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Conserved domains on  [gi|817522522|ref|WP_046578478|]
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LysR family transcriptional regulator [Burkholderia gladioli]

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 ...
 98-297 2.13e-72

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: 221.55  E-value: 2.13e-72
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  98 GTIRISAPRALGRFLIHPNIPDFLAAHPAVDVVLKLDDRQLDPVDDQVDIVFRITDDPPPGLVGRKLMRIEHVVCATPAY 177
Cdd:cd08422    1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVASPAY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522 178 LARHGRPAHPRELAAHGCITLSEDPVDTRWRFERGGGTVAVDVRGRYVANHSGVRLEAVLADLGIGGVPRFVAAAALEDG 257
Cdd:cd08422   81 LARHGTPQTPEDLARHRCLGYRLPGRPLRWRFRRGGGEVEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAEDLASG 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 817522522 258 RVEQVLPDWlfkTNYYGDAWAFCSPSRHTAPKIRSFLAFI 297
Cdd:cd08422  161 RLVRVLPDW---RPPPLPIYAVYPSRRHLPAKVRAFIDFL 197
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
10-68 1.81e-20

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


:

Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 82.82  E-value: 1.81e-20
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 817522522   10 MDEMATFVKVAEAGSFSEAARRLGSTPSAVSRSIARLERALGTRLILRSTRRLRLSDEG 68
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
 
Name Accession Description Interval E-value
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 98-297 2.13e-72

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: 221.55  E-value: 2.13e-72
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  98 GTIRISAPRALGRFLIHPNIPDFLAAHPAVDVVLKLDDRQLDPVDDQVDIVFRITDDPPPGLVGRKLMRIEHVVCATPAY 177
Cdd:cd08422    1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVASPAY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522 178 LARHGRPAHPRELAAHGCITLSEDPVDTRWRFERGGGTVAVDVRGRYVANHSGVRLEAVLADLGIGGVPRFVAAAALEDG 257
Cdd:cd08422   81 LARHGTPQTPEDLARHRCLGYRLPGRPLRWRFRRGGGEVEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAEDLASG 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 817522522 258 RVEQVLPDWlfkTNYYGDAWAFCSPSRHTAPKIRSFLAFI 297
Cdd:cd08422  161 RLVRVLPDW---RPPPLPIYAVYPSRRHLPAKVRAFIDFL 197
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
11-303 7.62e-55

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 178.52  E-value: 7.62e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  11 DEMATFVKVAEAGSFSEAARRLGSTPSAVSRSIARLERALGTRLILRSTRRLRLSDEGLEALRHAGELVAAAKAVMSLAE 90
Cdd:COG0583    4 RQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAELR 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  91 RRSAEPAGTIRISAPRALGRFLIHPNIPDFLAAHPAVDVVLKLD--DRQLDPV-DDQVDIVFRITDDPPPGLVGRKLMRI 167
Cdd:COG0583   84 ALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGnsDRLVDALlEGELDLAIRLGPPPDPGLVARPLGEE 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522 168 EHVVCATPAY-LARHGRpahprelaahgcitlsedpvdtrwrfergggtvavdvrgryVANHSGVRLEAVLADLGIGGVP 246
Cdd:COG0583  164 RLVLVASPDHpLARRAP-----------------------------------------LVNSLEALLAAVAAGLGIALLP 202

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 817522522 247 RFVAAAALEDGRVEQV-LPDWLFKTNYYgdawAFCSPSRHTAPKIRSFLAFIAGRIGR 303
Cdd:COG0583  203 RFLAADELAAGRLVALpLPDPPPPRPLY----LVWRRRRHLSPAVRAFLDFLREALAE 256
PRK09801 PRK09801
LysR family transcriptional regulator;
8-304 8.20e-45

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 154.42  E-value: 8.20e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522   8 PLMDEMATFVKVAEAGSFSEAARRLGSTPSAVSRSIARLERALGTRLILRSTRRLRLSDEGLEALRHAGELVAAAKAVMS 87
Cdd:PRK09801   6 PLAKDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVD 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  88 LAERRSAEPAGTIRISAPRALGRFLIHPNIPDFLAAHPAVDVVLKLDDRQLDPVDDQVDIVFRITDDPPPGLVGRKLMRI 167
Cdd:PRK09801  86 DVTQIKTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHFELFDRQIDLVQDNIDLDIRINDEIPDYYIAHLLTKN 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522 168 EHVVCATPAYLARHGRPAHPRELAAHGCITLSE-DPVDTRWRFERGGGTVAVDVRGRYVANHSGVRLEAVLADLGIGGVP 246
Cdd:PRK09801 166 KRILCAAPEYLQKYPQPQSLQELSRHDCLVTKErDMTHGIWELGNGQEKKSVKVSGHLSSNSGEIVLQWALEGKGIMLRS 245

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 817522522 247 RFVAAAALEDGRVEQVLPDWLFKTNyygdAWAFCSPSRHTAPKIRSFLAFIAG----RIGRP 304
Cdd:PRK09801 246 EWDVLPFLESGKLVQVLPEYAQSAN----IWAVYREPLYRSMKLRVCVEFLAAwcqqRLGKP 303
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 97-298 5.57e-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: 112.77  E-value: 5.57e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522   97 AGTIRISAPRALGRFLIHPNIPDFLAAHPAVDVVLKLDD--RQLDPVDD-QVDIVFRITDDPPPGLVGRKLMRIEHVVCA 173
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNseELLDLLLEgELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  174 TPAYLARHGRPAHPRELAAHGCITLSEDPvDTRWRFERGGGTVAVDVRGRYVANHSGVRLEAVLADLGIGGVPRFVAAAA 253
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLPPGS-GLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARE 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 817522522  254 LEDGR-VEQVLPDWLFKTNYygdaWAFCSPSRHTAPKIRSFLAFIA 298
Cdd:pfam03466 160 LADGRlVALPLPEPPLPREL----YLVWRKGRPLSPAVRAFIEFLR 201
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
10-68 1.81e-20

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 82.82  E-value: 1.81e-20
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 817522522   10 MDEMATFVKVAEAGSFSEAARRLGSTPSAVSRSIARLERALGTRLILRSTRRLRLSDEG 68
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 14-265 1.02e-13

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: 69.94  E-value: 1.02e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522   14 ATFVKVAEAGSFSEAARRLGSTPSAVSRSIARLERALGTRLILRsTRRLRLSDEGLEALRHA---GELVAAAKAVMSlAE 90
Cdd:TIGR03298   7 AALAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVR-TQPCRATEAGQRLLRHArqvRLLEAELLAELP-GL 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522   91 RRSAEPAGTIRISAPRALGRFLihPNIPDFLAAHPA-VDVVLKLDDRQLDPVDD-QVDIVFRITDDPPPGLVGRKLMRIE 168
Cdd:TIGR03298  85 APGAPTRLTIAVNADSLATWFL--PALAPVLAREGVlLDLVVEDQDHTAELLRSgEVLGAVTTEAKPVPGCRVVPLGAMR 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  169 HVVCATPAYLARH-GRPAHPRELAAHGCITLSEDPvDTRWRFERGGGTVAVDVRGRYVaNHSGVRLEAVLADLGIGGVPR 247
Cdd:TIGR03298 163 YLAVASPAFAARYfPDGVTAAALARAPVIVFNRKD-DLQDRFLRRLFGLPVSPPRHYV-PSSEGFVDAARAGLGWGMVPE 240

                         250
                  ....*....|....*...
gi 817522522  248 FVAAAALEDGRVEQVLPD 265
Cdd:TIGR03298 241 LQAEPHLAAGRLVELAPG 258
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
15-75 1.85e-10

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 60.59  E-value: 1.85e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 817522522  15 TFVKVAEAGSFSEAARRLGSTPSAVSRSIARLERALGTRLILRSTRRLRLSDEGLEALRHA 75
Cdd:PRK10094   9 TFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQA 69
HTH_MARR smart00347
helix_turn_helix multiple antibiotic resistance protein;
24-75 9.65e-05

helix_turn_helix multiple antibiotic resistance protein;


Pssm-ID: 197670 [Multi-domain]  Cd Length: 101  Bit Score: 40.66  E-value: 9.65e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 817522522    24 SFSEAARRLGSTPSAVSRSIARLERA-LGTRLILRSTRR---LRLSDEGLEALRHA 75
Cdd:smart00347  26 SVSELAKRLGVSPSTVTRVLDRLEKKgLVRREPSPEDRRsvlVSLTEEGRELIEQL 81
MarR COG1846
DNA-binding transcriptional regulator, MarR family [Transcription];
24-92 2.30e-04

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


Pssm-ID: 441451 [Multi-domain]  Cd Length: 142  Bit Score: 40.72  E-value: 2.30e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  24 SFSEAARRLGSTPSAVSRSIARLERAlgtRLILRST-------RRLRLSDEGLEALRHA----GELVAAAKAVMSLAERR 92
Cdd:COG1846   54 TQSELAERLGLTKSTVSRLLDRLEEK---GLVEREPdpedrraVLVRLTEKGRALLEEArpalEALLAELLAGLSEEELE 130
 
Name Accession Description Interval E-value
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 98-297 2.13e-72

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: 221.55  E-value: 2.13e-72
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  98 GTIRISAPRALGRFLIHPNIPDFLAAHPAVDVVLKLDDRQLDPVDDQVDIVFRITDDPPPGLVGRKLMRIEHVVCATPAY 177
Cdd:cd08422    1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVASPAY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522 178 LARHGRPAHPRELAAHGCITLSEDPVDTRWRFERGGGTVAVDVRGRYVANHSGVRLEAVLADLGIGGVPRFVAAAALEDG 257
Cdd:cd08422   81 LARHGTPQTPEDLARHRCLGYRLPGRPLRWRFRRGGGEVEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAEDLASG 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 817522522 258 RVEQVLPDWlfkTNYYGDAWAFCSPSRHTAPKIRSFLAFI 297
Cdd:cd08422  161 RLVRVLPDW---RPPPLPIYAVYPSRRHLPAKVRAFIDFL 197
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
11-303 7.62e-55

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 178.52  E-value: 7.62e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  11 DEMATFVKVAEAGSFSEAARRLGSTPSAVSRSIARLERALGTRLILRSTRRLRLSDEGLEALRHAGELVAAAKAVMSLAE 90
Cdd:COG0583    4 RQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAELR 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  91 RRSAEPAGTIRISAPRALGRFLIHPNIPDFLAAHPAVDVVLKLD--DRQLDPV-DDQVDIVFRITDDPPPGLVGRKLMRI 167
Cdd:COG0583   84 ALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGnsDRLVDALlEGELDLAIRLGPPPDPGLVARPLGEE 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522 168 EHVVCATPAY-LARHGRpahprelaahgcitlsedpvdtrwrfergggtvavdvrgryVANHSGVRLEAVLADLGIGGVP 246
Cdd:COG0583  164 RLVLVASPDHpLARRAP-----------------------------------------LVNSLEALLAAVAAGLGIALLP 202

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 817522522 247 RFVAAAALEDGRVEQV-LPDWLFKTNYYgdawAFCSPSRHTAPKIRSFLAFIAGRIGR 303
Cdd:COG0583  203 RFLAADELAAGRLVALpLPDPPPPRPLY----LVWRRRRHLSPAVRAFLDFLREALAE 256
PBP2_CrgA_like_8 cd08477
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 98-297 1.18e-50

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: 165.87  E-value: 1.18e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  98 GTIRISAPRALGRFLIHPNIPDFLAAHPAVDVVLKLDDRQLDPVDDQVDIVFRITDDPPPGLVGRKLMRIEHVVCATPAY 177
Cdd:cd08477    1 GKLRISAPVTFGSHVLTPALAEYLARYPDVRVDLVLSDRLVDLVEEGFDAAFRIGELADSSLVARPLAPYRMVLCASPDY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522 178 LARHGRPAHPRELAAHGCITLSEDPVDTRWRFERGGGTVAVDVRGRYVANHSGVRLEAVLADLGIGGVPRFVAAAALEDG 257
Cdd:cd08477   81 LARHGTPTTPEDLARHECLGFSYWRARNRWRLEGPGGEVKVPVSGRLTVNSGQALRVAALAGLGIVLQPEALLAEDLASG 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 817522522 258 RVEQVLPDWLFKTN-----YygdawafcSPSRHTAPKIRSFLAFI 297
Cdd:cd08477  161 RLVELLPDYLPPPRpmhllY--------PPDRRPTPKLRSFIDFL 197
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 96-297 3.97e-48

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: 159.55  E-value: 3.97e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  96 PAGTIRISAPRALGRFLIHPNIPDFLAAHPAVDVVLKLDDRQLDPVDDQVDIVFRITDDPPPGLVGRKLM-RIEHVVCAT 174
Cdd:cd08474    1 PAGTLRINAPRVAARLLLAPLLARFLARYPDIRLELVVDDGLVDIVAEGFDAGIRLGESVEKDMVAVPLGpPLRMAVVAS 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522 175 PAYLARHGRPAHPRELAAHGCIT--LSEDPVDTRWRFERGGGTVAVDVRGRYVANHSGVRLEAVLADLGIGGVPRFVAAA 252
Cdd:cd08474   81 PAYLARHGTPEHPRDLLNHRCIRyrFPTSGALYRWEFERGGRELEVDVEGPLILNDSDLMLDAALDGLGIAYLFEDLVAE 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 817522522 253 ALEDGRVEQVLPDWlfkTNYYGDAWAFCSPSRHTAPKIRSFLAFI 297
Cdd:cd08474  161 HLASGRLVRVLEDW---SPPFPGGYLYYPSRRRVPPALRAFIDFL 202
PBP2_CrgA_like_9 cd08479
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 98-297 4.38e-47

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: 156.99  E-value: 4.38e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  98 GTIRISAPRALGRFLIHPNIPDFLAAHPAVDVVLKLDDRQLDPVDDQVDIVFRITDDPPPGLVGRKLMRIEHVVCATPAY 177
Cdd:cd08479    1 GLLRVNASFGFGRRHIAPALSDFAKRYPELEVQLELTDRPVDLVEEGFDLDIRVGDLPDSSLIARKLAPNRRILCASPAY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522 178 LARHGRPAHPRELAAHGCITLSEDPVD-TRWRFERGGGTVAVDVRGRYVANHSGVRLEAVLADLGIGGVPRFVAAAALED 256
Cdd:cd08479   81 LERHGAPASPEDLARHDCLVIRENDEDfGLWRLRNGDGEATVRVRGALSSNDGEVVLQWALDGHGIILRSEWDVAPYLRS 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 817522522 257 GRVEQVLPDWLFKTnyyGDAWAFCSPSRHTAPKIRSFLAFI 297
Cdd:cd08479  161 GRLVRVLPDWQLPD---ADIWAVYPSRLSRSARVRVFVDFL 198
PRK09801 PRK09801
LysR family transcriptional regulator;
8-304 8.20e-45

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 154.42  E-value: 8.20e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522   8 PLMDEMATFVKVAEAGSFSEAARRLGSTPSAVSRSIARLERALGTRLILRSTRRLRLSDEGLEALRHAGELVAAAKAVMS 87
Cdd:PRK09801   6 PLAKDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVD 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  88 LAERRSAEPAGTIRISAPRALGRFLIHPNIPDFLAAHPAVDVVLKLDDRQLDPVDDQVDIVFRITDDPPPGLVGRKLMRI 167
Cdd:PRK09801  86 DVTQIKTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHFELFDRQIDLVQDNIDLDIRINDEIPDYYIAHLLTKN 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522 168 EHVVCATPAYLARHGRPAHPRELAAHGCITLSE-DPVDTRWRFERGGGTVAVDVRGRYVANHSGVRLEAVLADLGIGGVP 246
Cdd:PRK09801 166 KRILCAAPEYLQKYPQPQSLQELSRHDCLVTKErDMTHGIWELGNGQEKKSVKVSGHLSSNSGEIVLQWALEGKGIMLRS 245

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 817522522 247 RFVAAAALEDGRVEQVLPDWLFKTNyygdAWAFCSPSRHTAPKIRSFLAFIAG----RIGRP 304
Cdd:PRK09801 246 EWDVLPFLESGKLVQVLPEYAQSAN----IWAVYREPLYRSMKLRVCVEFLAAwcqqRLGKP 303
PBP2_CrgA_like_2 cd08471
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 98-300 1.90e-43

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 147.67  E-value: 1.90e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  98 GTIRISAPRALGRFLIHPNIPDFLAAHPAVDVVLKLDDRQLDPVDDQVDIVFRITDDPPPGLVGRKLMRIEHVVCATPAY 177
Cdd:cd08471    1 GLLTVTAPVLFGRLHVLPIITDFLDAYPEVSVRLLLLDRVVNLLEEGVDVAVRIGHLPDSSLVATRVGSVRRVVCASPAY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522 178 LARHGRPAHPRELAAHGCITLSEDPVDTRWRFERGGGTVAVDVRGRYVANHSGVRLEAVLADLGIGGVPRFVAAAALEDG 257
Cdd:cd08471   81 LARHGTPKHPDDLADHDCIAFTGLSPAPEWRFREGGKERSVRVRPRLTVNTVEAAIAAALAGLGLTRVLSYQVAEELAAG 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 817522522 258 RVEQVLPDwlfktnYYGDAWA---FCSPSRHTAPKIRSFLAFIAGR 300
Cdd:cd08471  161 RLQRVLED------FEPPPLPvhlVHPEGRLAPAKVRAFVDFAVPR 200
PBP2_CrgA_like_3 cd08472
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 98-300 2.05e-42

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 144.96  E-value: 2.05e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  98 GTIRISAPRALGRFLIHPNIPDFLAAHPAVDVVLKLDDRQLDPVDDQVDIVFRITDDPPPGLVGRKLMRIEHVVCATPAY 177
Cdd:cd08472    1 GRLRVDVPGSLARLLLIPALPDFLARYPDIELDLGVSDRPVDLIREGVDCVIRVGELADSSLVARRLGELRMVTCASPAY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522 178 LARHGRPAHPRELAAHGCITLSEdPVDTR---WRFERGGGTVAVDVRGRYVANHSGVRLEAVLADLGIGGVPRFVAAAAL 254
Cdd:cd08472   81 LARHGTPRHPEDLERHRAVGYFS-ARTGRvlpWEFQRDGEEREVKLPSRVSVNDSEAYLAAALAGLGIIQVPRFMVRPHL 159

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 817522522 255 EDGRVEQVLPDWLFKTNyygDAWAFCSPSRHTAPKIRSFLAFIAGR 300
Cdd:cd08472  160 ASGRLVEVLPDWRPPPL---PVSLLYPHRRHLSPRVRVFVDWVAEL 202
PBP2_CrgA_like_1 cd08470
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 98-299 8.86e-39

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding domain; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 1. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176159  Cd Length: 197  Bit Score: 135.52  E-value: 8.86e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  98 GTIRISAPRALGRFLIHPNIPDFLAAHPAVDVVLKLDDRQLDPVDDQVDIVFRITDDPPPGLVGRKLMRIEHVVCATPAY 177
Cdd:cd08470    1 GLLRITCPVAYGERFIAPLVNDFMQRYPKLEVDIELTNRVVDLVSEGFDLAIRLGRLTDSSLMARRLASRRHYVCASPAY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522 178 LARHGRPAHPRELAAHGCITLSEDpvdtRWRFERGGGTVAVDVRGRYVANHSGVRLEAVLADLGIGGVPRFVAAAALEDG 257
Cdd:cd08470   81 LERHGTPHSLADLDRHNCLLGTSD----HWRFQENGRERSVRVQGRWRCNSGVALLDAALKGMGLAQLPDYYVDEHLAAG 156

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 817522522 258 RVEQVLPDWLFKTNyygDAWAFCSPSRHTAPKIRSFLAFIAG 299
Cdd:cd08470  157 RLVPVLEDYRPPDE---GIWALYPHNRHLSPKVRLLVDYLAD 195
PBP2_CrgA_like_7 cd08476
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 98-297 1.35e-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 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: 129.67  E-value: 1.35e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  98 GTIRISAPrALGRFLIhPNIPDFLAAHPAVDVVLKLDDRQLDPVDDQVDIVFRITDDPPPGLVGRKLMRIEHVVCATPAY 177
Cdd:cd08476    1 GRLRVSLP-LVGGLLL-PVLAAFMQRYPEIELDLDFSDRLVDVIDEGFDAVIRTGELPDSRLMSRRLGSFRMVLVASPDY 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522 178 LARHGRPAHPRELAAHGCI------TLSEDPvdtrWRFERGGGTVAVDVRGRYVANHSGVRLEAVLADLGIGGVPRFVAA 251
Cdd:cd08476   79 LARHGTPETPADLAEHACLryrfptTGKLEP----WPLRGDGGDPELRLPTALVCNNIEALIEFALQGLGIACLPDFSVR 154

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 817522522 252 AALEDGRVEQVLPDWLFKTnyyGDAWAFCSPSRHTAPKIRSFLAFI 297
Cdd:cd08476  155 EALADGRLVTVLDDYVEER---GQFRLLWPSSRHLSPKLRVFVDFM 197
PBP2_CrgA_like_6 cd08475
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 98-291 2.90e-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 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: 128.83  E-value: 2.90e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  98 GTIRISAPRALGRFLIHPNIPDFLAAHPAVDVVLKLDDRQLDPVDDQVDIVFRITD-DPPPGLVGRKLMRIEHVVCATPA 176
Cdd:cd08475    1 GRLRIDLPVAFGRLCVAPLLLELARRHPELELELSFSDRFVDLIEEGIDLAVRIGElADSTGLVARRLGTQRMVLCASPA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522 177 YLARHGRPAHPRELAAHGCITLSEDPVDTRWRF-ERGGGTVAVDVRGRYVANHSGVRLEAVLADLGIGGVPRFVAAAALE 255
Cdd:cd08475   81 YLARHGTPRTLEDLAEHQCIAYGRGGQPLPWRLaDEQGRLVRFRPAPRLQFDDGEAIADAALAGLGIAQLPTWLVADHLQ 160

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 817522522 256 DGRVEQVLPDwlfKTNYYGDAWAFCSPSRHTAPKIR 291
Cdd:cd08475  161 RGELVEVLPE---LAPEGLPIHAVWPRTRHLPPKVR 193
PBP2_CrgA_like_4 cd08473
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 96-266 7.03e-35

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 125.36  E-value: 7.03e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  96 PAGTIRISAPRALGRFLIHPNIPDFLAAHPAVDVVLKLDDRQLDPVDDQVDIVFRITDDPP--PGLVGRKLMRIEHVVCA 173
Cdd:cd08473    1 PRGTVRVSCPPALAQELLAPLLPRFMAAYPQVRLQLEATNRRVDLIEEGIDVALRVRFPPLedSSLVMRVLGQSRQRLVA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522 174 TPAYLARHGRPAHPRELAAHGCITLSEDPVDTRWRFERG-GGTVAVDVRGRYVANHSGVRLEAVLADLGIGGVPRFVAAA 252
Cdd:cd08473   81 SPALLARLGRPRSPEDLAGLPTLSLGDVDGRHSWRLEGPdGESITVRHRPRLVTDDLLTLRQAALAGVGIALLPDHLCRE 160

                        170
                 ....*....|....
gi 817522522 253 ALEDGRVEQVLPDW 266
Cdd:cd08473  161 ALRAGRLVRVLPDW 174
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 10-266 3.35e-33

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 123.56  E-value: 3.35e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  10 MDEMATFVKVAEAGSFSEAARRLGSTPSAVSRSIARLERALGTRLILRSTRRLRLSDEGLEALRHAGELVAAAKAVMSLA 89
Cdd:PRK14997   4 LNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDAI 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  90 ERRSAEPAGTIRISAPRALGRFLIHPNIPDFLAAHPAVDVVLKLDDRQLDPVDDQVDIVFRITDDP--PPGLVGRKLMRI 167
Cdd:PRK14997  84 AALQVEPRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLEATNRRVDVVGEGVDVAIRVRPRPfeDSDLVMRVLADR 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522 168 EHVVCATPAYLARHGRPAHPRELAAHGCITLSEDPVDTRWR-FERGGGTVAVDVRGRYVANHSGVRLEAVLADLGIGGVP 246
Cdd:PRK14997 164 GHRLFASPDLIARMGIPSAPAELSHWPGLSLASGKHIHRWElYGPQGARAEVHFTPRMITTDMLALREAAMAGVGLVQLP 243

                        250       260
                 ....*....|....*....|
gi 817522522 247 RFVAAAALEDGRVEQVLPDW 266
Cdd:PRK14997 244 VLMVKEQLAAGELVAVLEEW 263
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 97-298 5.57e-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: 112.77  E-value: 5.57e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522   97 AGTIRISAPRALGRFLIHPNIPDFLAAHPAVDVVLKLDD--RQLDPVDD-QVDIVFRITDDPPPGLVGRKLMRIEHVVCA 173
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNseELLDLLLEgELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  174 TPAYLARHGRPAHPRELAAHGCITLSEDPvDTRWRFERGGGTVAVDVRGRYVANHSGVRLEAVLADLGIGGVPRFVAAAA 253
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLPPGS-GLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARE 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 817522522  254 LEDGR-VEQVLPDWLFKTNYygdaWAFCSPSRHTAPKIRSFLAFIA 298
Cdd:pfam03466 160 LADGRlVALPLPEPPLPREL----YLVWRKGRPLSPAVRAFIEFLR 201
PBP2_CrgA_like_10 cd08480
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 98-265 1.94e-29

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: 110.89  E-value: 1.94e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  98 GTIRISAPRALGRFLIHPNIPDFLAAHPAVDVVLKLDDRQLDPVDDQVDIVFRITDDPPPGLVGRKLMRIEHVVCATPAY 177
Cdd:cd08480    1 GRLRVNASVPFGTHFLLPLLPAFLARYPEILVDLSLTDEVVDLLAERTDVAIRVGPLPDSSLVARKLGESRRVIVASPSY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522 178 LARHGRPAHPRELAAHGCITLSEDPVDTRWRFERGGGTVAVDVRGRYVANHSGVRLEAVLADLGIGGVPRFVAAAALEDG 257
Cdd:cd08480   81 LARHGTPLTPQDLARHNCLGFNFRRALPDWPFRDGGRIVALPVSGNILVNDGEALRRLALAGAGLARLALFHVADDIAAG 160


                 ....*...
gi 817522522 258 RVEQVLPD 265
Cdd:cd08480  161 RLVPVLEE 168
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
13-264 6.72e-29

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 112.55  E-value: 6.72e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  13 MATFVKVAEAGSFSEAARRLGSTPSAVSRSIARLERALGTRLILRSTRRLRLSDEGLEALRHAGELVAAAKAVMSLAERR 92
Cdd:PRK10632   7 MSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQLYAF 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  93 SAEPAGTIRISAPRALGRFLIHPNIPDFLAAHPAVDVVLKLDDRQLDPVDDQVDIVFRITDDPPPGLVGRKLMRIEHVVC 172
Cdd:PRK10632  87 NNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTGIPAPDLIADGLDVVIRVGALQDSSLFSRRLGAMPMVVC 166

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522 173 ATPAYLARHGRPAHPRELAAHGCITLSEDPVDTRWRFERGGGTVAVDVRGRYVANHSGVRLEAVLADLGIGGVPRFVAAA 252
Cdd:PRK10632 167 AAKSYLAQYGTPEKPADLSSHSWLEYSVRPDNEFELIAPEGISTRLIPQGRFVTNDPQTLVRWLTAGAGIAYVPLMWVID 246

                        250
                 ....*....|..
gi 817522522 253 ALEDGRVEQVLP 264
Cdd:PRK10632 247 EINRGELEILFP 258
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 5-303 4.39e-27

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 107.24  E-value: 4.39e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522   5 QIPPLmdemaTFVKVAEAG----SFSEAARRLGSTPSAVSRSIARLERALGTRLILRSTRRLRLSDEGlealrhAGELVA 80
Cdd:PRK11139   4 RLPPL-----NALRAFEAAarhlSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEG------QRYFLD 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  81 AAKAVMSLAE------RRSAEpaGTIRISAPRALG-RFLIhPNIPDFLAAHPAVDVVLKLDDRQLDPVDDQVDIVFRITD 153
Cdd:PRK11139  73 IREIFDQLAEatrklrARSAK--GALTVSLLPSFAiQWLV-PRLSSFNEAHPDIDVRLKAVDRLEDFLRDDVDVAIRYGR 149

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522 154 DPPPGLVGRKLMRIEHVVCATPAYLARHGRPAHPRELAAHgciTL--SEDPVDtrWR-FERGGGTVAVDVRGRYVANHSG 230
Cdd:PRK11139 150 GNWPGLRVEKLLDEYLLPVCSPALLNGGKPLKTPEDLARH---TLlhDDSRED--WRaWFRAAGLDDLNVQQGPIFSHSS 224

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 817522522 231 VRLEAVLADLGIGGVPRFVAAAALEDGRVeqVLPdwlFKTNYYgDAWAF---CSPSRHTAPKIRSFLAFIAGRIGR 303
Cdd:PRK11139 225 MALQAAIHGQGVALGNRVLAQPEIEAGRL--VCP---FDTVLP-SPNAFylvCPDSQAELPKVAAFRQWLLAEAAQ 294
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 99-297 3.11e-22

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


Pssm-ID: 176123 [Multi-domain]  Cd Length: 194  Bit Score: 91.49  E-value: 3.11e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  99 TIRISAPRALG-RFLIhPNIPDFLAAHPAVDVVLKLDDRQLDPVDDQVDIVFRITDDPPPGLVGRKLMRIEHVVCATPAY 177
Cdd:cd08432    1 VLTVSVTPSFAaRWLI-PRLARFQARHPDIDLRLSTSDRLVDFAREGIDLAIRYGDGDWPGLEAERLMDEELVPVCSPAL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522 178 LARHgRPAHPRELAAHgciTL--SEDPVDTRWRFERGGGTVAVDVRGRYVANHSGVRLEAVLADLGIGGVPRFVAAAALE 255
Cdd:cd08432   80 LAGL-PLLSPADLARH---TLlhDATRPEAWQWWLWAAGVADVDARRGPRFDDSSLALQAAVAGLGVALAPRALVADDLA 155

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 817522522 256 DGRVEQVLPDWLFKTNYYgdaWAFCSPSRHTAPKIRSFLAFI 297
Cdd:cd08432  156 AGRLVRPFDLPLPSGGAY---YLVYPPGRAESPAVAAFRDWL 194
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
10-68 1.81e-20

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 82.82  E-value: 1.81e-20
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 817522522   10 MDEMATFVKVAEAGSFSEAARRLGSTPSAVSRSIARLERALGTRLILRSTRRLRLSDEG 68
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
13-186 6.83e-20

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 87.75  E-value: 6.83e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  13 MATFVKVAEAGSFSEAARRLGSTPSAVSRSIARLERALGTRLILRSTRRLRLSDEG---LEALRHAGELVAAAkavmsLA 89
Cdd:PRK10086  19 LHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGkrvFWALKSSLDTLNQE-----IL 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  90 ERRSAEPAGTIRISAPRALGRFLIHPNIPDFLAAHPAVDvvLKLDDRQlDPVDDQ---VDIVFRITDDPPPGLVGRKLMR 166
Cdd:PRK10086  94 DIKNQELSGTLTVYSRPSIAQCWLVPRLADFTRRYPSIS--LTILTGN-ENVNFQragIDLAIYFDDAPSAQLTHHFLMD 170

                        170       180
                 ....*....|....*....|....
gi 817522522 167 IEHV-VCaTPAYLARH---GRPAH 186
Cdd:PRK10086 171 EEILpVC-SPEYAERHaltGNPDN 193
PBP2_CrgA cd08478
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains ...
 96-297 1.77e-18

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: 81.62  E-value: 1.77e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  96 PAGTIRISAPRALGRFLIHPNIPDFLAAHPAVDVVLKLDDRQLDPVDDQVDIVFRITDDPPPGLVGRKLMRIEHVVCATP 175
Cdd:cd08478    1 PSGLLRVDAATPFVLHLLAPLIAKFRERYPDIELELVSNEGIIDLIERKTDVAIRIGELTDSTLHARPLGKSRLRILASP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522 176 AYLARHGRPAHPRELAAHGCITLSEDPVDTRWRFERGGGTVaVDVRGRYVANhSGVRLEAV-LADLGIGGVPRFVAAAAL 254
Cdd:cd08478   81 DYLARHGTPQSIEDLAQHQLLGFTEPASLNTWPIKDADGNL-LKIQPTITAS-SGETLRQLaLSGCGIACLSDFMTDKDI 158

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 817522522 255 EDGRVEQVLPDwlfKTN-YYGDAWAFCSPSRHTAPKIRSFLAFI 297
Cdd:cd08478  159 AEGRLIPLFAE---QTSdVRQPINAVYYRNTALSLRIRCFIDFL 199
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
10-265 2.53e-16

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 77.70  E-value: 2.53e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  10 MDEMATFVKVAEAGSFSEAARRLGSTPSAVSRSIARLERALGTRLILRsTRRLRLSDEGLEALRHAGEL-VAAAKAVMSL 88
Cdd:PRK13348   4 YKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQRLLRHLRQVaLLEADLLSTL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  89 AERRSAEPAGTIRISA-------PRALGRFLIHPNIpdflaahpAVDVVlklddrqldpVDDQV---------DIVFRIT 152
Cdd:PRK13348  83 PAERGSPPTLAIAVNAdslatwfLPALAAVLAGERI--------LLELI----------VDDQDhtfallergEVVGCVS 144

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522 153 DD--PPPGLVGRKLMRIEHVVCATPAYLARHgrpaHPRELAAHGcitLSEDPV------DT---RWrFERGGGTvavdVR 221
Cdd:PRK13348 145 TQpkPMRGCLAEPLGTMRYRCVASPAFAARY----FAQGLTRHS---ALKAPAvafnrkDTlqdSF-LEQLFGL----PV 212

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*....
gi 817522522 222 GRYV-----ANHSGVRleAVLADLGIGGVPRFVAAAALEDGRVEQVLPD 265
Cdd:PRK13348 213 GAYPrhyvpSTHAHLA--AIRHGLGYGMVPELLIGPLLAAGRLVDLAPG 259
PBP2_GcdR_like cd08481
The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, ...
 110-293 5.81e-15

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: 71.94  E-value: 5.81e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522 110 RFLIhPNIPDFLAAHPAVDVVLKLDDRQLDPVDDQVDIVFRITDDPPPGLVGRKLMRIEHVVCATPAYLARHGrPAHPRE 189
Cdd:cd08481   13 RWLI-PRLPDFLARHPDITVNLVTRDEPFDFSQGSFDAAIHFGDPVWPGAESEYLMDEEVVPVCSPALLAGRA-LAAPAD 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522 190 LAAHGCITLSEDPvdTRWR--FERGGGTVAVDVRG-RYvaNHSGVRLEAVLADLGIGGVPRFVAAAALEDGRVeQVLPDW 266
Cdd:cd08481   91 LAHLPLLQQTTRP--EAWRdwFEEVGLEVPTAYRGmRF--EQFSMLAQAAVAGLGVALLPRFLIEEELARGRL-VVPFNL 165

                        170       180
                 ....*....|....*....|....*...
gi 817522522 267 LFKTNYygdAWAFCSP-SRHTAPKIRSF 293
Cdd:cd08481  166 PLTSDK---AYYLVYPeDKAESPPVQAF 190
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 14-265 1.02e-13

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: 69.94  E-value: 1.02e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522   14 ATFVKVAEAGSFSEAARRLGSTPSAVSRSIARLERALGTRLILRsTRRLRLSDEGLEALRHA---GELVAAAKAVMSlAE 90
Cdd:TIGR03298   7 AALAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVR-TQPCRATEAGQRLLRHArqvRLLEAELLAELP-GL 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522   91 RRSAEPAGTIRISAPRALGRFLihPNIPDFLAAHPA-VDVVLKLDDRQLDPVDD-QVDIVFRITDDPPPGLVGRKLMRIE 168
Cdd:TIGR03298  85 APGAPTRLTIAVNADSLATWFL--PALAPVLAREGVlLDLVVEDQDHTAELLRSgEVLGAVTTEAKPVPGCRVVPLGAMR 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  169 HVVCATPAYLARH-GRPAHPRELAAHGCITLSEDPvDTRWRFERGGGTVAVDVRGRYVaNHSGVRLEAVLADLGIGGVPR 247
Cdd:TIGR03298 163 YLAVASPAFAARYfPDGVTAAALARAPVIVFNRKD-DLQDRFLRRLFGLPVSPPRHYV-PSSEGFVDAARAGLGWGMVPE 240

                         250
                  ....*....|....*...
gi 817522522  248 FVAAAALEDGRVEQVLPD 265
Cdd:TIGR03298 241 LQAEPHLAAGRLVELAPG 258
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 26-277 1.42e-12

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 66.94  E-value: 1.42e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  26 SEAARRLGSTPSAVSRSIARLERALGTRLILRSTRRL-RLSDEGLEALRHAGELVAAAKAVMSLAERRSAEPAGTIRISA 104
Cdd:PRK12682  20 TEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLkGLTEPGKAVLDVIERILREVGNIKRIGDDFSNQDSGTLTIAT 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522 105 PRALGRFLIHPNIPDFLAAHPAVDVVLKlddrQLDP-------VDDQVDIvfritddpppGLVGRKLMRIEHVVCaTPAY 177
Cdd:PRK12682 100 THTQARYVLPRVVAAFRKRYPKVNLSLH----QGSPdeiarmvISGEADI----------GIATESLADDPDLAT-LPCY 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522 178 LARHG---RPAHPreLAAHGCITL---SEDPVDTRWRFERGGGTV--AVDVRG---RYV--ANHSGVRLEAVLADLGIGg 244
Cdd:PRK12682 165 DWQHAvivPPDHP--LAQEERITLedlAEYPLITYHPGFTGRSRIdrAFAAAGlqpDIVleAIDSDVIKTYVRLGLGVG- 241

                        250       260       270
                 ....*....|....*....|....*....|....*.
gi 817522522 245 vprFVAAAALEDGRVE--QVLP-DWLFKTNyygDAW 277
Cdd:PRK12682 242 ---IVAEMAYRPDRDGdlVALPaGHLFGPN---TAW 271
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 99-297 3.45e-12

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: 64.16  E-value: 3.45e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  99 TIRISAPRALGRFLIHPNIPDFLAAHPAVDVVLKLDD-----RQLDpvDDQVDIVFRITDDPPPGLVGRKLMRIEHVVCA 173
Cdd:cd05466    1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGssellEALL--EGELDLAIVALPVDDPGLESEPLFEEPLVLVV 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522 174 TPAYLARHGRPAHPRELAAHGCITLSEDPVDTRWR---FERGGGTVAVdvrgRYVANHSGVRLEAVLADLGIGGVPRFvA 250
Cdd:cd05466   79 PPDHPLAKRKSVTLADLADEPLILFERGSGLRRLLdraFAEAGFTPNI----ALEVDSLEAIKALVAAGLGIALLPES-A 153

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 817522522 251 AAALEDGRVEQVLPDWLFKTNYYGDAWafcSPSRHTAPKIRSFLAFI 297
Cdd:cd05466  154 VEELADGGLVVLPLEDPPLSRTIGLVW---RKGRYLSPAARAFLELL 197
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 16-201 7.44e-12

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 64.59  E-value: 7.44e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  16 FVKVAEAGSFSEAARRLGSTPSAVSRSIARLERALGTRLILRSTRRLRLSDEGLEALRHA----GELVAAAKAVMSLAER 91
Cdd:PRK11242   9 FLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYArralQDLEAGRRAIHDVADL 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  92 RSaepaGTIRISAPRALGRFLIHPNIPDFLAAHPAVDVVLK---LDDRQLDPVDDQVDIVFRITDDPPPGLVGRKLM--R 166
Cdd:PRK11242  89 SR----GSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIRemsQERIEALLADDELDVGIAFAPVHSPEIEAQPLFteT 164

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 817522522 167 IEHVVCATPAyLARHGRPAHPRELAAHGCITLSED 201
Cdd:PRK11242 165 LALVVGRHHP-LAARRKALTLDELADEPLVLLSAE 198
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
15-75 1.85e-10

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 60.59  E-value: 1.85e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 817522522  15 TFVKVAEAGSFSEAARRLGSTPSAVSRSIARLERALGTRLILRSTRRLRLSDEGLEALRHA 75
Cdd:PRK10094   9 TFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQA 69
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
14-265 1.02e-09

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 58.25  E-value: 1.02e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  14 ATFVKVAEAGSFSEAARRLGSTPSAVSRSIARLERALGTRLILRsTRRLRLSDEGLEALRHAgELVAAAKAvmSLAERRS 93
Cdd:PRK03635   8 EALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRLLRHA-RQVRLLEA--ELLGELP 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  94 AEPAGTIRIS-APRAlgrflihpnipDFLA--AHPAVDVVLKLDDRQLD-PVDDQV---------DIVFRIT--DDPPPG 158
Cdd:PRK03635  84 ALDGTPLTLSiAVNA-----------DSLAtwFLPALAPVLARSGVLLDlVVEDQDhtaellrrgEVVGAVTtePQPVQG 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522 159 LVGRKLMRIEHVVCATPAYLARH-GRPAHPRELAAHGCITLSEDPvDTRWRFERGGGTVAVDVRGRYVANHSGVRLEAVL 237
Cdd:PRK03635 153 CRVDPLGAMRYLAVASPAFAARYfPDGVTAEALAKAPAVVFNRKD-DLQDRFLRQAFGLPPGSVPCHYVPSSEAFVRAAL 231

                        250       260
                 ....*....|....*....|....*...
gi 817522522 238 ADLGIGGVPRFVAAAALEDGRVEQVLPD 265
Cdd:PRK03635 232 AGLGWGMIPELQIEPELASGELVDLTPG 259
PRK09791 PRK09791
LysR family transcriptional regulator;
16-129 2.37e-09

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 57.46  E-value: 2.37e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  16 FVKVAEAGSFSEAARRLGSTPSAVSRSIARLERALGTRLILRSTRRLRLSDEGLEALRHAGELVAAAKAVMSLAERRSAE 95
Cdd:PRK09791  13 FVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQEDIRQRQGQ 92

                         90       100       110
                 ....*....|....*....|....*....|....
gi 817522522  96 PAGTIRISAPRALGRFLIHPNIPDFLAAHPAVDV 129
Cdd:PRK09791  93 LAGQINIGMGASIARSLMPAVISRFHQQHPQVKV 126
rbcR CHL00180
LysR transcriptional regulator; Provisional
 4-147 2.93e-09

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 56.95  E-value: 2.93e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522   4 NQIPPLMDEMATFVKVAEAGSFSEAARRLGSTPSAVSRSIARLERALGTRLILRSTRRLRLSDEGLEALRHAGELVA--- 80
Cdd:CHL00180   1 TDLPFTLDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILAlce 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 817522522  81 -AAKAVMSLAERRSaepaGTIRISAPRALGRFLIHPNIPDFLAAHPAVDVVLKLD-DRQL--DPVDDQVDI 147
Cdd:CHL00180  81 eTCRALEDLKNLQR----GTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHsTRRIawNVANGQIDI 147
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 12-272 1.53e-07

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 51.61  E-value: 1.53e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  12 EMATFVKVAEAGSFSEAARRLGSTPSAVSRSIARLERALGTRLILRSTRRLRLSDEGLEALRHAGELVAAAKAVMSLAER 91
Cdd:PRK10837   7 QLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQAVEIEQLFRE 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  92 RSaepaGTIRISAPRALGRFLIHPNIPDFLAAHPAVDVVLKLDDRQ--LDPVDD-QVDIVFRITDDPPPGLVGRKLMRIE 168
Cdd:PRK10837  87 DN----GALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNSQdvINAVLDfRVDIGLIEGPCHSPELISEPWLEDE 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522 169 HVVCATpaylarhgrPAHPrelAAHGCITLsEDPVDTRWRF-ERGGGTvavdvrgRYVANH------SGVRLE------- 234
Cdd:PRK10837 163 LVVFAA---------PDSP---LARGPVTL-EQLAAAPWILrERGSGT-------REIVDYlllshlPRFELAmelgnse 222

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*
gi 817522522 235 ----AVLADLGIGGVPRFVAAAALEDGRVEQV---LPDwLFKTNY 272
Cdd:PRK10837 223 aikhAVRHGLGISCLSRRVIADQLQAGTLVEVavpLPR-LMRTLY 266
PRK09986 PRK09986
LysR family transcriptional regulator;
16-204 4.57e-07

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 50.49  E-value: 4.57e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  16 FVKVAEAGSFSEAARRLGSTPSAVSRSIARLERALGTRLILRSTRRLrlsdegleALRHAGE--------LVAAAKAVMS 87
Cdd:PRK09986  15 FLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSV--------VLTHAGKilmeesrrLLDNAEQSLA 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  88 LAERRSAEPAGTIRIS-APRAL-GRFLihPNIPDFLAAHPAVDVVLK----------LDDRQLDpvddqVDIVFRITDDP 155
Cdd:PRK09986  87 RVEQIGRGEAGRIEIGiVGTALwGRLR--PAMRHFLKENPNVEWLLRelspsmqmaaLERRELD-----AGIWRMADLEP 159

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 817522522 156 PPGLVGRKLMRiEHVVCATPAYLARHGRPAHP-RELAAHGCITLSEDPVD 204
Cdd:PRK09986 160 NPGFTSRRLHE-SAFAVAVPEEHPLASRSSVPlKALRNEYFITLPFVHSD 208
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 10-105 4.94e-06

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 47.33  E-value: 4.94e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  10 MDEMATFVKVAEAGSFSEAARRLGSTPSAVSRSIARLERALGTRLILRSTRRLRLSDEGLEALRHAGE-LVAAAKAVMSL 88
Cdd:PRK15092  13 LDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKiLRFNDEACSSL 92

                         90
                 ....*....|....*..
gi 817522522  89 aerRSAEPAGTIRISAP 105
Cdd:PRK15092  93 ---MYSNLQGVLTIGAS 106
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 99-297 1.48e-05

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


Pssm-ID: 176112 [Multi-domain]  Cd Length: 201  Bit Score: 44.79  E-value: 1.48e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  99 TIRISAPRALGRFLIHPNIPDFLAAHPAVDVVLKLDDRQ--LDPV-DDQVDIVFRITDDPPPGLVGRKLMRIEHVVCATP 175
Cdd:cd08420    1 TLRIGASTTIGEYLLPRLLARFRKRYPEVRVSLTIGNTEeiAERVlDGEIDLGLVEGPVDHPDLIVEPFAEDELVLVVPP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522 176 AY-LARHGRPaHPRELAAHGCItlsedpvdtrWRfERGGGTVAV-------------DVRGRYVANHSGVRLEAVLADLG 241
Cdd:cd08420   81 DHpLAGRKEV-TAEELAAEPWI----------LR-EPGSGTREVferalaeagldglDLNIVMELGSTEAIKEAVEAGLG 148

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 817522522 242 IGGVPRFVAAAALEDGRVEQV-LPDWLFKTNYYgdawAFCSPSRHTAPKIRSFLAFI 297
Cdd:cd08420  149 ISILSRLAVRKELELGRLVALpVEGLRLTRPFS----LIYHKDKYLSPAAEAFLEFL 201
PBP2_HvrB cd08483
The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an ...
 100-258 1.50e-05

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: 44.64  E-value: 1.50e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522 100 IRISAPRALGRFLIHPNIPDFLAAHPAVDVVLKLDDRQLDPVDDQVDIVFRITDDPPPGLVGRKLMRIEHVVCATPAYLA 179
Cdd:cd08483    2 LTVTLTPSFASNWLMPRLGSFWAKHPEIELSLLPSADLVDLRPDGIDVAIRYGNGDWPGLESEPLTAAPFVVVAAPGLLG 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522 180 rhGRP-AHPRELAAHgcitlsedpvdtRWRFERGG----------GTVAVDVRGRYVANhSGVRLEAVLADLGIGGVPRF 248
Cdd:cd08483   82 --DRKvDSLADLAGL------------PWLQERGTneqrvwlasmGVVPDLERGVTFLP-GQLVLEAARAGLGLSIQARA 146

                        170
                 ....*....|
gi 817522522 249 VAAAALEDGR 258
Cdd:cd08483  147 LVEPDIAAGR 156
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 26-271 1.81e-05

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 45.42  E-value: 1.81e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  26 SEAARRLGSTPSAVSRSIARLERALGTRLILRSTRRLR-LSDEGLEALRHAGELVAAAKAVMSLAERRSAEPAGTIRISA 104
Cdd:PRK12683  20 TEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTgLTEPGKELLQIVERMLLDAENLRRLAEQFADRDSGHLTVAT 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522 105 PRALGRFLIHPNIPDFLAAHPAVDVVLklddRQLDP-------VDDQVDI-VFRITDDPPPGLVGRKLMRIEHVVCATPA 176
Cdd:PRK12683 100 THTQARYALPKVVRQFKEVFPKVHLAL----RQGSPqeiaemlLNGEADIgIATEALDREPDLVSFPYYSWHHVVVVPKG 175

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522 177 YLARHGRPAHPRELAAHGCITLSEDpVDTRWR----FERGGGTVAV-------DVRGRYVAnhsgvrleavlADLGIGGV 245
Cdd:PRK12683 176 HPLTGRENLTLEAIAEYPIITYDQG-FTGRSRidqaFAEAGLVPDIvltaldaDVIKTYVE-----------LGMGVGIV 243

                        250       260
                 ....*....|....*....|....*.
gi 817522522 246 PRfVAAAALEDGRVEQVLPDWLFKTN 271
Cdd:PRK12683 244 AA-MAYDPQRDTGLVALDTDHLFEAN 268
PBP2_AmpR cd08488
The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in ...
 115-264 2.46e-05

The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in control of the expression of beta-lactamase gene ampC, contains the type 2 periplasmic binding fold; AmpR acts as a transcriptional activator by binding to a DNA region immediately upstream of the ampC promoter. In the absence of a beta-lactam inducer, AmpR represses the synthesis of beta-lactamase, whereas expression is induced in the presence of a beta-lactam inducer. The AmpD, AmpG, and AmpR proteins are involved in the induction of AmpC-type beta-lactamase (class C) which produced by enterobacterial strains and many other gram-negative bacilli. The activation of ampC by AmpR requires ampG for induction or high-level expression of AmpC. It is probable that the AmpD and AmpG work together to modulate the ability of AmpR to activate ampC expression. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176177 [Multi-domain]  Cd Length: 191  Bit Score: 44.06  E-value: 2.46e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522 115 PNIPDFLAAHPAVDVVLKLDDRQLDPVDDQVDIVFRITDDPPPGLVGRKLMRIEHVVCATPAyLARHGRpaHPRELAAHg 194
Cdd:cd08488   17 PRLADFQNRHPFIDLRLSTNNNRVDIAAEGLDYAIRFGSGAWHGIDATRLFEAPLSPLCTPE-LARQLR--EPADLARH- 92

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 817522522 195 ciTLSEDPVDTRWR--FERGGGTVAVDVRGRYVANHSGVRLEAVLADLGIGGVPRFVAAAALEDGRVEQVLP 264
Cdd:cd08488   93 --TLLRSYRADEWPqwFEAAGVGHPCGLPNSIMFDSSLGMMEAALQGLGVALAPPSMFSRQLASGALVQPFA 162
PBP2_TrpI cd08482
The C-terminal substrate binding domain of LysR-type transcriptional regulator TrpI, which is ...
 108-258 8.84e-05

The C-terminal substrate binding domain of LysR-type transcriptional regulator TrpI, which is involved in control of tryptophan synthesis, contains type 2 periplasmic binding fold; TrpI and indoleglycerol phosphate (InGP), are required to activate transcription of the trpBA, the genes for tryptophan synthase. The trpBA is induced by the InGp substrate, rather than by tryptophan, but the exact mechanism of the activation event is not known. This substrate-binding domain of TrpI shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176171 [Multi-domain]  Cd Length: 195  Bit Score: 42.77  E-value: 8.84e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522 108 LGRFLIhPNIPDFLAAHPAVDVVLKLDDRQLDPVDDQVDIVFRITDDP-PPGLVGRKLMRiEHV--VCA---TPAYLARH 181
Cdd:cd08482   11 LMRWLI-PRLPAFQAALPDIDLQLSASDGPVDSLRDGIDAAIRFNDAPwPAGMQVIELFP-ERVgpVCSpslAPTVPLRQ 88

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 817522522 182 GRPAhpRELAAHGCITLSEDPVDTRWRFERGGGTVAVDVRGRYvaNHSGVRLEAVLADLGIGGVPRFVAAAALEDGR 258
Cdd:cd08482   89 APAA--ALLGAPLLHTRSRPQAWPDWAAAQGLAPEKLGTGQSF--EHFYYLLEAAVAGLGVAIAPWPLVRDDLASGR 161
PRK10341 PRK10341
transcriptional regulator TdcA;
6-68 9.37e-05

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 43.31  E-value: 9.37e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 817522522   6 IPPLMDEMATFVKVAEAGSFSEAARRLGSTPSAVSRSIARLERALGTRLILRSTRRLRLSDEG 68
Cdd:PRK10341   5 LLPKTQHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAG 67
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
16-154 9.49e-05

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 43.50  E-value: 9.49e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  16 FVKVAEAGSFSEAARRLGSTPSAVSRSIARLERALGTRLILRSTRRLRLSDEGL---EALRHAGELVAAakavmSLAERR 92
Cdd:PRK10082  19 FLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKifhSQIRHLLQQLES-----NLAELR 93

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  93 --SAEPAGTIRISAPRALGRFLIhPNI-----PDFLAAHPAVDVvlkldDRQLDPV-DDQVDIVFRITDD 154
Cdd:PRK10082  94 ggSDYAQRKIKIAAAHSLSLGLL-PSIisqmpPLFTWAIEAIDV-----DEAVDKLrEGQSDCIFSFHDE 157
HTH_MARR smart00347
helix_turn_helix multiple antibiotic resistance protein;
24-75 9.65e-05

helix_turn_helix multiple antibiotic resistance protein;


Pssm-ID: 197670 [Multi-domain]  Cd Length: 101  Bit Score: 40.66  E-value: 9.65e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 817522522    24 SFSEAARRLGSTPSAVSRSIARLERA-LGTRLILRSTRR---LRLSDEGLEALRHA 75
Cdd:smart00347  26 SVSELAKRLGVSPSTVTRVLDRLEKKgLVRREPSPEDRRsvlVSLTEEGRELIEQL 81
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 16-198 1.14e-04

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 43.06  E-value: 1.14e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  16 FVKVAEAGSFSEAARRLGSTPSAVSRSIARLERALGTRLILRSTRRLRLSDEGL---EALRHA----GELVAAAKavmSL 88
Cdd:PRK11013  12 FHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLrlfEEVQRSyyglDRIVSAAE---SL 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  89 AERRSAEpagtIRISAPRALGRFLIHPNIPDFLAAHPAVDVVLKlddRQLDPV------DDQVDIVFRITDDPPPGLVGR 162
Cdd:PRK11013  89 REFRQGQ----LSIACLPVFSQSLLPGLCQPFLARYPDVSLNIV---PQESPLleewlsAQRHDLGLTETLHTPAGTERT 161

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 817522522 163 KLMRIEHvVCATPAylarhgrpAHPreLAAHGCITL 198
Cdd:PRK11013 162 ELLTLDE-VCVLPA--------GHP--LAAKKVLTP 186
PRK12680 PRK12680
LysR family transcriptional regulator;
16-132 1.97e-04

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 42.30  E-value: 1.97e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  16 FVKVAEAG-SFSEAARRLGSTPSAVSRSIARLERALGTRLILRSTRRLR-LSDEGLEALRHAGELVAAAKAVMSLAERRS 93
Cdd:PRK12680   9 LVAIADAElNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLEsVTPAGVEVIERARAVLSEANNIRTYAANQR 88

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 817522522  94 AEPAGTIRISAPRALGRFLIHPNIPDFLAAHPAVDVVLK 132
Cdd:PRK12680  89 RESQGQLTLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQ 127
MarR COG1846
DNA-binding transcriptional regulator, MarR family [Transcription];
24-92 2.30e-04

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


Pssm-ID: 441451 [Multi-domain]  Cd Length: 142  Bit Score: 40.72  E-value: 2.30e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  24 SFSEAARRLGSTPSAVSRSIARLERAlgtRLILRST-------RRLRLSDEGLEALRHA----GELVAAAKAVMSLAERR 92
Cdd:COG1846   54 TQSELAERLGLTKSTVSRLLDRLEEK---GLVEREPdpedrraVLVRLTEKGRALLEEArpalEALLAELLAGLSEEELE 130
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
13-259 2.42e-04

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 42.31  E-value: 2.42e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  13 MATFVKVAEAGSFSEAARRLGSTPSAVSRSIARLERALGTRLILRSTRRLRLSDEGLEALRHAGELVAAakavMSLAERR 92
Cdd:PRK15421   7 LKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQ----ISQALQA 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  93 SAEPAGT-IRISAPRALGRFLIHPNIPDFLAAHPAVDVVLKLD---DRQLDPVDDQVDIVfrITDD--PPPGLVGRKLMR 166
Cdd:PRK15421  83 CNEPQQTrLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGvtfDPQPALQQGELDLV--MTSDilPRSGLHYSPMFD 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522 167 IEHVVCATPAYLARHGRPAHPRELAAHgciTLSEDPVDTR----WRFERGGGTVAVDVRGryvANHSGVRLEAVLADLGI 242
Cdd:PRK15421 161 YEVRLVLAPDHPLAAKTRITPEDLASE---TLLIYPVQRSrldvWRHFLQPAGVSPSLKS---VDNTLLLIQMVAARMGI 234

                        250
                 ....*....|....*..
gi 817522522 243 GGVPRFVAAAALEDGRV 259
Cdd:PRK15421 235 AALPHWVVESFERQGLV 251
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 19-68 3.18e-04

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 41.85  E-value: 3.18e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 817522522  19 VAEAGSFSEAARRLGSTPSAVSRSIARLERALGTRLILRSTRRLRLSDEG 68
Cdd:PRK11074  13 VARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAG 62
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
35-74 3.37e-04

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 41.34  E-value: 3.37e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 817522522  35 TPSAVSRSIARLERALGTRLILRSTRRLRLSDEGlEALRH 74
Cdd:PRK11716   4 SPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAG-EELRP 42
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
 104-264 4.26e-04

The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO operon, which is involved in the carbon dioxide fixation, contains the type 2 periplasmic binding fold; CbbR, a LysR-type transcriptional regulator, is required to activate expression of RubisCO, one of two unique enzymes in the Calvin-Benson-Bassham (CBB) cycle pathway. All plants, cyanobacteria, and many autotrophic bacteria use the CBB cycle to fix carbon dioxide. Thus, this cycle plays an essential role in assimilating CO2 into organic carbon on earth. The key CBB cycle enzyme is ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO), which catalyzes the actual CO2 fixation reaction. The CO2 concentration affects the expression of RubisCO genes. It has also shown that NADPH enhances the DNA-binding ability of the CbbR. RubisCO is composed of eight large (CbbL) and eight small subunits (CbbS). The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176111  Cd Length: 197  Bit Score: 40.57  E-value: 4.26e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522 104 APRALGRFLihpnipdflAAHPAVDVVLKLDDRQ--LDPVDD-QVDIVfrITDDPPPGL--VGRKLMRIEHVVCAtpayl 178
Cdd:cd08419   14 APRLLGAFC---------RRHPGVEVSLRVGNREqvLERLADnEDDLA--IMGRPPEDLdlVAEPFLDNPLVVIA----- 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522 179 arhgRPAHPreLAAHGCITLSE---DPVDTRwrfERGGGT-VAVDvrgRYVANHsGVRL-------------EAVLADLG 241
Cdd:cd08419   78 ----PPDHP--LAGQKRIPLERlarEPFLLR---EPGSGTrLAME---RFFAEH-GVTLrvrmelgsneaikQAVMAGLG 144

                        170       180
                 ....*....|....*....|...
gi 817522522 242 IGGVPRFVAAAALEDGRVeQVLP 264
Cdd:cd08419  145 LSVLSLHTLALELATGRL-AVLD 166
cbl PRK12679
HTH-type transcriptional regulator Cbl;
26-131 9.02e-04

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 40.18  E-value: 9.02e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  26 SEAARRLGSTPSAVSRSIARLERALGTRLILRSTRRLR-LSDEGLEALRHAGELVAAAKAVMSLAERRSAEPAGTIRISA 104
Cdd:PRK12679  20 TEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRLLgMTEPGKALLVIAERILNEASNVRRLADLFTNDTSGVLTIAT 99

                         90       100
                 ....*....|....*....|....*..
gi 817522522 105 PRALGRFLIHPNIPDFLAAHPAVDVVL 131
Cdd:PRK12679 100 THTQARYSLPEVIKAFRELFPEVRLEL 126
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
26-147 9.36e-04

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 40.35  E-value: 9.36e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  26 SEAARRLGSTPSAVSRSIARLERALGTRLILRSTRRLR-LSDEGLEALRHAGELVAAAKAVMSLAERRSAEPAGTIRISA 104
Cdd:PRK12684  20 TEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRgLTEPGRIILASVERILQEVENLKRVGKEFAAQDQGNLTIAT 99

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 817522522 105 PRALGRFLIHPNIPDFLAAHPAVdvvlKLDDRQLDP-------VDDQVDI 147
Cdd:PRK12684 100 THTQARYALPAAIKEFKKRYPKV----RLSILQGSPtqiaemvLHGQADL 145
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
15-87 2.57e-03

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 38.84  E-value: 2.57e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 817522522  15 TFVKVAEAGSFSEAARRLGSTPSAVSRSIARLERALGTRLILRSTRRLRLSDeglealrhAGE-LVAAAKAVMS 87
Cdd:PRK03601   8 TFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTA--------AGErLLPYAETLMN 73
PBP2_LTTR_beta_lactamase cd08484
The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase ...
 115-261 8.66e-03

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


Pssm-ID: 176173 [Multi-domain]  Cd Length: 189  Bit Score: 36.58  E-value: 8.66e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522 115 PNIPDFLAAHPAVDVVLKLDDRQLDPVDDQVDIVFRITDDPPPGLVGRKLMRIEHVVCATPAyLARhgRPAHPRELAAHg 194
Cdd:cd08484   17 PRLAEFRQLHPFIDLRLSTNNNRVDIAAEGLDFAIRFGEGAWPGTDATRLFEAPLSPLCTPE-LAR--RLSEPADLANE- 92

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 817522522 195 ciTLSEDPVDTRWR--FERGGGTVAVdVRGrYVANHSGVRLEAVLADLGIGGVPRFVAAAALEDGRVEQ 261
Cdd:cd08484   93 --TLLRSYRADEWPqwFEAAGVPPPP-ING-PVFDSSLLMVEAALQGAGVALAPPSMFSRELASGALVQ 157
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 99-251 9.95e-03

The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the catabolism of opines and that of related regulators, contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulators, OccR and NocR, involved in the catabolism of opines and that of LysR for lysine biosynthesis which clustered together in phylogenetic trees. Opines, such as octopine and nopaline, are low molecular weight compounds found in plant crown gall tumors that are produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. NocR and OccR belong to the family of LysR-type transcriptional regulators that positively regulates the catabolism of nopaline and octopine, respectively. Both nopaline and octopalin are arginine derivatives. In Agrobacterium tumefaciens, NocR regulates expression of the divergently transcribed nocB and nocR genes of the nopaline catabolism (noc) region. OccR protein activates the occQ operon of the Ti plasmid in response to octopine. This operon encodes proteins required for the uptake and catabolism of octopine. The occ operon also encodes the TraR protein, which is a quorum-sensing transcriptional regulator of the Ti plasmid tra regulon. LysR is the transcriptional activator of lysA gene encoding diaminopimelate decarboxylase, an enzyme that catalyses the decarboxylation of diaminopimelate to produce lysine. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176107 [Multi-domain]  Cd Length: 196  Bit Score: 36.39  E-value: 9.95e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522  99 TIRISAPRALGRFLIHPNIPDFLAAHPavDVVLKLDDRQLDPVDD-----QVDIVFRITDDPPPGLVGRKLMRIeHVVCA 173
Cdd:cd08415    1 TLRIAALPALALSLLPRAIARFRARHP--DVRISLHTLSSSTVVEavlsgQADLGLASLPLDHPGLESEPLASG-RAVCV 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817522522 174 TPA--YLARHGRpAHPRELAAHGCITLSEDpVDTRWRFERGGGTVAVDVRGRYVANHSGVRLEAVLADLGIGGVPRFVAA 251
Cdd:cd08415   78 LPPghPLARKDV-VTPADLAGEPLISLGRG-DPLRQRVDAAFERAGVEPRIVIETQLSHTACALVAAGLGVAIVDPLTAA 155
 
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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