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Conserved domains on  [gi|489192100|ref|WP_003101450|]
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MULTISPECIES: LysR family transcriptional regulator [Pseudomonas]

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 ...
 108-302 1.43e-71

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 cd08482:

Pssm-ID: 473866 [Multi-domain]  Cd Length: 195  Bit Score: 219.58  E-value: 1.43e-71
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100 108 ALVLSCEPTLLMRWLIPRIAGFMQEQPRLSIQLVAGGGPFAFGR-GIDLAIRRNDFPWPPGSHAHWLFDEQVGPVCRASD 186
Cdd:cd08482    1 PLVLSCSGSLLMRWLIPRLPAFQAALPDIDLQLSASDGPVDSLRdGIDAAIRFNDAPWPAGMQVIELFPERVGPVCSPSL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100 187 VERhFHLDAGPPGLRAVAPRLHTATRPQAWNTWTRLAGQAP-ATTEGQRFEHFYLSLQAAGAGLGVAIGPWQLVRDDLSA 265
Cdd:cd08482   81 APT-VPLRQAPAAALLGAPLLHTRSRPQAWPDWAAAQGLAPeKLGTGQSFEHFYYLLEAAVAGLGVAIAPWPLVRDDLAS 159

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 489192100 266 GLLAAPLGFLADGSSYHLLTPRPLqAGEPATLLLEWL 302
Cdd:cd08482  160 GRLVAPWGFIETGSHYVLLRPARL-RDSRAGALADWL 195
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
21-80 4.24e-19

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


:

Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 79.35  E-value: 4.24e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100   21 LNALRCFEAAARLENFSRAAEALCLTHGAISRAVRTLEEELGCALFERRGQRVFLSEAGR 80
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
 
Name Accession Description Interval E-value
PBP2_TrpI cd08482
The C-terminal substrate binding domain of LysR-type transcriptional regulator TrpI, which is ...
 108-302 1.43e-71

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: 219.58  E-value: 1.43e-71
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100 108 ALVLSCEPTLLMRWLIPRIAGFMQEQPRLSIQLVAGGGPFAFGR-GIDLAIRRNDFPWPPGSHAHWLFDEQVGPVCRASD 186
Cdd:cd08482    1 PLVLSCSGSLLMRWLIPRLPAFQAALPDIDLQLSASDGPVDSLRdGIDAAIRFNDAPWPAGMQVIELFPERVGPVCSPSL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100 187 VERhFHLDAGPPGLRAVAPRLHTATRPQAWNTWTRLAGQAP-ATTEGQRFEHFYLSLQAAGAGLGVAIGPWQLVRDDLSA 265
Cdd:cd08482   81 APT-VPLRQAPAAALLGAPLLHTRSRPQAWPDWAAAQGLAPeKLGTGQSFEHFYYLLEAAVAGLGVAIAPWPLVRDDLAS 159

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 489192100 266 GLLAAPLGFLADGSSYHLLTPRPLqAGEPATLLLEWL 302
Cdd:cd08482  160 GRLVAPWGFIETGSHYVLLRPARL-RDSRAGALADWL 195
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 16-302 7.27e-67

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 210.86  E-value: 7.27e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100  16 RRLPSLNALRCFEAAARLENFSRAAEALCLTHGAISRAVRTLEEELGCALFERRGQRVFLSEAGRRLLAGTGPALDLIER 95
Cdd:PRK11139   3 RRLPPLNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAE 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100  96 TGETLRAEAGPTALVLSCEPTLLMRWLIPRIAGFMQEQPRLSIQLVAGGGPFAFGRG-IDLAIRRNDFPWpPGSHAHWLF 174
Cdd:PRK11139  83 ATRKLRARSAKGALTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDRLEDFLRDdVDVAIRYGRGNW-PGLRVEKLL 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100 175 DEQVGPVC------------RASDVERHfhldagppglravaPRLHTATRpQAWNTWTRLAGQAPATTE-GQRFEHFYLS 241
Cdd:PRK11139 162 DEYLLPVCspallnggkplkTPEDLARH--------------TLLHDDSR-EDWRAWFRAAGLDDLNVQqGPIFSHSSMA 226

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489192100 242 LQAAGAGLGVAIGPWQLVRDDLSAGLLAAPL-GFLADGSSYHLLTPRPLQAGEPATLLLEWL 302
Cdd:PRK11139 227 LQAAIHGQGVALGNRVLAQPEIEAGRLVCPFdTVLPSPNAFYLVCPDSQAELPKVAAFRQWL 288
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
20-308 2.62e-46

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 156.95  E-value: 2.62e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100  20 SLNALRCFEAAARLENFSRAAEALCLTHGAISRAVRTLEEELGCALFERRGQRVFLSEAGRRLLAGTGPALDLIERTGET 99
Cdd:COG0583    2 DLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAE 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100 100 LRAEAGPTA--LVLSCEPTLLMRWLIPRIAGFMQEQPRLSIQLVAGGGPFAF----GRGIDLAIRRNDFPWPpGSHAHWL 173
Cdd:COG0583   82 LRALRGGPRgtLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVdallEGELDLAIRLGPPPDP-GLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100 174 FDEQVGPVCRASDverhfhldagppglravaprlhtatrpqawntwtRLAGQAPATTegqrfeHFYLSLQAAGAGLGVAI 253
Cdd:COG0583  161 GEERLVLVASPDH----------------------------------PLARRAPLVN------SLEALLAAVAAGLGIAL 200

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 489192100 254 GPWQLVRDDLSAGLLAA-PLGFLADGSSYHLLTPRPLQAGEPATLLLEWLRRSAAA 308
Cdd:COG0583  201 LPRFLAADELAAGRLVAlPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
21-80 4.24e-19

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 79.35  E-value: 4.24e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100   21 LNALRCFEAAARLENFSRAAEALCLTHGAISRAVRTLEEELGCALFERRGQRVFLSEAGR 80
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 109-307 5.92e-14

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: 69.24  E-value: 5.92e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100  109 LVLSCEPTLLMRWLIPRIAGFMQEQPRLSIQLVAGGGPFAFG----RGIDLAIRRNDFPWpPGSHAHWLFDEQVGPVCRa 184
Cdd:pfam03466   4 LRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDllleGELDLAIRRGPPDD-PGLEARPLGEEPLVLVAP- 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100  185 sdveRHFHLDAGPP-------GLRAVAPRLHTATRpQAWNTWTRLAGQAPATteGQRFEHFYLSLQAAGAGLGVAIGPWQ 257
Cdd:pfam03466  82 ----PDHPLARGEPvsledlaDEPLILLPPGSGLR-DLLDRALRAAGLRPRV--VLEVNSLEALLQLVAAGLGIALLPRS 154

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 489192100  258 LVRDDLSAGLLAA-PLGFLADGSSYHLLTPRPLQAGEPATLLLEWLRRSAA 307
Cdd:pfam03466 155 AVARELADGRLVAlPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREALA 205
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 21-141 9.62e-12

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: 64.56  E-value: 9.62e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100  21 LNALRCFEAAARLENFSRAAEALCLTHGAISRAVRTLEEELGCALFERRGQRVFLSEAGRRLLAGTGPALDLIERTGETL 100
Cdd:NF040786   3 LKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEEEF 82

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 489192100 101 RAEAGPTALVL----SCEPTLlmrWLIPRI-AGFMQEQPRLSIQLV 141
Cdd:NF040786  83 DRYGKESKGVLrigaSTIPGQ---YLLPELlKKFKEKYPNVRFKLM 125
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
23-84 5.08e-11

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 62.52  E-value: 5.08e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489192100  23 ALRCFEAAARLENFSRAAEALCLTHGAISRAVRTLEEELGCALFERRGQRVFLSEAGRRLLA 84
Cdd:PRK10094   6 TLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLS 67
 
Name Accession Description Interval E-value
PBP2_TrpI cd08482
The C-terminal substrate binding domain of LysR-type transcriptional regulator TrpI, which is ...
 108-302 1.43e-71

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: 219.58  E-value: 1.43e-71
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100 108 ALVLSCEPTLLMRWLIPRIAGFMQEQPRLSIQLVAGGGPFAFGR-GIDLAIRRNDFPWPPGSHAHWLFDEQVGPVCRASD 186
Cdd:cd08482    1 PLVLSCSGSLLMRWLIPRLPAFQAALPDIDLQLSASDGPVDSLRdGIDAAIRFNDAPWPAGMQVIELFPERVGPVCSPSL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100 187 VERhFHLDAGPPGLRAVAPRLHTATRPQAWNTWTRLAGQAP-ATTEGQRFEHFYLSLQAAGAGLGVAIGPWQLVRDDLSA 265
Cdd:cd08482   81 APT-VPLRQAPAAALLGAPLLHTRSRPQAWPDWAAAQGLAPeKLGTGQSFEHFYYLLEAAVAGLGVAIAPWPLVRDDLAS 159

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 489192100 266 GLLAAPLGFLADGSSYHLLTPRPLqAGEPATLLLEWL 302
Cdd:cd08482  160 GRLVAPWGFIETGSHYVLLRPARL-RDSRAGALADWL 195
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 16-302 7.27e-67

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 210.86  E-value: 7.27e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100  16 RRLPSLNALRCFEAAARLENFSRAAEALCLTHGAISRAVRTLEEELGCALFERRGQRVFLSEAGRRLLAGTGPALDLIER 95
Cdd:PRK11139   3 RRLPPLNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAE 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100  96 TGETLRAEAGPTALVLSCEPTLLMRWLIPRIAGFMQEQPRLSIQLVAGGGPFAFGRG-IDLAIRRNDFPWpPGSHAHWLF 174
Cdd:PRK11139  83 ATRKLRARSAKGALTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDRLEDFLRDdVDVAIRYGRGNW-PGLRVEKLL 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100 175 DEQVGPVC------------RASDVERHfhldagppglravaPRLHTATRpQAWNTWTRLAGQAPATTE-GQRFEHFYLS 241
Cdd:PRK11139 162 DEYLLPVCspallnggkplkTPEDLARH--------------TLLHDDSR-EDWRAWFRAAGLDDLNVQqGPIFSHSSMA 226

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489192100 242 LQAAGAGLGVAIGPWQLVRDDLSAGLLAAPL-GFLADGSSYHLLTPRPLQAGEPATLLLEWL 302
Cdd:PRK11139 227 LQAAIHGQGVALGNRVLAQPEIEAGRLVCPFdTVLPSPNAFYLVCPDSQAELPKVAAFRQWL 288
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 108-302 1.20e-49

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: 163.52  E-value: 1.20e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100 108 ALVLSCEPTLLMRWLIPRIAGFMQEQPRLSIQLVAGGGPFAFGR-GIDLAIRRNDFPWPpGSHAHWLFDEQVGPVCRASD 186
Cdd:cd08432    1 VLTVSVTPSFAARWLIPRLARFQARHPDIDLRLSTSDRLVDFAReGIDLAIRYGDGDWP-GLEAERLMDEELVPVCSPAL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100 187 VERHFHLdaGPPGLRAvAPRLHTATRPQAWNTWTRLAGQAPATTE-GQRFEHFYLSLQAAGAGLGVAIGPWQLVRDDLSA 265
Cdd:cd08432   80 LAGLPLL--SPADLAR-HTLLHDATRPEAWQWWLWAAGVADVDARrGPRFDDSSLALQAAVAGLGVALAPRALVADDLAA 156

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 489192100 266 GLLAAPLGF-LADGSSYHLLTPRPLQAGEPATLLLEWL 302
Cdd:cd08432  157 GRLVRPFDLpLPSGGAYYLVYPPGRAESPAVAAFRDWL 194
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
20-308 2.62e-46

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 156.95  E-value: 2.62e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100  20 SLNALRCFEAAARLENFSRAAEALCLTHGAISRAVRTLEEELGCALFERRGQRVFLSEAGRRLLAGTGPALDLIERTGET 99
Cdd:COG0583    2 DLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAE 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100 100 LRAEAGPTA--LVLSCEPTLLMRWLIPRIAGFMQEQPRLSIQLVAGGGPFAF----GRGIDLAIRRNDFPWPpGSHAHWL 173
Cdd:COG0583   82 LRALRGGPRgtLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVdallEGELDLAIRLGPPPDP-GLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100 174 FDEQVGPVCRASDverhfhldagppglravaprlhtatrpqawntwtRLAGQAPATTegqrfeHFYLSLQAAGAGLGVAI 253
Cdd:COG0583  161 GEERLVLVASPDH----------------------------------PLARRAPLVN------SLEALLAAVAAGLGIAL 200

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 489192100 254 GPWQLVRDDLSAGLLAA-PLGFLADGSSYHLLTPRPLQAGEPATLLLEWLRRSAAA 308
Cdd:COG0583  201 LPRFLAADELAAGRLVAlPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
14-307 2.23e-40

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 142.83  E-value: 2.23e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100  14 RRRRLPS--LNALRCFEAAARLENFSRAAEALCLTHGAISRAVRTLEEELGCALFERRGQRVFLSEAGRRLLAgtgpald 91
Cdd:PRK10086   7 RNRLLNGwqLSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFW------- 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100  92 LIERTGETLRAEAGPTA-------LVLSCEPTLLMRWLIPRIAGFMQEQPRLSIQLVAGGGPFAF-GRGIDLAIRRNDFP 163
Cdd:PRK10086  80 ALKSSLDTLNQEILDIKnqelsgtLTVYSRPSIAQCWLVPRLADFTRRYPSISLTILTGNENVNFqRAGIDLAIYFDDAP 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100 164 wPPGSHAHWLFDEQVGPVCRASDVERHfHLDAGPPGLRAVApRLHTAtrpQAWN---------TWTRLAG-QAPATTEGQ 233
Cdd:PRK10086 160 -SAQLTHHFLMDEEILPVCSPEYAERH-ALTGNPDNLRHCT-LLHDR---QAWSndsgtdewhSWAQHFGvNLLPPSSGI 233

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489192100 234 RFEHFYLSLQAAGAGLGVAIGPWQLVRDDLSAGLLAAPLGFLADGSSYH-LLTPRPLQAGEPATLLLEWLRRSAA 307
Cdd:PRK10086 234 GFDRSDLAVIAAMNHIGVAMGRKRLVQKRLASGELVAPFGDMEVKCHQHyYVTTLPGRQWPKIEAFIDWLKEQVK 308
PBP2_GcdR_like cd08481
The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, ...
 109-302 5.63e-35

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: 125.49  E-value: 5.63e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100 109 LVLSCEPTLLMRWLIPRIAGFMQEQPRLSIQLVAGGGPFAFGRG-IDLAIRRNDFPWPpGSHAHWLFDEQVGPVCRASDV 187
Cdd:cd08481    2 LELAVLPTFGTRWLIPRLPDFLARHPDITVNLVTRDEPFDFSQGsFDAAIHFGDPVWP-GAESEYLMDEEVVPVCSPALL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100 188 ERHfhlDAGPPGLRAVAPRLHTATRPQAWNTWTRLAG-QAPATTEGQRFEHFYLSLQAAGAGLGVAIGPWQLVRDDLSAG 266
Cdd:cd08481   81 AGR---ALAAPADLAHLPLLQQTTRPEAWRDWFEEVGlEVPTAYRGMRFEQFSMLAQAAVAGLGVALLPRFLIEEELARG 157

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 489192100 267 LLAAPLGF-LADGSSYHLLTPRPLQAGEPATLLLEWL 302
Cdd:cd08481  158 RLVVPFNLpLTSDKAYYLVYPEDKAESPPVQAFRDWL 194
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
21-80 4.24e-19

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 79.35  E-value: 4.24e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100   21 LNALRCFEAAARLENFSRAAEALCLTHGAISRAVRTLEEELGCALFERRGQRVFLSEAGR 80
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PBP2_HvrB cd08483
The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an ...
 108-302 2.78e-14

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: 70.07  E-value: 2.78e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100 108 ALVLSCEPTLLMRWLIPRIAGFMQEQPRLSIQLVAGGGPFAFGR-GIDLAIRRNDFPWPpGSHAHWLFDEQ---VGPVCR 183
Cdd:cd08483    1 PLTVTLTPSFASNWLMPRLGSFWAKHPEIELSLLPSADLVDLRPdGIDVAIRYGNGDWP-GLESEPLTAAPfvvVAAPGL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100 184 ASDVERhfhldAGPPGLRAVaPRLHTATRPQAWnTWTRLAGQAPATTEGQRFEHFYLSLQAAGAGLGVAIGPWQLVRDDL 263
Cdd:cd08483   80 LGDRKV-----DSLADLAGL-PWLQERGTNEQR-VWLASMGVVPDLERGVTFLPGQLVLEAARAGLGLSIQARALVEPDI 152

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 489192100 264 SAGLLAAPLGFLADGSSYHLLTpRPLQAGEPATLLLEWL 302
Cdd:cd08483  153 AAGRLTVLFEEEEEGLGYHIVT-RPGVLRPAAKAFVRWL 190
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 109-307 5.92e-14

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: 69.24  E-value: 5.92e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100  109 LVLSCEPTLLMRWLIPRIAGFMQEQPRLSIQLVAGGGPFAFG----RGIDLAIRRNDFPWpPGSHAHWLFDEQVGPVCRa 184
Cdd:pfam03466   4 LRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDllleGELDLAIRRGPPDD-PGLEARPLGEEPLVLVAP- 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100  185 sdveRHFHLDAGPP-------GLRAVAPRLHTATRpQAWNTWTRLAGQAPATteGQRFEHFYLSLQAAGAGLGVAIGPWQ 257
Cdd:pfam03466  82 ----PDHPLARGEPvsledlaDEPLILLPPGSGLR-DLLDRALRAAGLRPRV--VLEVNSLEALLQLVAAGLGIALLPRS 154

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 489192100  258 LVRDDLSAGLLAA-PLGFLADGSSYHLLTPRPLQAGEPATLLLEWLRRSAA 307
Cdd:pfam03466 155 AVARELADGRLVAlPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREALA 205
PBP2_BlaA cd08487
The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which ...
 116-291 2.61e-13

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


Pssm-ID: 176176 [Multi-domain]  Cd Length: 189  Bit Score: 67.18  E-value: 2.61e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100 116 TLLMRWLIPRIAGFMQEQPRLSIQLVAGGGPFAF-GRGIDLAIRRNDFPWpPGSHAHWLFDEQVGPVCRASDVERHFHld 194
Cdd:cd08487    9 TFAVGWLLPRLAEFRQLHPFIELRLRTNNNVVDLaTEGLDFAIRFGEGLW-PATHNERLLDAPLSVLCSPEIAKRLSH-- 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100 195 agPPGLraVAPRLHTATRPQAWNTWTRLAGQAPATTEGQRFEHFYLSLQAAGAGLGVAIGPWQLVRDDLSAGLLAAPLGF 274
Cdd:cd08487   86 --PADL--INETLLRSYRTDEWLQWFEAANMPPIKIRGPVFDSSRLMVEAAMQGAGVALAPAKMFSREIENGQLVQPFKI 161

                        170
                 ....*....|....*....
gi 489192100 275 LADGSSYHL--LTPRPLQA 291
Cdd:cd08487  162 EVETGSYWLtwLKSKPMTP 180
rbcR CHL00180
LysR transcriptional regulator; Provisional
 18-140 6.03e-12

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 65.04  E-value: 6.03e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100  18 LP-SLNALRCFEAAARLENFSRAAEALCLTHGAISRAVRTLEEELGCALFERRGQRVFLSEAGRRLLAGTGPALDLIErt 96
Cdd:CHL00180   3 LPfTLDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCE-- 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 489192100  97 gETLRA-------EAGptALVLSCEPTlLMRWLIPRIAG-FMQEQPRLSIQL 140
Cdd:CHL00180  81 -ETCRAledlknlQRG--TLIIGASQT-TGTYLMPRLIGlFRQRYPQINVQL 128
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 21-141 9.62e-12

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: 64.56  E-value: 9.62e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100  21 LNALRCFEAAARLENFSRAAEALCLTHGAISRAVRTLEEELGCALFERRGQRVFLSEAGRRLLAGTGPALDLIERTGETL 100
Cdd:NF040786   3 LKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEEEF 82

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 489192100 101 RAEAGPTALVL----SCEPTLlmrWLIPRI-AGFMQEQPRLSIQLV 141
Cdd:NF040786  83 DRYGKESKGVLrigaSTIPGQ---YLLPELlKKFKEKYPNVRFKLM 125
PBP2_LTTR_beta_lactamase cd08484
The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase ...
 116-302 3.02e-11

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: 61.23  E-value: 3.02e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100 116 TLLMRWLIPRIAGFMQEQPRLSIQLVAGGGPFAFGR-GIDLAIRRNDFPWPpGSHAHWLFDEQVGPVCRASDVERHFHld 194
Cdd:cd08484    9 TFAVGWLLPRLAEFRQLHPFIDLRLSTNNNRVDIAAeGLDFAIRFGEGAWP-GTDATRLFEAPLSPLCTPELARRLSE-- 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100 195 agPPGLRAVAprLHTATRPQAWNTWTRLAGQAPATTEGQRFEHFYLSLQAAGAGLGVAIGPWQLVRDDLSAGLLAAPLGF 274
Cdd:cd08484   86 --PADLANET--LLRSYRADEWPQWFEAAGVPPPPINGPVFDSSLLMVEAALQGAGVALAPPSMFSRELASGALVQPFKI 161

                        170       180
                 ....*....|....*....|....*...
gi 489192100 275 LADGSSYHLLTPRPLQAGEPATLLLEWL 302
Cdd:cd08484  162 TVSTGSYWLTRLKSKPETPAMSAFSQWL 189
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
23-84 5.08e-11

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 62.52  E-value: 5.08e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489192100  23 ALRCFEAAARLENFSRAAEALCLTHGAISRAVRTLEEELGCALFERRGQRVFLSEAGRRLLA 84
Cdd:PRK10094   6 TLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLS 67
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
28-139 7.10e-10

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 58.83  E-value: 7.10e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100  28 EAAARLENFSRAAEALCLTHGAISRAVRTLEEELGCALFERRGQRVF-LSEAGRRLLAGTGPAL---DLIERTGETLRAE 103
Cdd:PRK12684  11 EAVRQNFNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRgLTEPGRIILASVERILqevENLKRVGKEFAAQ 90

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 489192100 104 AGPTaLVLSCEPTlLMRWLIPR-IAGFMQEQP--RLSIQ 139
Cdd:PRK12684  91 DQGN-LTIATTHT-QARYALPAaIKEFKKRYPkvRLSIL 127
PRK09986 PRK09986
LysR family transcriptional regulator;
20-140 7.41e-10

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 58.58  E-value: 7.41e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100  20 SLNALRCFEAAARLENFSRAAEALCLTHGAISRAVRTLEEELGCALFERRGQRVFLSEAG-------RRLLAGTGPALDL 92
Cdd:PRK09986   8 DLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGkilmeesRRLLDNAEQSLAR 87

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 489192100  93 IERTGetlRAEAGptALVLSCEPTLLMRWLIPRIAGFMQEQPRLSIQL 140
Cdd:PRK09986  88 VEQIG---RGEAG--RIEIGIVGTALWGRLRPAMRHFLKENPNVEWLL 130
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 18-272 9.48e-10

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 58.46  E-value: 9.48e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100  18 LPSLNALRCFEAAARLENFSRAAEALCLTHGAISRAVRTLEEELGCALFERRGQRVFLSEAGRRLLAGTGPAL---DLIE 94
Cdd:PRK14997   1 KTDLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLveaQAAQ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100  95 RTGETLRAEagPTALV-LSCEPTLLMRWLIPRIAGFMQEQPRLSIQLVAGGGPF-AFGRGIDLAIRRNDFPWppgshahw 172
Cdd:PRK14997  81 DAIAALQVE--PRGIVkLTCPVTLLHVHIGPMLAKFMARYPDVSLQLEATNRRVdVVGEGVDVAIRVRPRPF-------- 150

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100 173 lfdEQVGPVCRASdVERHFHLDAGPpglrAVAPRLHTATRPQAWNTWTRLAGQAPATT--------EGQRFE-HF----- 238
Cdd:PRK14997 151 ---EDSDLVMRVL-ADRGHRLFASP----DLIARMGIPSAPAELSHWPGLSLASGKHIhrwelygpQGARAEvHFtprmi 222

                        250       260       270
                 ....*....|....*....|....*....|....*...
gi 489192100 239 ---YLSL-QAAGAGLGVAIGPWQLVRDDLSAGLLAAPL 272
Cdd:PRK14997 223 ttdMLALrEAAMAGVGLVQLPVLMVKEQLAAGELVAVL 260
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 20-80 4.35e-09

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 56.49  E-value: 4.35e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 489192100  20 SLNALRCFEAAARLENFSRAAEALCLTHGAISRAVRTLEEELGCALFERRGQRVFLSEAGR 80
Cdd:PRK11074   3 SEYSLEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGE 63
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 28-143 9.99e-09

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 55.38  E-value: 9.99e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100  28 EAAARLENFSRAAEALCLTHGAISRAVRTLEEELGCALFERRGQRVF-LSEAGRRLLagtgPALDLIERTGETLRA---- 102
Cdd:PRK12682  11 EAVRRNLNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKgLTEPGKAVL----DVIERILREVGNIKRigdd 86

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 489192100 103 ----EAGptALVLSCEPTlLMRWLIPR-IAGFMQEQPRLSIQLVAG 143
Cdd:PRK12682  87 fsnqDSG--TLTIATTHT-QARYVLPRvVAAFRKRYPKVNLSLHQG 129
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
23-134 3.25e-08

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 53.62  E-value: 3.25e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100  23 ALRCFEAAARLENFSRAAEALCLTHGAISRAVRTLEEELGCALFeRRGQRVFLSEAGRRLLAgtgpaldLIERTgETLRA 102
Cdd:PRK03635   6 QLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLL-VRTQPCRPTEAGQRLLR-------HARQV-RLLEA 76

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 489192100 103 EAGPTALVLSCEPTLLM---------RWLIPRIAGFMQEQP 134
Cdd:PRK03635  77 ELLGELPALDGTPLTLSiavnadslaTWFLPALAPVLARSG 117
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 20-143 7.31e-08

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 52.77  E-value: 7.31e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100  20 SLNALRCFEAAARLENFSRAAEALCLTHGAISRAVRTLEEELGCALFERRGQRVFLSEAGRRLLAgtgPALDLIERTGET 99
Cdd:PRK10837   4 TLRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYP---RALALLEQAVEI 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 489192100 100 ---LRAEAGptALVLSCEPTLLMRWLIPRIAGFMQEQPRLSIQLVAG 143
Cdd:PRK10837  81 eqlFREDNG--ALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVG 125
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 21-80 7.52e-08

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 52.65  E-value: 7.52e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100  21 LNALRCFEAAARLENFSRAAEALCLTHGAISRAVRTLEEELGCALFERRGQRVFLSEAGR 80
Cdd:PRK11242   3 LRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGE 62
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
24-141 1.45e-07

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 51.90  E-value: 1.45e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100  24 LRCFEAAARLENFSRAAEALCLTHGAISRAVRTLEEELGCALFErRGQRVFLSEAGRRLLAGTgPALDLIErtGETLR-- 101
Cdd:PRK13348   7 LEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLV-RGRPCRPTPAGQRLLRHL-RQVALLE--ADLLStl 82

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 489192100 102 --AEAGPTALVLSCEPTLLMRWLIPRIAGFMqEQPRLSIQLV 141
Cdd:PRK13348  83 paERGSPPTLAIAVNADSLATWFLPALAAVL-AGERILLELI 123
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
24-83 2.38e-07

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 51.17  E-value: 2.38e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100  24 LRCFEAAARLENFSRAAEALCLTHGAISRAVRTLEEELGCALFERRGQRVFLSEAGRRLL 83
Cdd:PRK03601   6 LKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLL 65
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
21-158 2.77e-07

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 51.30  E-value: 2.77e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100  21 LNALRCFEAAARLENFSRAAEALCLTHGAISRAVRTLEEELGCALFERRGQRVFLSEAGRRLLAGTGPALDLIERTGETL 100
Cdd:PRK10632   4 LKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQL 83

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 489192100 101 RA-EAGPTA-LVLSCEPTLLMRWLIPRIAGFMQEQPRLSIQLVAG-GGPFAFGRGIDLAIR 158
Cdd:PRK10632  84 YAfNNTPIGtLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTGiPAPDLIADGLDVVIR 144
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 28-83 3.44e-07

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 50.81  E-value: 3.44e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 489192100  28 EAAARLENFSRAAEALCLTHGAISRAVRTLEEELGCALFERRGQRVF-LSEAGRRLL 83
Cdd:PRK12683  11 EAVRQNFNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTgLTEPGKELL 67
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 21-83 3.76e-07

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 50.80  E-value: 3.76e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 489192100  21 LNALRCFEAAARLENFSRAAEALCLTHGAISRAVRTLEEELGCALFERRGQRVFLSEAGRRLL 83
Cdd:PRK15092  13 LDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLL 75
PBP2_AmpR cd08488
The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in ...
 116-302 4.10e-07

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: 49.45  E-value: 4.10e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100 116 TLLMRWLIPRIAGFMQEQPRLSIQLVAGGGPFAFG-RGIDLAIRRNDFPWPpGSHAHWLFDEQVGPVCrASDVERHFHld 194
Cdd:cd08488    9 TFAVGWLLPRLADFQNRHPFIDLRLSTNNNRVDIAaEGLDYAIRFGSGAWH-GIDATRLFEAPLSPLC-TPELARQLR-- 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100 195 aGPPGLRAVAprLHTATRPQAWNTWTRLAGQAPAT--TEGQRFEHFYLSLQAAGAGLGVAIGPWQLVRDDLSAGLLAAPL 272
Cdd:cd08488   85 -EPADLARHT--LLRSYRADEWPQWFEAAGVGHPCglPNSIMFDSSLGMMEAALQGLGVALAPPSMFSRQLASGALVQPF 161

                        170       180       190
                 ....*....|....*....|....*....|
gi 489192100 273 GFLADGSSYHLLTPRPLQAGEPATLLLEWL 302
Cdd:cd08488  162 ATTLSTGSYWLTRLQSRPETPAMSAFSAWL 191
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 21-83 6.91e-06

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 46.69  E-value: 6.91e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 489192100  21 LNALRCFEAAARLENFSRAAEALCLTHGAISRAVRTLEEELGCALFERRGQRVFLSEAGRRLL 83
Cdd:PRK09906   3 LRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFL 65
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 109-302 1.00e-05

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: 45.28  E-value: 1.00e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100 109 LVLSCEPTLLMRWLIPRIAGFMQEQPRLSIQLVAGGGPFAF-----GRgIDLAIRRnDFPWPPGSHAHWLFDEQVGPVCR 183
Cdd:cd05466    2 LRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLealleGE-LDLAIVA-LPVDDPGLESEPLFEEPLVLVVP 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100 184 ASdverhfHLDAGPPGLRA--------VAPRLHTATRpQAWNTWTRLAGQAPATTegQRFEHFYLSLQAAGAGLGVAIGP 255
Cdd:cd05466   80 PD------HPLAKRKSVTLadladeplILFERGSGLR-RLLDRAFAEAGFTPNIA--LEVDSLEAIKALVAAGLGIALLP 150

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 489192100 256 WQLVRDDLSAGLLAAPLGFLADGSSYHLLTPRPLQAGEPATLLLEWL 302
Cdd:cd05466  151 ESAVEELADGGLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
cbl PRK12679
HTH-type transcriptional regulator Cbl;
28-83 1.09e-05

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 46.34  E-value: 1.09e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 489192100  28 EAAARLENFSRAAEALCLTHGAISRAVRTLEEELGCALFERRGQRVF-LSEAGRRLL 83
Cdd:PRK12679  11 EAARQDYNLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRLLgMTEPGKALL 67
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
16-268 3.73e-05

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 44.62  E-value: 3.73e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100  16 RRLPSLNALR-CFEAAArlenfsrAAEALCLTHGAISRAVRTLEEELGCALFERRGQRVFLSEAGRRLLAGTGPALDLIE 94
Cdd:PRK15421   5 KHLKTLQALRnCGSLAA-------AAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQIS 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100  95 RTGETLRaEAGPTALVLSCEPTLLMRWLIPRIAGFMQEQPRLSIQLVAG----GGPFAFGRGIDLAIRRNDFPwPPGSHA 170
Cdd:PRK15421  78 QALQACN-EPQQTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGvtfdPQPALQQGELDLVMTSDILP-RSGLHY 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100 171 HWLFDEQVGPVCrASDVERHFHLDAGPPGLRAVAPRLHTATRPQ--AWNTWTRLAGQAPATtegQRFEHFYLSLQAAGAG 248
Cdd:PRK15421 156 SPMFDYEVRLVL-APDHPLAAKTRITPEDLASETLLIYPVQRSRldVWRHFLQPAGVSPSL---KSVDNTLLLIQMVAAR 231

                        250       260
                 ....*....|....*....|
gi 489192100 249 LGVAIGPWQLVRDDLSAGLL 268
Cdd:PRK15421 232 MGIAALPHWVVESFERQGLV 251
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
49-83 5.32e-05

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 44.04  E-value: 5.32e-05
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 489192100  49 AISRAVRTLEEELGCALFERRGQRVFLSEAGRRLL 83
Cdd:PRK11716   7 TLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELR 41
PRK10341 PRK10341
transcriptional regulator TdcA;
18-84 7.83e-05

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 43.70  E-value: 7.83e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489192100  18 LPSLNALRCFEAAARLENFSRAAEALCLTHGAISRAVRTLEEELGCALFERRGQRVFLSEAGRRLLA 84
Cdd:PRK10341   6 LPKTQHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLS 72
PRK09791 PRK09791
LysR family transcriptional regulator;
21-79 1.06e-04

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 43.21  E-value: 1.06e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 489192100  21 LNALRCFEAAARLENFSRAAEALCLTHGAISRAVRTLEEELGCALFERRGQRVFLSEAG 79
Cdd:PRK09791   7 IHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAG 65
nhaR PRK11062
transcriptional activator NhaR; Provisional
 37-79 1.81e-04

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 42.30  E-value: 1.81e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 489192100  37 SRAAEALCLTHGAISRAVRTLEEELGCALFERRGQRVFLSEAG 79
Cdd:PRK11062  22 VGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELG 64
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 24-84 1.88e-04

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 42.32  E-value: 1.88e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489192100  24 LRCFE---AAARLENFSRAAEALCLTHGAISRAVRTLEEELGCALFERRGQRVFLSEAGRRLLA 84
Cdd:PRK11151   3 IRDLEylvALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVD 66
cysB PRK12681
HTH-type transcriptional regulator CysB;
35-140 2.02e-04

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 42.19  E-value: 2.02e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100  35 NFSRAAEALCLTHGAISRAVRTLEEELGCALFERRGQRV-FLSEAGRRLLAGTGPALdlieRTGETLRAEAG----PTAL 109
Cdd:PRK12681  18 NVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLtQVTPAGEEIIRIAREIL----SKVESIKSVAGehtwPDKG 93

                         90       100       110
                 ....*....|....*....|....*....|...
gi 489192100 110 VLSCEPT-LLMRWLIPR-IAGFMQEQPRLSIQL 140
Cdd:PRK12681  94 SLYIATThTQARYALPPvIKGFIERYPRVSLHM 126
PBP2_CrgA_like_4 cd08473
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 106-268 2.15e-04

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: 41.39  E-value: 2.15e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100 106 PTALV-LSCEPTLLMRWLIPRIAGFMQEQPRLSIQLVAGGGPF-AFGRGIDLAIRRNDFPWPPGS-------------HA 170
Cdd:cd08473    1 PRGTVrVSCPPALAQELLAPLLPRFMAAYPQVRLQLEATNRRVdLIEEGIDVALRVRFPPLEDSSlvmrvlgqsrqrlVA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100 171 HWLFDEQVGPVCRASDVERHFHLDAGPPGLRAVaprlhtatrpqaWntwtRLAGQapattEGQRFEH----------FYL 240
Cdd:cd08473   81 SPALLARLGRPRSPEDLAGLPTLSLGDVDGRHS------------W----RLEGP-----DGESITVrhrprlvtddLLT 139

                        170       180
                 ....*....|....*....|....*...
gi 489192100 241 SLQAAGAGLGVAIGPWQLVRDDLSAGLL 268
Cdd:cd08473  140 LRQAALAGVGIALLPDHLCREALRAGRL 167
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 109-287 2.76e-04

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: 41.27  E-value: 2.76e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100 109 LVLSCEPTLLMRWLIPRIAGFMQEQPRLSIQLVAGGGPFAF-GRGIDLAIRRNDFPwPPGSHAHWLFD------------ 175
Cdd:cd08422    3 LRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLvEEGFDLAIRIGELP-DSSLVARRLGPvrrvlvaspayl 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100 176 EQVGPVCRASDVERHfhldagpPGLRavaprlhtATRPQAWNTWTRLAGQAPATTEGQ---RFEHFYLSLQAAGAGLGVA 252
Cdd:cd08422   82 ARHGTPQTPEDLARH-------RCLG--------YRLPGRPLRWRFRRGGGEVEVRVRgrlVVNDGEALRAAALAGLGIA 146

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 489192100 253 IGPWQLVRDDLSAGLLAAPL-GFLADGSSYHLLTPR 287
Cdd:cd08422  147 LLPDFLVAEDLASGRLVRVLpDWRPPPLPIYAVYPS 182
PRK09801 PRK09801
LysR family transcriptional regulator;
35-161 7.54e-04

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 40.79  E-value: 7.54e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489192100  35 NFSRAAEALCLTHGAISRAVRTLEEELGCALFERRGQRVFLSEAGRRLLAGTGPALDLIER-TGETLRAEAGPTALV-LS 112
Cdd:PRK09801  22 SFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRlVDDVTQIKTRPEGMIrIG 101

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 489192100 113 CEPTLLMRWLIPRIAGFMQEQPRLSIQLVagggpfAFGRGIDLA-------IRRND 161
Cdd:PRK09801 102 CSFGFGRSHIAPAITELMRNYPELQVHFE------LFDRQIDLVqdnidldIRIND 151
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
27-80 1.35e-03

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 39.65  E-value: 1.35e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 489192100  27 FEAAARLENFSRAAEALCLTHGAISRAVRTLEEELGCALFERRGQRVFLSEAGR 80
Cdd:PRK10082  19 FLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGK 72
 
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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