NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|126103173|gb|ABN75851|]
View 

transcriptional regulator, LysR family [Cereibacter sphaeroides ATCC 17029]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
Periplasmic_Binding_Protein_Type_2 super family cl21456
Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent ...
 91-290 1.02e-79

Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent the ligand-binding domains found in solute binding proteins that serve as initial receptors in the transport, signal transduction and channel gating. The PBP2 proteins share the same architecture as periplasmic binding proteins type 1 (PBP1), but have a different topology. They are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The origin of PBP module can be traced across the distant phyla, including eukaryotes, archebacteria, and prokaryotes. The majority of PBP2 proteins are involved in the uptake of a variety of soluble substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. 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 family includes ionotropic glutamate receptors and unorthodox sensor proteins involved in signal transduction. The substrate binding domain of the LysR transcriptional regulators and the oligopeptide-like transport systems also contain the type 2 periplasmic binding fold and thus they are significantly homologous to that of the PBP2; however, these two families are grouped into a separate hierarchy of the PBP2 superfamily due to the large number of protein sequences.


The actual alignment was detected with superfamily member cd08474:

Pssm-ID: 473866 [Multi-domain]  Cd Length: 202  Bit Score: 240.06  E-value: 1.02e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173  91 PSGMLRINASVQAGRAV-APLVLAFLRRYPEMRVDLVTEGRLVDIVAEGFDLGIRPADLVPRDMIALPLGHPVRHAVVAS 169
Cdd:cd08474    1 PAGTLRINAPRVAARLLlAPLLARFLARYPDIRLELVVDDGLVDIVAEGFDAGIRLGESVEKDMVAVPLGPPLRMAVVAS 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173 170 PDWLVRHPEPRSPADLDPDACLRVRLP-NGALLRWPFEKDGVPLPFEASGRLTVDEAAIARAAVLDGAGIGYFIEADVAE 248
Cdd:cd08474   81 PAYLARHGTPEHPRDLLNHRCIRYRFPtSGALYRWEFERGGRELEVDVEGPLILNDSDLMLDAALDGLGIAYLFEDLVAE 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 126103173 249 DIAAGRMIRLLEDWTPNRPGFSLYYSGRRNPSAGFTAFLAMA 290
Cdd:cd08474  161 HLASGRLVRVLEDWSPPFPGGYLYYPSRRRVPPALRAFIDFL 202
PRK09791 super family cl32411
LysR family transcriptional regulator;
8-137 1.55e-19

LysR family transcriptional regulator;


The actual alignment was detected with superfamily member PRK09791:

Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 86.35  E-value: 1.55e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173   8 LEAVLAIARKGSFRAAALDLGVSTTALSHTVARLEAGLGVRLFHRTTRSVALTEAGREFVARIAPALTEIRAALETVRSQ 87
Cdd:PRK09791  10 IRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQEDIRQR 89

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 126103173  88 RATPSGMLRINASVQAGRAVAPLVLA-FLRRYPEMRVDlVTEGRLVDIVAE 137
Cdd:PRK09791  90 QGQLAGQINIGMGASIARSLMPAVISrFHQQHPQVKVR-IMEGQLVSMINE 139
 
Name Accession Description Interval E-value
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 91-290 1.02e-79

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: 240.06  E-value: 1.02e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173  91 PSGMLRINASVQAGRAV-APLVLAFLRRYPEMRVDLVTEGRLVDIVAEGFDLGIRPADLVPRDMIALPLGHPVRHAVVAS 169
Cdd:cd08474    1 PAGTLRINAPRVAARLLlAPLLARFLARYPDIRLELVVDDGLVDIVAEGFDAGIRLGESVEKDMVAVPLGPPLRMAVVAS 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173 170 PDWLVRHPEPRSPADLDPDACLRVRLP-NGALLRWPFEKDGVPLPFEASGRLTVDEAAIARAAVLDGAGIGYFIEADVAE 248
Cdd:cd08474   81 PAYLARHGTPEHPRDLLNHRCIRYRFPtSGALYRWEFERGGRELEVDVEGPLILNDSDLMLDAALDGLGIAYLFEDLVAE 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 126103173 249 DIAAGRMIRLLEDWTPNRPGFSLYYSGRRNPSAGFTAFLAMA 290
Cdd:cd08474  161 HLASGRLVRVLEDWSPPFPGGYLYYPSRRRVPPALRAFIDFL 202
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
5-296 9.84e-48

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 160.03  E-value: 9.84e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173   5 LKGLEAVLAIARKGSFRAAALDLGVSTTALSHTVARLEAGLGVRLFHRTTRSVALTEAGREFVARIAPALTEIRAALETV 84
Cdd:COG0583    3 LRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAEL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173  85 RSQRATPSGMLRINASVQAGRA-VAPLVLAFLRRYPEMRVDLVTEG--RLVD-IVAEGFDLGIRPADLVPRDMIALPLGH 160
Cdd:COG0583   83 RALRGGPRGTLRIGAPPSLARYlLPPLLARFRARHPGVRLELREGNsdRLVDaLLEGELDLAIRLGPPPDPGLVARPLGE 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173 161 pVRHAVVASPDWLVRHPEPRspadldpdaclrvrlpngallrwpfekdgvplpfeasgrltVDEAAIARAAVLDGAGIGY 240
Cdd:COG0583  163 -ERLVLVASPDHPLARRAPL-----------------------------------------VNSLEALLAAVAAGLGIAL 200

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 126103173 241 FIEADVAEDIAAGRMIRL-LEDWTPNRPgFSLYYSGRRNPSAGFTAFLAMAREREAA 296
Cdd:COG0583  201 LPRFLAADELAAGRLVALpLPDPPPPRP-LYLVWRRRRHLSPAVRAFLDFLREALAE 256
PRK09801 PRK09801
LysR family transcriptional regulator;
6-272 9.33e-34

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 125.15  E-value: 9.33e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173   6 KGLEAVLAIARKGSFRAAALDLGVSTTALSHTVARLEAGLGVRLFHRTTRSVALTEAGREFVARIAPALTEIRAALETVR 85
Cdd:PRK09801   9 KDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVT 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173  86 SQRATPSGMLRINASVQAGRA-VAPLVLAFLRRYPEMRVDLVTEGRLVDIVAEGFDLGIRPADLVPRDMIALPLGHPVRh 164
Cdd:PRK09801  89 QIKTRPEGMIRIGCSFGFGRShIAPAITELMRNYPELQVHFELFDRQIDLVQDNIDLDIRINDEIPDYYIAHLLTKNKR- 167

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173 165 AVVASPDWLVRHPEPRSPADLDPDACLRVRLPNGALLRWPF----EKDGVplpfEASGRLTVDEAAIARAAVLDGAGIGY 240
Cdd:PRK09801 168 ILCAAPEYLQKYPQPQSLQELSRHDCLVTKERDMTHGIWELgngqEKKSV----KVSGHLSSNSGEIVLQWALEGKGIML 243

                        250       260       270
                 ....*....|....*....|....*....|..
gi 126103173 241 FIEADVAEDIAAGRMIRLLEDWTPNRPGFSLY 272
Cdd:PRK09801 244 RSEWDVLPFLESGKLVQVLPEYAQSANIWAVY 275
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 92-293 1.03e-21

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: 90.43  E-value: 1.03e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173   92 SGMLRINASVQAGRAVAPLVLA-FLRRYPEMRVDLVTEG--RLVDIVAEG-FDLGIRPADLVPRDMIALPLGHpVRHAVV 167
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLArFRERYPDVELELTEGNseELLDLLLEGeLDLAIRRGPPDDPGLEARPLGE-EPLVLV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173  168 ASPDWLVRHPEPRSPADLDPDACLRvrLPNGALLRWPFEKDGVPLPFEASGRLTVDEAAIARAAVLDGAGIGYFIEADVA 247
Cdd:pfam03466  80 APPDHPLARGEPVSLEDLADEPLIL--LPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVA 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 126103173  248 EDIAAGRMI-RLLEDWTPNRPgFSLYYSGRRNPSAGFTAFLAMARER 293
Cdd:pfam03466 158 RELADGRLVaLPLPEPPLPRE-LYLVWRKGRPLSPAVRAFIEFLREA 203
PRK09791 PRK09791
LysR family transcriptional regulator;
8-137 1.55e-19

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 86.35  E-value: 1.55e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173   8 LEAVLAIARKGSFRAAALDLGVSTTALSHTVARLEAGLGVRLFHRTTRSVALTEAGREFVARIAPALTEIRAALETVRSQ 87
Cdd:PRK09791  10 IRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQEDIRQR 89

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 126103173  88 RATPSGMLRINASVQAGRAVAPLVLA-FLRRYPEMRVDlVTEGRLVDIVAE 137
Cdd:PRK09791  90 QGQLAGQINIGMGASIARSLMPAVISrFHQQHPQVKVR-IMEGQLVSMINE 139
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
5-64 8.05e-19

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 78.20  E-value: 8.05e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173    5 LKGLEAVLAIARKGSFRAAALDLGVSTTALSHTVARLEAGLGVRLFHRTTRSVALTEAGR 64
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-143 6.39e-18

selenium metabolism-associated LysR family transcriptional regulator; LysR family transcriptional regulators regularly appear encoded adjacent to selenecysteine incorporation proteins such as SelB. This model represents one especially well-conserved subgroup of such transcription factors from species such as Merdimonas faecis, Sellimonas intestinalis, Syntrophotalea acetylenica, and Hydrogenivirga caldilitoris. Seed alignment members were selected by proximity to selB, but not all family members are expected to have similar genomic locations.


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 81.89  E-value: 6.39e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173   1 MDsgLKGLEAVLAIARKGSFRAAALDLGVSTTALSHTVARLEAGLGVRLFHRTTRSVALTEAGREFVARIAPALTEIRAA 80
Cdd:NF040786   1 MN--LKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKL 78

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 126103173  81 LETVRSQRATPSGMLRINASVQAGRAVAPLVLA-FLRRYPEMRVDLVTEG--RLVDIVAEG-FDLGI 143
Cdd:NF040786  79 EEEFDRYGKESKGVLRIGASTIPGQYLLPELLKkFKEKYPNVRFKLMISDsiKVIELLLEGeVDIGF 145
HTH_MARR smart00347
helix_turn_helix multiple antibiotic resistance protein;
27-81 4.63e-03

helix_turn_helix multiple antibiotic resistance protein;


Pssm-ID: 197670 [Multi-domain]  Cd Length: 101  Bit Score: 36.03  E-value: 4.63e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173    27 LGVSTTALSHTVARLE-AGLGVRLFH----RTTRsVALTEAGREFVARIAPALTEIRAAL 81
Cdd:smart00347  34 LGVSPSTVTRVLDRLEkKGLVRREPSpedrRSVL-VSLTEEGRELIEQLLEARSETLAEL 92
 
Name Accession Description Interval E-value
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 91-290 1.02e-79

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: 240.06  E-value: 1.02e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173  91 PSGMLRINASVQAGRAV-APLVLAFLRRYPEMRVDLVTEGRLVDIVAEGFDLGIRPADLVPRDMIALPLGHPVRHAVVAS 169
Cdd:cd08474    1 PAGTLRINAPRVAARLLlAPLLARFLARYPDIRLELVVDDGLVDIVAEGFDAGIRLGESVEKDMVAVPLGPPLRMAVVAS 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173 170 PDWLVRHPEPRSPADLDPDACLRVRLP-NGALLRWPFEKDGVPLPFEASGRLTVDEAAIARAAVLDGAGIGYFIEADVAE 248
Cdd:cd08474   81 PAYLARHGTPEHPRDLLNHRCIRYRFPtSGALYRWEFERGGRELEVDVEGPLILNDSDLMLDAALDGLGIAYLFEDLVAE 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 126103173 249 DIAAGRMIRLLEDWTPNRPGFSLYYSGRRNPSAGFTAFLAMA 290
Cdd:cd08474  161 HLASGRLVRVLEDWSPPFPGGYLYYPSRRRVPPALRAFIDFL 202
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 93-287 2.11e-60

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: 190.73  E-value: 2.11e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173  93 GMLRINASVQAGRA-VAPLVLAFLRRYPEMRVDLVTEGRLVDIVAEGFDLGIRPADLVPRDMIALPLGhPVRHAVVASPD 171
Cdd:cd08422    1 GRLRISAPVSFGRLhLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLG-PVRRVLVASPA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173 172 WLVRHPEPRSPADLDPDACLRVRLPnGALLRWPFEKDGVPLPFEASGRLTVDEAAIARAAVLDGAGIGYFIEADVAEDIA 251
Cdd:cd08422   80 YLARHGTPQTPEDLARHRCLGYRLP-GRPLRWRFRRGGGEVEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAEDLA 158

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 126103173 252 AGRMIRLLEDWTPNRPGFSLYYSGRRNPSAGFTAFL 287
Cdd:cd08422  159 SGRLVRVLPDWRPPPLPIYAVYPSRRHLPAKVRAFI 194
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
5-296 9.84e-48

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 160.03  E-value: 9.84e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173   5 LKGLEAVLAIARKGSFRAAALDLGVSTTALSHTVARLEAGLGVRLFHRTTRSVALTEAGREFVARIAPALTEIRAALETV 84
Cdd:COG0583    3 LRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAEL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173  85 RSQRATPSGMLRINASVQAGRA-VAPLVLAFLRRYPEMRVDLVTEG--RLVD-IVAEGFDLGIRPADLVPRDMIALPLGH 160
Cdd:COG0583   83 RALRGGPRGTLRIGAPPSLARYlLPPLLARFRARHPGVRLELREGNsdRLVDaLLEGELDLAIRLGPPPDPGLVARPLGE 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173 161 pVRHAVVASPDWLVRHPEPRspadldpdaclrvrlpngallrwpfekdgvplpfeasgrltVDEAAIARAAVLDGAGIGY 240
Cdd:COG0583  163 -ERLVLVASPDHPLARRAPL-----------------------------------------VNSLEALLAAVAAGLGIAL 200

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 126103173 241 FIEADVAEDIAAGRMIRL-LEDWTPNRPgFSLYYSGRRNPSAGFTAFLAMAREREAA 296
Cdd:COG0583  201 LPRFLAADELAAGRLVALpLPDPPPPRP-LYLVWRRRRHLSPAVRAFLDFLREALAE 256
PBP2_CrgA_like_8 cd08477
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-290 3.21e-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 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: 138.90  E-value: 3.21e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173  93 GMLRINASVQAG-RAVAPLVLAFLRRYPEMRVDLVTEGRLVDIVAEGFDLGIRPADLVPRDMIALPLGhPVRHAVVASPD 171
Cdd:cd08477    1 GKLRISAPVTFGsHVLTPALAEYLARYPDVRVDLVLSDRLVDLVEEGFDAAFRIGELADSSLVARPLA-PYRMVLCASPD 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173 172 WLVRHPEPRSPADLDPDACLRVrLPNGALLRWPFEKDGVPLPFEASGRLTVDEAAIARAAVLDGAGIGYFIEADVAEDIA 251
Cdd:cd08477   80 YLARHGTPTTPEDLARHECLGF-SYWRARNRWRLEGPGGEVKVPVSGRLTVNSGQALRVAALAGLGIVLQPEALLAEDLA 158

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 126103173 252 AGRMIRLLEDWTPNRPGFSLYYSGRRNPSAGFTAFLAMA 290
Cdd:cd08477  159 SGRLVELLPDYLPPPRPMHLLYPPDRRPTPKLRSFIDFL 197
PBP2_CrgA_like_2 cd08471
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-293 9.74e-38

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


Pssm-ID: 176160  Cd Length: 201  Bit Score: 132.26  E-value: 9.74e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173  93 GMLRINASVQAGRA-VAPLVLAFLRRYPEMRVDLVTEGRLVDIVAEGFDLGIRPADLVPRDMIALPLGHpVRHAVVASPD 171
Cdd:cd08471    1 GLLTVTAPVLFGRLhVLPIITDFLDAYPEVSVRLLLLDRVVNLLEEGVDVAVRIGHLPDSSLVATRVGS-VRRVVCASPA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173 172 WLVRHPEPRSPADLDPDACLRVRlPNGALLRWPFEKDGVPLPFEASGRLTVDEAAIARAAVLDGAGIGYFIEADVAEDIA 251
Cdd:cd08471   80 YLARHGTPKHPDDLADHDCIAFT-GLSPAPEWRFREGGKERSVRVRPRLTVNTVEAAIAAALAGLGLTRVLSYQVAEELA 158

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 126103173 252 AGRMIRLLEDWTPNRPGFSLYYSGRRNPSAGFTAFLAMARER 293
Cdd:cd08471  159 AGRLQRVLEDFEPPPLPVHLVHPEGRLAPAKVRAFVDFAVPR 200
PBP2_CrgA_like_9 cd08479
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-287 3.76e-36

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 128.10  E-value: 3.76e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173  93 GMLRINASVQAGRA-VAPLVLAFLRRYPEMRVDLVTEGRLVDIVAEGFDLGIRPADLVPRDMIALPLGhPVRHAVVASPD 171
Cdd:cd08479    1 GLLRVNASFGFGRRhIAPALSDFAKRYPELEVQLELTDRPVDLVEEGFDLDIRVGDLPDSSLIARKLA-PNRRILCASPA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173 172 WLVRHPEPRSPADLDPDACLRVRLPNGALLRWPFEKDGVPLPFEASGRLTVDEAAIARAAVLDGAGIGYFIEADVAEDIA 251
Cdd:cd08479   80 YLERHGAPASPEDLARHDCLVIRENDEDFGLWRLRNGDGEATVRVRGALSSNDGEVVLQWALDGHGIILRSEWDVAPYLR 159

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 126103173 252 AGRMIRLLEDWTPNRPGFSLYYSGRRNPSAGFTAFL 287
Cdd:cd08479  160 SGRLVRVLPDWQLPDADIWAVYPSRLSRSARVRVFV 195
PBP2_CrgA_like_7 cd08476
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-287 3.99e-34

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 7. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176165  Cd Length: 197  Bit Score: 123.12  E-value: 3.99e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173  93 GMLRInaSV-QAGRAVAPLVLAFLRRYPEMRVDLVTEGRLVDIVAEGFDLGIRPADLVPRDMIALPLGHpVRHAVVASPD 171
Cdd:cd08476    1 GRLRV--SLpLVGGLLLPVLAAFMQRYPEIELDLDFSDRLVDVIDEGFDAVIRTGELPDSRLMSRRLGS-FRMVLVASPD 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173 172 WLVRHPEPRSPADLDPDACLRVRLPN-GALLRWPFEKDGVPLPFEASGRLTVDEAAIARAAVLDGAGIGYFIEADVAEDI 250
Cdd:cd08476   78 YLARHGTPETPADLAEHACLRYRFPTtGKLEPWPLRGDGGDPELRLPTALVCNNIEALIEFALQGLGIACLPDFSVREAL 157

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 126103173 251 AAGRMIRLLEDWTPNRPGFSLYYSGRRNPSAGFTAFL 287
Cdd:cd08476  158 ADGRLVTVLDDYVEERGQFRLLWPSSRHLSPKLRVFV 194
PBP2_CrgA_like_1 cd08470
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-292 5.42e-34

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: 122.80  E-value: 5.42e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173  93 GMLRINASVQAG-RAVAPLVLAFLRRYPEMRVDLVTEGRLVDIVAEGFDLGIRPADLVPRDMIALPLGhPVRHAVVASPD 171
Cdd:cd08470    1 GLLRITCPVAYGeRFIAPLVNDFMQRYPKLEVDIELTNRVVDLVSEGFDLAIRLGRLTDSSLMARRLA-SRRHYVCASPA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173 172 WLVRHPEPRSPADLDPDACLRvrlpnGALLRWPFEKDGVPLPFEASGRLTVDEAAIARAAVLDGAGIGYFIEADVAEDIA 251
Cdd:cd08470   80 YLERHGTPHSLADLDRHNCLL-----GTSDHWRFQENGRERSVRVQGRWRCNSGVALLDAALKGMGLAQLPDYYVDEHLA 154

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 126103173 252 AGRMIRLLEDWTPNRPGFSLYYSGRRNPSAGFTAFLAMARE 292
Cdd:cd08470  155 AGRLVPVLEDYRPPDEGIWALYPHNRHLSPKVRLLVDYLAD 195
PRK09801 PRK09801
LysR family transcriptional regulator;
6-272 9.33e-34

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 125.15  E-value: 9.33e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173   6 KGLEAVLAIARKGSFRAAALDLGVSTTALSHTVARLEAGLGVRLFHRTTRSVALTEAGREFVARIAPALTEIRAALETVR 85
Cdd:PRK09801   9 KDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVT 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173  86 SQRATPSGMLRINASVQAGRA-VAPLVLAFLRRYPEMRVDLVTEGRLVDIVAEGFDLGIRPADLVPRDMIALPLGHPVRh 164
Cdd:PRK09801  89 QIKTRPEGMIRIGCSFGFGRShIAPAITELMRNYPELQVHFELFDRQIDLVQDNIDLDIRINDEIPDYYIAHLLTKNKR- 167

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173 165 AVVASPDWLVRHPEPRSPADLDPDACLRVRLPNGALLRWPF----EKDGVplpfEASGRLTVDEAAIARAAVLDGAGIGY 240
Cdd:PRK09801 168 ILCAAPEYLQKYPQPQSLQELSRHDCLVTKERDMTHGIWELgngqEKKSV----KVSGHLSSNSGEIVLQWALEGKGIML 243

                        250       260       270
                 ....*....|....*....|....*....|..
gi 126103173 241 FIEADVAEDIAAGRMIRLLEDWTPNRPGFSLY 272
Cdd:PRK09801 244 RSEWDVLPFLESGKLVQVLPEYAQSANIWAVY 275
PBP2_CrgA_like_3 cd08472
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-286 2.11e-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 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: 113.38  E-value: 2.11e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173  93 GMLRINASVQAGRA-VAPLVLAFLRRYPEMRVDLVTEGRLVDIVAEGFDLGIRPADLVPRDMIALPLGHpVRHAVVASPD 171
Cdd:cd08472    1 GRLRVDVPGSLARLlLIPALPDFLARYPDIELDLGVSDRPVDLIREGVDCVIRVGELADSSLVARRLGE-LRMVTCASPA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173 172 WLVRHPEPRSPADLDPDACLRVRLP-NGALLRWPFEKDGVPLPFEASGRLTVDEAAIARAAVLDGAGIGYFIEADVAEDI 250
Cdd:cd08472   80 YLARHGTPRHPEDLERHRAVGYFSArTGRVLPWEFQRDGEEREVKLPSRVSVNDSEAYLAAALAGLGIIQVPRFMVRPHL 159

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 126103173 251 AAGRMIRLLEDWTPNRPGFSLYYSGRRNPSAGFTAF 286
Cdd:cd08472  160 ASGRLVEVLPDWRPPPLPVSLLYPHRRHLSPRVRVF 195
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 14-277 9.59e-30

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 114.32  E-value: 9.59e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173  14 IARKGSFRAAALDLGVSTTALSHTVARLEAGLGVRLFHRTTRSVALTEAGREFVARIAPALTEIRAALETVRSQRATPSG 93
Cdd:PRK14997  13 VVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDAIAALQVEPRG 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173  94 MLRINASVQAGRA-VAPLVLAFLRRYPEMRVDLVTEGRLVDIVAEGFDLGI--RPADLVPRDMIALPLGHPvRHAVVASP 170
Cdd:PRK14997  93 IVKLTCPVTLLHVhIGPMLAKFMARYPDVSLQLEATNRRVDVVGEGVDVAIrvRPRPFEDSDLVMRVLADR-GHRLFASP 171

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173 171 DWLVRHPEPRSPADLDPDACLRVRlPNGALLRWP-FEKDGVPLPFEASGRLTVDEAAIARAAVLDGAGIGYFIEADVAED 249
Cdd:PRK14997 172 DLIARMGIPSAPAELSHWPGLSLA-SGKHIHRWElYGPQGARAEVHFTPRMITTDMLALREAAMAGVGLVQLPVLMVKEQ 250

                        250       260
                 ....*....|....*....|....*...
gi 126103173 250 IAAGRMIRLLEDWTPNRPGFSLYYSGRR 277
Cdd:PRK14997 251 LAAGELVAVLEEWEPRREVIHAVFPSRR 278
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
5-272 4.06e-29

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 112.93  E-value: 4.06e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173   5 LKGLEAVLAIARKGSFRAAALDLGVSTTALSHTVARLEAGLGVRLFHRTTRSVALTEAGREFVARIAPALTEIRAALETV 84
Cdd:PRK10632   4 LKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQL 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173  85 RSQRATPSGMLRI-NASVQAGRAVAPLVLAFLRRYPEMRVDLVTEGRLVDIVAEGFDLGIRPADLVPRDMIALPLGH-PV 162
Cdd:PRK10632  84 YAFNNTPIGTLRIgCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTGIPAPDLIADGLDVVIRVGALQDSSLFSRRLGAmPM 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173 163 rhAVVASPDWLVRHPEPRSPADLDPDACLR--VRLPNGALLRWPfekDGVPLPFEASGRLTVDEAAIARAAVLDGAGIGY 240
Cdd:PRK10632 164 --VVCAAKSYLAQYGTPEKPADLSSHSWLEysVRPDNEFELIAP---EGISTRLIPQGRFVTNDPQTLVRWLTAGAGIAY 238

                        250       260       270
                 ....*....|....*....|....*....|...
gi 126103173 241 FIEADVAEDIAAGRMIRLLEDWTPN-RPGFSLY 272
Cdd:PRK10632 239 VPLMWVIDEINRGELEILFPRYQSDpRPVYALY 271
PBP2_CrgA_like_10 cd08480
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-264 3.03e-28

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 10. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176169  Cd Length: 198  Bit Score: 107.42  E-value: 3.03e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173  93 GMLRINASVQAGR-AVAPLVLAFLRRYPEMRVDLVTEGRLVDIVAEGFDLGIRPADLVPRDMIALPLGHpVRHAVVASPD 171
Cdd:cd08480    1 GRLRVNASVPFGThFLLPLLPAFLARYPEILVDLSLTDEVVDLLAERTDVAIRVGPLPDSSLVARKLGE-SRRVIVASPS 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173 172 WLVRHPEPRSPADLDPDACLRVRLPNgALLRWPFEKDGVPLPFEASGRLTVDEAAIARAAVLDGAGIGYFIEADVAEDIA 251
Cdd:cd08480   80 YLARHGTPLTPQDLARHNCLGFNFRR-ALPDWPFRDGGRIVALPVSGNILVNDGEALRRLALAGAGLARLALFHVADDIA 158

                        170
                 ....*....|...
gi 126103173 252 AGRMIRLLEDWTP 264
Cdd:cd08480  159 AGRLVPVLEEYNP 171
PBP2_CrgA cd08478
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains ...
 91-287 1.76e-27

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: 105.50  E-value: 1.76e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173  91 PSGMLRIN-ASVQAGRAVAPLVLAFLRRYPEMRVDLVTEGRLVDIVAEGFDLGIRPADLVPRDMIALPLGHPVRHaVVAS 169
Cdd:cd08478    1 PSGLLRVDaATPFVLHLLAPLIAKFRERYPDIELELVSNEGIIDLIERKTDVAIRIGELTDSTLHARPLGKSRLR-ILAS 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173 170 PDWLVRHPEPRSPADLDPDACLRVRLPnGALLRWPFeKDGVPLPFEASGRLTVDEAAIARAAVLDGAGIGYFIEADVAED 249
Cdd:cd08478   80 PDYLARHGTPQSIEDLAQHQLLGFTEP-ASLNTWPI-KDADGNLLKIQPTITASSGETLRQLALSGCGIACLSDFMTDKD 157

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 126103173 250 IAAGRMIRLLEDWTPN--RPGFSLYYSGRRnPSAGFTAFL 287
Cdd:cd08478  158 IAEGRLIPLFAEQTSDvrQPINAVYYRNTA-LSLRIRCFI 196
PBP2_CrgA_like_4 cd08473
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 91-277 1.21e-26

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: 103.40  E-value: 1.21e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173  91 PSGMLRINASVQ-AGRAVAPLVLAFLRRYPEMRVDLVTEGRLVDIVAEGFDLGI--RPADLVPRDMIALPLGHpVRHAVV 167
Cdd:cd08473    1 PRGTVRVSCPPAlAQELLAPLLPRFMAAYPQVRLQLEATNRRVDLIEEGIDVALrvRFPPLEDSSLVMRVLGQ-SRQRLV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173 168 ASPDWLVRHPEPRSPADLdpdaclrVRLP------NGALLRWPFE-KDGVPLPFEASGRLTVDEAAIARAAVLDGAGIGY 240
Cdd:cd08473   80 ASPALLARLGRPRSPEDL-------AGLPtlslgdVDGRHSWRLEgPDGESITVRHRPRLVTDDLLTLRQAALAGVGIAL 152

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 126103173 241 FIEADVAEDIAAGRMIRLLEDWTPNRPGFSLYYSGRR 277
Cdd:cd08473  153 LPDHLCREALRAGRLVRVLPDWTPPRGIVHAVFPSRR 189
PBP2_CrgA_like_6 cd08475
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-264 4.88e-26

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: 101.86  E-value: 4.88e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173  93 GMLRINASVQAGRA-VAPLVLAFLRRYPEMRVDLVTEGRLVDIVAEGFDLGIR---PADlvPRDMIALPLGHPvRHAVVA 168
Cdd:cd08475    1 GRLRIDLPVAFGRLcVAPLLLELARRHPELELELSFSDRFVDLIEEGIDLAVRigeLAD--STGLVARRLGTQ-RMVLCA 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173 169 SPDWLVRHPEPRSPADLDPDACLrVRLPNGALLRWPF-EKDGVPLPFEASGRLTVDEAAIARAAVLDGAGIGYFIEADVA 247
Cdd:cd08475   78 SPAYLARHGTPRTLEDLAEHQCI-AYGRGGQPLPWRLaDEQGRLVRFRPAPRLQFDDGEAIADAALAGLGIAQLPTWLVA 156

                        170
                 ....*....|....*..
gi 126103173 248 EDIAAGRMIRLLEDWTP 264
Cdd:cd08475  157 DHLQRGELVEVLPELAP 173
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 5-261 9.48e-24

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 97.99  E-value: 9.48e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173   5 LKGLEAVLAIARKGSFRAAALDLGVSTTALSHTVARLEAGLGVRLFHRTTRSVALTEAGREFVARIAPALTEIRAALETV 84
Cdd:PRK11139   8 LNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEATRKL 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173  85 RSQRATPSgmLRINASVQ-AGRAVAPLVLAFLRRYPEMRVDLVTEGRLVDIVAEGFDLGIRPADLVPRDMIALPLgHPVR 163
Cdd:PRK11139  88 RARSAKGA--LTVSLLPSfAIQWLVPRLSSFNEAHPDIDVRLKAVDRLEDFLRDDVDVAIRYGRGNWPGLRVEKL-LDEY 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173 164 HAVVASPDWLVRHPEPRSPADLDPDACLRVRLPNGallrWP--FEKDGVPlPFEASGRLTVDEAAIARAAVLDGAGI--G 239
Cdd:PRK11139 165 LLPVCSPALLNGGKPLKTPEDLARHTLLHDDSRED----WRawFRAAGLD-DLNVQQGPIFSHSSMALQAAIHGQGValG 239

                        250       260
                 ....*....|....*....|..
gi 126103173 240 YFIEADvaEDIAAGRMIRLLED 261
Cdd:PRK11139 240 NRVLAQ--PEIEAGRLVCPFDT 259
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 92-293 1.03e-21

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: 90.43  E-value: 1.03e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173   92 SGMLRINASVQAGRAVAPLVLA-FLRRYPEMRVDLVTEG--RLVDIVAEG-FDLGIRPADLVPRDMIALPLGHpVRHAVV 167
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLArFRERYPDVELELTEGNseELLDLLLEGeLDLAIRRGPPDDPGLEARPLGE-EPLVLV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173  168 ASPDWLVRHPEPRSPADLDPDACLRvrLPNGALLRWPFEKDGVPLPFEASGRLTVDEAAIARAAVLDGAGIGYFIEADVA 247
Cdd:pfam03466  80 APPDHPLARGEPVSLEDLADEPLIL--LPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVA 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 126103173  248 EDIAAGRMI-RLLEDWTPNRPgFSLYYSGRRNPSAGFTAFLAMARER 293
Cdd:pfam03466 158 RELADGRLVaLPLPEPPLPRE-LYLVWRKGRPLSPAVRAFIEFLREA 203
PRK09791 PRK09791
LysR family transcriptional regulator;
8-137 1.55e-19

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 86.35  E-value: 1.55e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173   8 LEAVLAIARKGSFRAAALDLGVSTTALSHTVARLEAGLGVRLFHRTTRSVALTEAGREFVARIAPALTEIRAALETVRSQ 87
Cdd:PRK09791  10 IRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQEDIRQR 89

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 126103173  88 RATPSGMLRINASVQAGRAVAPLVLA-FLRRYPEMRVDlVTEGRLVDIVAE 137
Cdd:PRK09791  90 QGQLAGQINIGMGASIARSLMPAVISrFHQQHPQVKVR-IMEGQLVSMINE 139
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
5-64 8.05e-19

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 78.20  E-value: 8.05e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173    5 LKGLEAVLAIARKGSFRAAALDLGVSTTALSHTVARLEAGLGVRLFHRTTRSVALTEAGR 64
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-143 6.39e-18

selenium metabolism-associated LysR family transcriptional regulator; LysR family transcriptional regulators regularly appear encoded adjacent to selenecysteine incorporation proteins such as SelB. This model represents one especially well-conserved subgroup of such transcription factors from species such as Merdimonas faecis, Sellimonas intestinalis, Syntrophotalea acetylenica, and Hydrogenivirga caldilitoris. Seed alignment members were selected by proximity to selB, but not all family members are expected to have similar genomic locations.


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 81.89  E-value: 6.39e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173   1 MDsgLKGLEAVLAIARKGSFRAAALDLGVSTTALSHTVARLEAGLGVRLFHRTTRSVALTEAGREFVARIAPALTEIRAA 80
Cdd:NF040786   1 MN--LKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKL 78

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 126103173  81 LETVRSQRATPSGMLRINASVQAGRAVAPLVLA-FLRRYPEMRVDLVTEG--RLVDIVAEG-FDLGI 143
Cdd:NF040786  79 EEEFDRYGKESKGVLRIGASTIPGQYLLPELLKkFKEKYPNVRFKLMISDsiKVIELLLEGeVDIGF 145
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
5-143 2.88e-17

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 80.43  E-value: 2.88e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173   5 LKGLEAVLAIARKGSFRAAALDLGVSTTALSHTVARLEAGLGVRLFHRTTRSVALTEAGREFVARIAPALTEIRAALETV 84
Cdd:PRK10086  16 LSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLDTLNQEILDI 95

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 126103173  85 RSQRatPSGMLRINA--SVqAGRAVAPLVLAFLRRYPEMRVDLVTEGRLVDIVAEGFDLGI 143
Cdd:PRK10086  96 KNQE--LSGTLTVYSrpSI-AQCWLVPRLADFTRRYPSISLTILTGNENVNFQRAGIDLAI 153
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 12-186 5.50e-13

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 67.67  E-value: 5.50e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173  12 LAIARKGSFRAAALDLGVSTTALSHTVARLEAGLGVRLFHRTTRSVALTEAGREFVARIAPALTEIRAALETVRSQRATP 91
Cdd:PRK11242  10 LAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRRAIHDVADLS 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173  92 SGMLRINASVQ-AGRAVAPLVLAFLRRYP-------EMRVDLVTEGRLVDIVaegfDLGIRPADLVPRDMIALPLGHPVR 163
Cdd:PRK11242  90 RGSLRLAMTPTfTAYLIGPLIDAFHARYPgitltirEMSQERIEALLADDEL----DVGIAFAPVHSPEIEAQPLFTETL 165

                        170       180
                 ....*....|....*....|...
gi 126103173 164 HAVVASPDWLVRHPEPRSPADLD 186
Cdd:PRK11242 166 ALVVGRHHPLAARRKALTLDELA 188
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 8-121 5.72e-12

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 64.96  E-value: 5.72e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173   8 LEAVLAIARKGSFRAAALDLGVSTTALSHTVARLEAGLGVRLFHRTTRSVALTEAGREFVARiapALTEIRAALETVR-S 86
Cdd:PRK11074   7 LEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKE---ARSVIKKMQETRRqC 83

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 126103173  87 QRAT----PSGMLRINASVQAGRaVAPLVLAFLRRYPEM 121
Cdd:PRK11074  84 QQVAngwrGQLSIAVDNIVRPDR-TRQLIVDFYRHFDDV 121
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 114-286 2.37e-11

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: 61.44  E-value: 2.37e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173 114 FLRRYPEMRVDLVTEGRLVDIVAEGFDLGIRPADLVPRDMIALPLGhPVRHAVVASPDWLVRHPePRSPADLDPDACLRV 193
Cdd:cd08432   22 FQARHPDIDLRLSTSDRLVDFAREGIDLAIRYGDGDWPGLEAERLM-DEELVPVCSPALLAGLP-LLSPADLARHTLLHD 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173 194 RLPNGAlLRWPFEKDGVPLPFEASGrLTVDEAAIARAAVLDGAGIGYFIEADVAEDIAAGRMIRLLEDWTPNRPGFSLYY 273
Cdd:cd08432  100 ATRPEA-WQWWLWAAGVADVDARRG-PRFDDSSLALQAAVAGLGVALAPRALVADDLAAGRLVRPFDLPLPSGGAYYLVY 177

                        170
                 ....*....|...
gi 126103173 274 SGRRNPSAGFTAF 286
Cdd:cd08432  178 PPGRAESPAVAAF 190
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
8-185 9.53e-11

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 61.36  E-value: 9.53e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173   8 LEAVLAIARKGSFRAAALDLGVSTTALSHTVARLEAGLGVRLFHRTTRSVALTEAGREFVARIapalTEIRAALEtvrsq 87
Cdd:PRK10094   7 LRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQA----RDWLSWLE----- 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173  88 rATPSGMLRINASVQ------------AGRAVAPLVLAFLRRYPEMRVDL---VTEGRLVDIVAEGFDL--GIRPADLVP 150
Cdd:PRK10094  78 -SMPSELQQVNDGVErqvnivinnllyNPQAVAQLLAWLNERYPFTQFHIsrqIYMGVWDSLLYEGFSLaiGVTGTEALA 156

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 126103173 151 RDMIALPLGHPVRHAVVASPDWLVRHPEPRSPADL 185
Cdd:PRK10094 157 NTFSLDPLGSVQWRFVMAADHPLANVEEPLTEAQL 191
rbcR CHL00180
LysR transcriptional regulator; Provisional
 5-125 1.40e-10

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 60.80  E-value: 1.40e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173   5 LKGLEAVLAIARKGSFRAAALDLGVSTTALSHTVARLEAGLGVRLFHRTTRSVALTEAGREFV---ARIAPALTEIRAAL 81
Cdd:CHL00180   7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLrygNRILALCEETCRAL 86

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 126103173  82 ETVRSQRatpSGMLRINASVQAGRAVAPLVLA-FLRRYPEMRVDL 125
Cdd:CHL00180  87 EDLKNLQ---RGTLIIGASQTTGTYLMPRLIGlFRQRYPQINVQL 128
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
29-127 2.52e-10

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 59.83  E-value: 2.52e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173  29 VSTTALSHTVARLEAGLGVRLFHRTTRSVALTEAGREF--VARiaPALTEIRAALETVRSQRATPSGMLRINASVQAGRA 106
Cdd:PRK11716   3 VSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELrpFAQ--QTLLQWQQLRHTLDQQGPSLSGELSLFCSVTAAYS 80

                         90       100
                 ....*....|....*....|..
gi 126103173 107 VAPLVLA-FLRRYPEMRVDLVT 127
Cdd:PRK11716  81 HLPPILDrFRAEHPLVEIKLTT 102
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 5-164 9.54e-09

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 55.16  E-value: 9.54e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173   5 LKGLEAVLAIARKGSFRAAALDLGVSTTALSHTVARLEAGLGVRLFHRTTRSVALTEAGREFV--ARI--APALTEIRAA 80
Cdd:PRK09906   3 LRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLqdARAilEQAEKAKLRA 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173  81 LETVRSQRatpsgMLRINASVQAGRAVAPLVLAFLR-RYPEMRVDLV---TEGRLVDIVAEGFDLG-IRPAdlVPRDMI- 154
Cdd:PRK09906  83 RKIVQEDR-----QLTIGFVPSAEVNLLPKVLPMFRlRHPDTLIELVsliTTQQEEKLRRGELDVGfMRHP--VYSDEId 155

                        170       180
                 ....*....|....*....|.
gi 126103173 155 -----------ALPLGHPVRH 164
Cdd:PRK09906 156 ylelldeplvvVLPVDHPLAH 176
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 1-125 1.54e-08

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 54.69  E-value: 1.54e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173   1 MDSGLKGLEAVLAIARKGSFRAAALDLGVSTTALSHTVARLEAGLGVRLFHRTTRSVALTEAGREFVARiAPALTEIRAA 80
Cdd:PRK10837   1 MHITLRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPR-ALALLEQAVE 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 126103173  81 LETVRSQRatpSGMLRINASVQAGRAVAPLVLAFLRR-YPEMRVDL 125
Cdd:PRK10837  80 IEQLFRED---NGALRIYASSTIGNYILPAMIARYRRdYPQLPLEL 122
PRK12680 PRK12680
LysR family transcriptional regulator;
23-246 8.18e-08

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 52.70  E-value: 8.18e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173  23 AALDLGVSTTALSHTVARLEAGLGVRLFHRTTRSV-ALTEAGREFVARIAPALTEIRAALETVRSQRATPSGMLRINASV 101
Cdd:PRK12680  22 AAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLeSVTPAGVEVIERARAVLSEANNIRTYAANQRRESQGQLTLTTTH 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173 102 QAGRAVAPLVLAFLR-RYPEMRVDL--VTEGRLVDIVAEG-FDLGI-RPADLVPRDMIALPL-----------GHPVRHA 165
Cdd:PRK12680 102 TQARFVLPPAVAQIKqAYPQVSVHLqqAAESAALDLLGQGdADIAIvSTAGGEPSAGIAVPLyrwrrlvvvprGHALDTP 181

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173 166 VVAsPDW--LVRHPEprspadLDPDACLRvrlPNGALLRwPFEKDGVplpfEASGRLTVDEAAIARAAVLDGAGIGYFIE 243
Cdd:PRK12680 182 RRA-PDMaaLAEHPL------ISYESSTR---PGSSLQR-AFAQLGL----EPSIALTALDADLIKTYVRAGLGVGLLAE 246


                 ...
gi 126103173 244 ADV 246
Cdd:PRK12680 247 MAV 249
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 107-290 1.43e-07

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: 50.68  E-value: 1.43e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173 107 VAPLVLAFLRRYPEMRVDLVTEG--RLVDIVAEG-FDLGIRPADLVPRDMIALPLGHpVRHAVVASPDWLVRHPEPRSPA 183
Cdd:cd05466   15 LPPLLAAFRQRYPGVELSLVEGGssELLEALLEGeLDLAIVALPVDDPGLESEPLFE-EPLVLVVPPDHPLAKRKSVTLA 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173 184 DL--------DPDACLRVRlpngaLLRWpFEKDGVPLPFeasgRLTVDEAAIARAAVLDGAGIGyFIEADVAEDIAAGRM 255
Cdd:cd05466   94 DLadeplilfERGSGLRRL-----LDRA-FAEAGFTPNI----ALEVDSLEAIKALVAAGLGIA-LLPESAVEELADGGL 162

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 126103173 256 IRLLEDWTPNRPGFSLYYSGRRNPSAGFTAFLAMA 290
Cdd:cd05466  163 VVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
PRK09986 PRK09986
LysR family transcriptional regulator;
5-85 1.94e-07

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 51.26  E-value: 1.94e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173   5 LKGLEAVLAIARKGSFRAAALDLGVSTTALSHTVARLEAGLGVRLFHRTTRSVALTEAGREFVARIAPALTEIRAALETV 84
Cdd:PRK09986   9 LKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLARV 88


                 .
gi 126103173  85 R 85
Cdd:PRK09986  89 E 89
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
5-125 3.14e-07

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 50.79  E-value: 3.14e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173   5 LKGLEAVLAIARKGSFRAAALDLGVSTTALSHTVARLEAGLGVRLFHRTTRSVALTEAGREFVARIAPALTEIRAALETV 84
Cdd:PRK15421   4 VKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQAC 83

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 126103173  85 RSQRATpsgMLRINASVQAG-RAVAPLVLAFLRRYPEMRVDL 125
Cdd:PRK15421  84 NEPQQT---RLRIAIECHSCiQWLTPALENFHKNWPQVEMDF 122
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
6-64 4.49e-07

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 50.35  E-value: 4.49e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 126103173   6 KGLEAVLAIARKGSFRAAALDLGVSTTALSHTVARLEAGLGVRLFHRtTRSVALTEAGR 64
Cdd:PRK13348   5 KQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQ 62
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 8-121 1.25e-06

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 48.87  E-value: 1.25e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173   8 LEAVLAIARKGSFRAAALDLGVSTTALSHTVARLEAGLGVRLFHRTTRSVALTEAGREFVARIAPALTEIRAALETVRSQ 87
Cdd:PRK11151   6 LEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVLKEMASQQ 85

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 126103173  88 RATPSGMLRINASVQAGRAVAPLVLAFLRR-YPEM 121
Cdd:PRK11151  86 GETMSGPLHIGLIPTVGPYLLPHIIPMLHQtFPKL 120
PRK10341 PRK10341
transcriptional regulator TdcA;
6-158 2.48e-06

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 47.93  E-value: 2.48e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173   6 KGLEAVLAIARKGSFRAAALDLGVSTTALSHTVARLEAGLGVRLFHRTTRSVALTEAGREFVARIAPALTEIRAALETVR 85
Cdd:PRK10341  10 QHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEIN 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173  86 SQRATPSGMLRINASVQAGRAVAPLVL-AFLRRYPEMRVDLVtEGRLVDI---VAEG---FDLGIRPADLVPRDMIALPL 158
Cdd:PRK10341  90 GMSSEAVVDVSFGFPSLIGFTFMSDMInKFKEVFPKAQVSMY-EAQLSSFlpaIRDGrldFAIGTLSNEMKLQDLHVEPL 168
PBP2_HvrB cd08483
The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an ...
 109-261 8.37e-06

The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an activator of S-adenosyl-L-homocysteine hydrolase expression, contains the type 2 periplasmic binding fold; The transcriptional regulator HvrB of the LysR family is required for the light-dependent activation of both ahcY, which encoding the enzyme S-adenosyl-L-homocysteine hydrolase (AdoHcyase) that responsible for the reversible hydrolysis of AdoHcy to adenosine and homocysteine, and orf5, a gene of unknown. The topology of this C-terminal domain of HvrB is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176172 [Multi-domain]  Cd Length: 190  Bit Score: 45.41  E-value: 8.37e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173 109 PLVLAFLRRYPEMRVDLVTEGRLVDIVAEGFDLGIRPADLVPRDMIALPLGHPvRHAVVASPDwLVRHPEPRSPADLDPD 188
Cdd:cd08483   17 PRLGSFWAKHPEIELSLLPSADLVDLRPDGIDVAIRYGNGDWPGLESEPLTAA-PFVVVAAPG-LLGDRKVDSLADLAGL 94

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 126103173 189 ACLRVRLPNGALLrWpFEKDGVplPFEASGRLTVDEAAIARAAVLDGAGIGYFIEADVAEDIAAGRMIRLLED 261
Cdd:cd08483   95 PWLQERGTNEQRV-W-LASMGV--VPDLERGVTFLPGQLVLEAARAGLGLSIQARALVEPDIAAGRLTVLFEE 163
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
5-177 8.51e-06

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 46.51  E-value: 8.51e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173   5 LKGLEAVLAIARKG-SFRAAALDLGVSTTALSHTVARLEAGLGVRLFHRT-TRSVALTEAGREFVARIAPALTEIRAaLE 82
Cdd:PRK12684   3 LHQLRFVREAVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHgKRLRGLTEPGRIILASVERILQEVEN-LK 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173  83 TVRSQRAT-PSGMLRINAS-VQAGRAVAPLVLAFLRRYPEMRVDLV--TEGRLVDIVAEG-FDLGI--RPADLVPrDMIA 155
Cdd:PRK12684  82 RVGKEFAAqDQGNLTIATThTQARYALPAAIKEFKKRYPKVRLSILqgSPTQIAEMVLHGqADLAIatEAIADYK-ELVS 160

                        170       180
                 ....*....|....*....|..
gi 126103173 156 LPlGHPVRHAVVASPDwlvrHP 177
Cdd:PRK12684 161 LP-CYQWNHCVVVPPD----HP 177
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 5-177 9.03e-06

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 46.52  E-value: 9.03e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173   5 LKGLEAVLAIARKG-SFRAAALDLGVSTTALSHTVARLEAGLGVRLFHRT-TRSVALTEAGREFVARIAPALTEIRaALE 82
Cdd:PRK12682   3 LQQLRFVREAVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHgKRLKGLTEPGKAVLDVIERILREVG-NIK 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173  83 TVRSQRATP-SGMLRINASVQAGRAVAPLVLAFLR-RYPEMRVDL--VTEGRLVDIVAEGF-DLGI------RPADLVP- 150
Cdd:PRK12682  82 RIGDDFSNQdSGTLTIATTHTQARYVLPRVVAAFRkRYPKVNLSLhqGSPDEIARMVISGEaDIGIateslaDDPDLATl 161

                        170       180       190
                 ....*....|....*....|....*....|..
gi 126103173 151 -----RDMIALPLGHPVRHAVVASPDWLVRHP 177
Cdd:PRK12682 162 pcydwQHAVIVPPDHPLAQEERITLEDLAEYP 193
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
6-261 3.57e-05

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 44.66  E-value: 3.57e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173   6 KGLEAVLAIARKGSFRAAALDLGVSTTALSHTVARLEAGLGVRLFHRTTRSVALTEAGREFVARIAPALTEIRAALETVR 85
Cdd:PRK10082  14 KWLYDFLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESNLAELR 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173  86 SQRATPSGMLRINASVQAGRAVAPLVLAFLRRYPEMRVDLVTEGRLVDIVAEG---FDLGIRPADLV--PRDMIAL---- 156
Cdd:PRK10082  94 GGSDYAQRKIKIAAAHSLSLGLLPSIISQMPPLFTWAIEAIDVDEAVDKLREGqsdCIFSFHDEDLLeaPFDHIRLfesq 173

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173 157 --PLGHPVRHAvvaspDWLVRHPEPRSPADLDPDACLRVRLPNGALLRWPfekdgvPLPFeaSGRLTVDEAAIARAAVLD 234
Cdd:PRK10082 174 lfPVCASDEHG-----EALFNLAQPHFPLLNYSRNSYMGRLINRTLTRHS------ELSF--STFFVSSMSELLKQVALD 240

                        250       260
                 ....*....|....*....|....*..
gi 126103173 235 GAGIGYFIEADVAEDIAAGRMIRLLED 261
Cdd:PRK10082 241 GCGIAWLPEYAIQQEIRSGQLVVLNRD 267
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 23-177 4.05e-04

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 41.18  E-value: 4.05e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173  23 AALDLGVSTTALSHTVARLEAGLGVRLFHRT-TRSVALTEAGREF---VARIAPALTEIRAALETVRSQRatpSGMLRIN 98
Cdd:PRK12683  22 VANALYTSQSGVSKQIKDLEDELGVEIFIRRgKRLTGLTEPGKELlqiVERMLLDAENLRRLAEQFADRD---SGHLTVA 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173  99 AS-VQAGRAVAPLVLAFLRRYPEMRVDL--VTEGRLVDIVAEG-FDLGIRPADL--VPrDMIALPLgHPVRHAVVASPDw 172
Cdd:PRK12683  99 TThTQARYALPKVVRQFKEVFPKVHLALrqGSPQEIAEMLLNGeADIGIATEALdrEP-DLVSFPY-YSWHHVVVVPKG- 175


                 ....*
gi 126103173 173 lvrHP 177
Cdd:PRK12683 176 ---HP 177
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
8-64 6.20e-04

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 40.53  E-value: 6.20e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 126103173   8 LEAVLAIARKGSFRAAALDLGVSTTALSHTVARLEAGLGVRLFHRtTRSVALTEAGR 64
Cdd:PRK03635   7 LEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQ 62
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 1-171 3.31e-03

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 38.43  E-value: 3.31e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173   1 MDSGLKGLEAVLAIARKGSFRAAALDLGVSTTALSHTVARLEAGLGVRLFHRTT-RSVALTEAGREF--VARIAPALTEI 77
Cdd:PRK11013   2 AAVSLRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRgRLHPTVQGLRLFeeVQRSYYGLDRI 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173  78 RAALETVRSQRatpSGMLRINASVQAGRAVAPLVLA-FLRRYPEMRVDLVT-EGRLVD--IVAEGFDLGIRPADLVPR-- 151
Cdd:PRK11013  82 VSAAESLREFR---QGQLSIACLPVFSQSLLPGLCQpFLARYPDVSLNIVPqESPLLEewLSAQRHDLGLTETLHTPAgt 158

                        170       180
                 ....*....|....*....|....*....
gi 126103173 152 --------DMI-ALPLGHPVRHAVVASPD 171
Cdd:PRK11013 159 ertelltlDEVcVLPAGHPLAAKKVLTPD 187
PBP2_LTTR_beta_lactamase cd08484
The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase ...
 109-257 4.09e-03

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


Pssm-ID: 176173 [Multi-domain]  Cd Length: 189  Bit Score: 37.35  E-value: 4.09e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173 109 PLVLAFLRRYPEMRVDLVTEGRLVDIVAEGFDLGIRPADLVPRDMIALPL-GHPVrhAVVASPDWLvrhPEPRSPADldp 187
Cdd:cd08484   17 PRLAEFRQLHPFIDLRLSTNNNRVDIAAEGLDFAIRFGEGAWPGTDATRLfEAPL--SPLCTPELA---RRLSEPAD--- 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173 188 daclrvrLPNGALLR------WP--FEKDGVPLP------FEASgrLTVDEAAiaraavLDGAGIGYFIEADVAEDIAAG 253
Cdd:cd08484   89 -------LANETLLRsyradeWPqwFEAAGVPPPpingpvFDSS--LLMVEAA------LQGAGVALAPPSMFSRELASG 153


                 ....
gi 126103173 254 RMIR 257
Cdd:cd08484  154 ALVQ 157
HTH_MARR smart00347
helix_turn_helix multiple antibiotic resistance protein;
27-81 4.63e-03

helix_turn_helix multiple antibiotic resistance protein;


Pssm-ID: 197670 [Multi-domain]  Cd Length: 101  Bit Score: 36.03  E-value: 4.63e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173    27 LGVSTTALSHTVARLE-AGLGVRLFH----RTTRsVALTEAGREFVARIAPALTEIRAAL 81
Cdd:smart00347  34 LGVSPSTVTRVLDRLEkKGLVRREPSpedrRSVL-VSLTEEGRELIEQLLEARSETLAEL 92
cbl PRK12679
HTH-type transcriptional regulator Cbl;
27-177 5.00e-03

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 37.87  E-value: 5.00e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173  27 LGVSTTALSHTVARLEAGLGVRLF-HRTTRSVALTEAGREFVA---RIAPALTEIR--AALETVRSqratpSGMLRINAS 100
Cdd:PRK12679  26 LFTSQSGVSRHIRELEDELGIEIFiRRGKRLLGMTEPGKALLViaeRILNEASNVRrlADLFTNDT-----SGVLTIATT 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173 101 -VQAGRAVAPLVLAFLRRYPEMRVDLVtEGRLVDIVA----EGFDLGIRPADLVPRDMIA------------LPLGHPVR 163
Cdd:PRK12679 101 hTQARYSLPEVIKAFRELFPEVRLELI-QGTPQEIATllqnGEADIGIASERLSNDPQLVafpwfrwhhsllVPHDHPLT 179

                        170
                 ....*....|....
gi 126103173 164 HAVVASPDWLVRHP 177
Cdd:PRK12679 180 QITPLTLESIAKWP 193
PBP2_BlaA cd08487
The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which ...
 109-257 9.61e-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: 36.37  E-value: 9.61e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126103173 109 PLVLAFLRRYPEMRVDLVTEGRLVDIVAEGFDLGIR------PADLVPRDMIAlPLghpvrhAVVASPDWLVRHPEprsP 182
Cdd:cd08487   17 PRLAEFRQLHPFIELRLRTNNNVVDLATEGLDFAIRfgeglwPATHNERLLDA-PL------SVLCSPEIAKRLSH---P 86

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 126103173 183 ADLDPDACLRVRLPNgALLRWpFEKDGVPlPFEASGRLtVDEAAIARAAVLDGAGIGYFIEADVAEDIAAGRMIR 257
Cdd:cd08487   87 ADLINETLLRSYRTD-EWLQW-FEAANMP-PIKIRGPV-FDSSRLMVEAAMQGAGVALAPAKMFSREIENGQLVQ 157
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH