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Conserved domains on  [gi|294477897|gb|ADE87284|]
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transcriptional regulator, LysR family (plasmid) [Rhodobacter capsulatus SB 1003]

Protein Classification

Graphical summary

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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 ...
 91-287 1.97e-78

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: 236.59  E-value: 1.97e-78
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897  91 PSGRLRINASAQGGRAV-APLVLEFLNSHPQMQVDLVTEGRLVDIVAEGFDLGIRPADLVPRDMIALPLGAPARHAVVAA 169
Cdd:cd08474    1 PAGTLRINAPRVAARLLlAPLLARFLARYPDIRLELVVDDGLVDIVAEGFDAGIRLGESVEKDMVAVPLGPPLRMAVVAS 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897 170 PGWLARHPSPLSPADLDPDHCLRVRLP-NGALLRWPFEKDGRALPFEARGRLTVDDPAIARAAVLDGAGIGYFIEADVAE 248
Cdd:cd08474   81 PAYLARHGTPEHPRDLLNHRCIRYRFPtSGALYRWEFERGGRELEVDVEGPLILNDSDLMLDAALDGLGIAYLFEDLVAE 160

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 294477897 249 DIAAGRMVRLLADWTPNRPGFSLYYPGRRNASAGFTAFL 287
Cdd:cd08474  161 HLASGRLVRVLEDWSPPFPGGYLYYPSRRRVPPALRAFI 199
LysR_Sec_metab super family cl49002
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 5-143 2.78e-20

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.


The actual alignment was detected with superfamily member NF040786:

Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 88.44  E-value: 2.78e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897   5 LKALEAVQAIARRGSFRAAALDLGLSTTALSQTIARLEANLGVRLFNRTTRSVSLTEAGRDFAARTAPALAEIRAAMERV 84
Cdd:NF040786   3 LKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEEEF 82

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 294477897  85 RAQRDTPSGRLRINASAQGGRAVAPLVL-EFLNSHPQMQVDLVTEG--RLVDIVAEG-FDLGI 143
Cdd:NF040786  83 DRYGKESKGVLRIGASTIPGQYLLPELLkKFKEKYPNVRFKLMISDsiKVIELLLEGeVDIGF 145
 
Name Accession Description Interval E-value
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 91-287 1.97e-78

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: 236.59  E-value: 1.97e-78
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897  91 PSGRLRINASAQGGRAV-APLVLEFLNSHPQMQVDLVTEGRLVDIVAEGFDLGIRPADLVPRDMIALPLGAPARHAVVAA 169
Cdd:cd08474    1 PAGTLRINAPRVAARLLlAPLLARFLARYPDIRLELVVDDGLVDIVAEGFDAGIRLGESVEKDMVAVPLGPPLRMAVVAS 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897 170 PGWLARHPSPLSPADLDPDHCLRVRLP-NGALLRWPFEKDGRALPFEARGRLTVDDPAIARAAVLDGAGIGYFIEADVAE 248
Cdd:cd08474   81 PAYLARHGTPEHPRDLLNHRCIRYRFPtSGALYRWEFERGGRELEVDVEGPLILNDSDLMLDAALDGLGIAYLFEDLVAE 160

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 294477897 249 DIAAGRMVRLLADWTPNRPGFSLYYPGRRNASAGFTAFL 287
Cdd:cd08474  161 HLASGRLVRVLEDWSPPFPGGYLYYPSRRRVPPALRAFI 199
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
5-296 1.27e-48

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 162.34  E-value: 1.27e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897   5 LKALEAVQAIARRGSFRAAALDLGLSTTALSQTIARLEANLGVRLFNRTTRSVSLTEAGRDFAARTAPALAEIRAAMERV 84
Cdd:COG0583    3 LRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAEL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897  85 RAQRDTPSGRLRINAS-AQGGRAVAPLVLEFLNSHPQMQVDLVTEG--RLVD-IVAEGFDLGIRPADLVPRDMIALPLGa 160
Cdd:COG0583   83 RALRGGPRGTLRIGAPpSLARYLLPPLLARFRARHPGVRLELREGNsdRLVDaLLEGELDLAIRLGPPPDPGLVARPLG- 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897 161 PARHAVVAApgwlarhpsplspadldPDHCLrvrlpngallrwpfekdgralpfeARGRLTVDDPAIARAAVLDGAGIGY 240
Cdd:COG0583  162 EERLVLVAS-----------------PDHPL------------------------ARRAPLVNSLEALLAAVAAGLGIAL 200

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 294477897 241 FIEADVAEDIAAGRMVRLLADWTPNRPGFSLYYPGRRNASAGFTAFLALARQRAGA 296
Cdd:COG0583  201 LPRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
5-272 2.74e-35

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 129.11  E-value: 2.74e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897   5 LKALEAVQAIARRGSFRAAALDLGLSTTALSQTIARLEANLGVRLFNRTTRSVSLTEAGRDFAARTAPALAEIRAAMERV 84
Cdd:PRK10632   4 LKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQL 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897  85 RAQRDTPSGRLRINASAQGGRAV-APLVLEFLNSHPQMQVDLVTEGRLVDIVAEGFDLGIRPADLVPRDMIALPLGA-PA 162
Cdd:PRK10632  84 YAFNNTPIGTLRIGCSSTMAQNVlAGLTAKMLKEYPGLSVNLVTGIPAPDLIADGLDVVIRVGALQDSSLFSRRLGAmPM 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897 163 rhAVVAAPGWLARHPSPLSPADLD----------PDHCLRVRLPNGALLRwpfekdgralpFEARGRLTVDDPAIARAAV 232
Cdd:PRK10632 164 --VVCAAKSYLAQYGTPEKPADLSshswleysvrPDNEFELIAPEGISTR-----------LIPQGRFVTNDPQTLVRWL 230

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|.
gi 294477897 233 LDGAGIGYFIEADVAEDIAAGRMVRLLADWTPN-RPGFSLY 272
Cdd:PRK10632 231 TAGAGIAYVPLMWVIDEINRGELEILFPRYQSDpRPVYALY 271
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 92-295 3.75e-22

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: 91.58  E-value: 3.75e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897   92 SGRLRINAS-AQGGRAVAPLVLEFLNSHPQMQVDLVTEG--RLVDIVAEG-FDLGIRPADLVPRDMIALPLGaPARHAVV 167
Cdd:pfam03466   1 SGRLRIGAPpTLASYLLPPLLARFRERYPDVELELTEGNseELLDLLLEGeLDLAIRRGPPDDPGLEARPLG-EEPLVLV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897  168 AAPGWLARHPSPLSPADLDPDHCLRvrLPNGALLRWPFEKDGRALPFEARGRLTVDDPAIARAAVLDGAGIGYFIEADVA 247
Cdd:pfam03466  80 APPDHPLARGEPVSLEDLADEPLIL--LPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVA 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 294477897  248 EDIAAGRMV-RLLADWTPNRPgFSLYYPGRRNASAGFTAFLALARQRAG 295
Cdd:pfam03466 158 RELADGRLVaLPLPEPPLPRE-LYLVWRKGRPLSPAVRAFIEFLREALA 205
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 5-143 2.78e-20

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: 88.44  E-value: 2.78e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897   5 LKALEAVQAIARRGSFRAAALDLGLSTTALSQTIARLEANLGVRLFNRTTRSVSLTEAGRDFAARTAPALAEIRAAMERV 84
Cdd:NF040786   3 LKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEEEF 82

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 294477897  85 RAQRDTPSGRLRINASAQGGRAVAPLVL-EFLNSHPQMQVDLVTEG--RLVDIVAEG-FDLGI 143
Cdd:NF040786  83 DRYGKESKGVLRIGASTIPGQYLLPELLkKFKEKYPNVRFKLMISDsiKVIELLLEGeVDIGF 145
PRK09791 PRK09791
LysR family transcriptional regulator;
5-137 9.53e-20

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 87.12  E-value: 9.53e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897   5 LKALEAVQAIARRGSFRAAALDLGLSTTALSQTIARLEANLGVRLFNRTTRSVSLTEAGRDFAARTAPALAEIRAAMERV 84
Cdd:PRK09791   7 IHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQEDI 86

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 294477897  85 RAQRDTPSGRLRINASAQGGRAVAPLVL-EFLNSHPQMQVDlVTEGRLVDIVAE 137
Cdd:PRK09791  87 RQRQGQLAGQINIGMGASIARSLMPAVIsRFHQQHPQVKVR-IMEGQLVSMINE 139
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
5-64 2.85e-19

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 79.35  E-value: 2.85e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897    5 LKALEAVQAIARRGSFRAAALDLGLSTTALSQTIARLEANLGVRLFNRTTRSVSLTEAGR 64
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
 
Name Accession Description Interval E-value
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 91-287 1.97e-78

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: 236.59  E-value: 1.97e-78
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897  91 PSGRLRINASAQGGRAV-APLVLEFLNSHPQMQVDLVTEGRLVDIVAEGFDLGIRPADLVPRDMIALPLGAPARHAVVAA 169
Cdd:cd08474    1 PAGTLRINAPRVAARLLlAPLLARFLARYPDIRLELVVDDGLVDIVAEGFDAGIRLGESVEKDMVAVPLGPPLRMAVVAS 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897 170 PGWLARHPSPLSPADLDPDHCLRVRLP-NGALLRWPFEKDGRALPFEARGRLTVDDPAIARAAVLDGAGIGYFIEADVAE 248
Cdd:cd08474   81 PAYLARHGTPEHPRDLLNHRCIRYRFPtSGALYRWEFERGGRELEVDVEGPLILNDSDLMLDAALDGLGIAYLFEDLVAE 160

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 294477897 249 DIAAGRMVRLLADWTPNRPGFSLYYPGRRNASAGFTAFL 287
Cdd:cd08474  161 HLASGRLVRVLEDWSPPFPGGYLYYPSRRRVPPALRAFI 199
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 93-287 6.65e-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: 189.19  E-value: 6.65e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897  93 GRLRINASAQGGRA-VAPLVLEFLNSHPQMQVDLVTEGRLVDIVAEGFDLGIRPADLVPRDMIALPLGaPARHAVVAAPG 171
Cdd:cd08422    1 GRLRISAPVSFGRLhLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLG-PVRRVLVASPA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897 172 WLARHPSPLSPADLDPDHCLRVRLPnGALLRWPFEKDGRALPFEARGRLTVDDPAIARAAVLDGAGIGYFIEADVAEDIA 251
Cdd:cd08422   80 YLARHGTPQTPEDLARHRCLGYRLP-GRPLRWRFRRGGGEVEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAEDLA 158

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 294477897 252 AGRMVRLLADWTPNRPGFSLYYPGRRNASAGFTAFL 287
Cdd:cd08422  159 SGRLVRVLPDWRPPPLPIYAVYPSRRHLPAKVRAFI 194
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
5-296 1.27e-48

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 162.34  E-value: 1.27e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897   5 LKALEAVQAIARRGSFRAAALDLGLSTTALSQTIARLEANLGVRLFNRTTRSVSLTEAGRDFAARTAPALAEIRAAMERV 84
Cdd:COG0583    3 LRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAEL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897  85 RAQRDTPSGRLRINAS-AQGGRAVAPLVLEFLNSHPQMQVDLVTEG--RLVD-IVAEGFDLGIRPADLVPRDMIALPLGa 160
Cdd:COG0583   83 RALRGGPRGTLRIGAPpSLARYLLPPLLARFRARHPGVRLELREGNsdRLVDaLLEGELDLAIRLGPPPDPGLVARPLG- 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897 161 PARHAVVAApgwlarhpsplspadldPDHCLrvrlpngallrwpfekdgralpfeARGRLTVDDPAIARAAVLDGAGIGY 240
Cdd:COG0583  162 EERLVLVAS-----------------PDHPL------------------------ARRAPLVNSLEALLAAVAAGLGIAL 200

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 294477897 241 FIEADVAEDIAAGRMVRLLADWTPNRPGFSLYYPGRRNASAGFTAFLALARQRAGA 296
Cdd:COG0583  201 LPRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
PBP2_CrgA_like_8 cd08477
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-277 3.01e-39

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


Pssm-ID: 176166  Cd Length: 197  Bit Score: 136.21  E-value: 3.01e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897  93 GRLRINASAQ-GGRAVAPLVLEFLNSHPQMQVDLVTEGRLVDIVAEGFDLGIRPADLVPRDMIALPLgAPARHAVVAAPG 171
Cdd:cd08477    1 GKLRISAPVTfGSHVLTPALAEYLARYPDVRVDLVLSDRLVDLVEEGFDAAFRIGELADSSLVARPL-APYRMVLCASPD 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897 172 WLARHPSPLSPADLDPDHCLRVrLPNGALLRWPFEKDGRALPFEARGRLTVDDPAIARAAVLDGAGIGYFIEADVAEDIA 251
Cdd:cd08477   80 YLARHGTPTTPEDLARHECLGF-SYWRARNRWRLEGPGGEVKVPVSGRLTVNSGQALRVAALAGLGIVLQPEALLAEDLA 158

                        170       180
                 ....*....|....*....|....*..
gi 294477897 252 AGRMVRLLADWTP-NRPGFSLYYPGRR 277
Cdd:cd08477  159 SGRLVELLPDYLPpPRPMHLLYPPDRR 185
PBP2_CrgA_like_9 cd08479
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-287 1.29e-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: 129.64  E-value: 1.29e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897  93 GRLRINASAQGGRA-VAPLVLEFLNSHPQMQVDLVTEGRLVDIVAEGFDLGIRPADLVPRDMIALPLgAPARHAVVAAPG 171
Cdd:cd08479    1 GLLRVNASFGFGRRhIAPALSDFAKRYPELEVQLELTDRPVDLVEEGFDLDIRVGDLPDSSLIARKL-APNRRILCASPA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897 172 WLARHPSPLSPADLDPDHCLRVRLPNGALLRWPFEKDGRALPFEARGRLTVDDPAIARAAVLDGAGIGYFIEADVAEDIA 251
Cdd:cd08479   80 YLERHGAPASPEDLARHDCLVIRENDEDFGLWRLRNGDGEATVRVRGALSSNDGEVVLQWALDGHGIILRSEWDVAPYLR 159

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 294477897 252 AGRMVRLLADWTPNRPGFSLYYPGRRNASAGFTAFL 287
Cdd:cd08479  160 SGRLVRVLPDWQLPDADIWAVYPSRLSRSARVRVFV 195
PBP2_CrgA_like_2 cd08471
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-293 3.08e-36

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


Pssm-ID: 176160  Cd Length: 201  Bit Score: 128.41  E-value: 3.08e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897  93 GRLRINASAQGGRA-VAPLVLEFLNSHPQMQVDLVTEGRLVDIVAEGFDLGIRPADLVPRDMIALPLGApARHAVVAAPG 171
Cdd:cd08471    1 GLLTVTAPVLFGRLhVLPIITDFLDAYPEVSVRLLLLDRVVNLLEEGVDVAVRIGHLPDSSLVATRVGS-VRRVVCASPA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897 172 WLARHPSPLSPADLdPDHCLRVRLPNGALLRWPFEKDGRALPFEARGRLTVDDPAIARAAVLDGAGIGYFIEADVAEDIA 251
Cdd:cd08471   80 YLARHGTPKHPDDL-ADHDCIAFTGLSPAPEWRFREGGKERSVRVRPRLTVNTVEAAIAAALAGLGLTRVLSYQVAEELA 158

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 294477897 252 AGRMVRLLADWTPNRPGFSLYYPGRRNASAGFTAFLALARQR 293
Cdd:cd08471  159 AGRLQRVLEDFEPPPLPVHLVHPEGRLAPAKVRAFVDFAVPR 200
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
5-272 2.74e-35

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 129.11  E-value: 2.74e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897   5 LKALEAVQAIARRGSFRAAALDLGLSTTALSQTIARLEANLGVRLFNRTTRSVSLTEAGRDFAARTAPALAEIRAAMERV 84
Cdd:PRK10632   4 LKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQL 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897  85 RAQRDTPSGRLRINASAQGGRAV-APLVLEFLNSHPQMQVDLVTEGRLVDIVAEGFDLGIRPADLVPRDMIALPLGA-PA 162
Cdd:PRK10632  84 YAFNNTPIGTLRIGCSSTMAQNVlAGLTAKMLKEYPGLSVNLVTGIPAPDLIADGLDVVIRVGALQDSSLFSRRLGAmPM 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897 163 rhAVVAAPGWLARHPSPLSPADLD----------PDHCLRVRLPNGALLRwpfekdgralpFEARGRLTVDDPAIARAAV 232
Cdd:PRK10632 164 --VVCAAKSYLAQYGTPEKPADLSshswleysvrPDNEFELIAPEGISTR-----------LIPQGRFVTNDPQTLVRWL 230

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|.
gi 294477897 233 LDGAGIGYFIEADVAEDIAAGRMVRLLADWTPN-RPGFSLY 272
Cdd:PRK10632 231 TAGAGIAYVPLMWVIDEINRGELEILFPRYQSDpRPVYALY 271
PBP2_CrgA_like_1 cd08470
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-281 2.72e-33

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: 120.88  E-value: 2.72e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897  93 GRLRINAS-AQGGRAVAPLVLEFLNSHPQMQVDLVTEGRLVDIVAEGFDLGIRPADLVPRDMIALPLgAPARHAVVAAPG 171
Cdd:cd08470    1 GLLRITCPvAYGERFIAPLVNDFMQRYPKLEVDIELTNRVVDLVSEGFDLAIRLGRLTDSSLMARRL-ASRRHYVCASPA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897 172 WLARHPSPLSPADLDPDHCLRvrlpnGALLRWPFEKDGRALPFEARGRLTVDDPAIARAAVLDGAGIGYFIEADVAEDIA 251
Cdd:cd08470   80 YLERHGTPHSLADLDRHNCLL-----GTSDHWRFQENGRERSVRVQGRWRCNSGVALLDAALKGMGLAQLPDYYVDEHLA 154

                        170       180       190
                 ....*....|....*....|....*....|
gi 294477897 252 AGRMVRLLADWTPNRPGFSLYYPGRRNASA 281
Cdd:cd08470  155 AGRLVPVLEDYRPPDEGIWALYPHNRHLSP 184
PBP2_CrgA_like_7 cd08476
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-287 2.05e-32

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 118.50  E-value: 2.05e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897  93 GRLRINASaQGGRAVAPLVLEFLNSHPQMQVDLVTEGRLVDIVAEGFDLGIRPADLVPRDMIALPLGaPARHAVVAAPGW 172
Cdd:cd08476    1 GRLRVSLP-LVGGLLLPVLAAFMQRYPEIELDLDFSDRLVDVIDEGFDAVIRTGELPDSRLMSRRLG-SFRMVLVASPDY 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897 173 LARHPSPLSPADLDPDHCLRVRLPN-GALLRWPFEKDGRALPFEARGRLTVDDPAIARAAVLDGAGIGYFIEADVAEDIA 251
Cdd:cd08476   79 LARHGTPETPADLAEHACLRYRFPTtGKLEPWPLRGDGGDPELRLPTALVCNNIEALIEFALQGLGIACLPDFSVREALA 158

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 294477897 252 AGRMVRLLADWTPNRPGFSLYYPGRRNASAGFTAFL 287
Cdd:cd08476  159 DGRLVTVLDDYVEERGQFRLLWPSSRHLSPKLRVFV 194
PBP2_CrgA_like_3 cd08472
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-286 3.18e-31

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 115.30  E-value: 3.18e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897  93 GRLRINASAQGGRA-VAPLVLEFLNSHPQMQVDLVTEGRLVDIVAEGFDLGIRPADLVPRDMIALPLGApARHAVVAAPG 171
Cdd:cd08472    1 GRLRVDVPGSLARLlLIPALPDFLARYPDIELDLGVSDRPVDLIREGVDCVIRVGELADSSLVARRLGE-LRMVTCASPA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897 172 WLARHPSPLSPADLDPDHCLRVRLP-NGALLRWPFEKDGRALPFEARGRLTVDDPAIARAAVLDGAGIGYFIEADVAEDI 250
Cdd:cd08472   80 YLARHGTPRHPEDLERHRAVGYFSArTGRVLPWEFQRDGEEREVKLPSRVSVNDSEAYLAAALAGLGIIQVPRFMVRPHL 159

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 294477897 251 AAGRMVRLLADWTPNRPGFSLYYPGRRNASAGFTAF 286
Cdd:cd08472  160 ASGRLVEVLPDWRPPPLPVSLLYPHRRHLSPRVRVF 195
PRK09801 PRK09801
LysR family transcriptional regulator;
6-272 7.01e-30

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 114.75  E-value: 7.01e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897   6 KALEAVQAIARRGSFRAAALDLGLSTTALSQTIARLEANLGVRLFNRTTRSVSLTEAGRDFAARTAPALAEIRAAMERVR 85
Cdd:PRK09801   9 KDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVT 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897  86 AQRDTPSGRLRINASAQGGRA-VAPLVLEFLNSHPQMQVDLVTEGRLVDIVAEGFDLGIRPADLVPRDMIALPLGAPARh 164
Cdd:PRK09801  89 QIKTRPEGMIRIGCSFGFGRShIAPAITELMRNYPELQVHFELFDRQIDLVQDNIDLDIRINDEIPDYYIAHLLTKNKR- 167

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897 165 AVVAAPGWLARHPSPLSPADLDPDHCLRVRLPNGALLRWPFEKDGRALPFEARGRLTVDDPAIARAAVLDGAGIGYFIEA 244
Cdd:PRK09801 168 ILCAAPEYLQKYPQPQSLQELSRHDCLVTKERDMTHGIWELGNGQEKKSVKVSGHLSSNSGEIVLQWALEGKGIMLRSEW 247

                        250       260
                 ....*....|....*....|....*...
gi 294477897 245 DVAEDIAAGRMVRLLADWTPNRPGFSLY 272
Cdd:PRK09801 248 DVLPFLESGKLVQVLPEYAQSANIWAVY 275
PBP2_CrgA_like_10 cd08480
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-264 1.21e-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: 108.58  E-value: 1.21e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897  93 GRLRINASAQ-GGRAVAPLVLEFLNSHPQMQVDLVTEGRLVDIVAEGFDLGIRPADLVPRDMIALPLGApARHAVVAAPG 171
Cdd:cd08480    1 GRLRVNASVPfGTHFLLPLLPAFLARYPEILVDLSLTDEVVDLLAERTDVAIRVGPLPDSSLVARKLGE-SRRVIVASPS 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897 172 WLARHPSPLSPADLDPDHCLRVRLPNgALLRWPFEKDGRALPFEARGRLTVDDPAIARAAVLDGAGIGYFIEADVAEDIA 251
Cdd:cd08480   80 YLARHGTPLTPQDLARHNCLGFNFRR-ALPDWPFRDGGRIVALPVSGNILVNDGEALRRLALAGAGLARLALFHVADDIA 158

                        170
                 ....*....|...
gi 294477897 252 AGRMVRLLADWTP 264
Cdd:cd08480  159 AGRLVPVLEEYNP 171
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 14-277 2.89e-27

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 107.77  E-value: 2.89e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897  14 IARRGSFRAAALDLGLSTTALSQTIARLEANLGVRLFNRTTRSVSLTEAGRDFAARTAPALAEIRAAMERVRAQRDTPSG 93
Cdd:PRK14997  13 VVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDAIAALQVEPRG 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897  94 RLRINASAQGGRA-VAPLVLEFLNSHPQMQVDLVTEGRLVDIVAEGFDLGI--RPADLVPRDMIALPLgAPARHAVVAAP 170
Cdd:PRK14997  93 IVKLTCPVTLLHVhIGPMLAKFMARYPDVSLQLEATNRRVDVVGEGVDVAIrvRPRPFEDSDLVMRVL-ADRGHRLFASP 171

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897 171 GWLARHPSPLSPADLdpDHCLRVRLPNGA-LLRWP-FEKDGRALPFEARGRLTVDDPAIARAAVLDGAGIGYFIEADVAE 248
Cdd:PRK14997 172 DLIARMGIPSAPAEL--SHWPGLSLASGKhIHRWElYGPQGARAEVHFTPRMITTDMLALREAAMAGVGLVQLPVLMVKE 249

                        250       260
                 ....*....|....*....|....*....
gi 294477897 249 DIAAGRMVRLLADWTPNRPGFSLYYPGRR 277
Cdd:PRK14997 250 QLAAGELVAVLEEWEPRREVIHAVFPSRR 278
PBP2_CrgA_like_6 cd08475
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-264 2.63e-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: 102.63  E-value: 2.63e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897  93 GRLRINASAQGGRA-VAPLVLEFLNSHPQMQVDLVTEGRLVDIVAEGFDLGIR---PADlvPRDMIALPLGApARHAVVA 168
Cdd:cd08475    1 GRLRIDLPVAFGRLcVAPLLLELARRHPELELELSFSDRFVDLIEEGIDLAVRigeLAD--STGLVARRLGT-QRMVLCA 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897 169 APGWLARHPSPLSPADLDpDHCLRVRLPNGALLRWPF-EKDGRALPFEARGRLTVDDPAIARAAVLDGAGIGYFIEADVA 247
Cdd:cd08475   78 SPAYLARHGTPRTLEDLA-EHQCIAYGRGGQPLPWRLaDEQGRLVRFRPAPRLQFDDGEAIADAALAGLGIAQLPTWLVA 156

                        170
                 ....*....|....*..
gi 294477897 248 EDIAAGRMVRLLADWTP 264
Cdd:cd08475  157 DHLQRGELVEVLPELAP 173
PBP2_CrgA_like_4 cd08473
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 91-277 6.27e-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: 101.48  E-value: 6.27e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897  91 PSGRLRINASAQGGRA-VAPLVLEFLNSHPQMQVDLVTEGRLVDIVAEGFDLGI--RPADLVPRDMIALPLGApARHAVV 167
Cdd:cd08473    1 PRGTVRVSCPPALAQElLAPLLPRFMAAYPQVRLQLEATNRRVDLIEEGIDVALrvRFPPLEDSSLVMRVLGQ-SRQRLV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897 168 AAPGWLARHPSPLSPADLdpdhclrVRLP------NGALLRWPFE-KDGRALPFEARGRLTVDDPAIARAAVLDGAGIGY 240
Cdd:cd08473   80 ASPALLARLGRPRSPEDL-------AGLPtlslgdVDGRHSWRLEgPDGESITVRHRPRLVTDDLLTLRQAALAGVGIAL 152

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 294477897 241 FIEADVAEDIAAGRMVRLLADWTPNRPGFSLYYPGRR 277
Cdd:cd08473  153 LPDHLCREALRAGRLVRVLPDWTPPRGIVHAVFPSRR 189
PBP2_CrgA cd08478
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains ...
 91-277 1.15e-22

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: 92.79  E-value: 1.15e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897  91 PSGRLRIN-ASAQGGRAVAPLVLEFLNSHPQMQVDLVTEGRLVDIVAEGFDLGIRPADLVPRDMIALPLGAPARHaVVAA 169
Cdd:cd08478    1 PSGLLRVDaATPFVLHLLAPLIAKFRERYPDIELELVSNEGIIDLIERKTDVAIRIGELTDSTLHARPLGKSRLR-ILAS 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897 170 PGWLARHPSPLSPADLDPDHCLRVRLPnGALLRWPFeKDGRALPFEARGRLTVDDPAIARAAVLDGAGIGYFIEADVAED 249
Cdd:cd08478   80 PDYLARHGTPQSIEDLAQHQLLGFTEP-ASLNTWPI-KDADGNLLKIQPTITASSGETLRQLALSGCGIACLSDFMTDKD 157

                        170       180       190
                 ....*....|....*....|....*....|
gi 294477897 250 IAAGRMVRLLADWTPN--RPGFSLYYPGRR 277
Cdd:cd08478  158 IAEGRLIPLFAEQTSDvrQPINAVYYRNTA 187
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 92-295 3.75e-22

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: 91.58  E-value: 3.75e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897   92 SGRLRINAS-AQGGRAVAPLVLEFLNSHPQMQVDLVTEG--RLVDIVAEG-FDLGIRPADLVPRDMIALPLGaPARHAVV 167
Cdd:pfam03466   1 SGRLRIGAPpTLASYLLPPLLARFRERYPDVELELTEGNseELLDLLLEGeLDLAIRRGPPDDPGLEARPLG-EEPLVLV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897  168 AAPGWLARHPSPLSPADLDPDHCLRvrLPNGALLRWPFEKDGRALPFEARGRLTVDDPAIARAAVLDGAGIGYFIEADVA 247
Cdd:pfam03466  80 APPDHPLARGEPVSLEDLADEPLIL--LPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVA 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 294477897  248 EDIAAGRMV-RLLADWTPNRPgFSLYYPGRRNASAGFTAFLALARQRAG 295
Cdd:pfam03466 158 RELADGRLVaLPLPEPPLPRE-LYLVWRKGRPLSPAVRAFIEFLREALA 205
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 5-286 8.03e-21

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 89.90  E-value: 8.03e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897   5 LKALEAVQAIARRGSFRAAALDLGLSTTALSQTIARLEANLGVRLFNRTTRSVSLTEAGRDFAARTAPALAEIRAAMERV 84
Cdd:PRK11139   8 LNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEATRKL 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897  85 RAQRDTpsGRLRINASAQ-GGRAVAPLVLEFLNSHPQMQVDLVTEGRLVDIVAEGFDLGIRPADLVPRDMIALPLgAPAR 163
Cdd:PRK11139  88 RARSAK--GALTVSLLPSfAIQWLVPRLSSFNEAHPDIDVRLKAVDRLEDFLRDDVDVAIRYGRGNWPGLRVEKL-LDEY 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897 164 HAVVAAPGWLARHPSPLSPADLdpdhclrVRLPngaLLR------WP--FEKDGRAlPFEARGRLTVDDPAIARAAVLDG 235
Cdd:PRK11139 165 LLPVCSPALLNGGKPLKTPEDL-------ARHT---LLHddsredWRawFRAAGLD-DLNVQQGPIFSHSSMALQAAIHG 233

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|...
gi 294477897 236 AGI--GYFIEADvaEDIAAGRMVRLLADWTPNRPGFSLYYPGRRNASAGFTAF 286
Cdd:PRK11139 234 QGValGNRVLAQ--PEIEAGRLVCPFDTVLPSPNAFYLVCPDSQAELPKVAAF 284
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 5-143 2.78e-20

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: 88.44  E-value: 2.78e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897   5 LKALEAVQAIARRGSFRAAALDLGLSTTALSQTIARLEANLGVRLFNRTTRSVSLTEAGRDFAARTAPALAEIRAAMERV 84
Cdd:NF040786   3 LKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEEEF 82

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 294477897  85 RAQRDTPSGRLRINASAQGGRAVAPLVL-EFLNSHPQMQVDLVTEG--RLVDIVAEG-FDLGI 143
Cdd:NF040786  83 DRYGKESKGVLRIGASTIPGQYLLPELLkKFKEKYPNVRFKLMISDsiKVIELLLEGeVDIGF 145
PRK09791 PRK09791
LysR family transcriptional regulator;
5-137 9.53e-20

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 87.12  E-value: 9.53e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897   5 LKALEAVQAIARRGSFRAAALDLGLSTTALSQTIARLEANLGVRLFNRTTRSVSLTEAGRDFAARTAPALAEIRAAMERV 84
Cdd:PRK09791   7 IHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQEDI 86

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 294477897  85 RAQRDTPSGRLRINASAQGGRAVAPLVL-EFLNSHPQMQVDlVTEGRLVDIVAE 137
Cdd:PRK09791  87 RQRQGQLAGQINIGMGASIARSLMPAVIsRFHQQHPQVKVR-IMEGQLVSMINE 139
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
5-64 2.85e-19

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 79.35  E-value: 2.85e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897    5 LKALEAVQAIARRGSFRAAALDLGLSTTALSQTIARLEANLGVRLFNRTTRSVSLTEAGR 64
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 113-286 1.21e-14

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


Pssm-ID: 176123 [Multi-domain]  Cd Length: 194  Bit Score: 70.69  E-value: 1.21e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897 113 EFLNSHPQMQVDLVTEGRLVDIVAEGFDLGIRPADLVPRDMIALPLgAPARHAVVAAPGWLARHPsPLSPADLDPDHCLR 192
Cdd:cd08432   21 RFQARHPDIDLRLSTSDRLVDFAREGIDLAIRYGDGDWPGLEAERL-MDEELVPVCSPALLAGLP-LLSPADLARHTLLH 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897 193 VRLPNGAllRWPFEKDGRALPFEARGRLTVDDPAIARAAVLDGAGIGYFIEADVAEDIAAGRMVRLLADWTPNRPGFSLY 272
Cdd:cd08432   99 DATRPEA--WQWWLWAAGVADVDARRGPRFDDSSLALQAAVAGLGVALAPRALVADDLAAGRLVRPFDLPLPSGGAYYLV 176

                        170
                 ....*....|....
gi 294477897 273 YPGRRNASAGFTAF 286
Cdd:cd08432  177 YPPGRAESPAVAAF 190
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
5-143 3.88e-14

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 71.19  E-value: 3.88e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897   5 LKALEAVQAIARRGSFRAAALDLGLSTTALSQTIARLEANLGVRLFNRTTRSVSLTEAGRDFAARTAPALAEIRAAMERV 84
Cdd:PRK10086  16 LSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLDTLNQEILDI 95

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 294477897  85 RAQRdtPSGRLRINAS---AQGgrAVAPLVLEFLNSHPQMQVDLVTEGRLVDIVAEGFDLGI 143
Cdd:PRK10086  96 KNQE--LSGTLTVYSRpsiAQC--WLVPRLADFTRRYPSISLTILTGNENVNFQRAGIDLAI 153
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 13-186 1.28e-13

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 69.60  E-value: 1.28e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897  13 AIARRGSFRAAALDLGLSTTALSQTIARLEANLGVRLFNRTTRSVSLTEAGRDFAARTAPALAEIRAAMERVRAQRDTPS 92
Cdd:PRK11242  11 AVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRRAIHDVADLSR 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897  93 GRLRINASAQ-GGRAVAPLVLEFLNSHPQMQVDL--VTEGRLVDIVAEG-FDLGIRPADLVPRDMIALPLGAPARHAVVA 168
Cdd:PRK11242  91 GSLRLAMTPTfTAYLIGPLIDAFHARYPGITLTIreMSQERIEALLADDeLDVGIAFAPVHSPEIEAQPLFTETLALVVG 170

                        170
                 ....*....|....*...
gi 294477897 169 APGWLARHPSPLSPADLD 186
Cdd:PRK11242 171 RHHPLAARRKALTLDELA 188
rbcR CHL00180
LysR transcriptional regulator; Provisional
 5-125 4.02e-13

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 68.51  E-value: 4.02e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897   5 LKALEAVQAIARRGSFRAAALDLGLSTTALSQTIARLEANLGVRLFNRTTRSVSLTEAGR---DFAARTApALAEiraam 81
Cdd:CHL00180   7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGElllRYGNRIL-ALCE----- 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 294477897  82 ERVRA---QRDTPSGRLRINASAQGGRAVAPLVLE-FLNSHPQMQVDL 125
Cdd:CHL00180  81 ETCRAledLKNLQRGTLIIGASQTTGTYLMPRLIGlFRQRYPQINVQL 128
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
6-185 5.09e-13

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 67.91  E-value: 5.09e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897   6 KALEAVQAIARRGSFRAAALDLGLSTTALSQTIARLEANLGVRLFNRTTRSVSLTEAGRDFAARTAPALAEIRAAMERVR 85
Cdd:PRK10094   5 ETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPSELQ 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897  86 AQRD--TPSGRLRINASAQGGRAVAPLvLEFLN---SHPQMQVD-LVTEGRLVDIVAEGFDL--GIRPADLVPRDMIALP 157
Cdd:PRK10094  85 QVNDgvERQVNIVINNLLYNPQAVAQL-LAWLNeryPFTQFHISrQIYMGVWDSLLYEGFSLaiGVTGTEALANTFSLDP 163

                        170       180
                 ....*....|....*....|....*...
gi 294477897 158 LGAPARHAVVAAPGWLARHPSPLSPADL 185
Cdd:PRK10094 164 LGSVQWRFVMAADHPLANVEEPLTEAQL 191
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 7-87 6.35e-12

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 64.58  E-value: 6.35e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897   7 ALEAVQAIARRGSFRAAALDLGLSTTALSQTIARLEANLGVRLFNRTTRSVSLTEAGRDFaartapaLAEIRAA---MER 83
Cdd:PRK11074   6 SLEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWF-------VKEARSVikkMQE 78


                 ....
gi 294477897  84 VRAQ 87
Cdd:PRK11074  79 TRRQ 82
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 1-127 8.99e-11

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 61.32  E-value: 8.99e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897   1 MEagLKALEAVQAIARRGSFRAAALDLGLSTTALSQTIARLEANLGVRLFNRTTRSVSLTEAGRDF--AARTAPALAEIR 78
Cdd:PRK09906   1 ME--LRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFlqDARAILEQAEKA 78

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 294477897  79 AAMERVRAQRDTpsgRLRINASAQGGRAVAPLVL-EFLNSHPQMQVDLVT 127
Cdd:PRK09906  79 KLRARKIVQEDR---QLTIGFVPSAEVNLLPKVLpMFRLRHPDTLIELVS 125
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
29-127 1.16e-10

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 60.60  E-value: 1.16e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897  29 LSTTALSQTIARLEANLGVRLFNRTTRSVSLTEAG---RDFAARTapaLAEIRAAMERVRAQRDTPSGRLRINASAQGGR 105
Cdd:PRK11716   3 VSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGeelRPFAQQT---LLQWQQLRHTLDQQGPSLSGELSLFCSVTAAY 79

                         90       100
                 ....*....|....*....|...
gi 294477897 106 AVAPLVLE-FLNSHPQMQVDLVT 127
Cdd:PRK11716  80 SHLPPILDrFRAEHPLVEIKLTT 102
PRK09986 PRK09986
LysR family transcriptional regulator;
5-125 1.55e-09

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 57.81  E-value: 1.55e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897   5 LKALEAVQAIARRGSFRAAALDLGLSTTALSQTIARLEANLGVRLFNRTTRSVSLTEAGRDFAARTAPALAEIRAAMERV 84
Cdd:PRK09986   9 LKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLARV 88

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 294477897  85 RAQRDTPSGRLRIN--ASAQGGRaVAPLVLEFLNSHPQMQVDL 125
Cdd:PRK09986  89 EQIGRGEAGRIEIGivGTALWGR-LRPAMRHFLKENPNVEWLL 130
PRK10341 PRK10341
transcriptional regulator TdcA;
6-158 5.11e-09

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 56.41  E-value: 5.11e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897   6 KALEAVQAIARRGSFRAAALDLGLSTTALSQTIARLEANLGVRLFNRTTRSVSLTEAGRDFAARTAPALAEIRAAMERVR 85
Cdd:PRK10341  10 QHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEIN 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897  86 AQRDTPSGRLRINASAQGGRAVAPLVL-EFLNSHPQMQVDLVtEGRLVDI---VAEG---FDLGIRPADLVPRDMIALPL 158
Cdd:PRK10341  90 GMSSEAVVDVSFGFPSLIGFTFMSDMInKFKEVFPKAQVSMY-EAQLSSFlpaIRDGrldFAIGTLSNEMKLQDLHVEPL 168
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 94-290 8.34e-08

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: 51.45  E-value: 8.34e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897  94 RLRINAS-AQGGRAVAPLVLEFLNSHPQMQVDLVTEG--RLVDIVAEG-FDLGIRPADLVPRDMIALPLGApARHAVVAA 169
Cdd:cd05466    1 TLRIGASpSIAAYLLPPLLAAFRQRYPGVELSLVEGGssELLEALLEGeLDLAIVALPVDDPGLESEPLFE-EPLVLVVP 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897 170 PGWLARHPSPLSPADLDpDHCLrVRLPNGALLRWPFEKDGRALPFEARGRLTVDDPAIARAAVLDGAGIGyFIEADVAED 249
Cdd:cd05466   80 PDHPLAKRKSVTLADLA-DEPL-ILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIA-LLPESAVEE 156

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 294477897 250 IAAGRMVRLLADWTPNRPGFSLYYPGRRNASAGFTAFLALA 290
Cdd:cd05466  157 LADGGLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 1-112 2.01e-07

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 51.23  E-value: 2.01e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897   1 MEAGLKALEAVQAIARRGSFRAAALDLGLSTTALSQTIARLEANLGVRLFNRTTRSVSLTEAGRDFAARtAPALAEIRAA 80
Cdd:PRK10837   1 MHITLRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPR-ALALLEQAVE 79

                         90       100       110
                 ....*....|....*....|....*....|..
gi 294477897  81 MERVrAQRDtpSGRLRINASAQGGRAVAPLVL 112
Cdd:PRK10837  80 IEQL-FRED--NGALRIYASSTIGNYILPAMI 108
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
5-125 3.47e-07

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 50.79  E-value: 3.47e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897   5 LKALEAVQAIARRGSFRAAALDLGLSTTALSQTIARLEANLGVRLFNRTTRSVSLTEAGRDFAARTAPALAEIRAAMERV 84
Cdd:PRK15421   4 VKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQAC 83

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 294477897  85 RAQRDTpsgRLRINASAQGG-RAVAPLVLEFLNSHPQMQVDL 125
Cdd:PRK15421  84 NEPQQT---RLRIAIECHSCiQWLTPALENFHKNWPQVEMDF 122
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
8-64 6.84e-07

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 49.58  E-value: 6.84e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 294477897   8 LEAVQAIARRGSFRAAALDLGLSTTALSQTIARLEANLGVRLFNRtTRSVSLTEAGR 64
Cdd:PRK13348   7 LEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQ 62
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
19-261 8.24e-07

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 49.67  E-value: 8.24e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897  19 SFRAAALDLGLSTTALSQTIARLEANLGVRLFNRTTRSVSLTEAGRDFAARTAPALAEIRAAMERVRAQRDTPSGRLRIN 98
Cdd:PRK10082  27 NFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESNLAELRGGSDYAQRKIKIA 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897  99 ASAQGGRAVAPLVLEFLNSHPQMQVDLVTEGRLVDIVAEG---FDLGIRPADLV--PRDMIAL------PLGAPARHAvv 167
Cdd:PRK10082 107 AAHSLSLGLLPSIISQMPPLFTWAIEAIDVDEAVDKLREGqsdCIFSFHDEDLLeaPFDHIRLfesqlfPVCASDEHG-- 184

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897 168 AAPGWLARHPSPLspadLD-PDHCLRVRLPNGALLRwpfekdGRALPFEARGRLTVDDpaIARAAVLDGAGIGYFIEADV 246
Cdd:PRK10082 185 EALFNLAQPHFPL----LNySRNSYMGRLINRTLTR------HSELSFSTFFVSSMSE--LLKQVALDGCGIAWLPEYAI 252

                        250
                 ....*....|....*
gi 294477897 247 AEDIAAGRMVRLLAD 261
Cdd:PRK10082 253 QQEIRSGQLVVLNRD 267
PBP2_HvrB cd08483
The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an ...
 114-278 1.05e-05

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


Pssm-ID: 176172 [Multi-domain]  Cd Length: 190  Bit Score: 45.41  E-value: 1.05e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897 114 FLNSHPQMQVDLVTEGRLVDIVAEGFDLGIRPADLVPRDMIALPLGAPArHAVVAAPGWLARHPSpLSPADLDPDHCLRV 193
Cdd:cd08483   22 FWAKHPEIELSLLPSADLVDLRPDGIDVAIRYGNGDWPGLESEPLTAAP-FVVVAAPGLLGDRKV-DSLADLAGLPWLQE 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897 194 RLPNGALLrWpFEKDGraLPFEARGRLTVDDPAIARAAVLDGAGIGYFIEADVAEDIAAGRMVRLLADWTPNRPGFSLYY 273
Cdd:cd08483  100 RGTNEQRV-W-LASMG--VVPDLERGVTFLPGQLVLEAARAGLGLSIQARALVEPDIAAGRLTVLFEEEEEGLGYHIVTR 175


                 ....*
gi 294477897 274 PGRRN 278
Cdd:cd08483  176 PGVLR 180
PRK12680 PRK12680
LysR family transcriptional regulator;
23-167 3.31e-05

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 44.61  E-value: 3.31e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897  23 AALDLGLSTTALSQTIARLEANLGVRLFNRTTRSV-SLTEAGRDFAARTAPALAEIRAAMERVRAQRDTPSGRLRINASA 101
Cdd:PRK12680  22 AAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLeSVTPAGVEVIERARAVLSEANNIRTYAANQRRESQGQLTLTTTH 101

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 294477897 102 QGGRAV-APLVLEFLNSHPQMQVDL--VTEGRLVDIVAEG-FDLGI-RPADLVPRDMIALPLGAPARHAVV 167
Cdd:PRK12680 102 TQARFVlPPAVAQIKQAYPQVSVHLqqAAESAALDLLGQGdADIAIvSTAGGEPSAGIAVPLYRWRRLVVV 172
PBP2_LTTR_beta_lactamase cd08484
The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase ...
 109-257 3.63e-05

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


Pssm-ID: 176173 [Multi-domain]  Cd Length: 189  Bit Score: 43.51  E-value: 3.63e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897 109 PLVLEFLNSHPQMQVDLVTEGRLVDIVAEGFDLGIRPADLVPRDMIALPL-GAPArhAVVAAPGwLARHPSplSPADldp 187
Cdd:cd08484   17 PRLAEFRQLHPFIDLRLSTNNNRVDIAAEGLDFAIRFGEGAWPGTDATRLfEAPL--SPLCTPE-LARRLS--EPAD--- 88

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 294477897 188 dhclrvrLPNGALLR------WP--FEKDGrALPFEARGrlTVDDPAIARA-AVLDGAGIGYFIEADVAEDIAAGRMVR 257
Cdd:cd08484   89 -------LANETLLRsyradeWPqwFEAAG-VPPPPING--PVFDSSLLMVeAALQGAGVALAPPSMFSRELASGALVQ 157
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 8-97 3.73e-05

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 44.64  E-value: 3.73e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897   8 LEAVQAIARRGSFRAAALDLGLSTTALSQTIARLEANLGVRLFNRTTRSVSLTEAGRDFAARTAPALAEIRAAMERVRAQ 87
Cdd:PRK11151   6 LEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVLKEMASQQ 85

                         90
                 ....*....|
gi 294477897  88 RDTPSGRLRI 97
Cdd:PRK11151  86 GETMSGPLHI 95
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
6-64 5.92e-05

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 43.61  E-value: 5.92e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 294477897   6 KALEAVQAIARRGSFRAAALDLGLSTTALSQTIARLEANLGVRLFNRtTRSVSLTEAGR 64
Cdd:PRK03635   5 KQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQ 62
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 5-185 1.12e-04

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 43.06  E-value: 1.12e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897   5 LKALEAVQAIARRG-SFRAAALDLGLSTTALSQTIARLEANLGVRLFNRT-TRSVSLTEAGRDFAARTAPALAEIRaAME 82
Cdd:PRK12682   3 LQQLRFVREAVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHgKRLKGLTEPGKAVLDVIERILREVG-NIK 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897  83 RVRAQRDTP-SGRLRINASAQGGRAVAPLVL-EFLNSHPQMQVDL--VTEGRLVDIVAEGF-DLGIRPADLVP-RDMIAL 156
Cdd:PRK12682  82 RIGDDFSNQdSGTLTIATTHTQARYVLPRVVaAFRKRYPKVNLSLhqGSPDEIARMVISGEaDIGIATESLADdPDLATL 161

                        170       180
                 ....*....|....*....|....*....
gi 294477897 157 PLgAPARHAVVAAPGWLARHPSPLSPADL 185
Cdd:PRK12682 162 PC-YDWQHAVIVPPDHPLAQEERITLEDL 189
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
5-177 1.23e-03

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 39.96  E-value: 1.23e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897   5 LKALEAVQAIARRG-SFRAAALDLGLSTTALSQTIARLEANLGVRLFNRT-TRSVSLTEAGRDFAARTAPALAEI----R 78
Cdd:PRK12684   3 LHQLRFVREAVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHgKRLRGLTEPGRIILASVERILQEVenlkR 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897  79 AAMErvRAQRDTpsGRLRINASAQGGRAVAPLVL-EFLNSHPQMQVDLV--TEGRLVDIVAEG-FDLGI--RPADLVPrD 152
Cdd:PRK12684  83 VGKE--FAAQDQ--GNLTIATTHTQARYALPAAIkEFKKRYPKVRLSILqgSPTQIAEMVLHGqADLAIatEAIADYK-E 157

                        170       180
                 ....*....|....*....|....*
gi 294477897 153 MIALPlGAPARHAVVAAPGwlarHP 177
Cdd:PRK12684 158 LVSLP-CYQWNHCVVVPPD----HP 177
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 18-64 1.34e-03

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 39.67  E-value: 1.34e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 294477897  18 GSFRAAALDLGLSTTALSQTIARLEANLGVRLFNRTTRSVSLTEAGR 64
Cdd:PRK11233  16 GSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGK 62
PBP2_HupR cd08431
The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which ...
 109-280 2.79e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which regulates expression of the heme uptake receptor HupA; contains the type 2 periplasmic binding fold; HupR, a member of the LysR family, activates hupA transcription under low-iron conditions in the presence of hemin. The expression of many iron-uptake genes, such as hupA, is regulated at the transcriptional level by iron and an iron-binding repressor protein called Fur (ferric uptake regulation). Under iron-abundant conditions with heme, the active Fur repressor protein represses transcription of the iron-uptake gene hupA, and prevents transcriptional activation via HupR. Under low-iron conditions with heme, the Fur repressor is inactive and transcription of the hupA is allowed. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176122 [Multi-domain]  Cd Length: 195  Bit Score: 38.02  E-value: 2.79e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897 109 PLVLEFLNSHPQMQVDLVTE---GRLVDIVAEGFDLGIRPADLVPRDMIAL-PLGAPARHAVVAAPGWLARHPSPLSPAD 184
Cdd:cd08431   17 PLIAEFYQLNKATRIRLSEEvlgGTWDALASGRADLVIGATGELPPGGVKTrPLGEVEFVFAVAPNHPLAKLDGPLDASA 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897 185 LDpDHCLRVrlpngallrwpFEKDGRALP------FEARGRLTVDDPAIARAAVLDGAGIGYFIEADVAEDIAAGRMVrL 258
Cdd:cd08431   97 IK-QYPAIV-----------VADTSRNLPprssglLEGQDRIRVPTMQAKIDAQVLGLGVGYLPRHLAKPELASGELV-E 163

                        170       180
                 ....*....|....*....|..
gi 294477897 259 LADWTPNRPGfSLYYPGRRNAS 280
Cdd:cd08431  164 KALEDPRPPQ-ELFLAWRKDQR 184
PBP2_GcdR_like cd08481
The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, ...
 103-286 6.79e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, contains the type 2 periplasmic binding fold; GcdR is involved in the glutaconate/glutarate-specific activation of the Pg promoter driving expression of a glutaryl-CoA dehydrogenase-encoding gene (gcdH). The GcdH protein is essential for the anaerobic catabolism of many aromatic compounds and some alicyclic and dicarboxylic acids. The structural topology of this substrate-binding domain is most similar to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176170 [Multi-domain]  Cd Length: 194  Bit Score: 36.89  E-value: 6.79e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897 103 GGRAVAPLVLEFLNSHPQMQVDLVTEGRLVDIVAEGFDLGIRPADLVPRDMIALPLGAPARhAVVAAPGWLARHPsPLSP 182
Cdd:cd08481   11 GTRWLIPRLPDFLARHPDITVNLVTRDEPFDFSQGSFDAAIHFGDPVWPGAESEYLMDEEV-VPVCSPALLAGRA-LAAP 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294477897 183 ADLdpdhclrVRLPngaLLR-------WP--FEKDGRALPFEARGRLtVDDPAIARAAVLDGAGIGYFIEADVAEDIAAG 253
Cdd:cd08481   89 ADL-------AHLP---LLQqttrpeaWRdwFEEVGLEVPTAYRGMR-FEQFSMLAQAAVAGLGVALLPRFLIEEELARG 157

                        170       180       190
                 ....*....|....*....|....*....|...
gi 294477897 254 RMVRLLADWTPNRPGFSLYYPGRRNASAGFTAF 286
Cdd:cd08481  158 RLVVPFNLPLTSDKAYYLVYPEDKAESPPVQAF 190
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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