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Conserved domains on  [gi|15595321|ref|NP_248813|]
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transcriptional regulator [Pseudomonas aeruginosa PAO1]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 10444056)

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

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 92-289 1.95e-67

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: 208.83  E-value: 1.95e-67
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321  92 GELRLAAPVGFSGTLITQALKPLLENHRQLRLQLFFQDERIDLVAERIDLAIRVGNLADSSLVARHLGDWSSVLCAAPAY 171
Cdd:cd08422   1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVASPAY 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321 172 LRQRAPINRPEQLTEVDWISLNTSNHLNHLTLSGPGGEVcKLRLEPRVAANGMLAVRQFTLDGLGVSYQPLPEVRDALND 251
Cdd:cd08422  81 LARHGTPQTPEDLARHRCLGYRLPGRPLRWRFRRGGGEV-EVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAEDLAS 159

                       170       180       190
                ....*....|....*....|....*....|....*...
gi 15595321 252 GRLQQLLPEWRIPGLGIYAVTPRREAQPAKVKVAIEAL 289
Cdd:cd08422 160 GRLVRVLPDWRPPPLPIYAVYPSRRHLPAKVRAFIDFL 197
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
4-63 1.00e-19

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


:

Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 80.89  E-value: 1.00e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321     4 LKGMAIFATVVDKGSMAAAAQSLGMTPSAVSQQIRKLESRAQVTLLHRTTRRLTLTEAGE 63
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
 
Name Accession Description Interval E-value
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 92-289 1.95e-67

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: 208.83  E-value: 1.95e-67
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321  92 GELRLAAPVGFSGTLITQALKPLLENHRQLRLQLFFQDERIDLVAERIDLAIRVGNLADSSLVARHLGDWSSVLCAAPAY 171
Cdd:cd08422   1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVASPAY 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321 172 LRQRAPINRPEQLTEVDWISLNTSNHLNHLTLSGPGGEVcKLRLEPRVAANGMLAVRQFTLDGLGVSYQPLPEVRDALND 251
Cdd:cd08422  81 LARHGTPQTPEDLARHRCLGYRLPGRPLRWRFRRGGGEV-EVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAEDLAS 159

                       170       180       190
                ....*....|....*....|....*....|....*...
gi 15595321 252 GRLQQLLPEWRIPGLGIYAVTPRREAQPAKVKVAIEAL 289
Cdd:cd08422 160 GRLVRVLPDWRPPPLPIYAVYPSRRHLPAKVRAFIDFL 197
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-294 8.35e-60

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 191.23  E-value: 8.35e-60
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321   1 MDsLKGMAIFATVVDKGSMAAAAQSLGMTPSAVSQQIRKLESRAQVTLLHRTTRRLTLTEAGEAFYRSCAQMLAIAEEAE 80
Cdd:COG0583   1 MD-LRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAE 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321  81 RRLGEWRDAPVGELRLAAPVGFSGTLITQALKPLLENHRQLRLQLF--FQDERID-LVAERIDLAIRVGNLADSSLVARH 157
Cdd:COG0583  80 AELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELRegNSDRLVDaLLEGELDLAIRLGPPPDPGLVARP 159

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321 158 LGDWSSVLCAAPAY-LRQRAPInrpeqltevdwislntsnhlnhltlsgpggevcklrleprvaANGMLAVRQFTLDGLG 236
Cdd:COG0583 160 LGEERLVLVASPDHpLARRAPL------------------------------------------VNSLEALLAAVAAGLG 197

                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 15595321 237 VSYQPLPEVRDALNDGRLQQLLPEWRIPGLGIYAVTPRREAQPAKVKVAIEALRRAFA 294
Cdd:COG0583 198 IALLPRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALA 255
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
1-294 1.53e-54

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 179.57  E-value: 1.53e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321    1 MDSLKGMAIFATVVDKGSMAAAAQSLGMTPSAVSQQIRKLESRAQVTLLHRTTRRLTLTEAGEAFYRSCAQMLAIAEEAE 80
Cdd:PRK10632   1 MERLKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVH 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321   81 RRLGEWRDAPVGELRlaapVGFSGTLITQALKPL----LENHRQLRLQLFFQDERIDLVAERIDLAIRVGNLADSSLVAR 156
Cdd:PRK10632  81 EQLYAFNNTPIGTLR----IGCSSTMAQNVLAGLtakmLKEYPGLSVNLVTGIPAPDLIADGLDVVIRVGALQDSSLFSR 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321  157 HLGDWSSVLCAAPAYLRQRAPINRPEQLTEVDWISLNTSNHlNHLTLSGPGGEVCKLRLEPRVAANGMLAVRQFTLDGLG 236
Cdd:PRK10632 157 RLGAMPMVVCAAKSYLAQYGTPEKPADLSSHSWLEYSVRPD-NEFELIAPEGISTRLIPQGRFVTNDPQTLVRWLTAGAG 235

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 15595321  237 VSYQPLPEVRDALNDGRLQQLLPEWRIPGLGIYAVTPRREAQPAKVKVAIEALRRAFA 294
Cdd:PRK10632 236 IAYVPLMWVIDEINRGELEILFPRYQSDPRPVYALYTEKDKLPLKVQVCINYLTDYFV 293
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 92-294 5.85e-30

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


Pssm-ID: 460931 [Multi-domain]  Cd Length: 205  Bit Score: 112.38  E-value: 5.85e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321    92 GELRLAAPVGFSGTLITQALKPLLENHRQLRLQLFFQD--ERIDLVAE-RIDLAIRVGNLADSSLVARHLGDWSSVLCAA 168
Cdd:pfam03466   2 GRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNseELLDLLLEgELDLAIRRGPPDDPGLEARPLGEEPLVLVAP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321   169 PAY-LRQRAPInRPEQLTEVDWISLNTSNHLNHLTLSGPGGEvcKLRLEPRVAANGMLAVRQFTLDGLGVSYQPLPEVRD 247
Cdd:pfam03466  82 PDHpLARGEPV-SLEDLADEPLILLPPGSGLRDLLDRALRAA--GLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAR 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 15595321   248 ALNDGRLQQL-LPEWRIPgLGIYAVTPRREAQPAKVKVAIEALRRAFA 294
Cdd:pfam03466 159 ELADGRLVALpLPEPPLP-RELYLVWRKGRPLSPAVRAFIEFLREALA 205
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
4-63 1.00e-19

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 80.89  E-value: 1.00e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321     4 LKGMAIFATVVDKGSMAAAAQSLGMTPSAVSQQIRKLESRAQVTLLHRTTRRLTLTEAGE 63
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
10-97 4.04e-12

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 65.18  E-value: 4.04e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321   10 FATVVDKGSMAAAAQSLGMTPSAVSQQIRKLESRAQVTLLHRtTRRLTLTEAGEAFYRSCAQMLAIAEEAERRLGEWRDA 89
Cdd:PRK03635  10 LAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRLLRHARQVRLLEAELLGELPALDGT 88


                 ....*...
gi 15595321   90 PVgELRLA 97
Cdd:PRK03635  89 PL-TLSIA 95
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 10-260 4.83e-12

transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity. [Cellular processes, Toxin production and resistance, DNA metabolism, DNA replication, recombination, and repair, Regulatory functions, DNA interactions]


Pssm-ID: 274509 [Multi-domain]  Cd Length: 292  Bit Score: 64.94  E-value: 4.83e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321    10 FATVVDKGSMAAAAQSLGMTPSAVSQQIRKLESRAQVTLLHRtTRRLTLTEAGEAFYRSCAQMLAIAEEAERRLGEWRDA 89
Cdd:TIGR03298   9 LAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVR-TQPCRATEAGQRLLRHARQVRLLEAELLAELPGLAPG 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321    90 PVGELRLAAPVGFSGTLITQALKPLLENHRqLRLQLFFQDEriDLVAERI---DLAIRVGNLAD--SSLVARHLGDWSSV 164
Cdd:TIGR03298  88 APTRLTIAVNADSLATWFLPALAPVLAREG-VLLDLVVEDQ--DHTAELLrsgEVLGAVTTEAKpvPGCRVVPLGAMRYL 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321   165 LCAAPAYLR------------QRAPI---NRPEQLtEVDWISlntsnHLNHLTLSGPGGEVcklrlePRVAANGmlavrQ 229
Cdd:TIGR03298 165 AVASPAFAAryfpdgvtaaalARAPVivfNRKDDL-QDRFLR-----RLFGLPVSPPRHYV------PSSEGFV-----D 227

                         250       260       270
                  ....*....|....*....|....*....|.
gi 15595321   230 FTLDGLGVSYQPLPEVRDALNDGRLQQLLPE 260
Cdd:TIGR03298 228 AARAGLGWGMVPELQAEPHLAAGRLVELAPG 258
HTH_MARR smart00347
helix_turn_helix multiple antibiotic resistance protein;
18-83 7.59e-04

helix_turn_helix multiple antibiotic resistance protein;


Pssm-ID: 197670 [Multi-domain]  Cd Length: 101  Bit Score: 38.34  E-value: 7.59e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321     18 SMAAAAQSLGMTPSAVSQQIRKLESRAQVTLLH----RTTRRLTLTEAGEAFYRscaQMLAIAEEAERRL 83
Cdd:smart00347  26 SVSELAKRLGVSPSTVTRVLDRLEKKGLVRREPspedRRSVLVSLTEEGRELIE---QLLEARSETLAEL 92
MarR COG1846
DNA-binding transcriptional regulator, MarR family [Transcription];
18-83 8.80e-04

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


Pssm-ID: 441451 [Multi-domain]  Cd Length: 142  Bit Score: 38.80  E-value: 8.80e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15595321  18 SMAAAAQSLGMTPSAVSQQIRKLESRAqvtLLHRTT-------RRLTLTEAGEAFYRscaQMLAIAEEAERRL 83
Cdd:COG1846  54 TQSELAERLGLTKSTVSRLLDRLEEKG---LVEREPdpedrraVLVRLTEKGRALLE---EARPALEALLAEL 120
 
Name Accession Description Interval E-value
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 92-289 1.95e-67

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: 208.83  E-value: 1.95e-67
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321  92 GELRLAAPVGFSGTLITQALKPLLENHRQLRLQLFFQDERIDLVAERIDLAIRVGNLADSSLVARHLGDWSSVLCAAPAY 171
Cdd:cd08422   1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVASPAY 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321 172 LRQRAPINRPEQLTEVDWISLNTSNHLNHLTLSGPGGEVcKLRLEPRVAANGMLAVRQFTLDGLGVSYQPLPEVRDALND 251
Cdd:cd08422  81 LARHGTPQTPEDLARHRCLGYRLPGRPLRWRFRRGGGEV-EVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAEDLAS 159

                       170       180       190
                ....*....|....*....|....*....|....*...
gi 15595321 252 GRLQQLLPEWRIPGLGIYAVTPRREAQPAKVKVAIEAL 289
Cdd:cd08422 160 GRLVRVLPDWRPPPLPIYAVYPSRRHLPAKVRAFIDFL 197
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-294 8.35e-60

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 191.23  E-value: 8.35e-60
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321   1 MDsLKGMAIFATVVDKGSMAAAAQSLGMTPSAVSQQIRKLESRAQVTLLHRTTRRLTLTEAGEAFYRSCAQMLAIAEEAE 80
Cdd:COG0583   1 MD-LRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAE 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321  81 RRLGEWRDAPVGELRLAAPVGFSGTLITQALKPLLENHRQLRLQLF--FQDERID-LVAERIDLAIRVGNLADSSLVARH 157
Cdd:COG0583  80 AELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELRegNSDRLVDaLLEGELDLAIRLGPPPDPGLVARP 159

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321 158 LGDWSSVLCAAPAY-LRQRAPInrpeqltevdwislntsnhlnhltlsgpggevcklrleprvaANGMLAVRQFTLDGLG 236
Cdd:COG0583 160 LGEERLVLVASPDHpLARRAPL------------------------------------------VNSLEALLAAVAAGLG 197

                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 15595321 237 VSYQPLPEVRDALNDGRLQQLLPEWRIPGLGIYAVTPRREAQPAKVKVAIEALRRAFA 294
Cdd:COG0583 198 IALLPRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALA 255
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
1-294 1.53e-54

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 179.57  E-value: 1.53e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321    1 MDSLKGMAIFATVVDKGSMAAAAQSLGMTPSAVSQQIRKLESRAQVTLLHRTTRRLTLTEAGEAFYRSCAQMLAIAEEAE 80
Cdd:PRK10632   1 MERLKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVH 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321   81 RRLGEWRDAPVGELRlaapVGFSGTLITQALKPL----LENHRQLRLQLFFQDERIDLVAERIDLAIRVGNLADSSLVAR 156
Cdd:PRK10632  81 EQLYAFNNTPIGTLR----IGCSSTMAQNVLAGLtakmLKEYPGLSVNLVTGIPAPDLIADGLDVVIRVGALQDSSLFSR 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321  157 HLGDWSSVLCAAPAYLRQRAPINRPEQLTEVDWISLNTSNHlNHLTLSGPGGEVCKLRLEPRVAANGMLAVRQFTLDGLG 236
Cdd:PRK10632 157 RLGAMPMVVCAAKSYLAQYGTPEKPADLSSHSWLEYSVRPD-NEFELIAPEGISTRLIPQGRFVTNDPQTLVRWLTAGAG 235

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 15595321  237 VSYQPLPEVRDALNDGRLQQLLPEWRIPGLGIYAVTPRREAQPAKVKVAIEALRRAFA 294
Cdd:PRK10632 236 IAYVPLMWVIDEINRGELEILFPRYQSDPRPVYALYTEKDKLPLKVQVCINYLTDYFV 293
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 1-294 3.92e-47

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 160.16  E-value: 3.92e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321    1 MDSLKGMAIFATVVDKGSMAAAAQSLGMTPSAVSQQIRKLESRAQVTLLHRTTRRLTLTEAGEAFYRSCAQMLAIAEEAE 80
Cdd:PRK14997   1 KTDLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321   81 RRLGEWRDAPVGELRLAAPVGFSGTLITQALKPLLENHRQLRLQLFFQDERIDLVAERIDLAIRV--GNLADSSLVARHL 158
Cdd:PRK14997  81 DAIAALQVEPRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLEATNRRVDVVGEGVDVAIRVrpRPFEDSDLVMRVL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321  159 GDWSSVLCAAPAYLRQRAPINRPEQLTEVDWISLNTSNHLNHLTLSGPGGEVCKLRLEPRVAANGMLAVRQFTLDGLGVS 238
Cdd:PRK14997 161 ADRGHRLFASPDLIARMGIPSAPAELSHWPGLSLASGKHIHRWELYGPQGARAEVHFTPRMITTDMLALREAAMAGVGLV 240

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 15595321  239 YQPLPEVRDALNDGRLQQLLPEWRIPGLGIYAVTPRREAQPAKVKVAIEALRRAFA 294
Cdd:PRK14997 241 QLPVLMVKEQLAAGELVAVLEEWEPRREVIHAVFPSRRGLLPSVRALVDFLTEEYA 296
PBP2_CrgA_like_4 cd08473
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 90-289 7.99e-44

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 148.47  E-value: 7.99e-44
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321  90 PVGELRLAAPVGFSGTLITQALKPLLENHRQLRLQLFFQDERIDLVAERIDLAIRV--GNLADSSLVARHLGDWSSVLCA 167
Cdd:cd08473   1 PRGTVRVSCPPALAQELLAPLLPRFMAAYPQVRLQLEATNRRVDLIEEGIDVALRVrfPPLEDSSLVMRVLGQSRQRLVA 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321 168 APAYLRQRAPINRPEQLTEVDWISLNTSNHLNHLTLSGPGGEVCKLRLEPRVAANGMLAVRQFTLDGLGVSYQPLPEVRD 247
Cdd:cd08473  81 SPALLARLGRPRSPEDLAGLPTLSLGDVDGRHSWRLEGPDGESITVRHRPRLVTDDLLTLRQAALAGVGIALLPDHLCRE 160

                       170       180       190       200
                ....*....|....*....|....*....|....*....|..
gi 15595321 248 ALNDGRLQQLLPEWRIPGLGIYAVTPRREAQPAKVKVAIEAL 289
Cdd:cd08473 161 ALRAGRLVRVLPDWTPPRGIVHAVFPSRRGLLPAVRALIDFL 202
PBP2_CrgA_like_8 cd08477
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-289 2.74e-41

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: 141.60  E-value: 2.74e-41
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321  92 GELRLAAPVGFSGTLITQALKPLLENHRQLRLQLFFQDERIDLVAERIDLAIRVGNLADSSLVARHLGDWSSVLCAAPAY 171
Cdd:cd08477   1 GKLRISAPVTFGSHVLTPALAEYLARYPDVRVDLVLSDRLVDLVEEGFDAAFRIGELADSSLVARPLAPYRMVLCASPDY 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321 172 LRQRAPINRPEQLTEVDWISLNTSNHLNHLTLSGPGGEVcKLRLEPRVAANGMLAVRQFTLDGLGVSYQPLPEVRDALND 251
Cdd:cd08477  81 LARHGTPTTPEDLARHECLGFSYWRARNRWRLEGPGGEV-KVPVSGRLTVNSGQALRVAALAGLGIVLQPEALLAEDLAS 159

                       170       180       190
                ....*....|....*....|....*....|....*...
gi 15595321 252 GRLQQLLPEWRIPGLGIYAVTPRREAQPAKVKVAIEAL 289
Cdd:cd08477 160 GRLVELLPDYLPPPRPMHLLYPPDRRPTPKLRSFIDFL 197
PBP2_CrgA_like_9 cd08479
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-289 5.82e-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: 5.82e-39
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321  92 GELRLAAPVGFSGTLITQALKPLLENHRQLRLQLFFQDERIDLVAERIDLAIRVGNLADSSLVARHLGDWSSVLCAAPAY 171
Cdd:cd08479   1 GLLRVNASFGFGRRHIAPALSDFAKRYPELEVQLELTDRPVDLVEEGFDLDIRVGDLPDSSLIARKLAPNRRILCASPAY 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321 172 LRQRAPINRPEQLTEVDWISLNTSNHLNHL-TLSGPGGEVcKLRLEPRVAANGMLAVRQFTLDGLGVSYQPLPEVRDALN 250
Cdd:cd08479  81 LERHGAPASPEDLARHDCLVIRENDEDFGLwRLRNGDGEA-TVRVRGALSSNDGEVVLQWALDGHGIILRSEWDVAPYLR 159

                       170       180       190
                ....*....|....*....|....*....|....*....
gi 15595321 251 DGRLQQLLPEWRIPGLGIYAVTPRREAQPAKVKVAIEAL 289
Cdd:cd08479 160 SGRLVRVLPDWQLPDADIWAVYPSRLSRSARVRVFVDFL 198
PBP2_CrgA_like_6 cd08475
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-289 5.33e-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 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: 133.06  E-value: 5.33e-38
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321  92 GELRLAAPVGFSGTLITQALKPLLENHRQLRLQLFFQDERIDLVAERIDLAIRVGNLADSS-LVARHLGDWSSVLCAAPA 170
Cdd:cd08475   1 GRLRIDLPVAFGRLCVAPLLLELARRHPELELELSFSDRFVDLIEEGIDLAVRIGELADSTgLVARRLGTQRMVLCASPA 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321 171 YLRQRAPINRPEQLTEVDWISLNTSNHLNHLTLSGPGGEVCKLRLEPRVAANGMLAVRQFTLDGLGVSYQPLPEVRDALN 250
Cdd:cd08475  81 YLARHGTPRTLEDLAEHQCIAYGRGGQPLPWRLADEQGRLVRFRPAPRLQFDDGEAIADAALAGLGIAQLPTWLVADHLQ 160

                       170       180       190
                ....*....|....*....|....*....|....*....
gi 15595321 251 DGRLQQLLPEWRIPGLGIYAVTPRREAQPAKVKVAIEAL 289
Cdd:cd08475 161 RGELVEVLPELAPEGLPIHAVWPRTRHLPPKVRAAVDAL 199
PBP2_CrgA_like_2 cd08471
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-293 5.05e-36

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: 128.03  E-value: 5.05e-36
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321  92 GELRLAAPVGFSGTLITQALKPLLENHRQLRLQLFFQDERIDLVAERIDLAIRVGNLADSSLVARHLGDWSSVLCAAPAY 171
Cdd:cd08471   1 GLLTVTAPVLFGRLHVLPIITDFLDAYPEVSVRLLLLDRVVNLLEEGVDVAVRIGHLPDSSLVATRVGSVRRVVCASPAY 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321 172 LRQRAPINRPEQLTEVDWISLNTSNHLNHLTLsGPGGEVCKLRLEPRVAANGMLAVRQFTLDGLGV----SYQplpeVRD 247
Cdd:cd08471  81 LARHGTPKHPDDLADHDCIAFTGLSPAPEWRF-REGGKERSVRVRPRLTVNTVEAAIAAALAGLGLtrvlSYQ----VAE 155

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*.
gi 15595321 248 ALNDGRLQQLLPEWRIPGLGIYAVTPRREAQPAKVkvaiealrRAF 293
Cdd:cd08471 156 ELAAGRLQRVLEDFEPPPLPVHLVHPEGRLAPAKV--------RAF 193
PRK09801 PRK09801
LysR family transcriptional regulator;
5-290 1.24e-35

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 130.16  E-value: 1.24e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321    5 KGMAIFATVVDKGSMAAAAQSLGMTPSAVSQQIRKLESRAQVTLLHRTTRRLTLTEAGEAFYRSCAQMLAIAEEAERRLG 84
Cdd:PRK09801   9 KDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVT 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321   85 EWRDAPVGELRLAAPVGFSGTLITQALKPLLENHRQLRLQLFFQDERIDLVAERIDLAIRVGNLADSSLVARHLGDWSSV 164
Cdd:PRK09801  89 QIKTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHFELFDRQIDLVQDNIDLDIRINDEIPDYYIAHLLTKNKRI 168

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321  165 LCAAPAYLRQRAPINRPEQLTEVDWISLNTSNHLNHLTLSGPGGEVCKLRLEPRVAANGMLAVRQFTLDGLGVSYQPLPE 244
Cdd:PRK09801 169 LCAAPEYLQKYPQPQSLQELSRHDCLVTKERDMTHGIWELGNGQEKKSVKVSGHLSSNSGEIVLQWALEGKGIMLRSEWD 248

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*.
gi 15595321  245 VRDALNDGRLQQLLPEWrIPGLGIYAVTPRREAQPAKVKVAIEALR 290
Cdd:PRK09801 249 VLPFLESGKLVQVLPEY-AQSANIWAVYREPLYRSMKLRVCVEFLA 293
PBP2_CrgA_like_3 cd08472
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-287 1.22e-34

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


Pssm-ID: 176161  Cd Length: 202  Bit Score: 124.55  E-value: 1.22e-34
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321  92 GELRLAAPVGFSGTLITQALKPLLENHRQLRLQLFFQDERIDLVAERIDLAIRVGNLADSSLVARHLGDWSSVLCAAPAY 171
Cdd:cd08472   1 GRLRVDVPGSLARLLLIPALPDFLARYPDIELDLGVSDRPVDLIREGVDCVIRVGELADSSLVARRLGELRMVTCASPAY 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321 172 LRQRAPINRPEQLTE---VDWISlntsnHLNHLTLS---GPGGEVCKLRLEPRVAANGMLAVRQFTLDGLGVSYQPLPEV 245
Cdd:cd08472  81 LARHGTPRHPEDLERhraVGYFS-----ARTGRVLPwefQRDGEEREVKLPSRVSVNDSEAYLAAALAGLGIIQVPRFMV 155

                       170       180       190       200
                ....*....|....*....|....*....|....*....|..
gi 15595321 246 RDALNDGRLQQLLPEWRIPGLGIYAVTPRREAQPAKVKVAIE 287
Cdd:cd08472 156 RPHLASGRLVEVLPDWRPPPLPVSLLYPHRRHLSPRVRVFVD 197
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 90-289 2.28e-31

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


Pssm-ID: 176163 [Multi-domain]  Cd Length: 202  Bit Score: 116.02  E-value: 2.28e-31
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321  90 PVGELRLAAPVGFSGTLITQALKPLLENHRQLRLQLFFQDERIDLVAERIDLAIRVGNLADSSLVARHLG-DWSSVLCAA 168
Cdd:cd08474   1 PAGTLRINAPRVAARLLLAPLLARFLARYPDIRLELVVDDGLVDIVAEGFDAGIRLGESVEKDMVAVPLGpPLRMAVVAS 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321 169 PAYLRQRAPINRPEQLTEVDWIS--LNTSNHLNHLTLSGPGGEVcKLRLEPRVAANGMLAVRQFTLDGLGVSYQPLPEVR 246
Cdd:cd08474  81 PAYLARHGTPEHPRDLLNHRCIRyrFPTSGALYRWEFERGGREL-EVDVEGPLILNDSDLMLDAALDGLGIAYLFEDLVA 159

                       170       180       190       200
                ....*....|....*....|....*....|....*....|...
gi 15595321 247 DALNDGRLQQLLPEWRIPGLGIYAVTPRREAQPAKVKVAIEAL 289
Cdd:cd08474 160 EHLASGRLVRVLEDWSPPFPGGYLYYPSRRRVPPALRAFIDFL 202
PBP2_CrgA_like_1 cd08470
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-292 2.74e-31

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: 115.87  E-value: 2.74e-31
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321  92 GELRLAAPVGFSGTLITQALKPLLENHRQLRLQLFFQDERIDLVAERIDLAIRVGNLADSSLVARHLGDWSSVLCAAPAY 171
Cdd:cd08470   1 GLLRITCPVAYGERFIAPLVNDFMQRYPKLEVDIELTNRVVDLVSEGFDLAIRLGRLTDSSLMARRLASRRHYVCASPAY 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321 172 LRQRAPINRPEQLTEVDWIsLNTSNHLNHLTlsgpGGEVCKLRLEPRVAANGMLAVRQFTLDGLGVSYQPLPEVRDALND 251
Cdd:cd08470  81 LERHGTPHSLADLDRHNCL-LGTSDHWRFQE----NGRERSVRVQGRWRCNSGVALLDAALKGMGLAQLPDYYVDEHLAA 155

                       170       180       190       200
                ....*....|....*....|....*....|....*....|.
gi 15595321 252 GRLQQLLPEWRIPGLGIYAVTPRREAQPAKVKVAIEALRRA 292
Cdd:cd08470 156 GRLVPVLEDYRPPDEGIWALYPHNRHLSPKVRLLVDYLADA 196
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 92-294 5.85e-30

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


Pssm-ID: 460931 [Multi-domain]  Cd Length: 205  Bit Score: 112.38  E-value: 5.85e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321    92 GELRLAAPVGFSGTLITQALKPLLENHRQLRLQLFFQD--ERIDLVAE-RIDLAIRVGNLADSSLVARHLGDWSSVLCAA 168
Cdd:pfam03466   2 GRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNseELLDLLLEgELDLAIRRGPPDDPGLEARPLGEEPLVLVAP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321   169 PAY-LRQRAPInRPEQLTEVDWISLNTSNHLNHLTLSGPGGEvcKLRLEPRVAANGMLAVRQFTLDGLGVSYQPLPEVRD 247
Cdd:pfam03466  82 PDHpLARGEPV-SLEDLADEPLILLPPGSGLRDLLDRALRAA--GLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAR 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 15595321   248 ALNDGRLQQL-LPEWRIPgLGIYAVTPRREAQPAKVKVAIEALRRAFA 294
Cdd:pfam03466 159 ELADGRLVALpLPEPPLP-RELYLVWRKGRPLSPAVRAFIEFLREALA 205
PBP2_CrgA_like_7 cd08476
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-286 2.84e-27

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: 105.02  E-value: 2.84e-27
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321  92 GELRLAAPVGfsGTLITQALKPLLENHRQLRLQLFFQDERIDLVAERIDLAIRVGNLADSSLVARHLGDWSSVLCAAPAY 171
Cdd:cd08476   1 GRLRVSLPLV--GGLLLPVLAAFMQRYPEIELDLDFSDRLVDVIDEGFDAVIRTGELPDSRLMSRRLGSFRMVLVASPDY 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321 172 LRQRAPINRPEQLTEVDWI--SLNTSNHLNHLTLSGPGGEVcKLRLEPRVAANGMLAVRQFTLDGLGVSYQPLPEVRDAL 249
Cdd:cd08476  79 LARHGTPETPADLAEHACLryRFPTTGKLEPWPLRGDGGDP-ELRLPTALVCNNIEALIEFALQGLGIACLPDFSVREAL 157

                       170       180       190
                ....*....|....*....|....*....|....*..
gi 15595321 250 NDGRLQQLLPEWRIPGLGIYAVTPRREAQPAKVKVAI 286
Cdd:cd08476 158 ADGRLVTVLDDYVEERGQFRLLWPSSRHLSPKLRVFV 194
PBP2_CrgA cd08478
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains ...
 90-289 5.19e-25

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: 99.34  E-value: 5.19e-25
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321  90 PVGELRLAAPVGFSGTLITQALKPLLENHRQLRLQLFFQDERIDLVAERIDLAIRVGNLADSSLVARHLGDWSSVLCAAP 169
Cdd:cd08478   1 PSGLLRVDAATPFVLHLLAPLIAKFRERYPDIELELVSNEGIIDLIERKTDVAIRIGELTDSTLHARPLGKSRLRILASP 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321 170 AYLRQRAPINRPEQLTEVDWISLNTSNHLNHLTLSGPGGEvcKLRLEPRVAANGMLAVRQFTLDGLGVSYQPLPEVRDAL 249
Cdd:cd08478  81 DYLARHGTPQSIEDLAQHQLLGFTEPASLNTWPIKDADGN--LLKIQPTITASSGETLRQLALSGCGIACLSDFMTDKDI 158

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....
gi 15595321 250 NDGRLQQLLPE----WRIPglgIYAVTPRREAQPAKVKVAIEAL 289
Cdd:cd08478 159 AEGRLIPLFAEqtsdVRQP---INAVYYRNTALSLRIRCFIDFL 199
PBP2_CrgA_like_10 cd08480
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-289 1.76e-23

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: 95.10  E-value: 1.76e-23
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321  92 GELRLAAPVGFSGTLITQALKPLLENHRQLRLQLFFQDERIDLVAERIDLAIRVGNLADSSLVARHLGDWSSVLCAAPAY 171
Cdd:cd08480   1 GRLRVNASVPFGTHFLLPLLPAFLARYPEILVDLSLTDEVVDLLAERTDVAIRVGPLPDSSLVARKLGESRRVIVASPSY 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321 172 LRQRAPINRPEQLTEVDWISLNTSNHLNHLTLSGPGGEVCKLRLEPRVAANGMlAVRQFTLDGLGVSYQPLPEVRDALND 251
Cdd:cd08480  81 LARHGTPLTPQDLARHNCLGFNFRRALPDWPFRDGGRIVALPVSGNILVNDGE-ALRRLALAGAGLARLALFHVADDIAA 159

                       170       180       190       200
                ....*....|....*....|....*....|....*....|
gi 15595321 252 GRLQQLLPEWRiPG--LGIYAVTPRREAQPAKVKVAIEAL 289
Cdd:cd08480 160 GRLVPVLEEYN-PGdrEPIHAVYVGGGRLPARVRAFLDFL 198
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
4-63 1.00e-19

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 80.89  E-value: 1.00e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321     4 LKGMAIFATVVDKGSMAAAAQSLGMTPSAVSQQIRKLESRAQVTLLHRTTRRLTLTEAGE 63
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 18-283 1.73e-17

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 80.66  E-value: 1.73e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321   18 SMAAAAQSLGMTPSAVSQQIRKLESRAQVTLLHRTTRRLTLTEAGEAFY---RSCAQMLAIAEEAERRLGEwrdapVGEL 94
Cdd:PRK11139  22 SFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFldiREIFDQLAEATRKLRARSA-----KGAL 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321   95 RLAAPVGFSGTLITQALKPLLENHRQLRLQLFFQDERIDLVAERIDLAIRVGNLADSSLVARHL-GDWSSVLCaAPAYLR 173
Cdd:PRK11139  97 TVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDRLEDFLRDDVDVAIRYGRGNWPGLRVEKLlDEYLLPVC-SPALLN 175

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321  174 QRAPINRPEQL---------TEVDWisLNTSNHLNHLTLSGPGGEvcklrleprVAANGMLAVrQFTLDGLGVSYQPLPE 244
Cdd:PRK11139 176 GGKPLKTPEDLarhtllhddSREDW--RAWFRAAGLDDLNVQQGP---------IFSHSSMAL-QAAIHGQGVALGNRVL 243

                        250       260       270
                 ....*....|....*....|....*....|....*....
gi 15595321  245 VRDALNDGRLQQLLPEWRIPGLGIYAVTPRREAQPAKVK 283
Cdd:PRK11139 244 AQPEIEAGRLVCPFDTVLPSPNAFYLVCPDSQAELPKVA 282
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
4-184 9.07e-16

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 76.19  E-value: 9.07e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321    4 LKGMAIFATVVDKGSMAAAAQSLGMTPSAVSQQIRKLESRAQVTLLHRTTRRLTLTEAGEAFYRSCAQMLA-IAEEA-ER 81
Cdd:PRK10086  16 LSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLDtLNQEIlDI 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321   82 RLGEwrdaPVGELRLAAPVGFSGTLITQALKPLLENHRQLRLQLFFQDERIDLVAERIDLAIRVGNLADSSLVARHLGDW 161
Cdd:PRK10086  96 KNQE----LSGTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTILTGNENVNFQRAGIDLAIYFDDAPSAQLTHHFLMDE 171

                        170       180
                 ....*....|....*....|...
gi 15595321  162 SSVLCAAPAYLRQRAPINRPEQL 184
Cdd:PRK10086 172 EILPVCSPEYAERHALTGNPDNL 194
rbcR CHL00180
LysR transcriptional regulator; Provisional
 3-239 1.26e-14

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 72.75  E-value: 1.26e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321    3 SLKGMAIFATVVDKGSMAAAAQSLGMTPSAVSQQIRKLESRAQVTLLHRTTRRLTLTEAGEAFYRSCAQMLAIAEEAERR 82
Cdd:CHL00180   6 TLDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRA 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321   83 LGEWRDAPVGELRlaapVGFSGTLITQALKPLLE----NHRQLRLQLFFQDERI---DLVAERIDLAIrVG--------- 146
Cdd:CHL00180  86 LEDLKNLQRGTLI----IGASQTTGTYLMPRLIGlfrqRYPQINVQLQVHSTRRiawNVANGQIDIAI-VGgevptelkk 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321  147 NLADSSLVARHLgdwssVLCAAPAYLRQRAPINRPEQLTEVDWISLNTSNHLNHL---TLSGPGGEVCKLRLEprVAANG 223
Cdd:CHL00180 161 ILEITPYVEDEL-----ALIIPKSHPFAKLKKIQKEDLYRLNFITLDSNSTIRKVidnILIQNGIDSKRFKIE--MELNS 233

                        250
                 ....*....|....*.
gi 15595321  224 MLAVRQFTLDGLGVSY 239
Cdd:CHL00180 234 IEAIKNAVQSGLGAAF 249
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 94-283 3.76e-14

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: 69.53  E-value: 3.76e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321  94 LRLAAPVGFSGTLITQALKPLLENHRQLRLQLFFQDERIDLVAERIDLAIRVGNLADSSLVARHLGDWSSVLCAAPAYLR 173
Cdd:cd08432   2 LTVSVTPSFAARWLIPRLARFQARHPDIDLRLSTSDRLVDFAREGIDLAIRYGDGDWPGLEAERLMDEELVPVCSPALLA 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321 174 QRAPInRPEQLTEVDWISLNTSNHLNHLTLSGPGGEVCKLRLEPRVAANGMLAvrQFTLDGLGVSYQPLPEVRDALNDGR 253
Cdd:cd08432  82 GLPLL-SPADLARHTLLHDATRPEAWQWWLWAAGVADVDARRGPRFDDSSLAL--QAAVAGLGVALAPRALVADDLAAGR 158

                       170       180       190
                ....*....|....*....|....*....|
gi 15595321 254 LQQLLPEWRIPGLGIYAVTPRREAQPAKVK 283
Cdd:cd08432 159 LVRPFDLPLPSGGAYYLVYPPGRAESPAVA 188
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 93-289 1.35e-13

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: 68.01  E-value: 1.35e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321  93 ELRLAAPVGFSGTLITQALKPLLENHRQLRLQLFF--QDERIDLVAE-RIDLAIRVGNLADSSLVARHLGDWSSVLCAAP 169
Cdd:cd05466   1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEggSSELLEALLEgELDLAIVALPVDDPGLESEPLFEEPLVLVVPP 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321 170 AYLRQRAPINRPEQLTEVDWISLNTSNHLNHLTLsgpggEVC-KLRLEPRVA--ANGMLAVRQFTLDGLGVSYqpLPE-V 245
Cdd:cd05466  81 DHPLAKRKSVTLADLADEPLILFERGSGLRRLLD-----RAFaEAGFTPNIAleVDSLEAIKALVAAGLGIAL--LPEsA 153

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....
gi 15595321 246 RDALNDGRLQQLLPEWRIPGLGIYAVTPRREAQPAKVKVAIEAL 289
Cdd:cd05466 154 VEELADGGLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
10-97 4.04e-12

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 65.18  E-value: 4.04e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321   10 FATVVDKGSMAAAAQSLGMTPSAVSQQIRKLESRAQVTLLHRtTRRLTLTEAGEAFYRSCAQMLAIAEEAERRLGEWRDA 89
Cdd:PRK03635  10 LAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRLLRHARQVRLLEAELLGELPALDGT 88


                 ....*...
gi 15595321   90 PVgELRLA 97
Cdd:PRK03635  89 PL-TLSIA 95
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 10-260 4.83e-12

transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity. [Cellular processes, Toxin production and resistance, DNA metabolism, DNA replication, recombination, and repair, Regulatory functions, DNA interactions]


Pssm-ID: 274509 [Multi-domain]  Cd Length: 292  Bit Score: 64.94  E-value: 4.83e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321    10 FATVVDKGSMAAAAQSLGMTPSAVSQQIRKLESRAQVTLLHRtTRRLTLTEAGEAFYRSCAQMLAIAEEAERRLGEWRDA 89
Cdd:TIGR03298   9 LAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVR-TQPCRATEAGQRLLRHARQVRLLEAELLAELPGLAPG 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321    90 PVGELRLAAPVGFSGTLITQALKPLLENHRqLRLQLFFQDEriDLVAERI---DLAIRVGNLAD--SSLVARHLGDWSSV 164
Cdd:TIGR03298  88 APTRLTIAVNADSLATWFLPALAPVLAREG-VLLDLVVEDQ--DHTAELLrsgEVLGAVTTEAKpvPGCRVVPLGAMRYL 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321   165 LCAAPAYLR------------QRAPI---NRPEQLtEVDWISlntsnHLNHLTLSGPGGEVcklrlePRVAANGmlavrQ 229
Cdd:TIGR03298 165 AVASPAFAAryfpdgvtaaalARAPVivfNRKDDL-QDRFLR-----RLFGLPVSPPRHYV------PSSEGFV-----D 227

                         250       260       270
                  ....*....|....*....|....*....|.
gi 15595321   230 FTLDGLGVSYQPLPEVRDALNDGRLQQLLPE 260
Cdd:TIGR03298 228 AARAGLGWGMVPELQAEPHLAAGRLVELAPG 258
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
5-130 1.56e-11

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 63.84  E-value: 1.56e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321    5 KGMAIFATVVDKGSMAAAAQSLGMTPSAVSQQIRKLESRAQVTLLHRtTRRLTLTEAGEAFYRSCAQMLAIAEEAERRLG 84
Cdd:PRK13348   5 KQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQRLLRHLRQVALLEADLLSTLP 83

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 15595321   85 EWRDAPVgelRLAAPVGfSGTLIT---QALKPLLENHRqLRLQLFFQDE 130
Cdd:PRK13348  84 AERGSPP---TLAIAVN-ADSLATwflPALAAVLAGER-ILLELIVDDQ 127
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 10-143 9.96e-11

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 61.13  E-value: 9.96e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321   10 FATVVDKGSMAAAAQSLGMTPSAVSQQIRKLESRAQVTLLHRTTRRLTLTEAGEAFYRSCAQMLAIAEEAERRLGEWRDA 89
Cdd:PRK11242   9 FLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRRAIHDVADL 88

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 15595321   90 PVGELRLAAPVGFSGTLITQALKPLLENHRQLRLQLF-FQDERID--LVAERIDLAI 143
Cdd:PRK11242  89 SRGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIReMSQERIEalLADDELDVGI 145
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
10-95 5.87e-10

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 59.05  E-value: 5.87e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321   10 FATVVDKGSMAAAAQSLGMTPSAVSQQIRKLESRAQVTLLHRTTRRLTLTEAGEAFYRSCAQMLaiaeeaerrlgEWRDA 89
Cdd:PRK10094  10 FIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWL-----------SWLES 78


                 ....*.
gi 15595321   90 PVGELR 95
Cdd:PRK10094  79 MPSELQ 84
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 3-204 5.84e-09

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 55.85  E-value: 5.84e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321    3 SLKGMAIFATVVDKGSMAAAAQSLGMTPSAVSQQIRKLESRAQVTLLHRTTRRLTLTEAGEAFYRSCAQMLAIAEEAER- 81
Cdd:PRK10837   4 TLRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQAVEIEQl 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321   82 -RLGEwrdapvGELRLAApvgfSGTLITQALKPLLENHRQ----LRLQLFFQDER--IDLVAE-RIDLAIRVGNLADSSL 153
Cdd:PRK10837  84 fREDN------GALRIYA----SSTIGNYILPAMIARYRRdypqLPLELSVGNSQdvINAVLDfRVDIGLIEGPCHSPEL 153

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 15595321  154 VARH-LGDWSSVLCAAPAYLRQRaPINRpEQLTEVDWI----SLNTSNHLNHLTLS 204
Cdd:PRK10837 154 ISEPwLEDELVVFAAPDSPLARG-PVTL-EQLAAAPWIlrerGSGTREIVDYLLLS 207
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 4-82 1.63e-08

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 54.78  E-value: 1.63e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15595321    4 LKGMAIFATVVDKGSMAAAAQSLGMTPSAVSQQIRKLESRAQVTLLHRTTRRLTLTEAGEAFYRSCAQMLAIAEEAERR 82
Cdd:PRK09906   3 LRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKLR 81
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
28-189 1.83e-08

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 54.44  E-value: 1.83e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321   28 MTPSAVSQQIRKLESRAQVTLLHRTTRRLTLTEAGEAFYRSCAQMLAIAEEAERRLGEWRDAPVGELRLAAPVgfsgtli 107
Cdd:PRK11716   3 VSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSLFCSV------- 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321  108 TQA---LKPLLEN----HRQLRLQLFFQD--ERIDLV-AERIDLAI--RVGNLAdSSLVARHLGDwSSVLCAAPaylRQR 175
Cdd:PRK11716  76 TAAyshLPPILDRfraeHPLVEIKLTTGDaaDAVEKVqSGEADLAIaaKPETLP-ASVAFSPIDE-IPLVLIAP---ALP 150

                        170
                 ....*....|....
gi 15595321  176 APINRPEQLTEVDW 189
Cdd:PRK11716 151 CPVRQQLSQEKPDW 164
nhaR PRK11062
transcriptional activator NhaR; Provisional
 10-78 3.99e-08

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 53.47  E-value: 3.99e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15595321   10 FATVVDKGSMAAAAQSLGMTPSAVSQQIRKLESRAQVTLLHRTTRRLTLTEAGEAFYRSCAQMLAIAEE 78
Cdd:PRK11062  12 FWMVCKEGSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGELVFRYADKMFTLSQE 80
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 12-97 8.56e-08

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 52.64  E-value: 8.56e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321   12 TVVDKGSMAAAAQSLGMTPSAVSQQIRKLESRAQVTLLHRTTRRLTLTEAGEAFY---RSC-AQMLAIAEEAERRLGEWR 87
Cdd:PRK11074  12 AVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVkeaRSViKKMQETRRQCQQVANGWR 91

                         90
                 ....*....|
gi 15595321   88 dapvGELRLA 97
Cdd:PRK11074  92 ----GQLSIA 97
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 10-119 1.22e-07

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 51.99  E-value: 1.22e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321   10 FATVVDKGSMAAAAQSLGMTPSAVSQQIRKLESRAQVTLLHRTTRRLTLTEAGEAFY-------RSCAQmlaiAEEAERR 82
Cdd:PRK11233   9 FVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYtharailRQCEQ----AQLAVHN 84

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 15595321   83 LGEwrdapvgELRLAAPVGFS-GTLITQALKPLLENHR 119
Cdd:PRK11233  85 VGQ-------ALSGQVSIGLApGTAASSLTMPLLQAVR 115
PRK10341 PRK10341
transcriptional regulator TdcA;
5-126 2.14e-07

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 51.40  E-value: 2.14e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321    5 KGMAIFATVVDKGSMAAAAQSLGMTPSAVSQQIRKLESRAQVTLLHRTTRRLTLTEAGEAFYrscAQMLAIAEEAERRLG 84
Cdd:PRK10341  10 QHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLL---SRSESITREMKNMVN 86

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 15595321   85 EWR---DAPVGELRLAAP--VGFsgTLITQALKPLLENHRQLRLQLF 126
Cdd:PRK10341  87 EINgmsSEAVVDVSFGFPslIGF--TFMSDMINKFKEVFPKAQVSMY 131
PBP2_GcdR_like cd08481
The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, ...
 111-282 2.34e-06

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: 47.29  E-value: 2.34e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321 111 LKPLLENHRQLRLQLFFQDERIDLVAERIDLAIRVGNLADSSLVARHLGDWSSVLCAAPAYLRQRaPINRPEQLTEV--- 187
Cdd:cd08481  19 LPDFLARHPDITVNLVTRDEPFDFSQGSFDAAIHFGDPVWPGAESEYLMDEEVVPVCSPALLAGR-ALAAPADLAHLpll 97

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321 188 ----------DWISLNTSNHLNhlTLSGPGGEVCKLRLEprvaangmlAVRQftldGLGVSYQPLPEVRDALNDGRLQQL 257
Cdd:cd08481  98 qqttrpeawrDWFEEVGLEVPT--AYRGMRFEQFSMLAQ---------AAVA----GLGVALLPRFLIEEELARGRLVVP 162

                       170       180
                ....*....|....*....|....*
gi 15595321 258 LPEWRIPGLGIYAVTPRREAQPAKV 282
Cdd:cd08481 163 FNLPLTSDKAYYLVYPEDKAESPPV 187
PBP2_HvrB cd08483
The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an ...
 132-285 5.51e-06

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: 46.18  E-value: 5.51e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321 132 IDLVAERIDLAIRVGNladsslvarhlGDWSS-----------VLCAAPAYLRQRaPINRPEQLTEVDWISLNTSNHLNH 200
Cdd:cd08483  40 VDLRPDGIDVAIRYGN-----------GDWPGlesepltaapfVVVAAPGLLGDR-KVDSLADLAGLPWLQERGTNEQRV 107

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321 201 LTLSgpGGEVCKLRLEPRVAANGML--AVRQftldGLGVSYQPLPEVRDALNDGRLqQLLPEWRIPGLGIYAVT-PRREA 277
Cdd:cd08483 108 WLAS--MGVVPDLERGVTFLPGQLVleAARA----GLGLSIQARALVEPDIAAGRL-TVLFEEEEEGLGYHIVTrPGVLR 180


                ....*...
gi 15595321 278 QPAKVKVA 285
Cdd:cd08483 181 PAAKAFVR 188
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
1-191 1.12e-05

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 46.16  E-value: 1.12e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321    1 MDSLKGMAIFATVVDKGSMAAAAQSLGMTPSAVSQQIRKLESRAQVTLLHRTTRRLTLTEAGEAFYRSCAQMLAiaeEAE 80
Cdd:PRK15421   1 MIEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLP---QIS 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321   81 RRLGEWRDAPVGELRLAapvgFSGTLITQALKPLLENHRQL--RLQLFFQ-----DERIDLVAERIDLAIRVGNLADSSL 153
Cdd:PRK15421  78 QALQACNEPQQTRLRIA----IECHSCIQWLTPALENFHKNwpQVEMDFKsgvtfDPQPALQQGELDLVMTSDILPRSGL 153

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 15595321  154 VARHLGDWSSVLCAAPAYlrqraPINRPEQLTEVDWIS 191
Cdd:PRK15421 154 HYSPMFDYEVRLVLAPDH-----PLAAKTRITPEDLAS 186
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 10-62 1.22e-05

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 46.17  E-value: 1.22e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 15595321   10 FATVVDKGSMAAAAQSLGMTPSAVSQQIRKLESRAQVTLLHRTTRRLTLTEAG 62
Cdd:PRK15092  19 FVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHG 71
PRK09791 PRK09791
LysR family transcriptional regulator;
10-85 4.10e-05

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 44.37  E-value: 4.10e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321   10 FATVVDKGSMAAAAQSLGMTPSAVSQQIRKLESRAQVTLLHRTTRRLTLTEAGEAFYRSCAQML----AIAEEAERRLGE 85
Cdd:PRK09791  13 FVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILeelrAAQEDIRQRQGQ 92
PRK09986 PRK09986
LysR family transcriptional regulator;
3-79 1.64e-04

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 42.40  E-value: 1.64e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15595321    3 SLKGMAIFATVVDKGSMAAAAQSLGMTPSAVSQQIRKLESRAQVTLLHRTTRRLTLTEAGEAFYRSCAQMLAIAEEA 79
Cdd:PRK09986   8 DLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQS 84
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 22-110 4.43e-04

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 41.18  E-value: 4.43e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321   22 AAQSLGMTPSAVSQQIRKLESRAQVTLLHRTTRRLT-LTEAGEAFYRSCAQMLAIAEEAERRLGEWRDAPVGELRLAapv 100
Cdd:PRK12683  22 VANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTgLTEPGKELLQIVERMLLDAENLRRLAEQFADRDSGHLTVA--- 98

                         90
                 ....*....|
gi 15595321  101 gfsgTLITQA 110
Cdd:PRK12683  99 ----TTHTQA 104
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 22-85 4.68e-04

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 41.17  E-value: 4.68e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15595321   22 AAQSLGMTPSAVSQQIRKLESRAQVTLLHRTTRRLTLTEAGeafyrscaqmLAIAEEAERRLGE 85
Cdd:PRK11151  21 AADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAG----------LLLVDQARTVLRE 74
HTH_MARR smart00347
helix_turn_helix multiple antibiotic resistance protein;
18-83 7.59e-04

helix_turn_helix multiple antibiotic resistance protein;


Pssm-ID: 197670 [Multi-domain]  Cd Length: 101  Bit Score: 38.34  E-value: 7.59e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321     18 SMAAAAQSLGMTPSAVSQQIRKLESRAQVTLLH----RTTRRLTLTEAGEAFYRscaQMLAIAEEAERRL 83
Cdd:smart00347  26 SVSELAKRLGVSPSTVTRVLDRLEKKGLVRREPspedRRSVLVSLTEEGRELIE---QLLEARSETLAEL 92
MarR COG1846
DNA-binding transcriptional regulator, MarR family [Transcription];
18-83 8.80e-04

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


Pssm-ID: 441451 [Multi-domain]  Cd Length: 142  Bit Score: 38.80  E-value: 8.80e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15595321  18 SMAAAAQSLGMTPSAVSQQIRKLESRAqvtLLHRTT-------RRLTLTEAGEAFYRscaQMLAIAEEAERRL 83
Cdd:COG1846  54 TQSELAERLGLTKSTVSRLLDRLEEKG---LVEREPdpedrraVLVRLTEKGRALLE---EARPALEALLAEL 120
cysB PRK12681
HTH-type transcriptional regulator CysB;
21-110 2.15e-03

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 39.11  E-value: 2.15e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321   21 AAAQSLGMTPSAVSQQIRKLESRAQVTLLHRTTRRLT-LTEAGEAFYRSCAQMLAIAEEAERRLGEWRDAPVGELRLAap 99
Cdd:PRK12681  21 ATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTqVTPAGEEIIRIAREILSKVESIKSVAGEHTWPDKGSLYIA-- 98

                         90
                 ....*....|.
gi 15595321  100 vgfsgTLITQA 110
Cdd:PRK12681  99 -----TTHTQA 104
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
22-63 2.31e-03

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 38.84  E-value: 2.31e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 15595321   22 AAQSLGMTPSAVSQQIRKLESRAQVTLLHRTTRRLTLTEAGE 63
Cdd:PRK03601  21 AAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGE 62
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 21-191 5.27e-03

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 38.05  E-value: 5.27e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321   21 AAAQSLGMTPSAVSQQIRKLESRAQVTLLHRTTRRLT-LTEAGEAFYRSCAQMLAIAEEAERRLGEWRDAPVGELRLAap 99
Cdd:PRK12682  21 EAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKgLTEPGKAVLDVIERILREVGNIKRIGDDFSNQDSGTLTIA-- 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595321  100 vgfsgTLITQA---LKPLLENHRQL--RLQLFFQDERIDLVAERI-----DLAIRVGNLAD-SSLVARHLGDWSSVLCAA 168
Cdd:PRK12682  99 -----TTHTQAryvLPRVVAAFRKRypKVNLSLHQGSPDEIARMVisgeaDIGIATESLADdPDLATLPCYDWQHAVIVP 173

                        170       180
                 ....*....|....*....|....
gi 15595321  169 PAY-LRQRAPInRPEQLTEVDWIS 191
Cdd:PRK12682 174 PDHpLAQEERI-TLEDLAEYPLIT 196
 
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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