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Conserved domains on  [gi|743333428|gb|KID39791|]
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transcriptional regulator [Pseudoalteromonas distincta]

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 ...
 96-290 1.21e-69

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: 214.61  E-value: 1.21e-69
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428  96 GLLKISCPVNVGMQLIVPAINTFKRQYPKIQIDLQLTDDVVDIIKNGFDFAIRGVALSDSNLQATKLTTMSTCICGAPEY 175
Cdd:cd08422    1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVASPAY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428 176 FAHFGKPKTPLELAEHQWVVYQLGSK--TLTLQKDGKKHDITMQGGLSTNNAAARTAFVEAGHGIGRIPLYDAWPKVQAG 253
Cdd:cd08422   81 LARHGTPQTPEDLARHRCLGYRLPGRplRWRFRRGGGEVEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAEDLASG 160

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 743333428 254 LLEIILDDYKSKDIELYGVFPPGAAGSKKLRLFIDYL 290
Cdd:cd08422  161 RLVRVLPDWRPPPLPIYAVYPSRRHLPAKVRAFIDFL 197
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
8-66 1.35e-19

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


:

Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 80.51  E-value: 1.35e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 743333428    8 LKSMVVFAQIVEQGSLTAAAKQLGLTRAVASYHLKKLETQLEVTLLNRSTRTMALTEAG 66
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 ...
 96-290 1.21e-69

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: 214.61  E-value: 1.21e-69
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428  96 GLLKISCPVNVGMQLIVPAINTFKRQYPKIQIDLQLTDDVVDIIKNGFDFAIRGVALSDSNLQATKLTTMSTCICGAPEY 175
Cdd:cd08422    1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVASPAY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428 176 FAHFGKPKTPLELAEHQWVVYQLGSK--TLTLQKDGKKHDITMQGGLSTNNAAARTAFVEAGHGIGRIPLYDAWPKVQAG 253
Cdd:cd08422   81 LARHGTPQTPEDLARHRCLGYRLPGRplRWRFRRGGGEVEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAEDLASG 160

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 743333428 254 LLEIILDDYKSKDIELYGVFPPGAAGSKKLRLFIDYL 290
Cdd:cd08422  161 RLVRVLPDWRPPPLPIYAVYPSRRHLPAKVRAFIDFL 197
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
8-294 1.39e-62

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 198.55  E-value: 1.39e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428   8 LKSMVVFAQIVEQGSLTAAAKQLGLTRAVASYHLKKLETQLEVTLLNRSTRTMALTEAGIAYYERCRIITEQANAANQQI 87
Cdd:COG0583    3 LRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAEL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428  88 ENIKSEPQGLLKISCPVNVGMQLIVPAINTFKRQYPKIQIDLQL--TDDVVDIIKNG-FDFAIRGVALSDSNLQATKLTT 164
Cdd:COG0583   83 RALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREgnSDRLVDALLEGeLDLAIRLGPPPDPGLVARPLGE 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428 165 MSTCICGAPEYfahfgkpktplELAEHQWVVyqlgsktltlqkdgkkhditmqgglstNNAAARTAFVEAGHGIGRIPLY 244
Cdd:COG0583  163 ERLVLVASPDH-----------PLARRAPLV---------------------------NSLEALLAAVAAGLGIALLPRF 204

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|
gi 743333428 245 DAWPKVQAGLLEIILDDYKSKDIELYGVFPPGAAGSKKLRLFIDYLKAYF 294
Cdd:COG0583  205 LAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREAL 254
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
6-296 7.66e-56

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 183.04  E-value: 7.66e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428   6 EQLKSMVVFAQIVEQGSLTAAAKQLGLTRAVASYHLKKLETQLEVTLLNRSTRTMALTEAGIAYYERCRIITEQANAANQ 85
Cdd:PRK10632   2 ERLKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHE 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428  86 QIENIKSEPQGLLKISCPVNVGMQLIVPAINTFKRQYPKIQIDLQLTDDVVDIIKNGFDFAIRGVALSDSNLQATKLTTM 165
Cdd:PRK10632  82 QLYAFNNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTGIPAPDLIADGLDVVIRVGALQDSSLFSRRLGAM 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428 166 STCICGAPEYFAHFGKPKTPLELAEHQWVVY--QLGSKTLTLQKDGKKHDITMQGGLSTNNAAARTAFVEAGHGIGRIPL 243
Cdd:PRK10632 162 PMVVCAAKSYLAQYGTPEKPADLSSHSWLEYsvRPDNEFELIAPEGISTRLIPQGRFVTNDPQTLVRWLTAGAGIAYVPL 241

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|...
gi 743333428 244 YDAWPKVQAGLLEIILDDYKSKDIELYGVFPPGAAGSKKLRLFIDYLKAYFVK 296
Cdd:PRK10632 242 MWVIDEINRGELEILFPRYQSDPRPVYALYTEKDKLPLKVQVCINYLTDYFVE 294
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 95-294 2.39e-33

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: 121.63  E-value: 2.39e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428   95 QGLLKISCPVNVGMQLIVPAINTFKRQYPKIQIDLQL--TDDVVDIIKNG-FDFAIRGVALSDSNLQATKLTTMSTCICG 171
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEgnSEELLDLLLEGeLDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428  172 APEYFAHFGKPKTPLELAEHQWVVYQLGSKTLT-LQKDGKKHDITMQGGLSTNNAAARTAFVEAGHGIGRIPLYDAWPKV 250
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLPPGSGLRDlLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAREL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 743333428  251 QAGLLEII-LDDYKSKdIELYGVFPPGAAGSKKLRLFIDYLKAYF 294
Cdd:pfam03466 161 ADGRLVALpLPEPPLP-RELYLVWRKGRPLSPAVRAFIEFLREAL 204
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
8-66 1.35e-19

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 80.51  E-value: 1.35e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 743333428    8 LKSMVVFAQIVEQGSLTAAAKQLGLTRAVASYHLKKLETQLEVTLLNRSTRTMALTEAG 66
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
14-66 3.41e-07

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 50.74  E-value: 3.41e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 743333428  14 FAQIVEQGSLTAAAKQLGLTRAVASYHLKKLETQLEVTLLNRsTRTMALTEAG 66
Cdd:PRK13348  10 LAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAG 61
ModE COG2005
DNA-binding transcriptional regulator ModE (molybdenum-dependent) [Transcription];
16-90 4.44e-05

DNA-binding transcriptional regulator ModE (molybdenum-dependent) [Transcription];


Pssm-ID: 441608 [Multi-domain]  Cd Length: 118  Bit Score: 42.12  E-value: 4.44e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428  16 QIVEQGSLTAAAKQLGLtravaSY-----HLKKLETQLEVTLLNRST------RTmALTEAG---IAYYErcRIITEQAN 81
Cdd:COG2005   29 AIDETGSISAAAKAMGM-----SYkrawdLIDAMNNLLGEPLVERQTggkgggGA-RLTPEGrrlLALYR--RLEAEAQR 100


                 ....*....
gi 743333428  82 AANQQIENI 90
Cdd:COG2005  101 ALAALFEEL 109
 
Name Accession Description Interval E-value
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 96-290 1.21e-69

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: 214.61  E-value: 1.21e-69
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428  96 GLLKISCPVNVGMQLIVPAINTFKRQYPKIQIDLQLTDDVVDIIKNGFDFAIRGVALSDSNLQATKLTTMSTCICGAPEY 175
Cdd:cd08422    1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVASPAY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428 176 FAHFGKPKTPLELAEHQWVVYQLGSK--TLTLQKDGKKHDITMQGGLSTNNAAARTAFVEAGHGIGRIPLYDAWPKVQAG 253
Cdd:cd08422   81 LARHGTPQTPEDLARHRCLGYRLPGRplRWRFRRGGGEVEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAEDLASG 160

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 743333428 254 LLEIILDDYKSKDIELYGVFPPGAAGSKKLRLFIDYL 290
Cdd:cd08422  161 RLVRVLPDWRPPPLPIYAVYPSRRHLPAKVRAFIDFL 197
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
8-294 1.39e-62

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 198.55  E-value: 1.39e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428   8 LKSMVVFAQIVEQGSLTAAAKQLGLTRAVASYHLKKLETQLEVTLLNRSTRTMALTEAGIAYYERCRIITEQANAANQQI 87
Cdd:COG0583    3 LRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAEL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428  88 ENIKSEPQGLLKISCPVNVGMQLIVPAINTFKRQYPKIQIDLQL--TDDVVDIIKNG-FDFAIRGVALSDSNLQATKLTT 164
Cdd:COG0583   83 RALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREgnSDRLVDALLEGeLDLAIRLGPPPDPGLVARPLGE 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428 165 MSTCICGAPEYfahfgkpktplELAEHQWVVyqlgsktltlqkdgkkhditmqgglstNNAAARTAFVEAGHGIGRIPLY 244
Cdd:COG0583  163 ERLVLVASPDH-----------PLARRAPLV---------------------------NSLEALLAAVAAGLGIALLPRF 204

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|
gi 743333428 245 DAWPKVQAGLLEIILDDYKSKDIELYGVFPPGAAGSKKLRLFIDYLKAYF 294
Cdd:COG0583  205 LAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREAL 254
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
6-296 7.66e-56

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 183.04  E-value: 7.66e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428   6 EQLKSMVVFAQIVEQGSLTAAAKQLGLTRAVASYHLKKLETQLEVTLLNRSTRTMALTEAGIAYYERCRIITEQANAANQ 85
Cdd:PRK10632   2 ERLKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHE 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428  86 QIENIKSEPQGLLKISCPVNVGMQLIVPAINTFKRQYPKIQIDLQLTDDVVDIIKNGFDFAIRGVALSDSNLQATKLTTM 165
Cdd:PRK10632  82 QLYAFNNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTGIPAPDLIADGLDVVIRVGALQDSSLFSRRLGAM 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428 166 STCICGAPEYFAHFGKPKTPLELAEHQWVVY--QLGSKTLTLQKDGKKHDITMQGGLSTNNAAARTAFVEAGHGIGRIPL 243
Cdd:PRK10632 162 PMVVCAAKSYLAQYGTPEKPADLSSHSWLEYsvRPDNEFELIAPEGISTRLIPQGRFVTNDPQTLVRWLTAGAGIAYVPL 241

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|...
gi 743333428 244 YDAWPKVQAGLLEIILDDYKSKDIELYGVFPPGAAGSKKLRLFIDYLKAYFVK 296
Cdd:PRK10632 242 MWVIDEINRGELEILFPRYQSDPRPVYALYTEKDKLPLKVQVCINYLTDYFVE 294
PBP2_CrgA_like_3 cd08472
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 96-290 3.40e-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 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: 164.99  E-value: 3.40e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428  96 GLLKISCPVNVGMQLIVPAINTFKRQYPKIQIDLQLTDDVVDIIKNGFDFAIRGVALSDSNLQATKLTTMSTCICGAPEY 175
Cdd:cd08472    1 GRLRVDVPGSLARLLLIPALPDFLARYPDIELDLGVSDRPVDLIREGVDCVIRVGELADSSLVARRLGELRMVTCASPAY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428 176 FAHFGKPKTPLELAEHQWVVYQLGSKT----LTLQKDGKKHDITMQGGLSTNNAAARTAFVEAGHGIGRIPLYDAWPKVQ 251
Cdd:cd08472   81 LARHGTPRHPEDLERHRAVGYFSARTGrvlpWEFQRDGEEREVKLPSRVSVNDSEAYLAAALAGLGIIQVPRFMVRPHLA 160

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 743333428 252 AGLLEIILDDYKSKDIELYGVFPPGAAGSKKLRLFIDYL 290
Cdd:cd08472  161 SGRLVEVLPDWRPPPLPVSLLYPHRRHLSPRVRVFVDWV 199
PBP2_CrgA_like_1 cd08470
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 96-292 1.15e-43

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: 148.23  E-value: 1.15e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428  96 GLLKISCPVNVGMQLIVPAINTFKRQYPKIQIDLQLTDDVVDIIKNGFDFAIRGVALSDSNLQATKLTTMSTCICGAPEY 175
Cdd:cd08470    1 GLLRITCPVAYGERFIAPLVNDFMQRYPKLEVDIELTNRVVDLVSEGFDLAIRLGRLTDSSLMARRLASRRHYVCASPAY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428 176 FAHFGKPKTPLELAEHQwvVYQLGSKTLTLQKDGKKHDITMQGGLSTNNAAARTAFVEAGHGIGRIPLYDAWPKVQAGLL 255
Cdd:cd08470   81 LERHGTPHSLADLDRHN--CLLGTSDHWRFQENGRERSVRVQGRWRCNSGVALLDAALKGMGLAQLPDYYVDEHLAAGRL 158

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 743333428 256 EIILDDYKSKDIELYGVFPPGAAGSKKLRLFIDYLKA 292
Cdd:cd08470  159 VPVLEDYRPPDEGIWALYPHNRHLSPKVRLLVDYLAD 195
PRK09801 PRK09801
LysR family transcriptional regulator;
1-293 4.89e-42

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 147.49  E-value: 4.89e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428   1 MKVSFEQLKSMVVFAQIVEQGSLTAAAKQLGLTRAVASYHLKKLETQLEVTLLNRSTRTMALTEAGIAYYERCRIITEQA 80
Cdd:PRK09801   1 MLNSWPLAKDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428  81 NAANQQIENIKSEPQGLLKISCPVNVGMQLIVPAINTFKRQYPKIQIDLQLTDDVVDIIKNGFDFAIR-GVALSDSNLqA 159
Cdd:PRK09801  81 QRLVDDVTQIKTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHFELFDRQIDLVQDNIDLDIRiNDEIPDYYI-A 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428 160 TKLTTMSTCICGAPEYFAHFGKPKTPLELAEHQWVVYQLGSKTLTLQKDG---KKHDITMQGGLSTNNAAARTAFVEAGH 236
Cdd:PRK09801 160 HLLTKNKRILCAAPEYLQKYPQPQSLQELSRHDCLVTKERDMTHGIWELGngqEKKSVKVSGHLSSNSGEIVLQWALEGK 239

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 743333428 237 GIGRIPLYDAWPKVQAGLLEIILDDYkSKDIELYGVFPPGAAGSKKLRLFIDYLKAY 293
Cdd:PRK09801 240 GIMLRSEWDVLPFLESGKLVQVLPEY-AQSANIWAVYREPLYRSMKLRVCVEFLAAW 295
PBP2_CrgA_like_2 cd08471
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 96-290 6.55e-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 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: 143.43  E-value: 6.55e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428  96 GLLKISCPVNVGMQLIVPAINTFKRQYPKIQIDLQLTDDVVDIIKNGFDFAIRGVALSDSNLQATKLTTMSTCICGAPEY 175
Cdd:cd08471    1 GLLTVTAPVLFGRLHVLPIITDFLDAYPEVSVRLLLLDRVVNLLEEGVDVAVRIGHLPDSSLVATRVGSVRRVVCASPAY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428 176 FAHFGKPKTPLELAEHQWVVYQLGSKTL--TLQKDGKKHDITMQGGLSTNNAAARTAFVEAGHGIGRIPLYDAWPKVQAG 253
Cdd:cd08471   81 LARHGTPKHPDDLADHDCIAFTGLSPAPewRFREGGKERSVRVRPRLTVNTVEAAIAAALAGLGLTRVLSYQVAEELAAG 160

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 743333428 254 LLEIILDDYKSKDIELYGVFPPGAAGSKKLRLFIDYL 290
Cdd:cd08471  161 RLQRVLEDFEPPPLPVHLVHPEGRLAPAKVRAFVDFA 197
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 8-290 2.84e-40

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 142.44  E-value: 2.84e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428   8 LKSMVVFAQIVEQGSLTAAAKQLGLTRAVASYHLKKLETQLEVTLLNRSTRTMALTEAGIAYYERCRIITEQANAANQQI 87
Cdd:PRK14997   4 LNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDAI 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428  88 ENIKSEPQGLLKISCPVNVGMQLIVPAINTFKRQYPKIQIDLQLTDDVVDIIKNGFDFAI--RGVALSDSNLQATKLTTM 165
Cdd:PRK14997  84 AALQVEPRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLEATNRRVDVVGEGVDVAIrvRPRPFEDSDLVMRVLADR 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428 166 STCICGAPEYFAHFGKPKTPLELaeHQWVVYQLGS-----KTLTLQKDGKKHDITMQGGLSTNNAAARTAFVEAGHGIGR 240
Cdd:PRK14997 164 GHRLFASPDLIARMGIPSAPAEL--SHWPGLSLASgkhihRWELYGPQGARAEVHFTPRMITTDMLALREAAMAGVGLVQ 241

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|
gi 743333428 241 IPLYDAWPKVQAGLLEIILDDYKSKDIELYGVFPPGAAGSKKLRLFIDYL 290
Cdd:PRK14997 242 LPVLMVKEQLAAGELVAVLEEWEPRREVIHAVFPSRRGLLPSVRALVDFL 291
PBP2_CrgA_like_7 cd08476
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 96-290 4.70e-40

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 138.53  E-value: 4.70e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428  96 GLLKISCPVnVGMqLIVPAINTFKRQYPKIQIDLQLTDDVVDIIKNGFDFAIRGVALSDSNLQATKLTTMSTCICGAPEY 175
Cdd:cd08476    1 GRLRVSLPL-VGG-LLLPVLAAFMQRYPEIELDLDFSDRLVDVIDEGFDAVIRTGELPDSRLMSRRLGSFRMVLVASPDY 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428 176 FAHFGKPKTPLELAEHQWVVYQL--GSKTLT--LQKDGKKHDITMQGGLSTNNAAARTAFVEAGHGIGRIPLYDAWPKVQ 251
Cdd:cd08476   79 LARHGTPETPADLAEHACLRYRFptTGKLEPwpLRGDGGDPELRLPTALVCNNIEALIEFALQGLGIACLPDFSVREALA 158

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 743333428 252 AGLLEIILDDYKSKDIELYGVFPPGAAGSKKLRLFIDYL 290
Cdd:cd08476  159 DGRLVTVLDDYVEERGQFRLLWPSSRHLSPKLRVFVDFM 197
PBP2_CrgA_like_8 cd08477
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 96-290 7.24e-39

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 135.44  E-value: 7.24e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428  96 GLLKISCPVNVGMQLIVPAINTFKRQYPKIQIDLQLTDDVVDIIKNGFDFAIRGVALSDSNLQATKLTTMSTCICGAPEY 175
Cdd:cd08477    1 GKLRISAPVTFGSHVLTPALAEYLARYPDVRVDLVLSDRLVDLVEEGFDAAFRIGELADSSLVARPLAPYRMVLCASPDY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428 176 FAHFGKPKTPLELAEHQWV--VYQLGSKTLTLQKDGKKHDITMQGGLSTNNAAA-RTAFVeAGHGIGRIPLYDAWPKVQA 252
Cdd:cd08477   81 LARHGTPTTPEDLARHECLgfSYWRARNRWRLEGPGGEVKVPVSGRLTVNSGQAlRVAAL-AGLGIVLQPEALLAEDLAS 159

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 743333428 253 GLLEIILDDYKSKDIELYGVFPPGAAGSKKLRLFIDYL 290
Cdd:cd08477  160 GRLVELLPDYLPPPRPMHLLYPPDRRPTPKLRSFIDFL 197
PBP2_CrgA_like_9 cd08479
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 96-290 1.99e-37

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: 131.95  E-value: 1.99e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428  96 GLLKISCPVNVGMQLIVPAINTFKRQYPKIQIDLQLTDDVVDIIKNGFDFAIRGVALSDSNLQATKLTTMSTCICGAPEY 175
Cdd:cd08479    1 GLLRVNASFGFGRRHIAPALSDFAKRYPELEVQLELTDRPVDLVEEGFDLDIRVGDLPDSSLIARKLAPNRRILCASPAY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428 176 FAHFGKPKTPLELAEHQWVVYQLGSKTLT---LQKDGKKHDITMQGGLSTNNAAARTAFVEAGHGIGRIPLYDAWPKVQA 252
Cdd:cd08479   81 LERHGAPASPEDLARHDCLVIRENDEDFGlwrLRNGDGEATVRVRGALSSNDGEVVLQWALDGHGIILRSEWDVAPYLRS 160

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 743333428 253 GLLEIILDDYKSKDIELYGVFPPGAAGSKKLRLFIDYL 290
Cdd:cd08479  161 GRLVRVLPDWQLPDADIWAVYPSRLSRSARVRVFVDFL 198
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-290 2.11e-37

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: 131.81  E-value: 2.11e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428  94 PQGLLKISCPVNVGMQLIVPAINTFKRQYPKIQIDLQLTDDVVDIIKNGFDFAIR-GVALsDSNLQATKLT-TMSTCICG 171
Cdd:cd08474    1 PAGTLRINAPRVAARLLLAPLLARFLARYPDIRLELVVDDGLVDIVAEGFDAGIRlGESV-EKDMVAVPLGpPLRMAVVA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428 172 APEYFAHFGKPKTPLELAEHQWVVYQL-GSKTL---TLQKDGKKHDITMQGGLSTNNAAARTAFVEAGHGIGRIPLYDAW 247
Cdd:cd08474   80 SPAYLARHGTPEHPRDLLNHRCIRYRFpTSGALyrwEFERGGRELEVDVEGPLILNDSDLMLDAALDGLGIAYLFEDLVA 159

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 743333428 248 PKVQAGLLEIILDDYKSKDIELYGVFPPGAAGSKKLRLFIDYL 290
Cdd:cd08474  160 EHLASGRLVRVLEDWSPPFPGGYLYYPSRRRVPPALRAFIDFL 202
PBP2_CrgA_like_6 cd08475
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 96-290 9.86e-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 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: 124.98  E-value: 9.86e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428  96 GLLKISCPVNVGMQLIVPAINTFKRQYPKIQIDLQLTDDVVDIIKNGFDFAIRGVALSDS-NLQATKLTTMSTCICGAPE 174
Cdd:cd08475    1 GRLRIDLPVAFGRLCVAPLLLELARRHPELELELSFSDRFVDLIEEGIDLAVRIGELADStGLVARRLGTQRMVLCASPA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428 175 YFAHFGKPKTPLELAEHQWVVYQLGSKTLTLQ---KDGKKHDITMQGGLSTNNAAARTAFVEAGHGIGRIPLYDAWPKVQ 251
Cdd:cd08475   81 YLARHGTPRTLEDLAEHQCIAYGRGGQPLPWRladEQGRLVRFRPAPRLQFDDGEAIADAALAGLGIAQLPTWLVADHLQ 160

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 743333428 252 AGLLEIILDDYKSKDIELYGVFPPGAAGSKKLRLFIDYL 290
Cdd:cd08475  161 RGELVEVLPELAPEGLPIHAVWPRTRHLPPKVRAAVDAL 199
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 95-294 2.39e-33

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: 121.63  E-value: 2.39e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428   95 QGLLKISCPVNVGMQLIVPAINTFKRQYPKIQIDLQL--TDDVVDIIKNG-FDFAIRGVALSDSNLQATKLTTMSTCICG 171
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEgnSEELLDLLLEGeLDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428  172 APEYFAHFGKPKTPLELAEHQWVVYQLGSKTLT-LQKDGKKHDITMQGGLSTNNAAARTAFVEAGHGIGRIPLYDAWPKV 250
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLPPGSGLRDlLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAREL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 743333428  251 QAGLLEII-LDDYKSKdIELYGVFPPGAAGSKKLRLFIDYLKAYF 294
Cdd:pfam03466 161 ADGRLVALpLPEPPLP-RELYLVWRKGRPLSPAVRAFIEFLREAL 204
PBP2_CrgA_like_10 cd08480
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 96-290 2.16e-31

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 116.28  E-value: 2.16e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428  96 GLLKISCPVNVGMQLIVPAINTFKRQYPKIQIDLQLTDDVVDIIKNGFDFAIRGVALSDSNLQATKLTTMSTCICGAPEY 175
Cdd:cd08480    1 GRLRVNASVPFGTHFLLPLLPAFLARYPEILVDLSLTDEVVDLLAERTDVAIRVGPLPDSSLVARKLGESRRVIVASPSY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428 176 FAHFGKPKTPLELAEHQWVV--YQLGSKTLTLQKDGKKHDITMQGGLSTNNAAARTAFVEAGHGIGRIPLYDAWPKVQAG 253
Cdd:cd08480   81 LARHGTPLTPQDLARHNCLGfnFRRALPDWPFRDGGRIVALPVSGNILVNDGEALRRLALAGAGLARLALFHVADDIAAG 160

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 743333428 254 LLEIILDDYKSKDIE-LYGVFPPGAAGSKKLRLFIDYL 290
Cdd:cd08480  161 RLVPVLEEYNPGDREpIHAVYVGGGRLPARVRAFLDFL 198
PBP2_CrgA_like_4 cd08473
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-290 1.22e-30

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: 114.19  E-value: 1.22e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428  94 PQGLLKISCPVNVGMQLIVPAINTFKRQYPKIQIDLQLTDDVVDIIKNGFDFAI--RGVALSDSNLQATKLTTMSTCICG 171
Cdd:cd08473    1 PRGTVRVSCPPALAQELLAPLLPRFMAAYPQVRLQLEATNRRVDLIEEGIDVALrvRFPPLEDSSLVMRVLGQSRQRLVA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428 172 APEYFAHFGKPKTPLELAEHQWV----VYQLGSKTLTlQKDGKKHDITMQGGLSTNNAAARTAFVEAGHGIGRIPLYDAW 247
Cdd:cd08473   81 SPALLARLGRPRSPEDLAGLPTLslgdVDGRHSWRLE-GPDGESITVRHRPRLVTDDLLTLRQAALAGVGIALLPDHLCR 159

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 743333428 248 PKVQAGLLEIILDDYKSKDIELYGVFPPGAAGSKKLRLFIDYL 290
Cdd:cd08473  160 EALRAGRLVRVLPDWTPPRGIVHAVFPSRRGLLPAVRALIDFL 202
PBP2_CrgA cd08478
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains ...
 94-290 4.89e-26

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


Pssm-ID: 176167 [Multi-domain]  Cd Length: 199  Bit Score: 102.03  E-value: 4.89e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428  94 PQGLLKISCPVNVGMQLIVPAINTFKRQYPKIQIDLQLTDDVVDIIKNGFDFAIRGVALSDSNLQATKLTTMSTCICGAP 173
Cdd:cd08478    1 PSGLLRVDAATPFVLHLLAPLIAKFRERYPDIELELVSNEGIIDLIERKTDVAIRIGELTDSTLHARPLGKSRLRILASP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428 174 EYFAHFGKPKTPLELAEHQwvvyQLGSKTLT-------LQKDGKKHDItmQGGLSTNNAAARTAFVEAGHGIGRIPLYDA 246
Cdd:cd08478   81 DYLARHGTPQSIEDLAQHQ----LLGFTEPAslntwpiKDADGNLLKI--QPTITASSGETLRQLALSGCGIACLSDFMT 154

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 743333428 247 WPKVQAGLLEIILDDYKSKDIE-LYGVFPPGAAGSKKLRLFIDYL 290
Cdd:cd08478  155 DKDIAEGRLIPLFAEQTSDVRQpINAVYYRNTALSLRIRCFIDFL 199
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 22-292 2.25e-21

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 91.83  E-value: 2.25e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428  22 SLTAAAKQLGLTRAVASYHLKKLETQLEVTLLNRSTRTMALTEAGIAYYERCRIITEQANAANQQIENIKSEpqGLLKIS 101
Cdd:PRK11139  22 SFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEATRKLRARSAK--GALTVS 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428 102 CPVNVGMQLIVPAINTFKRQYPKIQIDLQLTDDVVDIIKNGFDFAIRGVALSDSNLQATKLTTMSTCICGAPEYFAHFGK 181
Cdd:PRK11139 100 LLPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDRLEDFLRDDVDVAIRYGRGNWPGLRVEKLLDEYLLPVCSPALLNGGKP 179

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428 182 PKTPLELAEHqwvvyqlgskTLtLQKDGKK--HDITMQGGLSTNNAAARTAF------VEA---GHGI--GRIPLydAWP 248
Cdd:PRK11139 180 LKTPEDLARH----------TL-LHDDSREdwRAWFRAAGLDDLNVQQGPIFshssmaLQAaihGQGValGNRVL--AQP 246

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....
gi 743333428 249 KVQAGLLEIILDDYKSKDIELYGVFPPGAAGSKKLRLFIDYLKA 292
Cdd:PRK11139 247 EIEAGRLVCPFDTVLPSPNAFYLVCPDSQAELPKVAAFRQWLLA 290
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
8-66 1.35e-19

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 80.51  E-value: 1.35e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 743333428    8 LKSMVVFAQIVEQGSLTAAAKQLGLTRAVASYHLKKLETQLEVTLLNRSTRTMALTEAG 66
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
7-180 4.98e-16

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 76.96  E-value: 4.98e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428   7 QLKSMVVFAQIVEQGSLTAAAKQLGLTRAVASYHLKKLETQLEVTLLNRSTRTMALTEAGiayyERCRIITEQA-NAANQ 85
Cdd:PRK10086  15 QLSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEG----KRVFWALKSSlDTLNQ 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428  86 QIENIKS-EPQGLLKISCPVNVGMQLIVPAINTFKRQYPKIQIDLQLTDDVVDIIKNGFDFAIRGVALSDSNLQATKLtt 164
Cdd:PRK10086  91 EILDIKNqELSGTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTILTGNENVNFQRAGIDLAIYFDDAPSAQLTHHFL-- 168

                        170
                 ....*....|....*....
gi 743333428 165 MSTCI---CgAPEYFAHFG 180
Cdd:PRK10086 169 MDEEIlpvC-SPEYAERHA 186
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 98-290 3.77e-15

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: 72.63  E-value: 3.77e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428  98 LKISCPVNVGMQLIVPAINTFKRQYPKIQIDLQ--LTDDVVDIIKNG-FDFAIRGVALSDSNLQATKLTTMSTCICGAPE 174
Cdd:cd05466    2 LRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVegGSSELLEALLEGeLDLAIVALPVDDPGLESEPLFEEPLVLVVPPD 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428 175 YFAHFGKPKTPLELAEHQWVVYQLGSKT-LTLQKDGKKHDITMQGGLSTNNAAARTAFVEAGHGIGRIPLYDAWPKVQAG 253
Cdd:cd05466   82 HPLAKRKSVTLADLADEPLILFERGSGLrRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEELADGG 161

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 743333428 254 LLEIILDDyKSKDIELYGVFPPGAAGSKKLRLFIDYL 290
Cdd:cd05466  162 LVVLPLED-PPLSRTIGLVWRKGRYLSPAARAFLELL 197
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 1-202 2.20e-14

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 72.03  E-value: 2.20e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428   1 MKVSFEQLKsmvVFAQIVEQGSLTAAAKQLGLTRAVASYHLKKLETQLEVTLLNRSTRTMALTEAGIAYYERCRIITEQA 80
Cdd:PRK10837   1 MHITLRQLE---VFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQA 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428  81 naanQQIENIKSEPQGLLKISCPVNVGMQLIVPAINTFKRQYPKIQIDLQLTDDvVDIIKNGFDFA-----IRGValsds 155
Cdd:PRK10837  78 ----VEIEQLFREDNGALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNS-QDVINAVLDFRvdiglIEGP----- 147

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 743333428 156 nlqatklttmstciCGAPEYFAH---------FGKPKTPL--------ELAEHQWVVYQLGSKT 202
Cdd:PRK10837 148 --------------CHSPELISEpwledelvvFAAPDSPLargpvtleQLAAAPWILRERGSGT 197
PRK09791 PRK09791
LysR family transcriptional regulator;
3-193 8.00e-13

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 67.48  E-value: 8.00e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428   3 VSFEQLKSmvvFAQIVEQGSLTAAAKQLGLTRAVASYHLKKLETQLEVTLLNRSTRTMALTEAGIAYYERCRIITEQANA 82
Cdd:PRK09791   5 VKIHQIRA---FVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRA 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428  83 ANQQIEniksepQGLLKISCPVNVGM-----QLIVPA-INTFKRQYPKIQIDL---QLTDDVVDIIKNGFDFAIRGVALS 153
Cdd:PRK09791  82 AQEDIR------QRQGQLAGQINIGMgasiaRSLMPAvISRFHQQHPQVKVRImegQLVSMINELRQGELDFTINTYYQG 155

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 743333428 154 --DSNLQATKLTTMSTCIcgapeyFAHFGKPK---TPL-ELAEHQW 193
Cdd:PRK09791 156 pyDHEFTFEKLLEKQFAV------FCRPGHPAigaRSLkQLLDYSW 195
rbcR CHL00180
LysR transcriptional regulator; Provisional
 4-130 3.94e-12

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 65.43  E-value: 3.94e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428   4 SFEQLKsmvVFAQIVEQGSLTAAAKQLGLTRAVASYHLKKLETQLEVTLLNRSTRTMALTEAG---IAYYERCRIITEQA 80
Cdd:CHL00180   6 TLDQLR---ILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGellLRYGNRILALCEET 82

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 743333428  81 NAANQQIENIKSepqGLLKISCPVNVGMQLIVPAINTFKRQYPKIQIDLQ 130
Cdd:CHL00180  83 CRALEDLKNLQR---GTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQ 129
PRK10341 PRK10341
transcriptional regulator TdcA;
9-197 2.00e-11

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 63.73  E-value: 2.00e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428   9 KSMVVFAQIVEQGSLTAAAKQLGLTRAVASYHLKKLETQLEVTLLNRSTRTMALTEAGIAYYERCRIITEQANAANQQIE 88
Cdd:PRK10341  10 QHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEIN 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428  89 NIKSEPQGLLKISCPVNVGMQLIVPAINTFKRQYPKIQIDL---QLTdDVVDIIKNG-FDFAIrGVALSDSNLQ------ 158
Cdd:PRK10341  90 GMSSEAVVDVSFGFPSLIGFTFMSDMINKFKEVFPKAQVSMyeaQLS-SFLPAIRDGrLDFAI-GTLSNEMKLQdlhvep 167

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 743333428 159 ---------ATKLTTMStcicgapeyfahfgKPKTPLELAEHQWVVYQ 197
Cdd:PRK10341 168 lfesefvlvASKSRTCT--------------GTTTLESLKNEQWVLPQ 201
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
14-150 7.72e-11

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 61.75  E-value: 7.72e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428  14 FAQIVEQGSLTAAAKQLGLTRAVASYHLKKLETQLEVTLLNRSTRTMALTEAGIAYYERCRIITEQANAANQQIENIKS- 92
Cdd:PRK10094  10 FIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPSELQQVNDg 89

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 743333428  93 -EPQgllkISCPVNVGM---QLIVPAINTFKRQYP--KIQIDLQLTDDVVD-IIKNGFDFAIrGV 150
Cdd:PRK10094  90 vERQ----VNIVINNLLynpQAVAQLLAWLNERYPftQFHISRQIYMGVWDsLLYEGFSLAI-GV 149
PRK09986 PRK09986
LysR family transcriptional regulator;
8-129 7.98e-11

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 61.66  E-value: 7.98e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428   8 LKSMVVFAQIVEQGSLTAAAKQLGLTRAVASYHLKKLETQLEVTLLNRSTRTMALTEAGIAYYERCRIITEQANAANQQI 87
Cdd:PRK09986   9 LKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLARV 88

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 743333428  88 ENIKSEPQGLLKISCpvnVGMQL---IVPAINTFKRQYPKIQIDL 129
Cdd:PRK09986  89 EQIGRGEAGRIEIGI---VGTALwgrLRPAMRHFLKENPNVEWLL 130
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 14-146 1.28e-10

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 61.13  E-value: 1.28e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428  14 FAQIVEQGSLTAAAKQLGLTRAVASYHLKKLETQLEVTLLNRSTRTMALTEAGIAYYERCRIITEQANAANQQIENIKSE 93
Cdd:PRK11242   9 FLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRRAIHDVADL 88

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 743333428  94 PQGLLKISCPVNVGMQLIVPAINTFKRQYPKIQIDLQ----------LTDDVVDIiknGFDFA 146
Cdd:PRK11242  89 SRGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIRemsqeriealLADDELDV---GIAFA 148
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 98-290 1.35e-09

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: 56.82  E-value: 1.35e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428  98 LKISCPVNVGMQLIVPAINTFKRQYPKIQIDLQLTDDVVDIIKNGFDFAIRGVALSDSNLQATKLTTMSTCICGAPEYFA 177
Cdd:cd08432    2 LTVSVTPSFAARWLIPRLARFQARHPDIDLRLSTSDRLVDFAREGIDLAIRYGDGDWPGLEAERLMDEELVPVCSPALLA 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428 178 HfGKPKTPLELAEHQW---VVYQLGSKTLTLQKDGkkHDITMQGGLSTNNA-----AARtafveAGHGIGRIPLYDAWPK 249
Cdd:cd08432   82 G-LPLLSPADLARHTLlhdATRPEAWQWWLWAAGV--ADVDARRGPRFDDSslalqAAV-----AGLGVALAPRALVADD 153

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 743333428 250 VQAGLLEIILDD-------YkskdielYGVFPPGAAGSKKLRLFIDYL 290
Cdd:cd08432  154 LAAGRLVRPFDLplpsggaY-------YLVYPPGRAESPAVAAFRDWL 194
PRK12680 PRK12680
LysR family transcriptional regulator;
3-239 1.44e-09

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 58.10  E-value: 1.44e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428   3 VSFEQLKSMVVFAQivEQGSLTAAAKQLGLTRAVASYHLKKLETQLEVTLLNRSTRTM-ALTEAGIAYYERCRIITEQAN 81
Cdd:PRK12680   1 MTLTQLRYLVAIAD--AELNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLeSVTPAGVEVIERARAVLSEAN 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428  82 AANQQIENIKSEPQGLLKISCPVNVGMQLIVPAINTFKRQYPKIQIDLQLT--DDVVDIIKNG-FDFAIRGVALSDSN-- 156
Cdd:PRK12680  79 NIRTYAANQRRESQGQLTLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQQAaeSAALDLLGQGdADIAIVSTAGGEPSag 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428 157 --LQATKLTTMSTCICGAPeyFAHFGKPKTPLELAEHQWVVYQLGSKTL-TLQKDGKKHDITMQGGLSTNNAAARTAFVE 233
Cdd:PRK12680 159 iaVPLYRWRRLVVVPRGHA--LDTPRRAPDMAALAEHPLISYESSTRPGsSLQRAFAQLGLEPSIALTALDADLIKTYVR 236


                 ....*.
gi 743333428 234 AGHGIG 239
Cdd:PRK12680 237 AGLGVG 242
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 14-125 2.36e-09

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 57.38  E-value: 2.36e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428  14 FAQIVEQGSLTAAAKQLGLTRAVASYHLKKLETQLEVTLLNRSTRTMALTEAGIAYYERCRIITEQANAANQQIENIKse 93
Cdd:PRK11233   9 FVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQLAVHNVG-- 86

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 743333428  94 pQGLlkiSCPVNVGM-------QLIVPAINTFKRQYPKI 125
Cdd:PRK11233  87 -QAL---SGQVSIGLapgtaasSLTMPLLQAVRAEFPGI 121
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 7-129 5.78e-09

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 55.93  E-value: 5.78e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428   7 QLKSMVVFAQIVEQGSLTAAAKQLGLTRAVASYHLKKLETQLEVTLLNRSTRTMALTEAGIAYYERCRIITEQANAANQQ 86
Cdd:PRK09906   2 ELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKLR 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 743333428  87 IENIkSEPQGLLKISCPVNVGMQLIVPAINTFKRQYPKIQIDL 129
Cdd:PRK09906  82 ARKI-VQEDRQLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIEL 123
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 111-290 1.90e-08

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: 53.65  E-value: 1.90e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428 111 IVPA-INTFKRQYPKIQIDLQL--TDDVVDIIKNG-FDFAIRGVALSDSNLQATKLTTMSTCICGAPEY-FAHfGKPKTP 185
Cdd:cd08420   14 LLPRlLARFRKRYPEVRVSLTIgnTEEIAERVLDGeIDLGLVEGPVDHPDLIVEPFAEDELVLVVPPDHpLAG-RKEVTA 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428 186 LELAEHQWVVYQLGSKT-----LTLQKDGKKHD---ITMQgglSTNNAAARTAfVEAGHGIGRIPLYDAWPKVQAGLLEI 257
Cdd:cd08420   93 EELAAEPWILREPGSGTrevfeRALAEAGLDGLdlnIVME---LGSTEAIKEA-VEAGLGISILSRLAVRKELELGRLVA 168

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 743333428 258 IlddyKSKDI----ELYGVFPPGAAGSKKLRLFIDYL 290
Cdd:cd08420  169 L----PVEGLrltrPFSLIYHKDKYLSPAAEAFLEFL 201
PBP2_HvrB cd08483
The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an ...
 98-290 4.73e-08

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: 52.35  E-value: 4.73e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428  98 LKISCPVNVGMQLIVPAINTFKRQYPKIQIDLQLTDDVVDIIKNGFDFAIR-GVAlSDSNLQATKLTTMSTCICGAPEYF 176
Cdd:cd08483    2 LTVTLTPSFASNWLMPRLGSFWAKHPEIELSLLPSADLVDLRPDGIDVAIRyGNG-DWPGLESEPLTAAPFVVVAAPGLL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428 177 AHfGKPKTPLELAEHQWvVYQLGSKTLTLQkdGKKHDITMQGGLST---NNAAARTAfVEAGHGIGRIPLYDAWPKVQAG 253
Cdd:cd08483   81 GD-RKVDSLADLAGLPW-LQERGTNEQRVW--LASMGVVPDLERGVtflPGQLVLEA-ARAGLGLSIQARALVEPDIAAG 155

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 743333428 254 LLEIIL-DDYKSKdiELYGVFPPGAAgSKKLRLFIDYL 290
Cdd:cd08483  156 RLTVLFeEEEEGL--GYHIVTRPGVL-RPAAKAFVRWL 190
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
7-242 1.02e-07

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 52.33  E-value: 1.02e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428   7 QLKSMVVFAQIVEQGSLTAAAKQLGLTRAVASYHLKKLETQLEVTLLNRSTRTMALTEAGiayyercRIITEQANAANQQ 86
Cdd:PRK15421   3 EVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQG-------EILLQLANQVLPQ 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428  87 IENIK---SEPQGL-LKISCPVNVGMQLIVPAINTFKRQYPKIQIDLQ--LTDDVVDIIKNG-FDFAIRGVALSDSNLQA 159
Cdd:PRK15421  76 ISQALqacNEPQQTrLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKsgVTFDPQPALQQGeLDLVMTSDILPRSGLHY 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428 160 TKLTTMSTCICGAPEYFAHFGKPKTPLELAEHQWVVYQLGSKTLT-----LQKDGKKHDITmqgglSTNNAAARTAFVEA 234
Cdd:PRK15421 156 SPMFDYEVRLVLAPDHPLAAKTRITPEDLASETLLIYPVQRSRLDvwrhfLQPAGVSPSLK-----SVDNTLLLIQMVAA 230


                 ....*...
gi 743333428 235 GHGIGRIP 242
Cdd:PRK15421 231 RMGIAALP 238
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
38-147 1.26e-07

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 51.74  E-value: 1.26e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428  38 SYHLKKLETQLEVTLLNRSTRTMALTEAGIAYYERCRIITEQANAANQQIENIKSEPQGLLKISCPVNVGMQLIVPAINT 117
Cdd:PRK11716   9 SRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSLFCSVTAAYSHLPPILDR 88

                         90       100       110
                 ....*....|....*....|....*....|...
gi 743333428 118 FKRQYPKIQIDLQLTD--DVVDIIKNG-FDFAI 147
Cdd:PRK11716  89 FRAEHPLVEIKLTTGDaaDAVEKVQSGeADLAI 121
PBP2_GcdR_like cd08481
The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, ...
 112-290 2.47e-07

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: 49.99  E-value: 2.47e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428 112 VPAINTFKRQYPKIQIDLQLTDDVVDIIKNGFDFAIRGVALSDSNLQATKLTTMSTCICGAPEYFAHFGkPKTPLELAE- 190
Cdd:cd08481   16 IPRLPDFLARHPDITVNLVTRDEPFDFSQGSFDAAIHFGDPVWPGAESEYLMDEEVVPVCSPALLAGRA-LAAPADLAHl 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428 191 ------------HQWvvyqlgsktltLQKDGKKHDITMQGGL----STNNAAARtafveAGHGIGRIPLYDAWPKVQAGL 254
Cdd:cd08481   95 pllqqttrpeawRDW-----------FEEVGLEVPTAYRGMRfeqfSMLAQAAV-----AGLGVALLPRFLIEEELARGR 158

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 743333428 255 LEIILDDYKSKDIELYGVFPPGAAGSKKLRLFIDYL 290
Cdd:cd08481  159 LVVPFNLPLTSDKAYYLVYPEDKAESPPVQAFRDWL 194
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
14-66 3.41e-07

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 50.74  E-value: 3.41e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 743333428  14 FAQIVEQGSLTAAAKQLGLTRAVASYHLKKLETQLEVTLLNRsTRTMALTEAG 66
Cdd:PRK13348  10 LAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAG 61
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 21-147 5.73e-07

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 49.94  E-value: 5.73e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428  21 GSLTAAAKQLGLTRAVASYHLKKLETQLEVTLLNRSTRTMALTEAGIAYYERCRIITEQANAANQQIENIKSEPQGLLKI 100
Cdd:PRK11074  17 GSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRRQCQQVANGWRGQLSI 96

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 743333428 101 SCPVNVGMQLIVPAINTFKRQYPKI--QIDLQLTDDVVDIIKNG-FDFAI 147
Cdd:PRK11074  97 AVDNIVRPDRTRQLIVDFYRHFDDVelIIRQEVFNGVWDALADGrVDIAI 146
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
16-130 4.38e-05

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 44.20  E-value: 4.38e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428  16 QIVEQG-SLTAAAKQLGLTRAVASYHLKKLETQLEVTLLNR-STRTMALTEAGiayyercRIITEQANAANQQIENIK-- 91
Cdd:PRK12684  11 EAVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRhGKRLRGLTEPG-------RIILASVERILQEVENLKrv 83

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 743333428  92 -----SEPQGLLKISCPVNVGMQLIVPAINTFKRQYPKIQIDLQ 130
Cdd:PRK12684  84 gkefaAQDQGNLTIATTHTQARYALPAAIKEFKKRYPKVRLSIL 127
ModE COG2005
DNA-binding transcriptional regulator ModE (molybdenum-dependent) [Transcription];
16-90 4.44e-05

DNA-binding transcriptional regulator ModE (molybdenum-dependent) [Transcription];


Pssm-ID: 441608 [Multi-domain]  Cd Length: 118  Bit Score: 42.12  E-value: 4.44e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428  16 QIVEQGSLTAAAKQLGLtravaSY-----HLKKLETQLEVTLLNRST------RTmALTEAG---IAYYErcRIITEQAN 81
Cdd:COG2005   29 AIDETGSISAAAKAMGM-----SYkrawdLIDAMNNLLGEPLVERQTggkgggGA-RLTPEGrrlLALYR--RLEAEAQR 100


                 ....*....
gi 743333428  82 AANQQIENI 90
Cdd:COG2005  101 ALAALFEEL 109
cbl PRK12679
HTH-type transcriptional regulator Cbl;
3-142 1.69e-04

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 42.49  E-value: 1.69e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428   3 VSFEQLKSMVVFAQivEQGSLTAAAKQLGLTRAVASYHLKKLETQLEVTL-LNRSTRTMALTEAGIAYYERCRIITEQAN 81
Cdd:PRK12679   1 MNFQQLKIIREAAR--QDYNLTEVANMLFTSQSGVSRHIRELEDELGIEIfIRRGKRLLGMTEPGKALLVIAERILNEAS 78

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 743333428  82 AANQQIENIKSEPQGLLKISCPVNVGMQLIVPAINTFKRQYPKIQIDL-QLT-DDVVDIIKNG 142
Cdd:PRK12679  79 NVRRLADLFTNDTSGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELiQGTpQEIATLLQNG 141
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 5-241 3.25e-04

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 41.57  E-value: 3.25e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428   5 FEQLKSMVvfaQIVEQG-SLTAAAKQLGLTRAVASYHLKKLETQLEVTLLNRS-TRTMALTEAGiayYERCRIITEQANA 82
Cdd:PRK12683   3 FQQLRIIR---EAVRQNfNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRgKRLTGLTEPG---KELLQIVERMLLD 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428  83 AnqqiENIK-------SEPQGLLKISCPVNVGMQLIVPAINTFKRQYPKIQIDLQLTD--DVVDIIKNG-FDFAIRGVAL 152
Cdd:PRK12683  77 A----ENLRrlaeqfaDRDSGHLTVATTHTQARYALPKVVRQFKEVFPKVHLALRQGSpqEIAEMLLNGeADIGIATEAL 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428 153 -SDSNLQATKLTTMSTCICGAPEYFAHFGKPKTPLELAEHQWVVYQLG----SKT-LTLQKDGKKHDITMqgglSTNNAA 226
Cdd:PRK12683 153 dREPDLVSFPYYSWHHVVVVPKGHPLTGRENLTLEAIAEYPIITYDQGftgrSRIdQAFAEAGLVPDIVL----TALDAD 228

                        250
                 ....*....|....*
gi 743333428 227 ARTAFVEAGHGIGRI 241
Cdd:PRK12683 229 VIKTYVELGMGVGIV 243
HTH_20 pfam12840
Helix-turn-helix domain; This domain represents a DNA-binding Helix-turn-helix domain found in ...
 11-45 1.60e-03

Helix-turn-helix domain; This domain represents a DNA-binding Helix-turn-helix domain found in transcriptional regulatory proteins.


Pssm-ID: 432824 [Multi-domain]  Cd Length: 61  Bit Score: 36.36  E-value: 1.60e-03
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 743333428   11 MVVFAQIVEQGSLTAA--AKQLGLTRAVASYHLKKLE 45
Cdd:pfam12840  13 LRILRALVGDEPLTASelARRLDISRNTLSYHLRKLE 49
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 38-129 2.58e-03

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 38.86  E-value: 2.58e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428  38 SYHLKKLETQLEVTLLNRSTRTMALTEAGIAYYERCRIITEQANA----ANQQIENIksepQGLLKISCPVNVG---MQL 110
Cdd:PRK11151  33 SGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVlkemASQQGETM----SGPLHIGLIPTVGpylLPH 108

                         90
                 ....*....|....*....
gi 743333428 111 IVPAIntfKRQYPKIQIDL 129
Cdd:PRK11151 109 IIPML---HQTFPKLEMYL 124
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
14-66 2.87e-03

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 38.60  E-value: 2.87e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 743333428  14 FAQIVEQGSLTAAAKQLGLTR-AVaSYHLKKLETQLEVTLLNRSTRTMAlTEAG 66
Cdd:PRK03635  10 LAAVVREGSFERAAQKLHITQsAV-SQRIKALEERVGQVLLVRTQPCRP-TEAG 61
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
 118-260 3.13e-03

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: 37.87  E-value: 3.13e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 743333428 118 FKRQYPKIQIDLQLT--DDVVDIIK-NGFDFAIRGVALSDSNLQATKLTTMSTCICGAPeyfAH--FGKPKTPLE-LAEH 191
Cdd:cd08419   21 FCRRHPGVEVSLRVGnrEQVLERLAdNEDDLAIMGRPPEDLDLVAEPFLDNPLVVIAPP---DHplAGQKRIPLErLARE 97

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 743333428 192 QWVVYQLGSKT-LTLQKDGKKHDITMQGGLSTN-NAAARTAfVEAGHGIGRIPLYDAWPKVQAGLLeIILD 260
Cdd:cd08419   98 PFLLREPGSGTrLAMERFFAEHGVTLRVRMELGsNEAIKQA-VMAGLGLSVLSLHTLALELATGRL-AVLD 166
PBP2_BlaA cd08487
The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which ...
 111-148 3.76e-03

The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which involved in control of the beta-lactamase gene expression; contains the type 2 periplasmic binding fold; This CD represents the C-terminal substrate binding domain of LysR-type transcriptional regulator, BlaA, that involved in control of the expression of beta-lactamase genes, blaA and blaB. Beta-lactamases are responsible for bacterial resistance to beta-lactam antibiotics such as penicillins. The blaA gene is located just upstream of blaB in the opposite direction and regulates the expression of the blaB. BlaA also negatively auto-regulates the expression of its own gene, blaA. BlaA (a constitutive class A penicllinase) belongs to the LysR family of transcriptional regulators, whereas BlaB (an inducible class C cephalosporinase or AmpC) can be referred to as a penicillin binding protein but it does not act as a beta-lactamase. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176176 [Multi-domain]  Cd Length: 189  Bit Score: 37.91  E-value: 3.76e-03
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 743333428 111 IVPAINTFKRQYPKIQIDLQLTDDVVDIIKNGFDFAIR 148
Cdd:cd08487   15 LLPRLAEFRQLHPFIELRLRTNNNVVDLATEGLDFAIR 52
PBP2_TrpI cd08482
The C-terminal substrate binding domain of LysR-type transcriptional regulator TrpI, which is ...
 98-148 4.43e-03

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: 37.38  E-value: 4.43e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 743333428  98 LKISCPVNVGMQLIVPAINTFKRQYPKIQIDLQLTDDVVDIIKNGFDFAIR 148
Cdd:cd08482    2 LVLSCSGSLLMRWLIPRLPAFQAALPDIDLQLSASDGPVDSLRDGIDAAIR 52
 
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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