVSKRIARLEEEigvQLLYRTT-------RKLTLTEAGKAMLHGAKN-VKQAAQEAMDAVS 83
Cdd:COG1846    54 TQSELAERLGLTKSTVSRLLDRLEEK---GLVEREPdpedrraVLVRLTEKGRALLEEARPaLEALLAELLAGLS 125
 
Name Accession Description Interval E-value
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 91-294 1.08e-79

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: 240.03  E-value: 1.08e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407  91 GHIKMSVPTISGDLILADAVAEFCNMHPGLTVDMSLNNRFVDLVDDGLDLVIRTGYLEDSSLIARHILDSQWVVCASPSY 170
Cdd:cd08422     1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVASPAY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407 171 IAKNGKPMQPKDLVEHNCLQYAYQtTGASEWQFLHskdgftDNDKYIVRVSGSFSTDNATALRKAALGGHGVAYVPRCLV 250
Cdd:cd08422    81 LARHGTPQTPEDLARHRCLGYRLP-GRPLRWRFRR------GGGEVEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLV 153

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1327307407 251 YHDIRNGQLVDIFPDLVGKKLGIYAVYPFTRQPPNKIKLLIEHI 294
Cdd:cd08422   154 AEDLASGRLVRVLPDWRPPPLPIYAVYPSRRHLPAKVRAFIDFL 197
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-297 3.02e-61

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 195.09  E-value: 3.02e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407   1 MRADDLILFSQVVELGSFSKVAEQNNLTNSVVSKRIARLEEEIGVQLLYRTTRKLTLTEAGKAMLHGAKNVKQAAQEAMD 80
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407  81 AVSGFGENVSGHIKMSVPTISGDLILADAVAEFCNMHPGLTVDMSLNN--RFVD-LVDDGLDLVIRTGYLEDSSLIARHI 157
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNsdRLVDaLLEGELDLAIRLGPPPDPGLVARPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407 158 LDSQWVVCASPSYIAKNGKPMqpkdlvehnclqyayqttgasewqflhskdgftdndkyivrvsgsfsTDNATALRKAAL 237
Cdd:COG0583   161 GEERLVLVASPDHPLARRAPL-----------------------------------------------VNSLEALLAAVA 193

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407 238 GGHGVAYVPRCLVYHDIRNGQLVDIFPDLVGKKLGIYAVYPFTRQPPNKIKLLIEHIRTR 297
Cdd:COG0583   194 AGLGIALLPRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREA 253
PBP2_CrgA_like_8 cd08477
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 91-294 9.07e-61

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: 192.06  E-value: 9.07e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407  91 GHIKMSVPTISGDLILADAVAEFCNMHPGLTVDMSLNNRFVDLVDDGLDLVIRTGYLEDSSLIARHILDSQWVVCASPSY 170
Cdd:cd08477     1 GKLRISAPVTFGSHVLTPALAEYLARYPDVRVDLVLSDRLVDLVEEGFDAAFRIGELADSSLVARPLAPYRMVLCASPDY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407 171 IAKNGKPMQPKDLVEHNCLQYAYqTTGASEWQFLHsKDGFTDndkyiVRVSGSFSTDNATALRKAALGGHGVAYVPRCLV 250
Cdd:cd08477    81 LARHGTPTTPEDLARHECLGFSY-WRARNRWRLEG-PGGEVK-----VPVSGRLTVNSGQALRVAALAGLGIVLQPEALL 153

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1327307407 251 YHDIRNGQLVDIFPDLVGKKLGIYAVYPFTRQPPNKIKLLIEHI 294
Cdd:cd08477   154 AEDLASGRLVELLPDYLPPPRPMHLLYPPDRRPTPKLRSFIDFL 197
PBP2_CrgA_like_3 cd08472
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 91-292 4.28e-55

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: 177.70  E-value: 4.28e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407  91 GHIKMSVPTISGDLILADAVAEFCNMHPGLTVDMSLNNRFVDLVDDGLDLVIRTGYLEDSSLIARHILDSQWVVCASPSY 170
Cdd:cd08472     1 GRLRVDVPGSLARLLLIPALPDFLARYPDIELDLGVSDRPVDLIREGVDCVIRVGELADSSLVARRLGELRMVTCASPAY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407 171 IAKNGKPMQPKDLVEHNCLQYAYQTTGAS-EWQFLhskdgfTDNDKYIVRVSGSFSTDNATALRKAALGGHGVAYVPRCL 249
Cdd:cd08472    81 LARHGTPRHPEDLERHRAVGYFSARTGRVlPWEFQ------RDGEEREVKLPSRVSVNDSEAYLAAALAGLGIIQVPRFM 154

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1327307407 250 VYHDIRNGQLVDIFPDLVGKKLGIYAVYPFTRQPPNKIKLLIE 292
Cdd:cd08472   155 VRPHLASGRLVEVLPDWRPPPLPVSLLYPHRRHLSPRVRVFVD 197
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
8-305 9.27e-50

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 167.24  E-value: 9.27e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407   8 LFSQVVELGSFSKVAEQNNLTNSVVSKRIARLEEEIGVQLLYRTTRKLTLTEAGKAMLHGAKNVKQAAQEAMDAVSGFGE 87
Cdd:PRK10632    9 VFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQLYAFNN 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407  88 NVSGHIKMSVPTISGDLILADAVAEFCNMHPGLTVDMSLNNRFVDLVDDGLDLVIRTGYLEDSSLIARHILDSQWVVCAS 167
Cdd:PRK10632   89 TPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTGIPAPDLIADGLDVVIRVGALQDSSLFSRRLGAMPMVVCAA 168

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407 168 PSYIAKNGKPMQPKDLVEHNCLQYAYQTtgASEWQfLHSKDGFTdndkyiVRVS--GSFSTDNATALRKAALGGHGVAYV 245
Cdd:PRK10632  169 KSYLAQYGTPEKPADLSSHSWLEYSVRP--DNEFE-LIAPEGIS------TRLIpqGRFVTNDPQTLVRWLTAGAGIAYV 239

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407 246 PRCLVYHDIRNGQLVDIFPDLVGKKLGIYAVYPFTRQPPNKIKLLIEhirtrYLTisHYF 305
Cdd:PRK10632  240 PLMWVIDEINRGELEILFPRYQSDPRPVYALYTEKDKLPLKVQVCIN-----YLT--DYF 292
PBP2_CrgA_like_1 cd08470
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 91-295 5.55e-47

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: 156.70  E-value: 5.55e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407  91 GHIKMSVPTISGDLILADAVAEFCNMHPGLTVDMSLNNRFVDLVDDGLDLVIRTGYLEDSSLIARHILDSQWVVCASPSY 170
Cdd:cd08470     1 GLLRITCPVAYGERFIAPLVNDFMQRYPKLEVDIELTNRVVDLVSEGFDLAIRLGRLTDSSLMARRLASRRHYVCASPAY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407 171 IAKNGKPMQPKDLVEHNCLQyayqttGASE-WQFLhsKDGFTDNdkyiVRVSGSFSTDNATALRKAALGGHGVAYVPRCL 249
Cdd:cd08470    81 LERHGTPHSLADLDRHNCLL------GTSDhWRFQ--ENGRERS----VRVQGRWRCNSGVALLDAALKGMGLAQLPDYY 148

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1327307407 250 VYHDIRNGQLVDIFPDLVGKKLGIYAVYPFTRQPPNKIKLLIEHIR 295
Cdd:cd08470   149 VDEHLAAGRLVPVLEDYRPPDEGIWALYPHNRHLSPKVRLLVDYLA 194
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 90-294 3.58e-45

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: 151.85  E-value: 3.58e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407  90 SGHIKMSVPTISGDLILADAVAEFCNMHPGLTVDMSLNNRFVDLVDDGLDLVIRTGYLEDSSLIARHILDSQ-WVVCASP 168
Cdd:cd08474     2 AGTLRINAPRVAARLLLAPLLARFLARYPDIRLELVVDDGLVDIVAEGFDAGIRLGESVEKDMVAVPLGPPLrMAVVASP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407 169 SYIAKNGKPMQPKDLVEHNCLQYAYQTTGASE-WQFlhSKDGftdnDKYIVRVSGSFSTDNATALRKAALGGHGVAYVPR 247
Cdd:cd08474    82 AYLARHGTPEHPRDLLNHRCIRYRFPTSGALYrWEF--ERGG----RELEVDVEGPLILNDSDLMLDAALDGLGIAYLFE 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 1327307407 248 CLVYHDIRNGQLVDIFPDLVGKKLGIYAVYPFTRQPPNKIKLLIEHI 294
Cdd:cd08474   156 DLVAEHLASGRLVRVLEDWSPPFPGGYLYYPSRRRVPPALRAFIDFL 202
PBP2_CrgA_like_6 cd08475
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 91-294 1.87e-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: 150.01  E-value: 1.87e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407  91 GHIKMSVPTISGDLILADAVAEFCNMHPGLTVDMSLNNRFVDLVDDGLDLVIRTGYLEDS-SLIARHILDSQWVVCASPS 169
Cdd:cd08475     1 GRLRIDLPVAFGRLCVAPLLLELARRHPELELELSFSDRFVDLIEEGIDLAVRIGELADStGLVARRLGTQRMVLCASPA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407 170 YIAKNGKPMQPKDLVEHNCLQYaYQTTGASEWQFLHSKDGFTDndkyiVRVSGSFSTDNATALRKAALGGHGVAYVPRCL 249
Cdd:cd08475    81 YLARHGTPRTLEDLAEHQCIAY-GRGGQPLPWRLADEQGRLVR-----FRPAPRLQFDDGEAIADAALAGLGIAQLPTWL 154

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 1327307407 250 VYHDIRNGQLVDIFPDLVGKKLGIYAVYPFTRQPPNKIKLLIEHI 294
Cdd:cd08475   155 VADHLQRGELVEVLPELAPEGLPIHAVWPRTRHLPPKVRAAVDAL 199
PBP2_CrgA_like_7 cd08476
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 91-294 1.36e-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 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: 145.08  E-value: 1.36e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407  91 GHIKMSVPTIsGDLILAdAVAEFCNMHPGLTVDMSLNNRFVDLVDDGLDLVIRTGYLEDSSLIARHILDSQWVVCASPSY 170
Cdd:cd08476     1 GRLRVSLPLV-GGLLLP-VLAAFMQRYPEIELDLDFSDRLVDVIDEGFDAVIRTGELPDSRLMSRRLGSFRMVLVASPDY 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407 171 IAKNGKPMQPKDLVEHNCLQYAYQTTGASE-WQfLHSKDGFTDndkyiVRVSGSFSTDNATALRKAALGGHGVAYVPRCL 249
Cdd:cd08476    79 LARHGTPETPADLAEHACLRYRFPTTGKLEpWP-LRGDGGDPE-----LRLPTALVCNNIEALIEFALQGLGIACLPDFS 152

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 1327307407 250 VYHDIRNGQLVDIFPDLVGKKLGIYAVYPFTRQPPNKIKLLIEHI 294
Cdd:cd08476   153 VREALADGRLVTVLDDYVEERGQFRLLWPSSRHLSPKLRVFVDFM 197
PBP2_CrgA_like_9 cd08479
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 91-294 4.87e-39

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: 136.19  E-value: 4.87e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407  91 GHIKMSVPTISGDLILADAVAEFCNMHPGLTVDMSLNNRFVDLVDDGLDLVIRTGYLEDSSLIARHILDSQWVVCASPSY 170
Cdd:cd08479     1 GLLRVNASFGFGRRHIAPALSDFAKRYPELEVQLELTDRPVDLVEEGFDLDIRVGDLPDSSLIARKLAPNRRILCASPAY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407 171 IAKNGKPMQPKDLVEHNCLQYAYQTTGASEWQFLHSKDGFTdndkyiVRVSGSFSTDNATALRKAALGGHGVAYVPRCLV 250
Cdd:cd08479    81 LERHGAPASPEDLARHDCLVIRENDEDFGLWRLRNGDGEAT------VRVRGALSSNDGEVVLQWALDGHGIILRSEWDV 154

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1327307407 251 YHDIRNGQLVDIFPDLVGKKLGIYAVYPFTRQPPNKIKLLIEHI 294
Cdd:cd08479   155 APYLRSGRLVRVLPDWQLPDADIWAVYPSRLSRSARVRVFVDFL 198
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 4-298 9.68e-39

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 138.20  E-value: 9.68e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407   4 DDLILFSQVVELGSFSKVAEQNNLTNSVVSKRIARLEEEIGVQLLYRTTRKLTLTEAGKAMLHGAKNVKQAAQEAMDAVS 83
Cdd:PRK14997    5 NDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDAIA 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407  84 GFGENVSGHIKMSVPTISGDLILADAVAEFCNMHPGLTVDMSLNNRFVDLVDDGLDLVIRT--GYLEDSSLIARHILDSQ 161
Cdd:PRK14997   85 ALQVEPRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLEATNRRVDVVGEGVDVAIRVrpRPFEDSDLVMRVLADRG 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407 162 WVVCASPSYIAKNGKPMQPKDLVEHNCLQYAyQTTGASEWQfLHSKDGftdnDKYIVRVSGSFSTDNATALRKAALGGHG 241
Cdd:PRK14997  165 HRLFASPDLIARMGIPSAPAELSHWPGLSLA-SGKHIHRWE-LYGPQG----ARAEVHFTPRMITTDMLALREAAMAGVG 238

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1327307407 242 VAYVPRCLVYHDIRNGQLVDIFPDLVGKKLGIYAVYPFTRQPPNKIKLLIEHIRTRY 298
Cdd:PRK14997  239 LVQLPVLMVKEQLAAGELVAVLEEWEPRREVIHAVFPSRRGLLPSVRALVDFLTEEY 295
PBP2_CrgA_like_4 cd08473
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 90-293 1.12e-38

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 135.38  E-value: 1.12e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407  90 SGHIKMSVPTISGDLILADAVAEFCNMHPGLTVDMSLNNRFVDLVDDGLDLVI--RTGYLEDSSLIARHILDSQWVVCAS 167
Cdd:cd08473     2 RGTVRVSCPPALAQELLAPLLPRFMAAYPQVRLQLEATNRRVDLIEEGIDVALrvRFPPLEDSSLVMRVLGQSRQRLVAS 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407 168 PSYIAKNGKPMQPKDLVEHNCLQYAYQTtGASEWQfLHSKDGftdnDKYIVRVSGSFSTDNATALRKAALGGHGVAYVPR 247
Cdd:cd08473    82 PALLARLGRPRSPEDLAGLPTLSLGDVD-GRHSWR-LEGPDG----ESITVRHRPRLVTDDLLTLRQAALAGVGIALLPD 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 1327307407 248 CLVYHDIRNGQLVDIFPDLVGKKLGIYAVYPfTRQ--PPnKIKLLIEH 293
Cdd:cd08473   156 HLCREALRAGRLVRVLPDWTPPRGIVHAVFP-SRRglLP-AVRALIDF 201
PBP2_CrgA_like_2 cd08471
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 91-297 1.24e-38

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 134.96  E-value: 1.24e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407  91 GHIKMSVPTISGDLILADAVAEFCNMHPGLTVDMSLNNRFVDLVDDGLDLVIRTGYLEDSSLIARHILDSQWVVCASPSY 170
Cdd:cd08471     1 GLLTVTAPVLFGRLHVLPIITDFLDAYPEVSVRLLLLDRVVNLLEEGVDVAVRIGHLPDSSLVATRVGSVRRVVCASPAY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407 171 IAKNGKPMQPKDLVEHNCLQYAyQTTGASEWQFLHSKDGFTdndkyiVRVSGSFSTDNATALRKAALGGHGVAyvpRCLV 250
Cdd:cd08471    81 LARHGTPKHPDDLADHDCIAFT-GLSPAPEWRFREGGKERS------VRVRPRLTVNTVEAAIAAALAGLGLT---RVLS 150

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 1327307407 251 YH---DIRNGQLVDIFPDLVGKKLGIYAVYPFTRQPPNKIKLLIEHIRTR 297
Cdd:cd08471   151 YQvaeELAAGRLQRVLEDFEPPPLPVHLVHPEGRLAPAKVRAFVDFAVPR 200
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 90-297 3.92e-38

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: 133.95  E-value: 3.92e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407  90 SGHIKMSVPTISGDLILADAVAEFCNMHPGLTVDMSLNN--RFVDLVDDG-LDLVIRTGYLEDSSLIARHILDSQWVVCA 166
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNseELLDLLLEGeLDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407 167 SPSYIAKNGKPMQPKDLVEHNCLQYAYQTTGASEWQFLHSKDGFtdndkyivRVSGSFSTDNATALRKAALGGHGVAYVP 246
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGL--------RPRVVLEVNSLEALLQLVAAGLGIALLP 152

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1327307407 247 RCLVYHDIRNGQLVDI-FPDLVGkKLGIYAVYPFTRQPPNKIKLLIEHIRTR 297
Cdd:pfam03466 153 RSAVARELADGRLVALpLPEPPL-PRELYLVWRKGRPLSPAVRAFIEFLREA 203
PBP2_CrgA_like_10 cd08480
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-292 7.72e-38

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 132.85  E-value: 7.72e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407  93 IKMSVPTisGDLILADAVAEFCNMHPGLTVDMSLNNRFVDLVDDGLDLVIRTGYLEDSSLIARHILDSQWVVCASPSYIA 172
Cdd:cd08480     5 VNASVPF--GTHFLLPLLPAFLARYPEILVDLSLTDEVVDLLAERTDVAIRVGPLPDSSLVARKLGESRRVIVASPSYLA 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407 173 KNGKPMQPKDLVEHNCLQYAYQTTgASEWQFlhsKDGFTDndkYIVRVSGSFSTDNATALRKAALGGHGVAYVPRCLVYH 252
Cdd:cd08480    83 RHGTPLTPQDLARHNCLGFNFRRA-LPDWPF---RDGGRI---VALPVSGNILVNDGEALRRLALAGAGLARLALFHVAD 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1327307407 253 DIRNGQLVDIFPDL-VGKKLGIYAVYPFTRQPPNKIKLLIE 292
Cdd:cd08480   156 DIAAGRLVPVLEEYnPGDREPIHAVYVGGGRLPARVRAFLD 196
PRK09801 PRK09801
LysR family transcriptional regulator;
3-283 9.18e-30

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 114.75  E-value: 9.18e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407   3 ADDLILFSQVVELGSFSKVAEQNNLTNSVVSKRIARLEEEIGVQLLYRTTRKLTLTEAGKAMLHGAKNVKQAAQEAMDAV 82
Cdd:PRK09801    8 AKDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDV 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407  83 SGFGENVSGHIKMSVPTISGDLILADAVAEFCNMHPGLTVDMSLNNRFVDLVDDGLDLVIRTGYLEDSSLIARHILDSQW 162
Cdd:PRK09801   88 TQIKTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHFELFDRQIDLVQDNIDLDIRINDEIPDYYIAHLLTKNKR 167

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407 163 VVCASPSYIAKNGKPMQPKDLVEHNCLQYAYQTTGASEWQFLHSKdgftdnDKYIVRVSGSFSTDNATALRKAALGGHGV 242
Cdd:PRK09801  168 ILCAAPEYLQKYPQPQSLQELSRHDCLVTKERDMTHGIWELGNGQ------EKKSVKVSGHLSSNSGEIVLQWALEGKGI 241

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|.
gi 1327307407 243 AYVPRCLVYHDIRNGQLVDIFPDLvGKKLGIYAVYpftRQP 283
Cdd:PRK09801  242 MLRSEWDVLPFLESGKLVQVLPEY-AQSANIWAVY---REP 278
PBP2_CrgA cd08478
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains ...
 105-294 2.26e-28

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: 108.19  E-value: 2.26e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407 105 ILADAVAEFCNMHPGLTVDMSLNNRFVDLVDDGLDLVIRTGYLEDSSLIARHILDSQWVVCASPSYIAKNGKPMQPKDLV 184
Cdd:cd08478    17 LLAPLIAKFRERYPDIELELVSNEGIIDLIERKTDVAIRIGELTDSTLHARPLGKSRLRILASPDYLARHGTPQSIEDLA 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407 185 EHNCLQYAyQTTGASEWQFLHSkdgftDNDKYivRVSGSFSTDNATALRKAALGGHGVAYVPRCLVYHDIRNGQLVDIF- 263
Cdd:cd08478    97 QHQLLGFT-EPASLNTWPIKDA-----DGNLL--KIQPTITASSGETLRQLALSGCGIACLSDFMTDKDIAEGRLIPLFa 168

                         170       180       190
                  ....*....|....*....|....*....|.
gi 1327307407 264 PDLVGKKLGIYAVYPFTRQPPNKIKLLIEHI 294
Cdd:cd08478   169 EQTSDVRQPINAVYYRNTALSLRIRCFIDFL 199
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 17-278 6.80e-28

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 109.55  E-value: 6.80e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407  17 SFSKVAEQNNLTNSVVSKRIARLEEEIGVQLLYRTTRKLTLTEAGKAMLHGAKNVKQAAQEAMDAVSGFGENvsGHIKMS 96
Cdd:PRK11139   22 SFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEATRKLRARSAK--GALTVS 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407  97 VPTISGDLILADAVAEFCNMHPGLTVDMSLNNRFVDLVDDGLDLVIRTGYLEDSSLIARHILDSQWVVCASPSYIAKNGK 176
Cdd:PRK11139  100 LLPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDRLEDFLRDDVDVAIRYGRGNWPGLRVEKLLDEYLLPVCSPALLNGGKP 179

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407 177 PMQPKDLVEHNCLqyayQTTGASEWQ--FLHSkdGFTDNDkyiVRVSGSFStdNATALRKAALGGHGVAYVPRCLVYHDI 254
Cdd:PRK11139  180 LKTPEDLARHTLL----HDDSREDWRawFRAA--GLDDLN---VQQGPIFS--HSSMALQAAIHGQGVALGNRVLAQPEI 248

                         250       260
                  ....*....|....*....|....
gi 1327307407 255 RNGQLVDIFPDLVGKKLGIYAVYP 278
Cdd:PRK11139  249 EAGRLVCPFDTVLPSPNAFYLVCP 272
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
17-292 5.40e-23

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 96.22  E-value: 5.40e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407  17 SFSKVAEQNNLTNSVVSKRIARLEEEIGVQLLYRTTRKLTLTEAGKAMLHG-AKNVKQAAQEAMDAVsgfGENVSGHIKM 95
Cdd:PRK10086   30 SFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWAlKSSLDTLNQEILDIK---NQELSGTLTV 106

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407  96 SV-PTISgDLILADAVAEFCNMHPGLTVDMSLNNRFVDLVDDGLDLVIRTGYLEDSSLIARHILDSQWV-VCaSPSYIAK 173
Cdd:PRK10086  107 YSrPSIA-QCWLVPRLADFTRRYPSISLTILTGNENVNFQRAGIDLAIYFDDAPSAQLTHHFLMDEEILpVC-SPEYAER 184

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407 174 NGKPMQPKDLVE----HNCLQYAYQtTGASEWQFLHSKDGFTDNDKyivRVSGSFS-TDNATAlrkAALGGHGVAYVPRC 248
Cdd:PRK10086  185 HALTGNPDNLRHctllHDRQAWSND-SGTDEWHSWAQHFGVNLLPP---SSGIGFDrSDLAVI---AAMNHIGVAMGRKR 257

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*
gi 1327307407 249 LVYHDIRNGQLVDIFPDLVGK-KLGIYAVYPFTRQPPnKIKLLIE 292
Cdd:PRK10086  258 LVQKRLASGELVAPFGDMEVKcHQHYYVTTLPGRQWP-KIEAFID 301
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 111-292 6.74e-22

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: 90.72  E-value: 6.74e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407 111 AEFCNMHPGLTVDMSLNNRFVDLVDDGLDLVIRTGYLEDSSLIARHILDSQWVVCASPSYIAKNGkPMQPKDLVEHNCLQ 190
Cdd:cd08432    20 ARFQARHPDIDLRLSTSDRLVDFAREGIDLAIRYGDGDWPGLEAERLMDEELVPVCSPALLAGLP-LLSPADLARHTLLH 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407 191 YAYQTTGASEWQFLHSKDGftdndkyiVRVSGSFSTDNATALRKAALGGHGVAYVPRCLVYHDIRNGQLVDIFPDLVGKK 270
Cdd:cd08432    99 DATRPEAWQWWLWAAGVAD--------VDARRGPRFDDSSLALQAAVAGLGVALAPRALVADDLAAGRLVRPFDLPLPSG 170

                         170       180
                  ....*....|....*....|..
gi 1327307407 271 LGIYAVYPFTRQPPNKIKLLIE 292
Cdd:cd08432   171 GAYYLVYPPGRAESPAVAAFRD 192
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
4-62 2.41e-21

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 85.13  E-value: 2.41e-21
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1327307407   4 DDLILFSQVVELGSFSKVAEQNNLTNSVVSKRIARLEEEIGVQLLYRTTRKLTLTEAGK 62
Cdd:pfam00126   2 RQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 92-294 1.79e-14

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: 70.71  E-value: 1.79e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407  92 HIKMSVPTISGDLILADAVAEFCNMHPGLTVDM--SLNNRFVDLVDDG-LDLVIRTGYLEDSSLIARHILDSQWVVCASP 168
Cdd:cd05466     1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLveGGSSELLEALLEGeLDLAIVALPVDDPGLESEPLFEEPLVLVVPP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407 169 SYIAKNGKPMQPKDLVEHNCLQYA--YQTTGASEWQFlhSKDGFTDNdkyIVrvsgsFSTDNATALRKAALGGHGVAYVP 246
Cdd:cd05466    81 DHPLAKRKSVTLADLADEPLILFErgSGLRRLLDRAF--AEAGFTPN---IA-----LEVDSLEAIKALVAAGLGIALLP 150

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 1327307407 247 RCLVyHDIRNGQLVDIFPDLVGKKLGIYAVYPFTRQPPNKIKLLIEHI 294
Cdd:cd05466   151 ESAV-EELADGGLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 9-142 5.23e-13

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 68.06  E-value: 5.23e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407   9 FSQVVELGSFSKVAEQNNLTNSVVSKRIARLEEEIGVQLLYRTTRKLTLTEAGKAMLHGAKNVKQAAQEAMDAVSGFGEN 88
Cdd:PRK11242    9 FLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRRAIHDVADL 88

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1327307407  89 VSGHIKMSV-PTISGDLIlADAVAEFCNMHPGLTVD---MSLNNRFVDLVDDGLDLVI 142
Cdd:PRK11242   89 SRGSLRLAMtPTFTAYLI-GPLIDAFHARYPGITLTireMSQERIEALLADDELDVGI 145
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
9-69 5.55e-13

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 67.91  E-value: 5.55e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1327307407   9 FSQVVELGSFSKVAEQNNLTNSVVSKRIARLEEEIGVQLLYRTTRKLTLTEAGKAMLHGAK 69
Cdd:PRK10094   10 FIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQAR 70
PBP2_HvrB cd08483
The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an ...
 110-284 5.05e-12

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: 63.52  E-value: 5.05e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407 110 VAEFCNMHPGLTVDMSLNNRFVDLVDDGLDLVIRTGYLEDSSLIARHILDSQWVVCASPSYIaKNGKPMQPKDLVEHNCL 189
Cdd:cd08483    19 LGSFWAKHPEIELSLLPSADLVDLRPDGIDVAIRYGNGDWPGLESEPLTAAPFVVVAAPGLL-GDRKVDSLADLAGLPWL 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407 190 QYAyqttGASEWQFLHSKDGFTDNDKYIVRVsgsfstDNATALRKAALGGHGVAYVPRCLVYHDIRNGQLVDIFpDLVGK 269
Cdd:cd08483    98 QER----GTNEQRVWLASMGVVPDLERGVTF------LPGQLVLEAARAGLGLSIQARALVEPDIAAGRLTVLF-EEEEE 166

                         170
                  ....*....|....*
gi 1327307407 270 KLGIYAVypfTRQPP 284
Cdd:cd08483   167 GLGYHIV---TRPGV 178
PBP2_GcdR_like cd08481
The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, ...
 117-278 1.05e-11

The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, contains the type 2 periplasmic binding fold; GcdR is involved in the glutaconate/glutarate-specific activation of the Pg promoter driving expression of a glutaryl-CoA dehydrogenase-encoding gene (gcdH). The GcdH protein is essential for the anaerobic catabolism of many aromatic compounds and some alicyclic and dicarboxylic acids. The structural topology of this substrate-binding domain is most similar 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: 176170 [Multi-domain]  Cd Length: 194  Bit Score: 62.70  E-value: 1.05e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407 117 HPGLTVDMSLNNRFVDLVDDGLDLVIRTGYLEDSSLIARHILDSQWVVCASPSYIAKNGkPMQPKDLVEHNCLQyayQTT 196
Cdd:cd08481    26 HPDITVNLVTRDEPFDFSQGSFDAAIHFGDPVWPGAESEYLMDEEVVPVCSPALLAGRA-LAAPADLAHLPLLQ---QTT 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407 197 GASEWQflhskDGFTDNDKYIVRVSGSFSTDNATALRKAALGGHGVAYVPRCLVYHDIRNGQLVDIFPDLVGKKLGIYAV 276
Cdd:cd08481   102 RPEAWR-----DWFEEVGLEVPTAYRGMRFEQFSMLAQAAVAGLGVALLPRFLIEEELARGRLVVPFNLPLTSDKAYYLV 176


                  ..
gi 1327307407 277 YP 278
Cdd:cd08481   177 YP 178
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 4-144 1.39e-10

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 61.20  E-value: 1.39e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407   4 DDLILFSQVVELGSFSKVAEQNNLTNSVVSKRIARLEEEIGVQLLYRTTRKLTLTEAGKAMLHGAKNVKQAAQEAmdAVS 83
Cdd:PRK15092   14 DLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEA--CSS 91

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1327307407  84 GFGENVSGHIKMSVPTISGDLILADAVAEFCNMHPGLTVDMSLN-NRFV-DLVDDG-LDLVIRT 144
Cdd:PRK15092   92 LMYSNLQGVLTIGASDDTADTILPFLLNRVSSVYPKLALDVRVKrNAFMmEMLESQeVDLAVTT 155
PRK10341 PRK10341
transcriptional regulator TdcA;
6-169 2.12e-10

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 60.65  E-value: 2.12e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407   6 LILFSQVVELGSFSKVAEQNNLTNSVVSKRIARLEEEIGVQLLYRTTRKLTLTEAGKAMLHGAKNVKQAAQEAMDAVSGF 85
Cdd:PRK10341   12 LVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEINGM 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407  86 GENVSGHIKMSVPTISGDLILADAVAEFCNMHPGLTVDM---SLNNrFVDLVDDG-LDLVIrtGYLEDSSLI----ARHI 157
Cdd:PRK10341   92 SSEAVVDVSFGFPSLIGFTFMSDMINKFKEVFPKAQVSMyeaQLSS-FLPAIRDGrLDFAI--GTLSNEMKLqdlhVEPL 168

                         170
                  ....*....|..
gi 1327307407 158 LDSQWVVCASPS 169
Cdd:PRK10341  169 FESEFVLVASKS 180
PBP2_BlaA cd08487
The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which ...
 110-263 2.71e-10

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: 58.71  E-value: 2.71e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407 110 VAEFCNMHPGLTVDMSLNNRFVDLVDDGLDLVIRTGYLEDSSLIARHILDSQWVVCASPSyIAKngKPMQPKDLVEHNCL 189
Cdd:cd08487    19 LAEFRQLHPFIELRLRTNNNVVDLATEGLDFAIRFGEGLWPATHNERLLDAPLSVLCSPE-IAK--RLSHPADLINETLL 95

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1327307407 190 QyAYQTtgaSEWQFLHSKDGFTDndkyiVRVSGSFsTDNATALRKAALGGHGVAYVPRCLVYHDIRNGQLVDIF 263
Cdd:cd08487    96 R-SYRT---DEWLQWFEAANMPP-----IKIRGPV-FDSSRLMVEAAMQGAGVALAPAKMFSREIENGQLVQPF 159
PRK09986 PRK09986
LysR family transcriptional regulator;
9-97 7.85e-10

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 58.58  E-value: 7.85e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407   9 FSQVVELGSFSKVAEQNNLTNSVVSKRIARLEEEIGVQLLYRTTRKLTLTEAGKAMLHGAKNVKQAAQEAMDAVSGFGEN 88
Cdd:PRK09986   15 FLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLARVEQIGRG 94


                  ....*....
gi 1327307407  89 VSGHIKMSV 97
Cdd:PRK09986   95 EAGRIEIGI 103
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
9-72 1.16e-09

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 58.06  E-value: 1.16e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1327307407   9 FSQVVELGSFSKVAEQNNLTNSVVSKRIARLEEEIGVQLLYRtTRKLTLTEAGKAMLHGAKNVK 72
Cdd:PRK13348   10 LAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQRLLRHLRQVA 72
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 1-128 3.45e-09

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 56.70  E-value: 3.45e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407   1 MRADDLILFSQVVELGSFSKVAEQNNLTNSVVSKRIARLEEEIGVQLLYRTTRKLTLTEAGKAMLHGA-----------K 69
Cdd:PRK09906    1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDAraileqaekakL 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407  70 NVKQAAQEAMDAVSGFgenvsghikmsVPtISGDLILADAVAEFCNMHPGLTVDM-SLNN 128
Cdd:PRK09906   81 RARKIVQEDRQLTIGF-----------VP-SAEVNLLPKVLPMFRLRHPDTLIELvSLIT 128
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 18-142 3.71e-09

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 56.58  E-value: 3.71e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407  18 FSKVAEQNNLTNSVVSKRIARLEEEIGVQLLYRTTRKLTLTEAGKAMLHGAKNVKQAAQEAMDAVSGFGENVSG--HIKM 95
Cdd:PRK11151   18 FRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVLKEMASQQGETMSGplHIGL 97

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1327307407  96 sVPTIsGDLILADAVAEFCNMHPGLtvDMSL----NNRFVDLVDDG-LDLVI 142
Cdd:PRK11151   98 -IPTV-GPYLLPHIIPMLHQTFPKL--EMYLheaqTHQLLAQLDSGkLDCAI 145
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 6-169 5.88e-09

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 55.85  E-value: 5.88e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407   6 LILFSQVVELGSFSKVAEQNNLTNSVVSKRIARLEEEIGVQLLYRTTRKLTLTEAGK-------AMLHGAKNVKQAAQEa 78
Cdd:PRK10837    8 LEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRllypralALLEQAVEIEQLFRE- 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407  79 mdavsgfgENvsGHIKMSVPTISGDLILADAVAEFCNMHPGLTVDMSLNNRfVDLVDDGLDLVIRTGYLE----DSSLIA 154
Cdd:PRK10837   87 --------DN--GALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNS-QDVINAVLDFRVDIGLIEgpchSPELIS 155

                         170
                  ....*....|....*
gi 1327307407 155 RHILDSQWVVCASPS 169
Cdd:PRK10837  156 EPWLEDELVVFAAPD 170
PBP2_LTTR_beta_lactamase cd08484
The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase ...
 111-274 6.37e-09

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: 54.68  E-value: 6.37e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407 111 AEFCNMHPGLTVDMSLNNRFVDLVDDGLDLVIRTGYLEDSSLIARHILDSQWVVCASPSyIAKNGKpmQPKDLVEHNCLQ 190
Cdd:cd08484    20 AEFRQLHPFIDLRLSTNNNRVDIAAEGLDFAIRFGEGAWPGTDATRLFEAPLSPLCTPE-LARRLS--EPADLANETLLR 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407 191 yAYQTtgaSEWQFLHSKDGFTdndkyiVRVSGSFSTDNATALRKAALGGHGVAYVPRCLVYHDIRNGQLVDIFPdlVGKK 270
Cdd:cd08484    97 -SYRA---DEWPQWFEAAGVP------PPPINGPVFDSSLLMVEAALQGAGVALAPPSMFSRELASGALVQPFK--ITVS 164


                  ....
gi 1327307407 271 LGIY 274
Cdd:cd08484   165 TGSY 168
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
9-266 6.68e-09

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 55.94  E-value: 6.68e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407   9 FSQVVELGSFSKVAEQNNLTNSVVSKRIARLEEEIGVQLLYRtTRKLTLTEAGKAMLHGAKNVKQAAQEAMDAVSGFGEn 88
Cdd:PRK03635   10 LAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRLLRHARQVRLLEAELLGELPALDG- 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407  89 vsGHIKMSVpTISGDLI---LADAVAEFCNMHpGLTVDMslnnrfvdLVDD---GLDL---------------------V 141
Cdd:PRK03635   88 --TPLTLSI-AVNADSLatwFLPALAPVLARS-GVLLDL--------VVEDqdhTAELlrrgevvgavttepqpvqgcrV 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407 142 IRTGYLEdssliarhildsqWVVCASPSYIAK---NGKPMQ-----------PKDLVEHnclQYAYQTTGASEWQFLH-- 205
Cdd:PRK03635  156 DPLGAMR-------------YLAVASPAFAARyfpDGVTAEalakapavvfnRKDDLQD---RFLRQAFGLPPGSVPChy 219

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1327307407 206 --SKDGFTDndkyivrvsgsfstdnatalrkAALGGHGVAYVPRCLVYHDIRNGQLVDIFPDL 266
Cdd:PRK03635  220 vpSSEAFVR----------------------AALAGLGWGMIPELQIEPELASGELVDLTPGR 260
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 9-93 1.12e-08

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 55.46  E-value: 1.12e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407   9 FSQVVELGSFSKVAEQNNLTNSVVSKRIARLEEEIGVQLLYRTTRKLTLTEAGKAMLHGAKNVKQAAQEAMDAVSGFGEN 88
Cdd:PRK11233    9 FVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQLAVHNVGQA 88


                  ....*
gi 1327307407  89 VSGHI 93
Cdd:PRK11233   89 LSGQV 93
PBP2_AmpR cd08488
The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in ...
 110-274 4.16e-08

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: 52.53  E-value: 4.16e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407 110 VAEFCNMHPGLTVDMSLNNRFVDLVDDGLDLVIRTGYLEDSSLIARHILDSQWVVCASPSyIAKNGKpmQPKDLVEHNCL 189
Cdd:cd08488    19 LADFQNRHPFIDLRLSTNNNRVDIAAEGLDYAIRFGSGAWHGIDATRLFEAPLSPLCTPE-LARQLR--EPADLARHTLL 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407 190 QyAYQttgASEWQFLHSKDGFTDNdkyiVRVSGSFSTDNATALRKAALGGHGVAYVPRCLVYHDIRNGQLVDIFPdlVGK 269
Cdd:cd08488    96 R-SYR---ADEWPQWFEAAGVGHP----CGLPNSIMFDSSLGMMEAALQGLGVALAPPSMFSRQLASGALVQPFA--TTL 165


                  ....*
gi 1327307407 270 KLGIY 274
Cdd:cd08488   166 STGSY 170
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
17-284 1.16e-07

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 52.36  E-value: 1.16e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407  17 SFSKVAEQNNLTNSVVSKRIARLEEEIGVQLLYRTTRKLTLTEAGKAMLHGAKNVKQAAQEAMDAVSGFGENVSGHIKMS 96
Cdd:PRK10082   27 NFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESNLAELRGGSDYAQRKIKIA 106

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407  97 VP-TISGDL---ILADAVAEFCNMHPGLTVDMSlnnrfVDLVDDGLDLVIRTGYLED---SSLIARHILDSQ-WVVCASP 168
Cdd:PRK10082  107 AAhSLSLGLlpsIISQMPPLFTWAIEAIDVDEA-----VDKLREGQSDCIFSFHDEDlleAPFDHIRLFESQlFPVCASD 181

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407 169 SYiaknGKPM----QPK-DLVEHNclQYAYQTTGASEWQFLHSKDGFtdndkyivrvSGSFSTDNATALRKAALGGHGVA 243
Cdd:PRK10082  182 EH----GEALfnlaQPHfPLLNYS--RNSYMGRLINRTLTRHSELSF----------STFFVSSMSELLKQVALDGCGIA 245

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|.
gi 1327307407 244 YVPRCLVYHDIRNGQLVDIFPDLVGKKLGIYAVYPFTRQPP 284
Cdd:PRK10082  246 WLPEYAIQQEIRSGQLVVLNRDELVIPIQAYAYRMNTRMNP 286
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
16-260 1.68e-07

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 51.94  E-value: 1.68e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407  16 GSFSKVAEQNNLTNSVVSKRIARLEEEIGVQLLYRTTRKLTLTEAGKAMLHGAKNVKQAAQEAMDAVSgfgENVSGHIKM 95
Cdd:PRK15421   17 GSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQACN---EPQQTRLRI 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407  96 SVPTISGDLILADAVAEFCNMHPGLTVDMSLNNRF---VDLVDDGLDLVIRTGYLEDSSLIARHILDSQWVVCASPSYIA 172
Cdd:PRK15421   94 AIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFdpqPALQQGELDLVMTSDILPRSGLHYSPMFDYEVRLVLAPDHPL 173

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407 173 KNGKPMQPKDLVEHNCLQYAYQTTGASEWQFLHSKDGFTDNDKyivrvsgsfSTDNATALRKAALGGHGVAYVPRCLVYH 252
Cdd:PRK15421  174 AAKTRITPEDLASETLLIYPVQRSRLDVWRHFLQPAGVSPSLK---------SVDNTLLLIQMVAARMGIAALPHWVVES 244


                  ....*...
gi 1327307407 253 DIRNGQLV 260
Cdd:PRK15421  245 FERQGLVV 252
rbcR CHL00180
LysR transcriptional regulator; Provisional
 4-153 3.05e-07

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 50.79  E-value: 3.05e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407   4 DDLILFSQVVELGSFSKVAEQNNLTNSVVSKRIARLEEEIGVQLLYRTTRKLTLTEAGKAMLHGAKNVKQAAQEAMDAVS 83
Cdd:CHL00180    8 DQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRALE 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407  84 GFGENVSGHIKMSVPTISGDLILADAVAEFCNMHPGLTVDMSLN----------NRFVDL------VDDGL-DLVIRTGY 146
Cdd:CHL00180   88 DLKNLQRGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHstrriawnvaNGQIDIaivggeVPTELkKILEITPY 167


                  ....*...
gi 1327307407 147 LEDS-SLI 153
Cdd:CHL00180  168 VEDElALI 175
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 14-118 3.49e-07

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 50.81  E-value: 3.49e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407  14 ELGSFSKVAEQN-NLT---------NSVVSKRIARLEEEIGVQLLYRTTRKLT-LTEAGKA-------MLHGAKNVKQAA 75
Cdd:PRK12683    5 QLRIIREAVRQNfNLTevanalytsQSGVSKQIKDLEDELGVEIFIRRGKRLTgLTEPGKEllqiverMLLDAENLRRLA 84

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1327307407  76 QEamdavsgFGENVSGHIKMSVPTISGDLILADAVAEFCNMHP 118
Cdd:PRK12683   85 EQ-------FADRDSGHLTVATTHTQARYALPKVVRQFKEVFP 120
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
25-97 2.59e-06

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 47.89  E-value: 2.59e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1327307407  25 NNLTNSVVSKRIARLEEEIGVQLLYRTTRKLTLTEAGKAMLHGAKNVKQAAQEAMDAVSGFGENVSGHIKM--SV 97
Cdd:PRK11716    1 MHVSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSLfcSV 75
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
21-84 1.50e-05

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 45.74  E-value: 1.50e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407  21 VAEQN-NLTNSV---------VSKRIARLEEEIGVQLLYRTTRKLT-LTEAGKA-------MLHGAKNVKQAAQEAMDAV 82
Cdd:PRK12684   12 AVRQNfNLTEAAkalytsqpgVSKAIIELEDELGVEIFTRHGKRLRgLTEPGRIilasverILQEVENLKRVGKEFAAQD 91


                  ..
gi 1327307407  83 SG 84
Cdd:PRK12684   92 QG 93
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 6-71 6.05e-05

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 43.78  E-value: 6.05e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1327307407   6 LILFSQVVELGSFSKVAEQNNLTNSVVSKRIARLEEEIGVQLLYRTTRKLTLTEAGKAMLHGAKNV 71
Cdd:PRK11074    7 LEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSV 72
PRK09791 PRK09791
LysR family transcriptional regulator;
9-187 9.69e-04

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 40.13  E-value: 9.69e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407   9 FSQVVELGSFSKVAEQNNLTNSVVSKRIARLEEEIGVQLLYRTTRKLTLTEAGKAMLHGAKNVKQ---AAQEamDAVSGF 85
Cdd:PRK09791   13 FVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEelrAAQE--DIRQRQ 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1327307407  86 GEnVSGHIKMSVPTISGDLILADAVAEFCNMHPGLTVDM---SLNNRFVDLVDDGLDLVIRTGYLE--DSSLIARHILDS 160
Cdd:PRK09791   91 GQ-LAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRImegQLVSMINELRQGELDFTINTYYQGpyDHEFTFEKLLEK 169

                         170       180       190
                  ....*....|....*....|....*....|.
gi 1327307407 161 QWVVcaspsyIAKNGKPMQP----KDLVEHN 187
Cdd:PRK09791  170 QFAV------FCRPGHPAIGarslKQLLDYS 194
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 19-65 2.57e-03

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 38.82  E-value: 2.57e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1327307407  19 SKVAEQNNLTNSVVSKRIARLEEEIGVQLLYRTTRKLT-LTEAGKAML 65
Cdd:PRK12682   20 TEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKgLTEPGKAVL 67
MarR COG1846
DNA-binding transcriptional regulator, MarR family [Transcription];
17-83 7.62e-03

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


Pssm-ID: 441451 [Multi-domain]  Cd Length: 142  Bit Score: 36.10  E-value: 7.62e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1327307407  17 SFSKVAEQNNLTNSVVSKRIARLEEEigvQLLYRTT-------RKLTLTEAGKAMLHGAKN-VKQAAQEAMDAVS 83
Cdd:COG1846    54 TQSELAERLGLTKSTVSRLLDRLEEK---GLVEREPdpedrraVLVRLTEKGRALLEEARPaLEALLAELLAGLS 125
cbl PRK12679
HTH-type transcriptional regulator Cbl;
19-65 7.73e-03

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 37.48  E-value: 7.73e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1327307407  19 SKVAEQNNLTNSVVSKRIARLEEEIGVQL-LYRTTRKLTLTEAGKAML 65
Cdd:PRK12679   20 TEVANMLFTSQSGVSRHIRELEDELGIEIfIRRGKRLLGMTEPGKALL 67
 
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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