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Conserved domains on  [gi|503616044|ref|WP_013850120|]
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MULTISPECIES: LysR family transcriptional regulator [Sinorhizobium]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 10444111)

LysR family transcriptional regulator contains an N-terminal DNA-binding domain and a C-terminal substrate-binding domain, which is involved in co-inducer recognition/response to activate the transcription of operons and regulons involved in very diverse functions

CATH:  3.40.190.10
Gene Ontology:  GO:0003700

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
PBP2_CrgA_like_2 cd08471
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
92-295 1.75e-89

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: 265.54  E-value: 1.75e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044  92 GMLTISSPPILGEEILRPILDDFLDLYPTVSVRLLLLDRFVNLVDEGVDIALRIGQLADSSLISTRLGGdVRRVVVASPR 171
Cdd:cd08471    1 GLLTVTAPVLFGRLHVLPIITDFLDAYPEVSVRLLLLDRVVNLLEEGVDVAVRIGHLPDSSLVATRVGS-VRRVVCASPA 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044 172 YLANHPRIEEPADLAKHQILAFTNFGLES-WSFTPAKGssvPRTIQFTPRCIVNSVRAAAASAAAGRGLTRLYSYHVAEY 250
Cdd:cd08471   80 YLARHGTPKHPDDLADHDCIAFTGLSPAPeWRFREGGK---ERSVRVRPRLTVNTVEAAIAAALAGLGLTRVLSYQVAEE 156
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 503616044 251 VRDGRLEIVLADAEHPPLPAHLIAPQGRMSVPKVRAFVDFAAPRL 295
Cdd:cd08471  157 LAAGRLQRVLEDFEPPPLPVHLVHPEGRLAPAKVRAFVDFAVPRL 201
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
4-63 1.97e-16

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


:

Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 72.03  E-value: 1.97e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044    4 IDAMKVFVAAIDEGSLAGAARRLKRSPTAVSRALSFLEAHVGVELLHRTTRTLKLSEAGQ 63
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
 
Name Accession Description Interval E-value
PBP2_CrgA_like_2 cd08471
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
92-295 1.75e-89

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: 265.54  E-value: 1.75e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044  92 GMLTISSPPILGEEILRPILDDFLDLYPTVSVRLLLLDRFVNLVDEGVDIALRIGQLADSSLISTRLGGdVRRVVVASPR 171
Cdd:cd08471    1 GLLTVTAPVLFGRLHVLPIITDFLDAYPEVSVRLLLLDRVVNLLEEGVDVAVRIGHLPDSSLVATRVGS-VRRVVCASPA 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044 172 YLANHPRIEEPADLAKHQILAFTNFGLES-WSFTPAKGssvPRTIQFTPRCIVNSVRAAAASAAAGRGLTRLYSYHVAEY 250
Cdd:cd08471   80 YLARHGTPKHPDDLADHDCIAFTGLSPAPeWRFREGGK---ERSVRVRPRLTVNTVEAAIAAALAGLGLTRVLSYQVAEE 156
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 503616044 251 VRDGRLEIVLADAEHPPLPAHLIAPQGRMSVPKVRAFVDFAAPRL 295
Cdd:cd08471  157 LAAGRLQRVLEDFEPPPLPVHLVHPEGRLAPAKVRAFVDFAVPRL 201
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-297 9.98e-52

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 170.82  E-value: 9.98e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044   1 MDrIDAMKVFVAAIDEGSLAGAARRLKRSPTAVSRALSFLEAHVGVELLHRTTRTLKLSEAGQRYAAACRRVLTDLEEAD 80
Cdd:COG0583    1 MD-LRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAE 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044  81 MLAGGERSAPRGMLTISSPPILGEEILRPILDDFLDLYPTVSVRLLLL--DRFVN-LVDEGVDIALRIGQLADSSLISTR 157
Cdd:COG0583   80 AELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGnsDRLVDaLLEGELDLAIRLGPPPDPGLVARP 159
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044 158 LgGDVRRVVVASPRY-LANHPRieepadlakhqilaftnfgleswsftpakgssvprtiqftprcIVNSVRAAAASAAAG 236
Cdd:COG0583  160 L-GEERLVLVASPDHpLARRAP-------------------------------------------LVNSLEALLAAVAAG 195
                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 503616044 237 RGLTRLYSYHVAEYVRDGRLEIVLADAEHPPLPAHLIAPQGRMSVPKVRAFVDFAAPRLRS 297
Cdd:COG0583  196 LGIALLPRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
10-305 7.78e-37

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 133.58  E-value: 7.78e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044  10 FVAAIDEGSLAGAARRLKRSPTAVSRALSFLEAHVGVELLHRTTRTLKLSEAGQRYAAACRRVLTDLEEADMLAGGERSA 89
Cdd:PRK14997  10 FVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDAIAALQVE 89
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044  90 PRGMLTISSPPILGEEILRPILDDFLDLYPTVSVRLLLLDRFVNLVDEGVDIALRI--GQLADSSLIsTRLGGDVRRVVV 167
Cdd:PRK14997  90 PRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLEATNRRVDVVGEGVDVAIRVrpRPFEDSDLV-MRVLADRGHRLF 168
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044 168 ASPRYLANHPRIEEPADLAKHQILAF-TNFGLESWSFTPAKGSSVprTIQFTPRCIVNSVRAAAASAAAGRGLTRLYSYH 246
Cdd:PRK14997 169 ASPDLIARMGIPSAPAELSHWPGLSLaSGKHIHRWELYGPQGARA--EVHFTPRMITTDMLALREAAMAGVGLVQLPVLM 246
                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 503616044 247 VAEYVRDGRLEIVLADAEHPPLPAHLIAPQGRMSVPKVRAFVDFaaprLRSEFARMAAE 305
Cdd:PRK14997 247 VKEQLAAGELVAVLEEWEPRREVIHAVFPSRRGLLPSVRALVDF----LTEEYARMVEE 301
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
91-296 5.19e-24

LysR substrate binding domain; The structure of this domain is known and is similar to the periplasmic binding proteins. This domain binds a variety of ligands that caries in size and structure, such as amino acids, sugar phosphates, organic acids, metal cations, flavonoids, C6-ring carboxylic acids, H2O2, HOCl, homocysteine, NADPH, ATP, sulphate, muropeptides, acetate, salicylate, citrate, phenol- and quinolone derivatives, acetylserines, fatty acid CoA, shikimate, chorismate, homocysteine, indole-3-acetic acid, Na(I), c-di-GMP, ppGpp and hydrogen peroxide (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 460931 [Multi-domain]  Cd Length: 205  Bit Score: 96.97  E-value: 5.19e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044   91 RGMLTISSPPILGEEILRPILDDFLDLYPTVSVRLLLLD--RFVNLVDEG-VDIALRIGQLADSSLISTRLGgDVRRVVV 167
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNseELLDLLLEGeLDLAIRRGPPDDPGLEARPLG-EEPLVLV 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044  168 ASPRY-LANHPRIEePADLAKHQILAFTNFGLESWSFTPAKGSsvpRTIQFTPRCIVNSVRAAAASAAAGRGLTRLYSYH 246
Cdd:pfam03466  80 APPDHpLARGEPVS-LEDLADEPLILLPPGSGLRDLLDRALRA---AGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSA 155
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 503616044  247 VAEYVRDGRLEIVLADAEHPPLPAHLIAPQGRMSVPKVRAFVDFAAPRLR 296
Cdd:pfam03466 156 VARELADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREALA 205
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
4-63 1.97e-16

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 72.03  E-value: 1.97e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044    4 IDAMKVFVAAIDEGSLAGAARRLKRSPTAVSRALSFLEAHVGVELLHRTTRTLKLSEAGQ 63
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
5-77 3.64e-09

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 56.74  E-value: 3.64e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 503616044   5 DAMKVFVAAIDEGSLAGAARRLKRSPTAVSRALSFLEAHVGVELLHRTTRTLKLSEAGQRYAAACRRVLTDLE 77
Cdd:PRK10094   5 ETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLE 77
 
Name Accession Description Interval E-value
PBP2_CrgA_like_2 cd08471
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
92-295 1.75e-89

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: 265.54  E-value: 1.75e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044  92 GMLTISSPPILGEEILRPILDDFLDLYPTVSVRLLLLDRFVNLVDEGVDIALRIGQLADSSLISTRLGGdVRRVVVASPR 171
Cdd:cd08471    1 GLLTVTAPVLFGRLHVLPIITDFLDAYPEVSVRLLLLDRVVNLLEEGVDVAVRIGHLPDSSLVATRVGS-VRRVVCASPA 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044 172 YLANHPRIEEPADLAKHQILAFTNFGLES-WSFTPAKGssvPRTIQFTPRCIVNSVRAAAASAAAGRGLTRLYSYHVAEY 250
Cdd:cd08471   80 YLARHGTPKHPDDLADHDCIAFTGLSPAPeWRFREGGK---ERSVRVRPRLTVNTVEAAIAAALAGLGLTRVLSYQVAEE 156
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 503616044 251 VRDGRLEIVLADAEHPPLPAHLIAPQGRMSVPKVRAFVDFAAPRL 295
Cdd:cd08471  157 LAAGRLQRVLEDFEPPPLPVHLVHPEGRLAPAKVRAFVDFAVPRL 201
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
92-290 1.37e-63

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: 199.20  E-value: 1.37e-63
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044  92 GMLTISSPPILGEEILRPILDDFLDLYPTVSVRLLLLDRFVNLVDEGVDIALRIGQLADSSLISTRLgGDVRRVVVASPR 171
Cdd:cd08422    1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRL-GPVRRVLVASPA 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044 172 YLANHPRIEEPADLAKHQILAFTNFG-LESWSFTPAKGssvPRTIQFTPRCIVNSVRAAAASAAAGRGLTRLYSYHVAEY 250
Cdd:cd08422   80 YLARHGTPQTPEDLARHRCLGYRLPGrPLRWRFRRGGG---EVEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAED 156
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 503616044 251 VRDGRLEIVLADAEHPPLPAHLIAPQGRMSVPKVRAFVDF 290
Cdd:cd08422  157 LASGRLVRVLPDWRPPPLPIYAVYPSRRHLPAKVRAFIDF 196
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-297 9.98e-52

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 170.82  E-value: 9.98e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044   1 MDrIDAMKVFVAAIDEGSLAGAARRLKRSPTAVSRALSFLEAHVGVELLHRTTRTLKLSEAGQRYAAACRRVLTDLEEAD 80
Cdd:COG0583    1 MD-LRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAE 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044  81 MLAGGERSAPRGMLTISSPPILGEEILRPILDDFLDLYPTVSVRLLLL--DRFVN-LVDEGVDIALRIGQLADSSLISTR 157
Cdd:COG0583   80 AELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGnsDRLVDaLLEGELDLAIRLGPPPDPGLVARP 159
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044 158 LgGDVRRVVVASPRY-LANHPRieepadlakhqilaftnfgleswsftpakgssvprtiqftprcIVNSVRAAAASAAAG 236
Cdd:COG0583  160 L-GEERLVLVASPDHpLARRAP-------------------------------------------LVNSLEALLAAVAAG 195
                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 503616044 237 RGLTRLYSYHVAEYVRDGRLEIVLADAEHPPLPAHLIAPQGRMSVPKVRAFVDFAAPRLRS 297
Cdd:COG0583  196 LGIALLPRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
PBP2_CrgA_like_8 cd08477
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
92-291 4.04e-43

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


Pssm-ID: 176166  Cd Length: 197  Bit Score: 146.61  E-value: 4.04e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044  92 GMLTISSPPILGEEILRPILDDFLDLYPTVSVRLLLLDRFVNLVDEGVDIALRIGQLADSSLISTRLgGDVRRVVVASPR 171
Cdd:cd08477    1 GKLRISAPVTFGSHVLTPALAEYLARYPDVRVDLVLSDRLVDLVEEGFDAAFRIGELADSSLVARPL-APYRMVLCASPD 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044 172 YLANHPRIEEPADLAKHQILAFTNFGLES-WSFTPAKGssvPRTIQFTPRCIVNSVRAAAASAAAGRGLTRLYSYHVAEY 250
Cdd:cd08477   80 YLARHGTPTTPEDLARHECLGFSYWRARNrWRLEGPGG---EVKVPVSGRLTVNSGQALRVAALAGLGIVLQPEALLAED 156
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 503616044 251 VRDGRLEIVLADAEHPPLPAHLIAPQGRMSVPKVRAFVDFA 291
Cdd:cd08477  157 LASGRLVELLPDYLPPPRPMHLLYPPDRRPTPKLRSFIDFL 197
PBP2_CrgA_like_3 cd08472
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
92-292 5.14e-40

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 138.80  E-value: 5.14e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044  92 GMLTISSPPILGEEILRPILDDFLDLYPTVSVRLLLLDRFVNLVDEGVDIALRIGQLADSSLISTRLgGDVRRVVVASPR 171
Cdd:cd08472    1 GRLRVDVPGSLARLLLIPALPDFLARYPDIELDLGVSDRPVDLIREGVDCVIRVGELADSSLVARRL-GELRMVTCASPA 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044 172 YLANHPRIEEPADLAKHQILAFTNFG---LESWSFTPAKGSsvpRTIQFTPRCIVNSVRAAAASAAAGRGLTRLYSYHVA 248
Cdd:cd08472   80 YLARHGTPRHPEDLERHRAVGYFSARtgrVLPWEFQRDGEE---REVKLPSRVSVNDSEAYLAAALAGLGIIQVPRFMVR 156
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 503616044 249 EYVRDGRLEIVLADAEHPPLPAHLIAPQGRMSVPKVRAFVDFAA 292
Cdd:cd08472  157 PHLASGRLVEVLPDWRPPPLPVSLLYPHRRHLSPRVRVFVDWVA 200
PBP2_CrgA_like_1 cd08470
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
92-295 5.55e-39

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: 135.90  E-value: 5.55e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044  92 GMLTISSPPILGEEILRPILDDFLDLYPTVSVRLLLLDRFVNLVDEGVDIALRIGQLADSSLISTRLgGDVRRVVVASPR 171
Cdd:cd08470    1 GLLRITCPVAYGERFIAPLVNDFMQRYPKLEVDIELTNRVVDLVSEGFDLAIRLGRLTDSSLMARRL-ASRRHYVCASPA 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044 172 YLANHPRIEEPADLAKHQILAFTNfglESWSFTpAKGSSVPRTIQFTPRCivNSVRAAAASAAAGRGLTRLYSYHVAEYV 251
Cdd:cd08470   80 YLERHGTPHSLADLDRHNCLLGTS---DHWRFQ-ENGRERSVRVQGRWRC--NSGVALLDAALKGMGLAQLPDYYVDEHL 153
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 503616044 252 RDGRLEIVLADAEHPPLPAHLIAPQGRMSVPKVRAFVDFAAPRL 295
Cdd:cd08470  154 AAGRLVPVLEDYRPPDEGIWALYPHNRHLSPKVRLLVDYLADAL 197
PBP2_CrgA_like_4 cd08473
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
90-290 5.62e-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 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: 136.15  E-value: 5.62e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044  90 PRGMLTISSPPILGEEILRPILDDFLDLYPTVSVRLLLLDRFVNLVDEGVDIALRIGQ--LADSSLISTRLgGDVRRVVV 167
Cdd:cd08473    1 PRGTVRVSCPPALAQELLAPLLPRFMAAYPQVRLQLEATNRRVDLIEEGIDVALRVRFppLEDSSLVMRVL-GQSRQRLV 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044 168 ASPRYLANHPRIEEPADLAKHQILAFTNFGLE-SWSFTPAKGSSvpRTIQFTPRCIVNSVRAAAASAAAGRGLTRLYSYH 246
Cdd:cd08473   80 ASPALLARLGRPRSPEDLAGLPTLSLGDVDGRhSWRLEGPDGES--ITVRHRPRLVTDDLLTLRQAALAGVGIALLPDHL 157
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 503616044 247 VAEYVRDGRLEIVLADAEHPPLPAHLIAPQGRMSVPKVRAFVDF 290
Cdd:cd08473  158 CREALRAGRLVRVLPDWTPPRGIVHAVFPSRRGLLPAVRALIDF 201
PBP2_CrgA_like_9 cd08479
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
92-290 7.81e-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: 135.80  E-value: 7.81e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044  92 GMLTISSPPILGEEILRPILDDFLDLYPTVSVRLLLLDRFVNLVDEGVDIALRIGQLADSSLISTRLGGDvRRVVVASPR 171
Cdd:cd08479    1 GLLRVNASFGFGRRHIAPALSDFAKRYPELEVQLELTDRPVDLVEEGFDLDIRVGDLPDSSLIARKLAPN-RRILCASPA 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044 172 YLANHPRIEEPADLAKHQILAF----TNFGLesWSFTPAKGssvPRTIQFTPRCIVNSVRAAAASAAAGRGLTRLYSYHV 247
Cdd:cd08479   80 YLERHGAPASPEDLARHDCLVIrendEDFGL--WRLRNGDG---EATVRVRGALSSNDGEVVLQWALDGHGIILRSEWDV 154
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 503616044 248 AEYVRDGRLEIVLADAEHPPLPAHLIAPQGRMSVPKVRAFVDF 290
Cdd:cd08479  155 APYLRSGRLVRVLPDWQLPDADIWAVYPSRLSRSARVRVFVDF 197
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
90-291 4.36e-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 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: 133.74  E-value: 4.36e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044  90 PRGMLTISSPPILGEEILRPILDDFLDLYPTVSVRLLLLDRFVNLVDEGVDIALRIGQLADSSLISTRLGGDVRRVVVAS 169
Cdd:cd08474    1 PAGTLRINAPRVAARLLLAPLLARFLARYPDIRLELVVDDGLVDIVAEGFDAGIRLGESVEKDMVAVPLGPPLRMAVVAS 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044 170 PRYLANHPRIEEPADLAKHQILAF---TNFGLESWSFTpaKGsSVPRTIQFTPRCIVNSVRAAAASAAAGRGLTRLYSYH 246
Cdd:cd08474   81 PAYLARHGTPEHPRDLLNHRCIRYrfpTSGALYRWEFE--RG-GRELEVDVEGPLILNDSDLMLDAALDGLGIAYLFEDL 157
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 503616044 247 VAEYVRDGRLEIVLADAEHPPLPAHLIAPQGRMSVPKVRAFVDFA 291
Cdd:cd08474  158 VAEHLASGRLVRVLEDWSPPFPGGYLYYPSRRRVPPALRAFIDFL 202
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
10-305 7.78e-37

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 133.58  E-value: 7.78e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044  10 FVAAIDEGSLAGAARRLKRSPTAVSRALSFLEAHVGVELLHRTTRTLKLSEAGQRYAAACRRVLTDLEEADMLAGGERSA 89
Cdd:PRK14997  10 FVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDAIAALQVE 89
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044  90 PRGMLTISSPPILGEEILRPILDDFLDLYPTVSVRLLLLDRFVNLVDEGVDIALRI--GQLADSSLIsTRLGGDVRRVVV 167
Cdd:PRK14997  90 PRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLEATNRRVDVVGEGVDVAIRVrpRPFEDSDLV-MRVLADRGHRLF 168
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044 168 ASPRYLANHPRIEEPADLAKHQILAF-TNFGLESWSFTPAKGSSVprTIQFTPRCIVNSVRAAAASAAAGRGLTRLYSYH 246
Cdd:PRK14997 169 ASPDLIARMGIPSAPAELSHWPGLSLaSGKHIHRWELYGPQGARA--EVHFTPRMITTDMLALREAAMAGVGLVQLPVLM 246
                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 503616044 247 VAEYVRDGRLEIVLADAEHPPLPAHLIAPQGRMSVPKVRAFVDFaaprLRSEFARMAAE 305
Cdd:PRK14997 247 VKEQLAAGELVAVLEEWEPRREVIHAVFPSRRGLLPSVRALVDF----LTEEYARMVEE 301
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
1-303 2.18e-36

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 132.58  E-value: 2.18e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044   1 MDRIDAMKVFVAAIDEGSLAGAARRLKRSPTAVSRALSFLEAHVGVELLHRTTRTLKLSEAGQRYAAACRRVLTDLEEAD 80
Cdd:PRK10632   1 MERLKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVH 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044  81 MLAGGERSAPRGMLTISSPPILGEEILRPILDDFLDLYPTVSVRLLLLDRFVNLVDEGVDIALRIGQLADSSLISTRLGG 160
Cdd:PRK10632  81 EQLYAFNNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTGIPAPDLIADGLDVVIRVGALQDSSLFSRRLGA 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044 161 dVRRVVVASPRYLANHPRIEEPADLAKHQILAFTNFGLESWSFTPAKGSSvprtIQFTP--RCIVNSVRAAAASAAAGRG 238
Cdd:PRK10632 161 -MPMVVCAAKSYLAQYGTPEKPADLSSHSWLEYSVRPDNEFELIAPEGIS----TRLIPqgRFVTNDPQTLVRWLTAGAG 235
                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 503616044 239 LTRLYSYHVAEYVRDGRLEIVLADAEHPPLPAHLIAPQgRMSVP-KVRAFVDFaaprLRSEFARMA 303
Cdd:PRK10632 236 IAYVPLMWVIDEINRGELEILFPRYQSDPRPVYALYTE-KDKLPlKVQVCINY----LTDYFVEVA 296
PBP2_CrgA_like_7 cd08476
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
92-290 1.23e-34

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 124.66  E-value: 1.23e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044  92 GMLTISSPPILGeeILRPILDDFLDLYPTVSVRLLLLDRFVNLVDEGVDIALRIGQLADSSLISTRLGGdVRRVVVASPR 171
Cdd:cd08476    1 GRLRVSLPLVGG--LLLPVLAAFMQRYPEIELDLDFSDRLVDVIDEGFDAVIRTGELPDSRLMSRRLGS-FRMVLVASPD 77
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044 172 YLANHPRIEEPADLAKHQILAF---TNFGLESWSFTPAKGS---SVPRTIqftprcIVNSVRAAAASAAAGRGLTRLYSY 245
Cdd:cd08476   78 YLARHGTPETPADLAEHACLRYrfpTTGKLEPWPLRGDGGDpelRLPTAL------VCNNIEALIEFALQGLGIACLPDF 151
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 503616044 246 HVAEYVRDGRLEIVLADAEHPPLPAHLIAPQGRMSVPKVRAFVDF 290
Cdd:cd08476  152 SVREALADGRLVTVLDDYVEERGQFRLLWPSSRHLSPKLRVFVDF 196
PBP2_CrgA_like_6 cd08475
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
92-289 5.09e-32

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 118.04  E-value: 5.09e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044  92 GMLTISSPPILGEEILRPILDDFLDLYPTVSVRLLLLDRFVNLVDEGVDIALRIGQLADSSLISTRLGGDVRRVVVASPR 171
Cdd:cd08475    1 GRLRIDLPVAFGRLCVAPLLLELARRHPELELELSFSDRFVDLIEEGIDLAVRIGELADSTGLVARRLGTQRMVLCASPA 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044 172 YLANHPRIEEPADLAKHQILAFTNFG-LESWSFTPAKGSSVPRTIqfTPRCIVNSVRAAAASAAAGRGLTRLYSYHVAEY 250
Cdd:cd08475   81 YLARHGTPRTLEDLAEHQCIAYGRGGqPLPWRLADEQGRLVRFRP--APRLQFDDGEAIADAALAGLGIAQLPTWLVADH 158
                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 503616044 251 VRDGRLEIVLADAEHPPLPAHLIAPQGRMSVPKVRAFVD 289
Cdd:cd08475  159 LQRGELVEVLPELAPEGLPIHAVWPRTRHLPPKVRAAVD 197
PBP2_CrgA_like_10 cd08480
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
92-290 3.19e-28

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: 107.81  E-value: 3.19e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044  92 GMLTISSPPILGEEILRPILDDFLDLYPTVSVRLLLLDRFVNLVDEGVDIALRIGQLADSSLISTRLgGDVRRVVVASPR 171
Cdd:cd08480    1 GRLRVNASVPFGTHFLLPLLPAFLARYPEILVDLSLTDEVVDLLAERTDVAIRVGPLPDSSLVARKL-GESRRVIVASPS 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044 172 YLANHPRIEEPADLAKHQILAFtNF--GLESWSFTPAkGSSVPRTIQFTPRCivNSVRAAAASAAAGRGLTRLYSYHVAE 249
Cdd:cd08480   80 YLARHGTPLTPQDLARHNCLGF-NFrrALPDWPFRDG-GRIVALPVSGNILV--NDGEALRRLALAGAGLARLALFHVAD 155
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 503616044 250 YVRDGRLEIVLAD-AEHPPLPAHLIAPQGRMSVPKVRAFVDF 290
Cdd:cd08480  156 DIAAGRLVPVLEEyNPGDREPIHAVYVGGGRLPARVRAFLDF 197
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
6-289 3.47e-27

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 107.62  E-value: 3.47e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044   6 AMKVFVAAIDEGSLAGAARRLKRSPTAVSRALSFLEAHVGVELLHRTTRTLKLSEAGQRYAAACRRVLTDLEEA--DMLA 83
Cdd:PRK11139  10 ALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEAtrKLRA 89
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044  84 GGERSAprgmLTISSPPILGEEILRPILDDFLDLYPTVSVRLLLLDRFVNLVDEGVDIALRIGQLADSSLISTRLGGDVr 163
Cdd:PRK11139  90 RSAKGA----LTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDRLEDFLRDDVDVAIRYGRGNWPGLRVEKLLDEY- 164
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044 164 RVVVASPRYLANHPRIEEPADLAKHQILA----------FTNFGLESWsfTPAKG---SSVPRTIQftprcivnsvraaa 230
Cdd:PRK11139 165 LLPVCSPALLNGGKPLKTPEDLARHTLLHddsredwrawFRAAGLDDL--NVQQGpifSHSSMALQ-------------- 228
                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 503616044 231 aSAAAGRG--LTRLySYHVAEyVRDGRLEIVLADAEHPPLPAHLIAPQGRMSVPKVRAFVD 289
Cdd:PRK11139 229 -AAIHGQGvaLGNR-VLAQPE-IEAGRLVCPFDTVLPSPNAFYLVCPDSQAELPKVAAFRQ 286
PBP2_CrgA cd08478
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains ...
90-290 6.40e-26

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: 101.65  E-value: 6.40e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044  90 PRGMLTI--SSPPILgeEILRPILDDFLDLYPTVSVRLLLLDRFVNLVDEGVDIALRIGQLADSSLiSTRLGGDVRRVVV 167
Cdd:cd08478    1 PSGLLRVdaATPFVL--HLLAPLIAKFRERYPDIELELVSNEGIIDLIERKTDVAIRIGELTDSTL-HARPLGKSRLRIL 77
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044 168 ASPRYLANHPRIEEPADLAKHQILAFTNFG-LESWSFTPAKGSsvprTIQFTPRCIVNSVRAAAASAAAGRGLTRLYSYH 246
Cdd:cd08478   78 ASPDYLARHGTPQSIEDLAQHQLLGFTEPAsLNTWPIKDADGN----LLKIQPTITASSGETLRQLALSGCGIACLSDFM 153
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 503616044 247 VAEYVRDGRLEIVLAD-AEHPPLPAHLIAPQGRMSVPKVRAFVDF 290
Cdd:cd08478  154 TDKDIAEGRLIPLFAEqTSDVRQPINAVYYRNTALSLRIRCFIDF 198
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
91-296 5.19e-24

LysR substrate binding domain; The structure of this domain is known and is similar to the periplasmic binding proteins. This domain binds a variety of ligands that caries in size and structure, such as amino acids, sugar phosphates, organic acids, metal cations, flavonoids, C6-ring carboxylic acids, H2O2, HOCl, homocysteine, NADPH, ATP, sulphate, muropeptides, acetate, salicylate, citrate, phenol- and quinolone derivatives, acetylserines, fatty acid CoA, shikimate, chorismate, homocysteine, indole-3-acetic acid, Na(I), c-di-GMP, ppGpp and hydrogen peroxide (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 460931 [Multi-domain]  Cd Length: 205  Bit Score: 96.97  E-value: 5.19e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044   91 RGMLTISSPPILGEEILRPILDDFLDLYPTVSVRLLLLD--RFVNLVDEG-VDIALRIGQLADSSLISTRLGgDVRRVVV 167
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNseELLDLLLEGeLDLAIRRGPPDDPGLEARPLG-EEPLVLV 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044  168 ASPRY-LANHPRIEePADLAKHQILAFTNFGLESWSFTPAKGSsvpRTIQFTPRCIVNSVRAAAASAAAGRGLTRLYSYH 246
Cdd:pfam03466  80 APPDHpLARGEPVS-LEDLADEPLILLPPGSGLRDLLDRALRA---AGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSA 155
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 503616044  247 VAEYVRDGRLEIVLADAEHPPLPAHLIAPQGRMSVPKVRAFVDFAAPRLR 296
Cdd:pfam03466 156 VARELADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREALA 205
PRK09801 PRK09801
LysR family transcriptional regulator;
7-262 1.09e-20

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 90.09  E-value: 1.09e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044   7 MKVFVAAIDEGSLAGAARRLKRSPTAVSRALSFLEAHVGVELLHRTTRTLKLSEAGQRYAAACRRVLTDLEEADMLAGGE 86
Cdd:PRK09801  11 LQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVTQI 90
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044  87 RSAPRGMLTISSPPILGEEILRPILDDFLDLYPTVSVRLLLLDRFVNLVDEGVDIALRIGQLADSSLISTRLGGDvRRVV 166
Cdd:PRK09801  91 KTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHFELFDRQIDLVQDNIDLDIRINDEIPDYYIAHLLTKN-KRIL 169
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044 167 VASPRYLANHPRIEEPADLAKHQILAFTNFGLESWSFTPAKGSSvPRTIQFTPRCIVNSVRAAAASAAAGRGLTRLYSYH 246
Cdd:PRK09801 170 CAAPEYLQKYPQPQSLQELSRHDCLVTKERDMTHGIWELGNGQE-KKSVKVSGHLSSNSGEIVLQWALEGKGIMLRSEWD 248
                        250
                 ....*....|....*.
gi 503616044 247 VAEYVRDGRLEIVLAD 262
Cdd:PRK09801 249 VLPFLESGKLVQVLPE 264
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
7-186 5.81e-18

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 82.36  E-value: 5.81e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044   7 MKVFVAAIDEGSLAGAARRLKRSPTAVSRALSFLEAHVGVELLHRTTRTLKLSEAGQRYAAACRRVLTDL-EEADMLAGG 85
Cdd:PRK10086  19 LHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLDTLnQEILDIKNQ 98
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044  86 ERSaprGMLTISSPPILGEEILRPILDDFLDLYPTVSVRLLLLDRFVNLVDEGVDIALRIGQLADSSLISTRLgGDVRRV 165
Cdd:PRK10086  99 ELS---GTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTILTGNENVNFQRAGIDLAIYFDDAPSAQLTHHFL-MDEEIL 174
                        170       180
                 ....*....|....*....|.
gi 503616044 166 VVASPRYLANHPRIEEPADLA 186
Cdd:PRK10086 175 PVCSPEYAERHALTGNPDNLR 195
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
94-289 1.31e-17

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: 79.16  E-value: 1.31e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044  94 LTISSPPILGEEILRPILDDFLDLYPTVSVRLLLLDRFVNLVDEGVDIALRIGQLADSSLISTRLgGDVRRVVVASPRYL 173
Cdd:cd08432    2 LTVSVTPSFAARWLIPRLARFQARHPDIDLRLSTSDRLVDFAREGIDLAIRYGDGDWPGLEAERL-MDEELVPVCSPALL 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044 174 ANHPRIeEPADLAKHQILAFTNFGLESWSFTPAKGSSVP---RTIQFtprcivNSVRAAAASAAAGRGLTRLYSYHVAEY 250
Cdd:cd08432   81 AGLPLL-SPADLARHTLLHDATRPEAWQWWLWAAGVADVdarRGPRF------DDSSLALQAAVAGLGVALAPRALVADD 153
                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 503616044 251 VRDGRLEIVLADAEHPPLPAHLIAPQGRMSVPKVRAFVD 289
Cdd:cd08432  154 LAAGRLVRPFDLPLPSGGAYYLVYPPGRAESPAVAAFRD 192
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
4-63 1.97e-16

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 72.03  E-value: 1.97e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044    4 IDAMKVFVAAIDEGSLAGAARRLKRSPTAVSRALSFLEAHVGVELLHRTTRTLKLSEAGQ 63
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
94-291 6.46e-10

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: 57.61  E-value: 6.46e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044  94 LTISSPPILGEEILRPILDDFLDLYPTVSVRLLLL--DRFVNLVDEG-VDIALRIGQLADSSLISTRLGGDvRRVVVASP 170
Cdd:cd05466    2 LRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGgsSELLEALLEGeLDLAIVALPVDDPGLESEPLFEE-PLVLVVPP 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044 171 RY-LANHPRIeEPADLAKHQILAFTNfGLESWSFTPAKGSSVPrtIQFTPRCIVNSVRAAAASAAAGRGLTrLYSYHVAE 249
Cdd:cd05466   81 DHpLAKRKSV-TLADLADEPLILFER-GSGLRRLLDRAFAEAG--FTPNIALEVDSLEAIKALVAAGLGIA-LLPESAVE 155
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 503616044 250 YVRDGRLEIVLADAEHPPLPAHLIAPQGRMSVPKVRAFVDFA 291
Cdd:cd05466  156 ELADGGLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
PBP2_GcdR_like cd08481
The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, ...
94-289 1.14e-09

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: 56.92  E-value: 1.14e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044  94 LTISSPPILGEEILRPILDDFLDLYPTVSVRLLLLDRFVNLVDEGVDIALRIGQLADSSLISTRLGGDVRrVVVASPRYL 173
Cdd:cd08481    2 LELAVLPTFGTRWLIPRLPDFLARHPDITVNLVTRDEPFDFSQGSFDAAIHFGDPVWPGAESEYLMDEEV-VPVCSPALL 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044 174 ANHPrIEEPADLAKHQIL-------AFTNF----GLESwsFTPAKGssvPRTIQFTPrcIVNSVRAaaasaaaGRGLTRL 242
Cdd:cd08481   81 AGRA-LAAPADLAHLPLLqqttrpeAWRDWfeevGLEV--PTAYRG---MRFEQFSM--LAQAAVA-------GLGVALL 145
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 503616044 243 YSYHVAEYVRDGRLEIVLADAEHPPLPAHLIAPQGRMSVPKVRAFVD 289
Cdd:cd08481  146 PRFLIEEELARGRLVVPFNLPLTSDKAYYLVYPEDKAESPPVQAFRD 192
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
5-77 3.64e-09

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 56.74  E-value: 3.64e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 503616044   5 DAMKVFVAAIDEGSLAGAARRLKRSPTAVSRALSFLEAHVGVELLHRTTRTLKLSEAGQRYAAACRRVLTDLE 77
Cdd:PRK10094   5 ETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLE 77
PBP2_HvrB cd08483
The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an ...
94-289 4.09e-09

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: 55.43  E-value: 4.09e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044  94 LTISSPPILGEEILRPILDDFLDLYPTVSVRLLLLDRFVNLVDEGVDIALRIGQLADSSLISTRLGGdVRRVVVASPRYL 173
Cdd:cd08483    2 LTVTLTPSFASNWLMPRLGSFWAKHPEIELSLLPSADLVDLRPDGIDVAIRYGNGDWPGLESEPLTA-APFVVVAAPGLL 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044 174 ANHPrIEEPADLAKHQIL--AFTNfglESWSFTPAKG---SSVPRTIQFTPRCIVNSVRaaaasaaAGRGLTRLYSYHVA 248
Cdd:cd08483   81 GDRK-VDSLADLAGLPWLqeRGTN---EQRVWLASMGvvpDLERGVTFLPGQLVLEAAR-------AGLGLSIQARALVE 149
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 503616044 249 EYVRDGRLeIVLADAEHPPLPAHLIAPQGRMSvPKVRAFVD 289
Cdd:cd08483  150 PDIAAGRL-TVLFEEEEEGLGYHIVTRPGVLR-PAAKAFVR 188
rbcR CHL00180
LysR transcriptional regulator; Provisional
4-143 4.34e-09

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 56.57  E-value: 4.34e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044   4 IDAMKVFVAAIDEGSLAGAARRLKRSPTAVSRALSFLEAHVGVELLHRTTRTLKLSEAGQ---RYAaacRRVLTDLEEAD 80
Cdd:CHL00180   7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGElllRYG---NRILALCEETC 83
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 503616044  81 MLAGGERSAPRGMLTISSPPILGEEILRPILDDFLDLYPTVSVRLLL-LDRFV--NLVDEGVDIAL 143
Cdd:CHL00180  84 RALEDLKNLQRGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVhSTRRIawNVANGQIDIAI 149
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
10-142 1.04e-08

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 55.35  E-value: 1.04e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044  10 FVAAIDEGSLAGAARRLKRSPTAVSRALSFLEAHVGVELLHRTTRTLKLSEAGQRYAAACRRVLTDLEEADMLAGGERSA 89
Cdd:PRK11242   9 FLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRRAIHDVADL 88
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 503616044  90 PRGMLTISSPPILGEEILRPILDDFLDLYP--TVSVRLLLLDRF-VNLVDEGVDIA 142
Cdd:PRK11242  89 SRGSLRLAMTPTFTAYLIGPLIDAFHARYPgiTLTIREMSQERIeALLADDELDVG 144
PRK10341 PRK10341
transcriptional regulator TdcA;
9-154 6.94e-08

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 52.94  E-value: 6.94e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044   9 VFVAAIDEGSLAGAARRLKRSPTAVSRALSFLEAHVGVELLHRTTRTLKLSEAGQRYAAACRRVLTDLEEADMLAGGERS 88
Cdd:PRK10341  14 VFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEINGMSS 93
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 503616044  89 APRGMLTISSPPILGEEILRPILDDFLDLYPTVSVRLL--LLDRFVNLVDEG-VDIAlrIGQLADSSLI 154
Cdd:PRK10341  94 EAVVDVSFGFPSLIGFTFMSDMINKFKEVFPKAQVSMYeaQLSSFLPAIRDGrLDFA--IGTLSNEMKL 160
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
8-96 3.64e-07

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 50.74  E-value: 3.64e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044   8 KVFVAAIDEGSLAGAARRLKRSPTAVSRALSFLEAHVGVELLHRtTRTLKLSEAGQRYAAACRRVltDLEEADMLAG-GE 86
Cdd:PRK13348   8 EALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQRLLRHLRQV--ALLEADLLSTlPA 84
                         90
                 ....*....|
gi 503616044  87 RSAPRGMLTI 96
Cdd:PRK13348  85 ERGSPPTLAI 94
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
7-148 1.62e-06

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 48.61  E-value: 1.62e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044   7 MKVFVAAIDEGSLAGAARRLKRSPTAVSRALSFLEAHVGVELLHRTTRTLKLSEAGQRYAAACRRVLTDLEEADMLAGGE 86
Cdd:PRK09906   6 LRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKLRARKI 85
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 503616044  87 RSAPRgMLTISSPPILGEEILRPILDDFLDLYPTVSVRLllldrfVNLVDEGVDIALRIGQL 148
Cdd:PRK09906  86 VQEDR-QLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIEL------VSLITTQQEEKLRRGEL 140
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
17-146 4.25e-06

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 47.63  E-value: 4.25e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044  17 GSLAGAARRLKRSPTAVSRALSFLEAHVGVELLHRTTRTLKLSEAGQRYAAACRRVLTDLEEadMLAGGERSAP--RGML 94
Cdd:PRK11074  17 GSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQE--TRRQCQQVANgwRGQL 94
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 503616044  95 TISSPPILGEEILRPILDDFLDLYPtvSVRLLLLDRFVN-----LVDEGVDIAlrIG 146
Cdd:PRK11074  95 SIAVDNIVRPDRTRQLIVDFYRHFD--DVELIIRQEVFNgvwdaLADGRVDIA--IG 147
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
9-123 9.14e-06

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 46.52  E-value: 9.14e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044   9 VFVAAIDEGSLAGAARRLKRSPTAVSRALSFLEAHVGVELLHRTTRTLKLSEAGQRYAAACRRVLTDLEEADMLAGGERS 88
Cdd:PRK11013  11 IFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLFEEVQRSYYGLDRIVSAAESLRE 90
                         90       100       110
                 ....*....|....*....|....*....|....*
gi 503616044  89 APRGMLTISSPPILGEEILRPILDDFLDLYPTVSV 123
Cdd:PRK11013  91 FRQGQLSIACLPVFSQSLLPGLCQPFLARYPDVSL 125
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
1-193 1.25e-05

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 46.16  E-value: 1.25e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044   1 MDRIDAMKVFVAAIDEGSLAGAARRLKRSPTAVSRALSFLEAHVGVELLHRTTRTLKLSEAGQRYAAACRRVLTDLEEAd 80
Cdd:PRK15421   1 MIEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQA- 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044  81 MLAGGERSAPRGMLTISSPPILgeEILRPILDDFLDLYPTVSVRL---LLLDRFVNLVDEGVDIALRIGQLADSSLISTR 157
Cdd:PRK15421  80 LQACNEPQQTRLRIAIECHSCI--QWLTPALENFHKNWPQVEMDFksgVTFDPQPALQQGELDLVMTSDILPRSGLHYSP 157
                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 503616044 158 LGGDVRRVVVASPRYLANHPRIeEPADLAKHQILAF 193
Cdd:PRK15421 158 MFDYEVRLVLAPDHPLAAKTRI-TPEDLASETLLIY 192
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
18-280 1.71e-05

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 45.82  E-value: 1.71e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044  18 SLAGAARRLkrSPTAVSRALSFLEAHVGVELLHRTTRTLKLSEAGQRYAAACRRVLTDLEE-ADMLAGGERSAPRgMLTI 96
Cdd:PRK10082  29 SQAAVSRNV--SQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESnLAELRGGSDYAQR-KIKI 105
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044  97 SSPPILGEEILRPILDdflDLYPTVSVRLLLLDrfvnlVDEGVDiALRIGQladSSLISTRLGGDVRRVVVASPRYL--- 173
Cdd:PRK10082 106 AAAHSLSLGLLPSIIS---QMPPLFTWAIEAID-----VDEAVD-KLREGQ---SDCIFSFHDEDLLEAPFDHIRLFesq 173
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044 174 -----ANHPRIEEPADLAKhqilafTNFGLESWSFTPAKGSSVPRT------IQFTPRCIVNSVRAAAASAAAGRGLTRL 242
Cdd:PRK10082 174 lfpvcASDEHGEALFNLAQ------PHFPLLNYSRNSYMGRLINRTltrhseLSFSTFFVSSMSELLKQVALDGCGIAWL 247
                        250       260       270
                 ....*....|....*....|....*....|....*...
gi 503616044 243 YSYHVAEYVRDGRLEIVLADAEHPPLPAHLIAPQGRMS 280
Cdd:PRK10082 248 PEYAIQQEIRSGQLVVLNRDELVIPIQAYAYRMNTRMN 285
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
4-123 1.78e-05

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 45.79  E-value: 1.78e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044   4 IDAMKVFVAAIDEGSLAGAARRLKRSPTAVSRALSFLEAHVGVELLHRTTRTLKLSEAGQRYAAACRRVLTDLEEADMLA 83
Cdd:PRK15092  13 LDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEACSSL 92
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 503616044  84 ggERSAPRGMLTISSPPILGEEILRPILDDFLDLYPTVSV 123
Cdd:PRK15092  93 --MYSNLQGVLTIGASDDTADTILPFLLNRVSSVYPKLAL 130
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
5-83 3.46e-05

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 44.76  E-value: 3.46e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 503616044   5 DAMKVFVAAIDEGSLAGAARRLKRSPTAVSRALSFLEAHVGVELLHRtTRTLKLSEAGQRYAAACRRVLtdLEEADMLA 83
Cdd:PRK03635   5 KQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRLLRHARQVR--LLEAELLG 80
PBP2_LTTR_beta_lactamase cd08484
The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase ...
107-191 6.06e-05

The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase genes, contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators, BlaA and AmpR, that are involved in control of the expression of beta-lactamase genes. Beta-lactamases are responsible for bacterial resistance to beta-lactam antibiotics such as penicillins. BlaA (a constitutive class A penicillinase) belongs to the LysR family of transcriptional regulators, while BlaB (an inducible class C cephalosporinase or AmpC) can be referred to as a penicillin-binding protein, but it does not act as a beta-lactamase. AmpR regulates the expression of beta-lactamases in many enterobacterial strains and many other gram-negative bacilli. In contrast to BlaA, AmpR acts an activator only in the presence of the beta-lactam inducer. In the absence of the inducer, AmpR acts as a repressor. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176173 [Multi-domain]  Cd Length: 189  Bit Score: 43.13  E-value: 6.06e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044 107 LRPILDDFLDLYPTVSVRLLLLDRFVNLVDEGVDIALRIGQLADSSLISTRLgGDVRRVVVASPRyLAnhPRIEEPADLA 186
Cdd:cd08484   15 LLPRLAEFRQLHPFIDLRLSTNNNRVDIAAEGLDFAIRFGEGAWPGTDATRL-FEAPLSPLCTPE-LA--RRLSEPADLA 90

                 ....*
gi 503616044 187 KHQIL 191
Cdd:cd08484   91 NETLL 95
PRK09986 PRK09986
LysR family transcriptional regulator;
3-202 6.25e-05

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 43.94  E-value: 6.25e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044   3 RID--AMKVFVAAIDEGSLAGAARRLKRSPTAVSRALSFLEAHVGVELLHRTTRTLKLSEAGQRYAAACRRVLTDLEEAd 80
Cdd:PRK09986   6 RIDlkLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQS- 84
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044  81 mLAG----GERSAPRGMLTISSPPILGEeiLRPILDDFLDLYPTVSVRL----------LLLDRfvnLVDEGVDIALRIG 146
Cdd:PRK09986  85 -LARveqiGRGEAGRIEIGIVGTALWGR--LRPAMRHFLKENPNVEWLLrelspsmqmaALERR---ELDAGIWRMADLE 158
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 503616044 147 QLADssLISTRLGGDVRRVVVASPRYLANHPRIeePADLAKHQILAFTNFGLESWS 202
Cdd:PRK09986 159 PNPG--FTSRRLHESAFAVAVPEEHPLASRSSV--PLKALRNEYFITLPFVHSDWG 210
PBP2_BlaA cd08487
The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which ...
107-191 9.43e-05

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: 42.53  E-value: 9.43e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044 107 LRPILDDFLDLYPTVSVRLLLLDRFVNLVDEGVDIALRIGQLADSSLISTRLgGDVRRVVVASPRYLanhPRIEEPADLA 186
Cdd:cd08487   15 LLPRLAEFRQLHPFIELRLRTNNNVVDLATEGLDFAIRFGEGLWPATHNERL-LDAPLSVLCSPEIA---KRLSHPADLI 90

                 ....*
gi 503616044 187 KHQIL 191
Cdd:cd08487   91 NETLL 95
cbl PRK12679
HTH-type transcriptional regulator Cbl;
12-125 1.16e-04

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 43.26  E-value: 1.16e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044  12 AAIDEGSLAGAARRLKRSPTAVSRALSFLEAHVGVEL-LHRTTRTLKLSEAGQRYAAACRRVLTDLEEADMLAGGERSAP 90
Cdd:PRK12679  12 AARQDYNLTEVANMLFTSQSGVSRHIRELEDELGIEIfIRRGKRLLGMTEPGKALLVIAERILNEASNVRRLADLFTNDT 91
                         90       100       110
                 ....*....|....*....|....*....|....*
gi 503616044  91 RGMLTISSPPILGEEILRPILDDFLDLYPTVSVRL 125
Cdd:PRK12679  92 SGVLTIATTHTQARYSLPEVIKAFRELFPEVRLEL 126
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
7-186 3.12e-04

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 41.60  E-value: 3.12e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044   7 MKVFVAAIDEGSLAGAARRLKRSPTAVSRALSFLEAHVGVELLHRTTRTLKLSEAGQ-RYAaacrRVLTDLEEA----DM 81
Cdd:PRK10837   8 LEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRlLYP----RALALLEQAveieQL 83
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044  82 LAGGErsaprGMLTISSPPILGEEILRPILDDFLDLYPTVSVRLLL---LDRFVNLVDEGVDIALRIGQLADSSLISTRL 158
Cdd:PRK10837  84 FREDN-----GALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVgnsQDVINAVLDFRVDIGLIEGPCHSPELISEPW 158
                        170       180
                 ....*....|....*....|....*...
gi 503616044 159 GGDvRRVVVASPrylaNHPRIEEPADLA 186
Cdd:PRK10837 159 LED-ELVVFAAP----DSPLARGPVTLE 181
PRK12680 PRK12680
LysR family transcriptional regulator;
7-125 4.05e-04

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 41.53  E-value: 4.05e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044   7 MKVFVAAID-EGSLAGAARRLKRSPTAVSRALSFLEAHVGVELLHRTTRTLK-LSEAGQRYAAACRRVLTDLEEADMLAG 84
Cdd:PRK12680   6 LRYLVAIADaELNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLEsVTPAGVEVIERARAVLSEANNIRTYAA 85
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 503616044  85 GERSAPRGMLTISSPPILGEEILRPILDDFLDLYPTVSVRL 125
Cdd:PRK12680  86 NQRRESQGQLTLTTTHTQARFVLPPAVAQIKQAYPQVSVHL 126
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
29-125 4.84e-04

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 40.96  E-value: 4.84e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044  29 SPTAVSRALSFLEAHVGVELLHRTTRTLKLSEAGQRYAAACRRVLTDLEEAdmlaggersapRGMLTISSPPILGE---- 104
Cdd:PRK11716   4 SPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQL-----------RHTLDQQGPSLSGElslf 72
                         90       100
                 ....*....|....*....|....*...
gi 503616044 105 -------EILRPILDDFLDLYPTVSVRL 125
Cdd:PRK11716  73 csvtaaySHLPPILDRFRAEHPLVEIKL 100
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
94-291 8.89e-04

C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which activates the transcription of the cysJI operon encoding sulfite reductase, contains the type 2 periplasmic binding fold; CysL, also known as YwfK, is a regular of sulfur metabolism in Bacillus subtilis. Sulfur is required for the synthesis of proteins and essential cofactors in all living organism. Sulfur can be assimilated either from inorganic sources (sulfate and thiosulfate), or from organic sources (sulfate esters, sulfamates, and sulfonates). CysL activates the transcription of the cysJI operon encoding sulfite reductase, which reduces sulfite to sulfide. Both cysL mutant and cysJI mutant are unable to grow using sulfate or sulfite as the sulfur source. Like other LysR-type regulators, CysL also negatively regulates its own transcription. In Escherichia coli, three LysR-type activators are involved in the regulation of sulfur metabolism: CysB, Cbl and MetR. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176112 [Multi-domain]  Cd Length: 201  Bit Score: 39.78  E-value: 8.89e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044  94 LTISSPPILGEEILRPILDDFLDLYPTVSVRLL------LLDRfvnLVDEGVDIALRIGQLADSSLISTRLGGDvRRVVV 167
Cdd:cd08420    2 LRIGASTTIGEYLLPRLLARFRKRYPEVRVSLTignteeIAER---VLDGEIDLGLVEGPVDHPDLIVEPFAED-ELVLV 77
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044 168 ASPRY-LANHPRIeEPADLAKHQIL--------------AFTNFGLeswsftpaKGSSVPRTIQFT-PRCIVNSVRaaaa 231
Cdd:cd08420   78 VPPDHpLAGRKEV-TAEELAAEPWIlrepgsgtrevferALAEAGL--------DGLDLNIVMELGsTEAIKEAVE---- 144
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 503616044 232 saaAGRGLTRLYSYHVAEYVRDGRLEIVlaDAEHPPL--PAHLIAPQGRMSVPKVRAFVDFA 291
Cdd:cd08420  145 ---AGLGISILSRLAVRKELELGRLVAL--PVEGLRLtrPFSLIYHKDKYLSPAAEAFLEFL 201
PBP2_AmpR cd08488
The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in ...
107-191 1.17e-03

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: 39.44  E-value: 1.17e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044 107 LRPILDDFLDLYPTVSVRLLLLDRFVNLVDEGVDIALRIGQLADSSLISTRLGGdVRRVVVASPRyLANHPRieEPADLA 186
Cdd:cd08488   15 LLPRLADFQNRHPFIDLRLSTNNNRVDIAAEGLDYAIRFGSGAWHGIDATRLFE-APLSPLCTPE-LARQLR--EPADLA 90

                 ....*
gi 503616044 187 KHQIL 191
Cdd:cd08488   91 RHTLL 95
PRK09791 PRK09791
LysR family transcriptional regulator;
3-126 1.19e-03

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 40.13  E-value: 1.19e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044   3 RIDAMKVFVAAIDEGSLAGAARRLKRSPTAVSRALSFLEAHVGVELLHRTTRTLKLSEAGQRYAAACRRVLTDLEEADML 82
Cdd:PRK09791   6 KIHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQED 85
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 503616044  83 AGGERSAPRGMLTISSPPILGEEILRPILDDFLDLYPTVSVRLL 126
Cdd:PRK09791  86 IRQRQGQLAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRIM 129
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
7-79 1.65e-03

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 39.67  E-value: 1.65e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 503616044   7 MKVFVAAIDEGSLAGAARRLKRSPTAVSRALSFLEAHVGVELLHRTTRTLKLSEAGQRYAAACRRVLTDLEEA 79
Cdd:PRK11233   6 LKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQA 78
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
19-193 2.49e-03

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 38.82  E-value: 2.49e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044  19 LAGAARRLKRSPTAVSRALSFLEAHVGVELLHRTTRTLK-LSEAGQRYAAACRRVLTDLEEADMLaGGERSAPR-GMLTI 96
Cdd:PRK12682  19 LTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKgLTEPGKAVLDVIERILREVGNIKRI-GDDFSNQDsGTLTI 97
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044  97 SSPPILGEEILRPILDDFLDLYPTVSVRLLLL--DRFVNLVDEGV-DIALRIGQLAD-SSLISTRLGGDVRRVVVASPRY 172
Cdd:PRK12682  98 ATTHTQARYVLPRVVAAFRKRYPKVNLSLHQGspDEIARMVISGEaDIGIATESLADdPDLATLPCYDWQHAVIVPPDHP 177
                        170       180
                 ....*....|....*....|.
gi 503616044 173 LANHPRIEEPaDLAKHQILAF 193
Cdd:PRK12682 178 LAQEERITLE-DLAEYPLITY 197
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
18-126 5.62e-03

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 38.03  E-value: 5.62e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044  18 SLAGAARRLKRSPTAVSRALSFLEAHVGVELLHRT-TRTLKLSEAGQRYAAACRRVLTDLEEADMLAGGERSAPRGMLTI 96
Cdd:PRK12684  18 NLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHgKRLRGLTEPGRIILASVERILQEVENLKRVGKEFAAQDQGNLTI 97
                         90       100       110
                 ....*....|....*....|....*....|
gi 503616044  97 SSPPILGEEILRPILDDFLDLYPTVSVRLL 126
Cdd:PRK12684  98 ATTHTQARYALPAAIKEFKKRYPKVRLSIL 127
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
19-125 7.54e-03

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 37.33  E-value: 7.54e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044  19 LAGAARRLKRSPTAVSRALSFLEAHVGVELLHRT-TRTLKLSEAGQRYAAACRRVLTDLEEADMLAGGERSAPRGMLTIS 97
Cdd:PRK12683  19 LTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRgKRLTGLTEPGKELLQIVERMLLDAENLRRLAEQFADRDSGHLTVA 98
                         90       100
                 ....*....|....*....|....*...
gi 503616044  98 SPPILGEEILRPILDDFLDLYPTVSVRL 125
Cdd:PRK12683  99 TTHTQARYALPKVVRQFKEVFPKVHLAL 126
PBP2_LeuO cd08466
The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an ...
95-192 9.06e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an activator of leucine synthesis operon, contains the type 2 periplasmic binding fold; LeuO, a LysR-type transcriptional regulator, was originally identified as an activator of the leucine synthesis operon (leuABCD). Subsequently, LeuO was found to be not a specific regulator of the leu gene but a global regulator of unrelated various genes. LeuO activates bglGFB (utilization of beta-D-glucoside) and represses cadCBA (lysine decarboxylation) and dsrA (encoding a regulatory small RNA for translational control of rpoS and hns). LeuO also regulates the yjjQ-bglJ operon which coding for a LuxR-type transcription factor. In Salmonella enterica serovar Typhi, LeuO is a positive regulator of ompS1 (encoding an outer membrane), ompS2 (encoding a pathogenicity determinant), and assT, while LeuO represses the expression of OmpX and Tpx. Both osmS1 and osmS2 influence virulence in the mouse model of Salmonella. In Vibrio cholerae, LeuO is involved in control of biofilm formation and in the stringent response. 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: 176155 [Multi-domain]  Cd Length: 200  Bit Score: 36.85  E-value: 9.06e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503616044  95 TISSPPILGEEILRPILDDFLDLYPTVSVRLLLL---DRFVNLVDEGVDIALRIGQLADSSLISTRLGGDvRRVVVASpr 171
Cdd:cd08466    3 NIAANETLDLLLLPRLLARLKQLAPNISLRESPSseeDLFEDLRLQEVDLVIDYVPFRDPSFKSELLFED-ELVCVAR-- 79
                         90       100
                 ....*....|....*....|.
gi 503616044 172 ylANHPRIEEPadLAKHQILA 192
Cdd:cd08466   80 --KDHPRIQGS--LSLEQYLA 96
 
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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