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Conserved domains on  [gi|745759150|ref|WP_039058362|]
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LysR family transcriptional regulator [Enterobacter sp. Bisph1]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 10444297)

LysR family transcriptional regulator containing an N-terminal helix-turn-helix DNA-binding domain and a C-terminal substrate binding domain; similar to CbbR, AmpR, GalR, YhaJ, and NmcR, which are positive transcriptional regulators of various genes

Gene Ontology:  GO:0003677|GO:0003700|GO:0001216
PubMed:  8257110|19047729
SCOP:  4000316

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 ...
 92-292 7.13e-87

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: 258.16  E-value: 7.13e-87
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150  92 PSGTLRLNVPQNIGPLFLDDLLVRFLVRYPLIRMEVASEARAIDIVAEGYDAGVRLAEAVPQDMIAVPLTADIRMRVVAT 171
Cdd:cd08474    1 PAGTLRINAPRVAARLLLAPLLARFLARYPDIRLELVVDDGLVDIVAEGFDAGIRLGESVEKDMVAVPLGPPLRMAVVAS 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150 172 PQWFAEHGTPQVPEDLYQHHGICMRM-SNGSNYRWELARRGQQFDIAVPPRLATSDLFTSIAAVRAGLGVGFLPGFYIEE 250
Cdd:cd08474   81 PAYLARHGTPEHPRDLLNHRCIRYRFpTSGALYRWEFERGGRELEVDVEGPLILNDSDLMLDAALDGLGIAYLFEDLVAE 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 745759150 251 DLRSGALVSVLDEWTQPFKGLCLYYPGHRHIPAALRTFIAFI 292
Cdd:cd08474  161 HLASGRLVRVLEDWSPPFPGGYLYYPSRRRVPPALRAFIDFL 202
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
9-65 1.31e-18

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


:

Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 77.81  E-value: 1.31e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 745759150    9 LEVVMAVMRRGSFRGAAQALSMSPTAVSNAIAGLESRLAIRLFHRTTRSVALTEAGQ 65
Cdd:pfam00126   4 LRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
 
Name Accession Description Interval E-value
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-292 7.13e-87

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: 258.16  E-value: 7.13e-87
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150  92 PSGTLRLNVPQNIGPLFLDDLLVRFLVRYPLIRMEVASEARAIDIVAEGYDAGVRLAEAVPQDMIAVPLTADIRMRVVAT 171
Cdd:cd08474    1 PAGTLRINAPRVAARLLLAPLLARFLARYPDIRLELVVDDGLVDIVAEGFDAGIRLGESVEKDMVAVPLGPPLRMAVVAS 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150 172 PQWFAEHGTPQVPEDLYQHHGICMRM-SNGSNYRWELARRGQQFDIAVPPRLATSDLFTSIAAVRAGLGVGFLPGFYIEE 250
Cdd:cd08474   81 PAYLARHGTPEHPRDLLNHRCIRYRFpTSGALYRWEFERGGRELEVDVEGPLILNDSDLMLDAALDGLGIAYLFEDLVAE 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 745759150 251 DLRSGALVSVLDEWTQPFKGLCLYYPGHRHIPAALRTFIAFI 292
Cdd:cd08474  161 HLASGRLVRVLEDWSPPFPGGYLYYPSRRRVPPALRAFIDFL 202
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
9-294 6.27e-56

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 181.22  E-value: 6.27e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150   9 LEVVMAVMRRGSFRGAAQALSMSPTAVSNAIAGLESRLAIRLFHRTTRSVALTEAGQRFVARIGPALREIQQAQEEIHSL 88
Cdd:COG0583    6 LRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAELRAL 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150  89 ADEPSGTLRLNVPQNIGPLFLDDLLVRFLVRYPLIRMEV--ASEARAID-IVAEGYDAGVRLAEAVPQDMIAVPLtADIR 165
Cdd:COG0583   86 RGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELreGNSDRLVDaLLEGELDLAIRLGPPPDPGLVARPL-GEER 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150 166 MRVVATPQwfaehgtpqvpedlyqhhgicmrmsngsnyrWELARRGQQFDiavpprlatsDLFTSIAAVRAGLGVGFLPG 245
Cdd:COG0583  165 LVLVASPD-------------------------------HPLARRAPLVN----------SLEALLAAVAAGLGIALLPR 203

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*....
gi 745759150 246 FYIEEDLRSGALVSVLDEWTQPFKGLCLYYPGHRHIPAALRTFIAFIRA 294
Cdd:COG0583  204 FLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLRE 252
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 15-292 9.19e-45

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 153.99  E-value: 9.19e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150  15 VMRRGSFRGAAQALSMSPTAVSNAIAGLESRLAIRLFHRTTRSVALTEAGQRFVARIGPALREIQQAQEEIHSLADEPSG 94
Cdd:PRK14997  13 VVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDAIAALQVEPRG 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150  95 TLRLNVPQNIGPLFLDDLLVRFLVRYPLIRMEVASEARAIDIVAEGYDAGVRLAEAVPQDM-IAVPLTADIRMRVVATPQ 173
Cdd:PRK14997  93 IVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLEATNRRVDVVGEGVDVAIRVRPRPFEDSdLVMRVLADRGHRLFASPD 172

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150 174 WFAEHGTPQVPEDLYQHHGICMrMSNGSNYRWEL-ARRGQQFDIAVPPRLATSDLFTSIAAVRAGLGVGFLPGFYIEEDL 252
Cdd:PRK14997 173 LIARMGIPSAPAELSHWPGLSL-ASGKHIHRWELyGPQGARAEVHFTPRMITTDMLALREAAMAGVGLVQLPVLMVKEQL 251

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|
gi 745759150 253 RSGALVSVLDEWTQPFKGLCLYYPGHRHIPAALRTFIAFI 292
Cdd:PRK14997 252 AAGELVAVLEEWEPRREVIHAVFPSRRGLLPSVRALVDFL 291
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 93-294 4.59e-30

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


Pssm-ID: 460931 [Multi-domain]  Cd Length: 205  Bit Score: 112.38  E-value: 4.59e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150   93 SGTLRLNVPQNIGPLFLDDLLVRFLVRYPLIRMEV--ASEARAIDIVAEG-YDAGVRLAEAVPQDMIAVPLtADIRMRVV 169
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELteGNSEELLDLLLEGeLDLAIRRGPPDDPGLEARPL-GEEPLVLV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150  170 ATPQWFAEHGTPQVPEDLYQHhgICMRMSNGSNYRWELARRGQQFDIAVPPRLATSDLFTSIAAVRAGLGVGFLPGFYIE 249
Cdd:pfam03466  80 APPDHPLARGEPVSLEDLADE--PLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVA 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 745759150  250 EDLRSGALVSVLDEWTQPFKGLCLYYPGHRHIPAALRTFIAFIRA 294
Cdd:pfam03466 158 RELADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLRE 202
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 6-293 6.02e-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: 87.67  E-value: 6.02e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150   6 LIELEVVMAVMRRGSFRGAAQALSMSPTAVSNAIAGLESRLAIRLFHRTTRSVALTEAGQRFVARIGPALREIQQAQEEI 85
Cdd:NF040786   3 LKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEEEF 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150  86 HSLADEPSGTLRL---NVPqniGPLFLDDLLVRFLVRYPLIRMEV--ASEARAIDIVAEG-YD---AGVRLAEAvpqDMI 156
Cdd:NF040786  83 DRYGKESKGVLRIgasTIP---GQYLLPELLKKFKEKYPNVRFKLmiSDSIKVIELLLEGeVDigfTGTKLEKK---RLV 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150 157 AVPLTADiRMrVVATP---QWFAEHGTPQVPEDLYQHHGIcMRmSNGSNYRWE----LARRG---QQFDIAvpprLATSD 226
Cdd:NF040786 157 YTPFYKD-RL-VLITPngtEKYRMLKEEISISELQKEPFI-MR-EEGSGTRKEaekaLKSLGislEDLNVV----ASLGS 228

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 745759150 227 LFTSIAAVRAGLGVGFLPGFYIEEDLRSGALVSVldewtqPFKGLclyyPGHRHI----------PAALRTFIAFIR 293
Cdd:NF040786 229 TEAIKQSVEAGLGISVISELAAEKEVERGRVLIF------PIPGL----PKNRDFylvynknrqlSPTAEAFLQFVK 295
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
9-65 1.31e-18

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 77.81  E-value: 1.31e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 745759150    9 LEVVMAVMRRGSFRGAAQALSMSPTAVSNAIAGLESRLAIRLFHRTTRSVALTEAGQ 65
Cdd:pfam00126   4 LRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 9-261 2.16e-13

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


Pssm-ID: 274509 [Multi-domain]  Cd Length: 292  Bit Score: 68.79  E-value: 2.16e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150    9 LEVVMAVMRRGSFRGAAQALSMSPTAVSNAIAGLESRLAIRLFHRtTRSVALTEAGQRFVARigpaLREIQQAQEEI--H 86
Cdd:TIGR03298   6 LAALAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVR-TQPCRATEAGQRLLRH----ARQVRLLEAELlaE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150   87 SLADEPSGTLRLNVPQN---IGPLFLdDLLVRFLVRYPLiRMEVASE--ARAIDIVAEGYDAGVRLAEAVP-QDMIAVPL 160
Cdd:TIGR03298  81 LPGLAPGAPTRLTIAVNadsLATWFL-PALAPVLAREGV-LLDLVVEdqDHTAELLRSGEVLGAVTTEAKPvPGCRVVPL 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150  161 TAdIRMRVVATP----QWFAEHGTpqvPEDLYQHHGICMRMSNGSNYRWeLARRGQQfdIAVPPR--LATSDLFtsIAAV 234
Cdd:TIGR03298 159 GA-MRYLAVASPafaaRYFPDGVT---AAALARAPVIVFNRKDDLQDRF-LRRLFGL--PVSPPRhyVPSSEGF--VDAA 229

                         250       260
                  ....*....|....*....|....*..
gi 745759150  235 RAGLGVGFLPGFYIEEDLRSGALVSVL 261
Cdd:TIGR03298 230 RAGLGWGMVPELQAEPHLAAGRLVELA 256
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 8-109 1.96e-06

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 48.49  E-value: 1.96e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150   8 ELEVVMAVMRRGSFRGAAQALSMSPTAVSNAIAGLESRLAIRLFHRTTRSVALTEAGQRFVARIGPALREIQQAQEEIHS 87
Cdd:PRK11151   5 DLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVLKEMASQ 84

                         90       100
                 ....*....|....*....|..
gi 745759150  88 LADEPSGTLRLNVPQNIGPLFL 109
Cdd:PRK11151  85 QGETMSGPLHIGLIPTVGPYLL 106
 
Name Accession Description Interval E-value
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-292 7.13e-87

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: 258.16  E-value: 7.13e-87
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150  92 PSGTLRLNVPQNIGPLFLDDLLVRFLVRYPLIRMEVASEARAIDIVAEGYDAGVRLAEAVPQDMIAVPLTADIRMRVVAT 171
Cdd:cd08474    1 PAGTLRINAPRVAARLLLAPLLARFLARYPDIRLELVVDDGLVDIVAEGFDAGIRLGESVEKDMVAVPLGPPLRMAVVAS 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150 172 PQWFAEHGTPQVPEDLYQHHGICMRM-SNGSNYRWELARRGQQFDIAVPPRLATSDLFTSIAAVRAGLGVGFLPGFYIEE 250
Cdd:cd08474   81 PAYLARHGTPEHPRDLLNHRCIRYRFpTSGALYRWEFERGGRELEVDVEGPLILNDSDLMLDAALDGLGIAYLFEDLVAE 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 745759150 251 DLRSGALVSVLDEWTQPFKGLCLYYPGHRHIPAALRTFIAFI 292
Cdd:cd08474  161 HLASGRLVRVLEDWSPPFPGGYLYYPSRRRVPPALRAFIDFL 202
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 94-292 1.07e-65

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: 204.21  E-value: 1.07e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150  94 GTLRLNVPQNIGPLFLDDLLVRFLVRYPLIRMEVASEARAIDIVAEGYDAGVRLAEAVPQDMIAVPLtADIRMRVVATPQ 173
Cdd:cd08422    1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRL-GPVRRVLVASPA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150 174 WFAEHGTPQVPEDLYQHHGICMRmSNGSNYRWELARRGQQFDIAVPPRLATSDLFTSIAAVRAGLGVGFLPGFYIEEDLR 253
Cdd:cd08422   80 YLARHGTPQTPEDLARHRCLGYR-LPGRPLRWRFRRGGGEVEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAEDLA 158

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 745759150 254 SGALVSVLDEWTQPFKGLCLYYPGHRHIPAALRTFIAFI 292
Cdd:cd08422  159 SGRLVRVLPDWRPPPLPIYAVYPSRRHLPAKVRAFIDFL 197
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
9-294 6.27e-56

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 181.22  E-value: 6.27e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150   9 LEVVMAVMRRGSFRGAAQALSMSPTAVSNAIAGLESRLAIRLFHRTTRSVALTEAGQRFVARIGPALREIQQAQEEIHSL 88
Cdd:COG0583    6 LRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAELRAL 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150  89 ADEPSGTLRLNVPQNIGPLFLDDLLVRFLVRYPLIRMEV--ASEARAID-IVAEGYDAGVRLAEAVPQDMIAVPLtADIR 165
Cdd:COG0583   86 RGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELreGNSDRLVDaLLEGELDLAIRLGPPPDPGLVARPL-GEER 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150 166 MRVVATPQwfaehgtpqvpedlyqhhgicmrmsngsnyrWELARRGQQFDiavpprlatsDLFTSIAAVRAGLGVGFLPG 245
Cdd:COG0583  165 LVLVASPD-------------------------------HPLARRAPLVN----------SLEALLAAVAAGLGIALLPR 203

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*....
gi 745759150 246 FYIEEDLRSGALVSVLDEWTQPFKGLCLYYPGHRHIPAALRTFIAFIRA 294
Cdd:COG0583  204 FLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLRE 252
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 15-292 9.19e-45

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 153.99  E-value: 9.19e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150  15 VMRRGSFRGAAQALSMSPTAVSNAIAGLESRLAIRLFHRTTRSVALTEAGQRFVARIGPALREIQQAQEEIHSLADEPSG 94
Cdd:PRK14997  13 VVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDAIAALQVEPRG 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150  95 TLRLNVPQNIGPLFLDDLLVRFLVRYPLIRMEVASEARAIDIVAEGYDAGVRLAEAVPQDM-IAVPLTADIRMRVVATPQ 173
Cdd:PRK14997  93 IVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLEATNRRVDVVGEGVDVAIRVRPRPFEDSdLVMRVLADRGHRLFASPD 172

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150 174 WFAEHGTPQVPEDLYQHHGICMrMSNGSNYRWEL-ARRGQQFDIAVPPRLATSDLFTSIAAVRAGLGVGFLPGFYIEEDL 252
Cdd:PRK14997 173 LIARMGIPSAPAELSHWPGLSL-ASGKHIHRWELyGPQGARAEVHFTPRMITTDMLALREAAMAGVGLVQLPVLMVKEQL 251

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|
gi 745759150 253 RSGALVSVLDEWTQPFKGLCLYYPGHRHIPAALRTFIAFI 292
Cdd:PRK14997 252 AAGELVAVLEEWEPRREVIHAVFPSRRGLLPSVRALVDFL 291
PBP2_CrgA_like_3 cd08472
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-289 1.02e-37

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 132.25  E-value: 1.02e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150  94 GTLRLNVPQNIGPLFLDDLLVRFLVRYPLIRMEVASEARAIDIVAEGYDAGVRLAEAVPQDMIAVPLtADIRMRVVATPQ 173
Cdd:cd08472    1 GRLRVDVPGSLARLLLIPALPDFLARYPDIELDLGVSDRPVDLIREGVDCVIRVGELADSSLVARRL-GELRMVTCASPA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150 174 WFAEHGTPQVPEDLYQHHGICMRM-SNGSNYRWELARRGQQFDIAVPPRLATSDLFTSIAAVRAGLGVGFLPGFYIEEDL 252
Cdd:cd08472   80 YLARHGTPRHPEDLERHRAVGYFSaRTGRVLPWEFQRDGEEREVKLPSRVSVNDSEAYLAAALAGLGIIQVPRFMVRPHL 159

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 745759150 253 RSGALVSVLDEWTQPFKGLCLYYPGHRHIPAALRTFI 289
Cdd:cd08472  160 ASGRLVEVLPDWRPPPLPVSLLYPHRRHLSPRVRVFV 196
PBP2_CrgA_like_4 cd08473
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-291 5.02e-37

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 130.75  E-value: 5.02e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150  92 PSGTLRLNVPQNIGPLFLDDLLVRFLVRYPLIRMEVASEARAIDIVAEGYDAGVRLAEAVPQD--MIAVPLtADIRMRVV 169
Cdd:cd08473    1 PRGTVRVSCPPALAQELLAPLLPRFMAAYPQVRLQLEATNRRVDLIEEGIDVALRVRFPPLEDssLVMRVL-GQSRQRLV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150 170 ATPQWFAEHGTPQVPEDLYQHHGICMrMSNGSNYRWEL-ARRGQQFDIAVPPRLATSDLFTSIAAVRAGLGVGFLPGFYI 248
Cdd:cd08473   80 ASPALLARLGRPRSPEDLAGLPTLSL-GDVDGRHSWRLeGPDGESITVRHRPRLVTDDLLTLRQAALAGVGIALLPDHLC 158

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 745759150 249 EEDLRSGALVSVLDEWTQPFKGLCLYYPGHRHIPAALRTFIAF 291
Cdd:cd08473  159 REALRAGRLVRVLPDWTPPRGIVHAVFPSRRGLLPAVRALIDF 201
PBP2_CrgA_like_7 cd08476
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-292 2.23e-35

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 126.21  E-value: 2.23e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150  94 GTLRLNVPQnIGPLFLDdLLVRFLVRYPLIRMEVASEARAIDIVAEGYDAGVRLAEAVPQDMIAVPLtADIRMRVVATPQ 173
Cdd:cd08476    1 GRLRVSLPL-VGGLLLP-VLAAFMQRYPEIELDLDFSDRLVDVIDEGFDAVIRTGELPDSRLMSRRL-GSFRMVLVASPD 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150 174 WFAEHGTPQVPEDLYQHHGICMRM-SNGSNYRWELARRGQQFDIAVPPRLATSDLFTSIAAVRAGLGVGFLPGFYIEEDL 252
Cdd:cd08476   78 YLARHGTPETPADLAEHACLRYRFpTTGKLEPWPLRGDGGDPELRLPTALVCNNIEALIEFALQGLGIACLPDFSVREAL 157

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 745759150 253 RSGALVSVLDEWTQPFKGLCLYYPGHRHIPAALRTFIAFI 292
Cdd:cd08476  158 ADGRLVTVLDDYVEERGQFRLLWPSSRHLSPKLRVFVDFM 197
PBP2_CrgA_like_1 cd08470
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-295 1.32e-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: 121.65  E-value: 1.32e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150  94 GTLRLNVPQNIGPLFLDDLLVRFLVRYPLIRMEVASEARAIDIVAEGYDAGVRLAEAVPQDMIAVPLtADIRMRVVATPQ 173
Cdd:cd08470    1 GLLRITCPVAYGERFIAPLVNDFMQRYPKLEVDIELTNRVVDLVSEGFDLAIRLGRLTDSSLMARRL-ASRRHYVCASPA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150 174 WFAEHGTPQVPEDLYQHHgiCMRmsnGSNYRWELARRGQQFDIAVPPRLATSDLFTSIAAVRAGLGVGFLPGFYIEEDLR 253
Cdd:cd08470   80 YLERHGTPHSLADLDRHN--CLL---GTSDHWRFQENGRERSVRVQGRWRCNSGVALLDAALKGMGLAQLPDYYVDEHLA 154

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 745759150 254 SGALVSVLDEWTQPFKGLCLYYPGHRHIPAALRTFIAFIRAG 295
Cdd:cd08470  155 AGRLVPVLEDYRPPDEGIWALYPHNRHLSPKVRLLVDYLADA 196
PBP2_CrgA_like_8 cd08477
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-292 1.03e-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 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: 119.26  E-value: 1.03e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150  94 GTLRLNVPQNIGPLFLDDLLVRFLVRYPLIRMEVASEARAIDIVAEGYDAGVRLAEAVPQDMIAVPLtADIRMRVVATPQ 173
Cdd:cd08477    1 GKLRISAPVTFGSHVLTPALAEYLARYPDVRVDLVLSDRLVDLVEEGFDAAFRIGELADSSLVARPL-APYRMVLCASPD 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150 174 WFAEHGTPQVPEDLYQHHgiCMRMSNGS-NYRWELARRGQQFDIAVPPRLATSDLFTSIAAVRAGLGVGFLPGFYIEEDL 252
Cdd:cd08477   80 YLARHGTPTTPEDLARHE--CLGFSYWRaRNRWRLEGPGGEVKVPVSGRLTVNSGQALRVAALAGLGIVLQPEALLAEDL 157

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 745759150 253 RSGALVSVLDEWTQPFKGLCLYYPGHRHIPAALRTFIAFI 292
Cdd:cd08477  158 ASGRLVELLPDYLPPPRPMHLLYPPDRRPTPKLRSFIDFL 197
PBP2_CrgA_like_2 cd08471
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-294 2.35e-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 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: 118.40  E-value: 2.35e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150  94 GTLRLNVPQNIGPLFLDDLLVRFLVRYPLIRMEVASEARAIDIVAEGYDAGVRLAEAVPQDMIAVPLtADIRMRVVATPQ 173
Cdd:cd08471    1 GLLTVTAPVLFGRLHVLPIITDFLDAYPEVSVRLLLLDRVVNLLEEGVDVAVRIGHLPDSSLVATRV-GSVRRVVCASPA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150 174 WFAEHGTPQVPEDLYQHHGIcMRMSNGSNYRWELARRGQQFDIAVPPRLATSDLFTSIAAVRAGLGVGFLPGFYIEEDLR 253
Cdd:cd08471   80 YLARHGTPKHPDDLADHDCI-AFTGLSPAPEWRFREGGKERSVRVRPRLTVNTVEAAIAAALAGLGLTRVLSYQVAEELA 158

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 745759150 254 SGALVSVLDEWTQPFKGLCLYYPGHRHIPAALRTFIAFIRA 294
Cdd:cd08471  159 AGRLQRVLEDFEPPPLPVHLVHPEGRLAPAKVRAFVDFAVP 199
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 93-294 4.59e-30

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


Pssm-ID: 460931 [Multi-domain]  Cd Length: 205  Bit Score: 112.38  E-value: 4.59e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150   93 SGTLRLNVPQNIGPLFLDDLLVRFLVRYPLIRMEV--ASEARAIDIVAEG-YDAGVRLAEAVPQDMIAVPLtADIRMRVV 169
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELteGNSEELLDLLLEGeLDLAIRRGPPDDPGLEARPL-GEEPLVLV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150  170 ATPQWFAEHGTPQVPEDLYQHhgICMRMSNGSNYRWELARRGQQFDIAVPPRLATSDLFTSIAAVRAGLGVGFLPGFYIE 249
Cdd:pfam03466  80 APPDHPLARGEPVSLEDLADE--PLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVA 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 745759150  250 EDLRSGALVSVLDEWTQPFKGLCLYYPGHRHIPAALRTFIAFIRA 294
Cdd:pfam03466 158 RELADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLRE 202
PRK09801 PRK09801
LysR family transcriptional regulator;
8-295 1.71e-29

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 113.98  E-value: 1.71e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150   8 ELEVVMAVMRRGSFRGAAQALSMSPTAVSNAIAGLESRLAIRLFHRTTRSVALTEAGQRFVARIGPALREIQQAQEEIHS 87
Cdd:PRK09801  10 DLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVTQ 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150  88 LADEPSGTLRLNVPQNIGPLFLDDLLVRFLVRYPLIRMEVASEARAIDIVAEGYDAGVRLAEAVPQDMIAVPLTADIRMr 167
Cdd:PRK09801  90 IKTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHFELFDRQIDLVQDNIDLDIRINDEIPDYYIAHLLTKNKRI- 168

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150 168 VVATPQWFAEHGTPQVPEDLYQHHGICMRMSNGSNYRWELARRGQQFDIAVPPRLATSDLFTSIAAVRAGLGVGFLPGFY 247
Cdd:PRK09801 169 LCAAPEYLQKYPQPQSLQELSRHDCLVTKERDMTHGIWELGNGQEKKSVKVSGHLSSNSGEIVLQWALEGKGIMLRSEWD 248

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*....
gi 745759150 248 IEEDLRSGALVSVLDEWTQPFKGLCLYY-PGHRHIpaALRTFIAFIRAG 295
Cdd:PRK09801 249 VLPFLESGKLVQVLPEYAQSANIWAVYRePLYRSM--KLRVCVEFLAAW 295
PBP2_CrgA_like_6 cd08475
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-286 1.25e-27

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 106.10  E-value: 1.25e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150  94 GTLRLNVPQNIGPLFLDDLLVRFLVRYPLIRMEVASEARAIDIVAEGYDAGVRLAE-AVPQDMIAVPLTADiRMRVVATP 172
Cdd:cd08475    1 GRLRIDLPVAFGRLCVAPLLLELARRHPELELELSFSDRFVDLIEEGIDLAVRIGElADSTGLVARRLGTQ-RMVLCASP 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150 173 QWFAEHGTPQVPEDLYQHHGIcMRMSNGSNYRWELARRGQQF-DIAVPPRLATSDLFTSIAAVRAGLGVGFLPGFYIEED 251
Cdd:cd08475   80 AYLARHGTPRTLEDLAEHQCI-AYGRGGQPLPWRLADEQGRLvRFRPAPRLQFDDGEAIADAALAGLGIAQLPTWLVADH 158

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 745759150 252 LRSGALVSVLDEWTQPfkGLCLY--YPGHRHIPAALR 286
Cdd:cd08475  159 LQRGELVEVLPELAPE--GLPIHavWPRTRHLPPKVR 193
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
13-257 2.20e-27

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 107.92  E-value: 2.20e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150  13 MAVMRR----GSFRGAAQALSMSPTAVSNAIAGLESRLAIRLFHRTTRSVALTEAGQRFVARIGPALREIQQAQEEIHSL 88
Cdd:PRK10632   7 MSVFAKvvefGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQLYAF 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150  89 ADEPSGTLRLNVPQNIGPLFLDDLLVRFLVRYPLIRMEVASEARAIDIVAEGYDAGVRLAEAVPQDMIAVPLTAdIRMRV 168
Cdd:PRK10632  87 NNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTGIPAPDLIADGLDVVIRVGALQDSSLFSRRLGA-MPMVV 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150 169 VATPQWFAEHGTPQVPEDLYQHHGICMRMSNGSNYrwEL-ARRGQQFDIAVPPRLATSDLFTSIAAVRAGLGVGFLPGFY 247
Cdd:PRK10632 166 CAAKSYLAQYGTPEKPADLSSHSWLEYSVRPDNEF--ELiAPEGISTRLIPQGRFVTNDPQTLVRWLTAGAGIAYVPLMW 243

                        250
                 ....*....|
gi 745759150 248 IEEDLRSGAL 257
Cdd:PRK10632 244 VIDEINRGEL 253
PBP2_CrgA_like_9 cd08479
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-292 7.60e-24

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: 95.74  E-value: 7.60e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150  94 GTLRLNVPQNIGPLFLDDLLVRFLVRYPLIRMEVASEARAIDIVAEGYDAGVRLAEAVPQDMIAVPLTADIRMrVVATPQ 173
Cdd:cd08479    1 GLLRVNASFGFGRRHIAPALSDFAKRYPELEVQLELTDRPVDLVEEGFDLDIRVGDLPDSSLIARKLAPNRRI-LCASPA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150 174 WFAEHGTPQVPEDLYQHHGICMRMSNGSNYRWELARRGQQFDIAVPPRLATSDlftSIAAVR---AGLGVGFLPGFYIEE 250
Cdd:cd08479   80 YLERHGAPASPEDLARHDCLVIRENDEDFGLWRLRNGDGEATVRVRGALSSND---GEVVLQwalDGHGIILRSEWDVAP 156

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 745759150 251 DLRSGALVSVLDEWTQPFKGLCLYYPGHRHIPAALRTFIAFI 292
Cdd:cd08479  157 YLRSGRLVRVLPDWQLPDADIWAVYPSRLSRSARVRVFVDFL 198
PBP2_CrgA_like_10 cd08480
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-292 2.14e-22

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: 92.01  E-value: 2.14e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150  94 GTLRLNVPQNIGPLFLDDLLVRFLVRYPLIRMEVASEARAIDIVAEGYDAGVRLAEAVPQDMIAVPLtADIRMRVVATPQ 173
Cdd:cd08480    1 GRLRVNASVPFGTHFLLPLLPAFLARYPEILVDLSLTDEVVDLLAERTDVAIRVGPLPDSSLVARKL-GESRRVIVASPS 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150 174 WFAEHGTPQVPEDLYQHHgiCMrmsnGSNYR-----WELARRGQQFDIAVPPRLATSDLFTSIAAVRAGLGVGFLPGFYI 248
Cdd:cd08480   80 YLARHGTPLTPQDLARHN--CL----GFNFRralpdWPFRDGGRIVALPVSGNILVNDGEALRRLALAGAGLARLALFHV 153

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 745759150 249 EEDLRSGALVSVLDEWT----QPFKGLclyYPGHRHIPAALRTFIAFI 292
Cdd:cd08480  154 ADDIAAGRLVPVLEEYNpgdrEPIHAV---YVGGGRLPARVRAFLDFL 198
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 20-263 1.94e-21

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 91.83  E-value: 1.94e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150  20 SFRGAAQALSMSPTAVSNAIAGLESRLAIRLFHRTTRSVALTEAGQRFVARIGPALREIQQAQEEIHSLADEpsGTLRLN 99
Cdd:PRK11139  22 SFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEATRKLRARSAK--GALTVS 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150 100 VPQNIGPLFLDDLLVRFLVRYPLIRMEVASEARAIDIVAEGYDAGVRLAEAVPQDMIAVPLTADIRMrVVATPQWFAEHG 179
Cdd:PRK11139 100 LLPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDRLEDFLRDDVDVAIRYGRGNWPGLRVEKLLDEYLL-PVCSPALLNGGK 178

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150 180 TPQVPEDLYQHHGIcmRMSNGSNYR-WelARRGQQFDIAVPPRLATSDLFTSIAAVRAGLGVGFLPGFYIEEDLRSGALV 258
Cdd:PRK11139 179 PLKTPEDLARHTLL--HDDSREDWRaW--FRAAGLDDLNVQQGPIFSHSSMALQAAIHGQGVALGNRVLAQPEIEAGRLV 254


                 ....*
gi 745759150 259 SVLDE 263
Cdd:PRK11139 255 CPFDT 259
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
6-289 2.46e-20

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 88.91  E-value: 2.46e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150   6 LIELEVVMAVMRRGSFRGAAQALSMSPTAVSNAIAGLESRLAIRLFHRTTRSVALTEAGQRFVARIGPALREIQQaqeEI 85
Cdd:PRK10086  16 LSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLDTLNQ---EI 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150  86 HSLAD-EPSGTLRLNVPQNIGPLFLDDLLVRFLVRYPLIRMEVASEARAIDIVAEGYDAGVRLAEAVPQDMIAVPLTaDI 164
Cdd:PRK10086  93 LDIKNqELSGTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTILTGNENVNFQRAGIDLAIYFDDAPSAQLTHHFLM-DE 171

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150 165 RMRVVATPQWFAEHGTPQVPEDLYQhhgiCMRM------SNGSNY-RWELARRGQQFDIAVPPRLAT---SDLFTsIAAV 234
Cdd:PRK10086 172 EILPVCSPEYAERHALTGNPDNLRH----CTLLhdrqawSNDSGTdEWHSWAQHFGVNLLPPSSGIGfdrSDLAV-IAAM 246

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 745759150 235 RaGLGVGFLPGFYIEEDLRSGALVSvldewtqPFKGLCL-----YY---PGHRHIPaALRTFI 289
Cdd:PRK10086 247 N-HIGVAMGRKRLVQKRLASGELVA-------PFGDMEVkchqhYYvttLPGRQWP-KIEAFI 300
PBP2_CrgA cd08478
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains ...
 92-292 4.18e-20

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: 85.85  E-value: 4.18e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150  92 PSGTLRLNVPQNIGPLFLDDLLVRFLVRYPLIRMEVASEARAIDIVAEGYDAGVRLAEAVPQDMIAVPLtADIRMRVVAT 171
Cdd:cd08478    1 PSGLLRVDAATPFVLHLLAPLIAKFRERYPDIELELVSNEGIIDLIERKTDVAIRIGELTDSTLHARPL-GKSRLRILAS 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150 172 PQWFAEHGTPQVPEDLYQHhgICMRMSN-GSNYRWELaRRGQQFDIAVPPRLATSDLFTSIAAVRAGLGVGFLPGFYIEE 250
Cdd:cd08478   80 PDYLARHGTPQSIEDLAQH--QLLGFTEpASLNTWPI-KDADGNLLKIQPTITASSGETLRQLALSGCGIACLSDFMTDK 156

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 745759150 251 DLRSGALVSVLDE----WTQPFKGlcLYYPGhRHIPAALRTFIAFI 292
Cdd:cd08478  157 DIAEGRLIPLFAEqtsdVRQPINA--VYYRN-TALSLRIRCFIDFL 199
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 6-293 6.02e-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: 87.67  E-value: 6.02e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150   6 LIELEVVMAVMRRGSFRGAAQALSMSPTAVSNAIAGLESRLAIRLFHRTTRSVALTEAGQRFVARIGPALREIQQAQEEI 85
Cdd:NF040786   3 LKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEEEF 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150  86 HSLADEPSGTLRL---NVPqniGPLFLDDLLVRFLVRYPLIRMEV--ASEARAIDIVAEG-YD---AGVRLAEAvpqDMI 156
Cdd:NF040786  83 DRYGKESKGVLRIgasTIP---GQYLLPELLKKFKEKYPNVRFKLmiSDSIKVIELLLEGeVDigfTGTKLEKK---RLV 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150 157 AVPLTADiRMrVVATP---QWFAEHGTPQVPEDLYQHHGIcMRmSNGSNYRWE----LARRG---QQFDIAvpprLATSD 226
Cdd:NF040786 157 YTPFYKD-RL-VLITPngtEKYRMLKEEISISELQKEPFI-MR-EEGSGTRKEaekaLKSLGislEDLNVV----ASLGS 228

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 745759150 227 LFTSIAAVRAGLGVGFLPGFYIEEDLRSGALVSVldewtqPFKGLclyyPGHRHI----------PAALRTFIAFIR 293
Cdd:NF040786 229 TEAIKQSVEAGLGISVISELAAEKEVERGRVLIF------PIPGL----PKNRDFylvynknrqlSPTAEAFLQFVK 295
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
9-65 1.31e-18

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 77.81  E-value: 1.31e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 745759150    9 LEVVMAVMRRGSFRGAAQALSMSPTAVSNAIAGLESRLAIRLFHRTTRSVALTEAGQ 65
Cdd:pfam00126   4 LRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 9-283 8.53e-18

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 81.53  E-value: 8.53e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150   9 LEVVMAVMRRGSFRGAAQALSMSPTAVSNAIAGLESRLAIRLFHRTTRSVALTEAGQRFVARIGPALREIQQAQEEIHSL 88
Cdd:PRK11074   7 LEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRRQCQQV 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150  89 ADEPSGTLRLNV-----PQNIGPLFLDdllvrFLVRYP----LIRMEVAS---EARAidivaegyDAGVRLAEAVPQdmi 156
Cdd:PRK11074  87 ANGWRGQLSIAVdnivrPDRTRQLIVD-----FYRHFDdvelIIRQEVFNgvwDALA--------DGRVDIAIGATR--- 150

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150 157 AVPLTADIRMRVVATPQW---------FAEHGTPQVPEDLYQHHGICM---------RMSngsnyrWELArrgQQFDIAV 218
Cdd:PRK11074 151 AIPVGGRFAFRDMGMLSWacvvssdhpLASMDGPLSDDELRPYPSLCLedtsrtlpkRIT------WLLD---NQRRLVV 221

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 745759150 219 PprlatsDLFTSIAAVRAGLGVGFLPGFYIEEDLRSGALVSVldEWTQPFK--GLCLYYPGHRHIPA 283
Cdd:PRK11074 222 P------DWESAINCLSAGLCVGMVPTHFAKPLINSGKLVEL--TLENPFPdsPCCLTWQQNDMSPA 280
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 95-292 8.74e-18

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: 79.57  E-value: 8.74e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150  95 TLRLNVPQNIGPLFLDDLLVRFLVRYPLIRMEV--ASEARAIDIVAEG-YDAGVRLAEAVPQDMIAVPLTADiRMRVVAT 171
Cdd:cd05466    1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLveGGSSELLEALLEGeLDLAIVALPVDDPGLESEPLFEE-PLVLVVP 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150 172 PQWFAEHGTPQVPEDLYQHHgICMRmSNGSNYRWELARRGQQFDIAVPPRLATSDLFTSIAAVRAGLGVGFLPGFYIEEd 251
Cdd:cd05466   80 PDHPLAKRKSVTLADLADEP-LILF-ERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEE- 156

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 745759150 252 LRSGALVSVLDEWTQPFKGLCLYYPGHRHIPAALRTFIAFI 292
Cdd:cd05466  157 LADGGLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 115-292 3.52e-17

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: 78.01  E-value: 3.52e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150 115 RFLVRYPLIRMEVASEARAIDIVAEGYDAGVRLAEAVPQDMIAVPLTADiRMRVVATPQWFAEHGTPQvPEDLYQHHGIC 194
Cdd:cd08432   21 RFQARHPDIDLRLSTSDRLVDFAREGIDLAIRYGDGDWPGLEAERLMDE-ELVPVCSPALLAGLPLLS-PADLARHTLLH 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150 195 MRMSNGSNYRWELARRGQQFDIAVPPRLATSDLftSIAAVRAGLGVGFLPGFYIEEDLRSGALVSVLDEWTQPFKGLCLY 274
Cdd:cd08432   99 DATRPEAWQWWLWAAGVADVDARRGPRFDDSSL--ALQAAVAGLGVALAPRALVADDLAAGRLVRPFDLPLPSGGAYYLV 176

                        170
                 ....*....|....*...
gi 745759150 275 YPGHRHIPAALRTFIAFI 292
Cdd:cd08432  177 YPPGRAESPAVAAFRDWL 194
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
9-259 6.44e-17

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 79.08  E-value: 6.44e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150   9 LEVVMAVMRRGSFRGAAQALSMSPTAVSNAIAGLESRLAIRLFHRTTRSVALTEAGQRFVARIGPALREIQQAQEEIHSL 88
Cdd:PRK10094   7 LRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPSELQQV 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150  89 AD--EPSGTLRLN----VPQNIGplfldDLLVRFLVRYPLIRMEVaseARAI------DIVAEGYD--AGVRLAEAVPQD 154
Cdd:PRK10094  87 NDgvERQVNIVINnllyNPQAVA-----QLLAWLNERYPFTQFHI---SRQIymgvwdSLLYEGFSlaIGVTGTEALANT 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150 155 MIAVPLtADIRMRVVATPQW-FAEHGTPQVPEDLYQHHGICMRMSNGSNYRWELARRGQQFDIAVPprlatsDLFTSIAA 233
Cdd:PRK10094 159 FSLDPL-GSVQWRFVMAADHpLANVEEPLTEAQLRRFPAVNIEDSARTLTKRVAWRLPGQKEIIVP------DMETKIAA 231

                        250       260
                 ....*....|....*....|....*.
gi 745759150 234 VRAGLGVGFLPGFYIEEDLRSGALVS 259
Cdd:PRK10094 232 HLAGVGIGFLPKSLCQSMIDNQQLVS 257
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 13-187 4.89e-16

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 76.53  E-value: 4.89e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150  13 MAVMRRGSFRGAAQALSMSPTAVSNAIAGLESRLAIRLFHRTTRSVALTEAGQRFVARIGPALREIQQAQEEIHSLADEP 92
Cdd:PRK11242  10 LAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRRAIHDVADLS 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150  93 SGTLRLNVPQNIGPLFLDDLLVRFLVRYPLIRM---EVASEARAIDIVAEGYDAGVRLAEAVPQDMIAVPLTADIRMRVV 169
Cdd:PRK11242  90 RGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLtirEMSQERIEALLADDELDVGIAFAPVHSPEIEAQPLFTETLALVV 169

                        170
                 ....*....|....*...
gi 745759150 170 ATPQWFAEHGTPQVPEDL 187
Cdd:PRK11242 170 GRHHPLAARRKALTLDEL 187
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 1-295 1.66e-15

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 75.11  E-value: 1.66e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150   1 MHRSgLIELEVVMAVMRRGSFRGAAQALSMSPTAVSNAIAGLESRLAIRLFHRTTRSVALTEAGQRFVARigpALREIQQ 80
Cdd:PRK10837   1 MHIT-LRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPR---ALALLEQ 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150  81 AQeEIHSLADEPSGTLRLNVPQNIGPLFLDDLLVRFLVRYPLIRME--VASEARAIDIVAEgYDAGVRLAEAVPQ--DMI 156
Cdd:PRK10837  77 AV-EIEQLFREDNGALRIYASSTIGNYILPAMIARYRRDYPQLPLElsVGNSQDVINAVLD-FRVDIGLIEGPCHspELI 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150 157 AVPLTADiRMRVVATPqwfaEHGTPQVP---EDLYQHHGIcMRmSNGSNYRWELAR----RGQQFDIAVpprlatsDLFT 229
Cdd:PRK10837 155 SEPWLED-ELVVFAAP----DSPLARGPvtlEQLAAAPWI-LR-ERGSGTREIVDYlllsHLPRFELAM-------ELGN 220

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 745759150 230 SIA---AVRAGLGVGFLPGFYIEEDLRSGALVSVLDEWTQPFKGLCLYYPGHRHIPAALRTFIAFIRAG 295
Cdd:PRK10837 221 SEAikhAVRHGLGISCLSRRVIADQLQAGTLVEVAVPLPRLMRTLYRIHHRQKHLSNALQRFLSYCQEA 289
rbcR CHL00180
LysR transcriptional regulator; Provisional
 6-260 6.66e-14

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 70.43  E-value: 6.66e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150   6 LIELEVVMAVMRRGSFRGAAQALSMSPTAVSNAIAGLESRLAIRLFHRTTRSVALTEAGQ---RFVARIGPALREIQQAQ 82
Cdd:CHL00180   7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGElllRYGNRILALCEETCRAL 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150  83 EEIHSLAdepSGTLRLNVPQNIGPLFLDDLLVRFLVRYPLI--RMEVASEARAIDIVAEG-YDAGVrLAEAVPQDMIAV- 158
Cdd:CHL00180  87 EDLKNLQ---RGTLIIGASQTTGTYLMPRLIGLFRQRYPQInvQLQVHSTRRIAWNVANGqIDIAI-VGGEVPTELKKIl 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150 159 ---PLTADIRMRVVATPQWFAEHGTPQvPEDLYQHHGICmrMSNGSNYRWELARRGQQFDIAVpPRLATSDLFTSI---- 231
Cdd:CHL00180 163 eitPYVEDELALIIPKSHPFAKLKKIQ-KEDLYRLNFIT--LDSNSTIRKVIDNILIQNGIDS-KRFKIEMELNSIeaik 238

                        250       260
                 ....*....|....*....|....*....
gi 745759150 232 AAVRAGLGVGFLPGFYIEEDLRSGALVSV 260
Cdd:CHL00180 239 NAVQSGLGAAFVSVSAIEKELELGLLHWI 267
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 9-261 2.16e-13

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


Pssm-ID: 274509 [Multi-domain]  Cd Length: 292  Bit Score: 68.79  E-value: 2.16e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150    9 LEVVMAVMRRGSFRGAAQALSMSPTAVSNAIAGLESRLAIRLFHRtTRSVALTEAGQRFVARigpaLREIQQAQEEI--H 86
Cdd:TIGR03298   6 LAALAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVR-TQPCRATEAGQRLLRH----ARQVRLLEAELlaE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150   87 SLADEPSGTLRLNVPQN---IGPLFLdDLLVRFLVRYPLiRMEVASE--ARAIDIVAEGYDAGVRLAEAVP-QDMIAVPL 160
Cdd:TIGR03298  81 LPGLAPGAPTRLTIAVNadsLATWFL-PALAPVLAREGV-LLDLVVEdqDHTAELLRSGEVLGAVTTEAKPvPGCRVVPL 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150  161 TAdIRMRVVATP----QWFAEHGTpqvPEDLYQHHGICMRMSNGSNYRWeLARRGQQfdIAVPPR--LATSDLFtsIAAV 234
Cdd:TIGR03298 159 GA-MRYLAVASPafaaRYFPDGVT---AAALARAPVIVFNRKDDLQDRF-LRRLFGL--PVSPPRhyVPSSEGF--VDAA 229

                         250       260
                  ....*....|....*....|....*..
gi 745759150  235 RAGLGVGFLPGFYIEEDLRSGALVSVL 261
Cdd:TIGR03298 230 RAGLGWGMVPELQAEPHLAAGRLVELA 256
PRK09791 PRK09791
LysR family transcriptional regulator;
8-127 5.21e-13

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 67.86  E-value: 5.21e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150   8 ELEVVMAVMRRGSFRGAAQALSMSPTAVSNAIAGLESRLAIRLFHRTTRSVALTEAGQRFVARIGPALREIQQAQEEIHS 87
Cdd:PRK09791   9 QIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQEDIRQ 88

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 745759150  88 LADEPSGTLRLNVPQNIGPLFLDDLLVRFLVRYPLIRMEV 127
Cdd:PRK09791  89 RQGQLAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRI 128
PRK10341 PRK10341
transcriptional regulator TdcA;
9-160 8.84e-13

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 67.58  E-value: 8.84e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150   9 LEVVMAVMRRGSFRGAAQALSMSPTAVSNAIAGLESRLAIRLFHRTTRSVALTEAGQRFVARIGPALREIQQAQEEIHSL 88
Cdd:PRK10341  12 LVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEINGM 91

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 745759150  89 ADEPSGTLRLNVPQNIGPLFLDDLLVRFLVRYPLIRMEVaSEARAIDIVAEGYDA------GVRLAEAVPQDMIAVPL 160
Cdd:PRK10341  92 SSEAVVDVSFGFPSLIGFTFMSDMINKFKEVFPKAQVSM-YEAQLSSFLPAIRDGrldfaiGTLSNEMKLQDLHVEPL 168
PBP2_GcdR_like cd08481
The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, ...
 95-292 2.19e-11

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: 61.54  E-value: 2.19e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150  95 TLRLNVPQNIGPLFLDDLLVRFLVRYPLIRMEVASEARAIDIVAEGYDAGVRLAEAVPQDMIAVPLTADIRMRVVAtPQW 174
Cdd:cd08481    1 TLELAVLPTFGTRWLIPRLPDFLARHPDITVNLVTRDEPFDFSQGSFDAAIHFGDPVWPGAESEYLMDEEVVPVCS-PAL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150 175 FAEHGtPQVPEDLYQ----HHgicmrmsNGSNYRWELARRGQQFDIAVPPRLATSDLFTSIA-AVRAGLGVGFLPGFYIE 249
Cdd:cd08481   80 LAGRA-LAAPADLAHlpllQQ-------TTRPEAWRDWFEEVGLEVPTAYRGMRFEQFSMLAqAAVAGLGVALLPRFLIE 151

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 745759150 250 EDLRSGALVSVLDEWTQPFKGLCLYYPGHRHIPAALRTFIAFI 292
Cdd:cd08481  152 EELARGRLVVPFNLPLTSDKAYYLVYPEDKAESPPVQAFRDWL 194
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
30-137 8.82e-11

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 60.99  E-value: 8.82e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150  30 MSPTAVSNAIAGLESRLAIRLFHRTTRSVALTEAGQRF--VARigPALREIQQAQEEIHSLADEPSGTLRlnvpqnigpL 107
Cdd:PRK11716   3 VSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELrpFAQ--QTLLQWQQLRHTLDQQGPSLSGELS---------L 71

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 745759150 108 F---------LDDLLVRFLVRYPL--IRMEVASEARAIDIV 137
Cdd:PRK11716  72 FcsvtaayshLPPILDRFRAEHPLveIKLTTGDAADAVEKV 112
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
8-261 1.04e-09

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 58.06  E-value: 1.04e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150   8 ELEVVMAVMRRGSFRGAAQALSMSPTAVSNAIAGLESRLAIRLFHRtTRSVALTEAGQRfVARIGPALReIQQAqEEIHS 87
Cdd:PRK13348   6 QLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQR-LLRHLRQVA-LLEA-DLLST 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150  88 LADEPSGTLRLNVPQNIgplflDDLLVRFLvryPLIRMEVASEARAIDIVAEGYD-AGVRLAE--------AVPQDM--- 155
Cdd:PRK13348  82 LPAERGSPPTLAIAVNA-----DSLATWFL---PALAAVLAGERILLELIVDDQDhTFALLERgevvgcvsTQPKPMrgc 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150 156 IAVPLTAdIRMRVVATP----QWFAE----HGTPQVPEDLYQHhgicmrmSNGSNYRWeLARRGQqfdiaVPPRLATSDL 227
Cdd:PRK13348 154 LAEPLGT-MRYRCVASPafaaRYFAQgltrHSALKAPAVAFNR-------KDTLQDSF-LEQLFG-----LPVGAYPRHY 219

                        250       260       270
                 ....*....|....*....|....*....|....*...
gi 745759150 228 FTSIA----AVRAGLGVGFLPGFYIEEDLRSGALVSVL 261
Cdd:PRK13348 220 VPSTHahlaAIRHGLGYGMVPELLIGPLLAAGRLVDLA 257
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
9-267 7.96e-09

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 55.55  E-value: 7.96e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150   9 LEVVMAVMRRGSFRGAAQALSMSPTAVSNAIAGLESRLAIRLFHRtTRSVALTEAGQRFVARigpaLREIQQAQEEI-HS 87
Cdd:PRK03635   7 LEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRLLRH----ARQVRLLEAELlGE 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150  88 LADEPSGTLRLNVPQN---IGPLFLdDLLVRFLVRYP-LIRMEVASEARAIDIVAEGYDAGVRLAEAVP-QDMIAVPLTA 162
Cdd:PRK03635  82 LPALDGTPLTLSIAVNadsLATWFL-PALAPVLARSGvLLDLVVEDQDHTAELLRRGEVVGAVTTEPQPvQGCRVDPLGA 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150 163 dIRMRVVATP----QWFAEHGTPQV----------PEDLYQHhgicmrmsngsnyRWelARRGQQFDIAVPPR--LATSD 226
Cdd:PRK03635 161 -MRYLAVASPafaaRYFPDGVTAEAlakapavvfnRKDDLQD-------------RF--LRQAFGLPPGSVPChyVPSSE 224

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|.
gi 745759150 227 LFtsIAAVRAGLGVGFLPGFYIEEDLRSGALVSVLDEWTQP 267
Cdd:PRK03635 225 AF--VRAALAGLGWGMIPELQIEPELASGELVDLTPGRPLD 263
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
9-259 1.56e-08

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 55.02  E-value: 1.56e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150   9 LEVVMAVMRRGSFRGAAQALSMSPTAVSNAIAGLESRLAIRLFHRTTRSVALTEAGQRFVARIGPALREIQQAQEEihsl 88
Cdd:PRK15421   7 LKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQA---- 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150  89 ADEPSGT-LRLNVPQNIGPLFLDDLLVRFLVRYPLIRMEvasearaidivaegYDAGVRL--AEAVPQDMIAVPLTADI- 164
Cdd:PRK15421  83 CNEPQQTrLRIAIECHSCIQWLTPALENFHKNWPQVEMD--------------FKSGVTFdpQPALQQGELDLVMTSDIl 148

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150 165 -------------RMRVVATPQWFAEHGTPQVPEDLYQHHGICMRMSNGsnyRWELARRGQQfDIAVPPRLATSD-LFTS 230
Cdd:PRK15421 149 prsglhyspmfdyEVRLVLAPDHPLAAKTRITPEDLASETLLIYPVQRS---RLDVWRHFLQ-PAGVSPSLKSVDnTLLL 224

                        250       260
                 ....*....|....*....|....*....
gi 745759150 231 IAAVRAGLGVGFLPGFYIEEDLRSGALVS 259
Cdd:PRK15421 225 IQMVAARMGIAALPHWVVESFERQGLVVT 253
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 95-292 2.90e-08

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


Pssm-ID: 176112 [Multi-domain]  Cd Length: 201  Bit Score: 52.88  E-value: 2.90e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150  95 TLRLNVPQNIGPLFLDDLLVRFLVRYPLIR--MEVASEARAIDIVAEG-YDAGVRLAEAVPQDMIAVPLTADiRMRVVAT 171
Cdd:cd08420    1 TLRIGASTTIGEYLLPRLLARFRKRYPEVRvsLTIGNTEEIAERVLDGeIDLGLVEGPVDHPDLIVEPFAED-ELVLVVP 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150 172 PQW-FAEHGTPQvPEDLYQHHGIcMRMSnGSNYRWELARRGQQFDIAvPPRLATSDLFTSI----AAVRAGLGVGFLPGF 246
Cdd:cd08420   80 PDHpLAGRKEVT-AEELAAEPWI-LREP-GSGTREVFERALAEAGLD-GLDLNIVMELGSTeaikEAVEAGLGISILSRL 155

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|..
gi 745759150 247 YIEEDLRSGALVSVldewtqPFKGLCLY------YPGHRHIPAALRTFIAFI 292
Cdd:cd08420  156 AVRKELELGRLVAL------PVEGLRLTrpfsliYHKDKYLSPAAEAFLEFL 201
PRK12680 PRK12680
LysR family transcriptional regulator;
24-254 1.91e-07

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 51.55  E-value: 1.91e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150  24 AAQALSMSPTAVSNAIAGLESRLAIRLFHRTTRSV-ALTEAGQRFVARIGPALREIQQAQEEIHSLADEPSGTLRLNVPQ 102
Cdd:PRK12680  22 AAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLeSVTPAGVEVIERARAVLSEANNIRTYAANQRRESQGQLTLTTTH 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150 103 NIGPLFLDDLLVRFLVRYP--LIRMEVASEARAIDIVAEGyDAGVRL---AEAVPQDMIAVPLTADIRMRVVATPQWFAE 177
Cdd:PRK12680 102 TQARFVLPPAVAQIKQAYPqvSVHLQQAAESAALDLLGQG-DADIAIvstAGGEPSAGIAVPLYRWRRLVVVPRGHALDT 180

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150 178 HGTPQVPEDLYQHHGICMRMSN--GSNYRWELARRGQQFDIAVPPRLAtsDLFTSIaaVRAGLGVGFLPGFYI---EEDL 252
Cdd:PRK12680 181 PRRAPDMAALAEHPLISYESSTrpGSSLQRAFAQLGLEPSIALTALDA--DLIKTY--VRAGLGVGLLAEMAVnanDEDL 256


                 ..
gi 745759150 253 RS 254
Cdd:PRK12680 257 RA 258
PBP2_TrpI cd08482
The C-terminal substrate binding domain of LysR-type transcriptional regulator TrpI, which is ...
 113-286 2.81e-07

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


Pssm-ID: 176171 [Multi-domain]  Cd Length: 195  Bit Score: 50.09  E-value: 2.81e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150 113 LVRFLVRYPLIRMEVASEARAIDIVAEGYDAGVRLAEA-VPQDMIAVPLtADIRMRVVATPQ----WFAEHGTPQVPEDL 187
Cdd:cd08482   19 LPAFQAALPDIDLQLSASDGPVDSLRDGIDAAIRFNDApWPAGMQVIEL-FPERVGPVCSPSlaptVPLRQAPAAALLGA 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150 188 YQHHgicmrmSNGSNYRW-ELARRGQQFDIAVPPRLATSDLFTSIAAVRAGLGVGFLPGFYIEEDLRSGALVSVLDeWTQ 266
Cdd:cd08482   98 PLLH------TRSRPQAWpDWAAAQGLAPEKLGTGQSFEHFYYLLEAAVAGLGVAIAPWPLVRDDLASGRLVAPWG-FIE 170

                        170       180
                 ....*....|....*....|
gi 745759150 267 PFKGLCLYYPGHRHIPAALR 286
Cdd:cd08482  171 TGSHYVLLRPARLRDSRAGA 190
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 8-109 1.96e-06

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 48.49  E-value: 1.96e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150   8 ELEVVMAVMRRGSFRGAAQALSMSPTAVSNAIAGLESRLAIRLFHRTTRSVALTEAGQRFVARIGPALREIQQAQEEIHS 87
Cdd:PRK11151   5 DLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVLKEMASQ 84

                         90       100
                 ....*....|....*....|..
gi 745759150  88 LADEPSGTLRLNVPQNIGPLFL 109
Cdd:PRK11151  85 QGETMSGPLHIGLIPTVGPYLL 106
PRK09986 PRK09986
LysR family transcriptional regulator;
2-80 2.63e-06

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 47.80  E-value: 2.63e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150   2 HRSGLIELEVVMAVMRRGSFRGAAQALSMSPTAVSNAIAGLESRLAIRLFHRTTRSVALTEAGQ-------RFVARIGPA 74
Cdd:PRK09986   5 YRIDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKilmeesrRLLDNAEQS 84


                 ....*.
gi 745759150  75 LREIQQ 80
Cdd:PRK09986  85 LARVEQ 90
nhaR PRK11062
transcriptional activator NhaR; Provisional
 15-65 9.71e-06

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 46.16  E-value: 9.71e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 745759150  15 VMRRGSFRGAAQALSMSPTAVSNAIAGLESRLAIRLFHRTTRSVALTEAGQ 65
Cdd:PRK11062  15 VCKEGSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGE 65
PBP2_LTTR_beta_lactamase cd08484
The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase ...
 113-269 2.13e-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: 44.28  E-value: 2.13e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150 113 LVRFLVRYPLIRMEVASEARAIDIVAEGYDAGVRLAEAVPQDMIAVPLtADIRMRVVATPQwFAEhgTPQVPEDLYQHhg 192
Cdd:cd08484   19 LAEFRQLHPFIDLRLSTNNNRVDIAAEGLDFAIRFGEGAWPGTDATRL-FEAPLSPLCTPE-LAR--RLSEPADLANE-- 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150 193 ICMRmsngsNYR---WElarrgQQFDIA-VPPRLATSDLFTS----IAAVRAGLGVGFLPGFYIEEDLRSGALVsvldew 264
Cdd:cd08484   93 TLLR-----SYRadeWP-----QWFEAAgVPPPPINGPVFDSsllmVEAALQGAGVALAPPSMFSRELASGALV------ 156


                 ....*
gi 745759150 265 tQPFK 269
Cdd:cd08484  157 -QPFK 160
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 108-292 2.69e-05

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; LysR-transcriptional regulators comprise 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, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to a name a few. 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: 176117 [Multi-domain]  Cd Length: 199  Bit Score: 44.22  E-value: 2.69e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150 108 FLDDLLVRFLVRYPLIRM--EVASEARAIDIVAEG-YDAGVRLAEAVPQDmIAVPLTADIRMRVVATPQW-FAEHGTPQV 183
Cdd:cd08426   14 LLPSLIARFRQRYPGVFFtvDVASTADVLEAVLSGeADIGLAFSPPPEPG-IRVHSRQPAPIGAVVPPGHpLARQPSVTL 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150 184 pEDLYQHHGICMRMSNGSNYRWE--LARRGQQFDiavpPRLATSDLFTSIAAVRAGLGVGFLPGFYIEEDLRSGALVSV- 260
Cdd:cd08426   93 -AQLAGYPLALPPPSFSLRQILDaaFARAGVQLE----PVLISNSIETLKQLVAAGGGISLLTELAVRREIRRGQLVAVp 167

                        170       180       190
                 ....*....|....*....|....*....|..
gi 745759150 261 LDEWTQPFKGLCLYYPGHRHIPAALRTFIAFI 292
Cdd:cd08426  168 LADPHMNHRQLELQTRAGRQLPAAASAFLQLL 199
PBP2_HvrB cd08483
The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an ...
 113-292 3.67e-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: 43.49  E-value: 3.67e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150 113 LVRFLVRYPLIRMEVASEARAIDIVAEGYDAGVRLAEAVPQDMIAVPLTADiRMRVVATPQWFAEHgTPQVPEDLYQHHG 192
Cdd:cd08483   19 LGSFWAKHPEIELSLLPSADLVDLRPDGIDVAIRYGNGDWPGLESEPLTAA-PFVVVAAPGLLGDR-KVDSLADLAGLPW 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150 193 IcmrMSNGSNYRWELAR-RGQQFDIAVPPRLATSDLftSIAAVRAGLGVGFLPGFYIEEDLRSGALVsVLDEWTQPFKGl 271
Cdd:cd08483   97 L---QERGTNEQRVWLAsMGVVPDLERGVTFLPGQL--VLEAARAGLGLSIQARALVEPDIAAGRLT-VLFEEEEEGLG- 169

                        170       180
                 ....*....|....*....|...
gi 745759150 272 clYYPGHRHIPA--ALRTFIAFI 292
Cdd:cd08483  170 --YHIVTRPGVLrpAAKAFVRWL 190
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
6-125 4.22e-05

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 44.20  E-value: 4.22e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150   6 LIELEVVMAVMRRG-SFRGAAQALSMSPTAVSNAIAGLESRLAIRLFHRT-TRSVALTEAGQRFVARIGPALREIQQAQE 83
Cdd:PRK12684   3 LHQLRFVREAVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHgKRLRGLTEPGRIILASVERILQEVENLKR 82

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 745759150  84 EIHSLADEPSGTL---------RLNVPQNIGplflddllvRFLVRYPLIRM 125
Cdd:PRK12684  83 VGKEFAAQDQGNLtiatthtqaRYALPAAIK---------EFKKRYPKVRL 124
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 19-94 5.56e-05

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 43.90  E-value: 5.56e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 745759150  19 GSFRGAAQALSMSPTAVSNAIAGLESRLAIRLFHRTTRSVALTEAGQRFVARIGPALREIQQAQEEIHSLADEPSG 94
Cdd:PRK11233  16 GSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQLAVHNVGQALSG 91
PBP2_HupR cd08431
The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which ...
 220-273 1.22e-04

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: 42.26  E-value: 1.22e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 745759150 220 PRLATSDLFTSIAAVRAGLGVGFLPGFYIEEDLRSGALVSVLDEWTQPFKGLCL 273
Cdd:cd08431  124 DRIRVPTMQAKIDAQVLGLGVGYLPRHLAKPELASGELVEKALEDPRPPQELFL 177
leuO PRK09508
leucine transcriptional activator; Reviewed
 9-98 1.88e-04

leucine transcriptional activator; Reviewed


Pssm-ID: 181918 [Multi-domain]  Cd Length: 314  Bit Score: 42.32  E-value: 1.88e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150   9 LEVVMAVMRRGSFRGAAQALSMSPTAVSNAIAGLESRLAIRLFHRTTRSVALTE-AGQRFvariGPALREIQQAQEEIHS 87
Cdd:PRK09508  27 LTVFDAVMQEQNITRAAHNLGMSQPAVSNAVARLKVMFNDELFVRYGRGIQPTArARQLF----GPVRQALQLVQNELPG 102

                         90
                 ....*....|.
gi 745759150  88 LADEPSGTLRL 98
Cdd:PRK09508 103 SGFEPESSERV 113
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 1-128 5.25e-04

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 41.13  E-value: 5.25e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150   1 MHRSGLIELEVVMAVMRRGSFRGAAQALSMSPTAVSNAIAGLESRLAIRLFHR-------TTRSVALTEAGQRF------ 67
Cdd:PRK11013   1 MAAVSLRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERvrgrlhpTVQGLRLFEEVQRSyygldr 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 745759150  68 VARIGPALREIQQAQEEIHSLadepsgtlrlnvpqnigPLF----LDDLLVRFLVRYPLIRMEVA 128
Cdd:PRK11013  81 IVSAAESLREFRQGQLSIACL-----------------PVFsqslLPGLCQPFLARYPDVSLNIV 128
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 6-71 2.21e-03

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 38.98  E-value: 2.21e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 745759150   6 LIELEVVMAVMRRGSFRGAAQALSMSPTAVSNAIAGLESRLAIRLFHRTTRSVALTEAGQRFV--ARI 71
Cdd:PRK09906   3 LRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLqdARA 70
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 9-127 2.41e-03

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 38.86  E-value: 2.41e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150   9 LEVVMAVMRRGSFRGAAQALSMSPTAVSNAIAGLESRLAIRLFHRTTRSVALTEAGQRFvarIGPAlREIQQAQEE---- 84
Cdd:PRK15092  16 LRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQL---LGYA-RKILRFNDEacss 91

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 745759150  85 -IHSLADepsGTLRLNVPQNIGPLFLDDLLVRFLVRYPLIRMEV 127
Cdd:PRK15092  92 lMYSNLQ---GVLTIGASDDTADTILPFLLNRVSSVYPKLALDV 132
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
15-68 4.60e-03

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 38.07  E-value: 4.60e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 745759150  15 VMRRGSFRGAAQALSMSPTAVSNAIAGLESRLAIRLFHRTTRSVALTEAGQRFV 68
Cdd:PRK03601  12 VSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLL 65
PBP2_AmpR cd08488
The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in ...
 113-268 5.64e-03

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


Pssm-ID: 176177 [Multi-domain]  Cd Length: 191  Bit Score: 37.13  E-value: 5.64e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 745759150 113 LVRFLVRYPLIRMEVASEARAIDIVAEGYDAGVRLAEAVPQDMIAVPLTaDIRMRVVATPQwFAEhgTPQVPEDLYQHhg 192
Cdd:cd08488   19 LADFQNRHPFIDLRLSTNNNRVDIAAEGLDYAIRFGSGAWHGIDATRLF-EAPLSPLCTPE-LAR--QLREPADLARH-- 92

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 745759150 193 ICMRMSNGSNYRWELARRGQQFDIAVPPRLATSDLFTSIAAVRAGLGVGFLPGFYIEEDLRSGALVsvldewtQPF 268
Cdd:cd08488   93 TLLRSYRADEWPQWFEAAGVGHPCGLPNSIMFDSSLGMMEAALQGLGVALAPPSMFSRQLASGALV-------QPF 161
 
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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