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Conserved domains on  [gi|15600486|ref|NP_253980|]
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transcriptional regulator [Pseudomonas aeruginosa PAO1]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 1001158)

LysR family HTH-containing transcriptional regulator

Gene Ontology:  GO:0003677|GO:0003700
PubMed:  19047729

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK11139 super family cl32646
DNA-binding transcriptional activator GcvA; Provisional
 1-295 1.51e-82

DNA-binding transcriptional activator GcvA; Provisional


The actual alignment was detected with superfamily member PRK11139:

Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 250.92  E-value: 1.51e-82
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486    1 MTRRLPPLYALRAFEAAARHASFTRAGEELAITQSAVSRHIRTLEEHFGCRLFERHGRQLQLTEPARLLLPGLRDGFDAL 80
Cdd:PRK11139   1 MSRRLPPLNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486   81 ERACTALR--VDDATLRLKAPSTLTLRWLLPRLSRFRHLNPDIEVQLTSAWMDvdsVDFQREPFDCAVLLGSGQFsPEWE 158
Cdd:PRK11139  81 AEATRKLRarSAKGALTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDRL---EDFLRDDVDVAIRYGRGNW-PGLR 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486  159 TAALFAEWLVPVCDP---DEAVEPWTLQRLRDSELLHPTpDRRDWRRWLQRTGLgEEVSLKGGQVFDTLELGIVAAARGY 235
Cdd:PRK11139 157 VEKLLDEYLLPVCSPallNGGKPLKTPEDLARHTLLHDD-SREDWRAWFRAAGL-DDLNVQQGPIFSHSSMALQAAIHGQ 234

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486  236 GVSIGDLVMVAEDVAQGRIGLPWPVAVASGESYHLVWPRARRGQERFQRLRDFLLAEVAA 295
Cdd:PRK11139 235 GVALGNRVLAQPEIEAGRLVCPFDTVLPSPNAFYLVCPDSQAELPKVAAFRQWLLAEAAQ 294
 
Name Accession Description Interval E-value
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 1-295 1.51e-82

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 250.92  E-value: 1.51e-82
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486    1 MTRRLPPLYALRAFEAAARHASFTRAGEELAITQSAVSRHIRTLEEHFGCRLFERHGRQLQLTEPARLLLPGLRDGFDAL 80
Cdd:PRK11139   1 MSRRLPPLNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486   81 ERACTALR--VDDATLRLKAPSTLTLRWLLPRLSRFRHLNPDIEVQLTSAWMDvdsVDFQREPFDCAVLLGSGQFsPEWE 158
Cdd:PRK11139  81 AEATRKLRarSAKGALTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDRL---EDFLRDDVDVAIRYGRGNW-PGLR 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486  159 TAALFAEWLVPVCDP---DEAVEPWTLQRLRDSELLHPTpDRRDWRRWLQRTGLgEEVSLKGGQVFDTLELGIVAAARGY 235
Cdd:PRK11139 157 VEKLLDEYLLPVCSPallNGGKPLKTPEDLARHTLLHDD-SREDWRAWFRAAGL-DDLNVQQGPIFSHSSMALQAAIHGQ 234

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486  236 GVSIGDLVMVAEDVAQGRIGLPWPVAVASGESYHLVWPRARRGQERFQRLRDFLLAEVAA 295
Cdd:PRK11139 235 GVALGNRVLAQPEIEAGRLVCPFDTVLPSPNAFYLVCPDSQAELPKVAAFRQWLLAEAAQ 294
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
7-295 4.72e-45

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 153.48  E-value: 4.72e-45
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486   7 PLYALRAFEAAARHASFTRAGEELAITQSAVSRHIRTLEEHFGCRLFERHGRQLQLTEPARLLLPGLRDGFDALERACTA 86
Cdd:COG0583   2 DLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAE 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486  87 LRVDDA----TLRLKAPSTLTLRWLLPRLSRFRHLNPDIEVQLTSAWMDVDSVDFQREPFDCAVLLGSGQfSPEWETAAL 162
Cdd:COG0583  82 LRALRGgprgTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPP-DPGLVARPL 160

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486 163 FAEWLVPVCDPDeavepwtlqrlrdsellHPTPDRRdwrrwlqrtglgeevslkggQVFDTLELGIVAAARGYGVSIGDL 242
Cdd:COG0583 161 GEERLVLVASPD-----------------HPLARRA--------------------PLVNSLEALLAAVAAGLGIALLPR 203

                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|...
gi 15600486 243 VMVAEDVAQGRIGLPWPVAVASGESYHLVWPRARRGQERFQRLRDFLLAEVAA 295
Cdd:COG0583 204 FLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 93-289 1.76e-41

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: 142.33  E-value: 1.76e-41
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486  93 TLRLKAPSTLTLRWLLPRLSRFRHLNPDIEVQLTSAWmdvDSVDFQREPFDCAVLLGSGQFsPEWETAALFAEWLVPVCD 172
Cdd:cd08432   1 VLTVSVTPSFAARWLIPRLARFQARHPDIDLRLSTSD---RLVDFAREGIDLAIRYGDGDW-PGLEAERLMDEELVPVCS 76

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486 173 PD--EAVEPWTLQRLRDSELLHPTpDRRDWRRWLQRTGLGEEVSLKGGQVFDTLELGIVAAARGYGVSIGDLVMVAEDVA 250
Cdd:cd08432  77 PAllAGLPLLSPADLARHTLLHDA-TRPEAWQWWLWAAGVADVDARRGPRFDDSSLALQAAVAGLGVALAPRALVADDLA 155

                       170       180       190
                ....*....|....*....|....*....|....*....
gi 15600486 251 QGRIGLPWPVAVASGESYHLVWPRARRGQERFQRLRDFL 289
Cdd:cd08432 156 AGRLVRPFDLPLPSGGAYYLVYPPGRAESPAVAAFRDWL 194
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 93-294 8.65e-23

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: 93.51  E-value: 8.65e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486    93 TLRLKAPSTLTLRWLLPRLSRFRHLNPDIEVQLTSAWMDvDSVDFQREP-FDCAVLLGSGQfSPEWETAALFAEWLVPVC 171
Cdd:pfam03466   3 RLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSE-ELLDLLLEGeLDLAIRRGPPD-DPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486   172 DPD---EAVEPWTLQRLRDSELLHPTPD---RRDWRRWLQRTGlgeeVSLKGGQVFDTLELGIVAAARGYGVSIGDLVMV 245
Cdd:pfam03466  81 PPDhplARGEPVSLEDLADEPLILLPPGsglRDLLDRALRAAG----LRPRVVLEVNSLEALLQLVAAGLGIALLPRSAV 156

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 15600486   246 AEDVAQGRI-GLPWPVAVASGEsYHLVWPRARRGQERFQRLRDFLLAEVA 294
Cdd:pfam03466 157 ARELADGRLvALPLPEPPLPRE-LYLVWRKGRPLSPAVRAFIEFLREALA 205
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 10-70 5.37e-08

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: 53.00  E-value: 5.37e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15600486    10 ALRAFEAAARHASFTRAGEELAITQSAVSRHIRTLEEHFGCRLFERhGRQLQLTEPARLLL 70
Cdd:TIGR03298   5 QLAALAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVR-TQPCRATEAGQRLL 64
 
Name Accession Description Interval E-value
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 1-295 1.51e-82

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 250.92  E-value: 1.51e-82
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486    1 MTRRLPPLYALRAFEAAARHASFTRAGEELAITQSAVSRHIRTLEEHFGCRLFERHGRQLQLTEPARLLLPGLRDGFDAL 80
Cdd:PRK11139   1 MSRRLPPLNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486   81 ERACTALR--VDDATLRLKAPSTLTLRWLLPRLSRFRHLNPDIEVQLTSAWMDvdsVDFQREPFDCAVLLGSGQFsPEWE 158
Cdd:PRK11139  81 AEATRKLRarSAKGALTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDRL---EDFLRDDVDVAIRYGRGNW-PGLR 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486  159 TAALFAEWLVPVCDP---DEAVEPWTLQRLRDSELLHPTpDRRDWRRWLQRTGLgEEVSLKGGQVFDTLELGIVAAARGY 235
Cdd:PRK11139 157 VEKLLDEYLLPVCSPallNGGKPLKTPEDLARHTLLHDD-SREDWRAWFRAAGL-DDLNVQQGPIFSHSSMALQAAIHGQ 234

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486  236 GVSIGDLVMVAEDVAQGRIGLPWPVAVASGESYHLVWPRARRGQERFQRLRDFLLAEVAA 295
Cdd:PRK11139 235 GVALGNRVLAQPEIEAGRLVCPFDTVLPSPNAFYLVCPDSQAELPKVAAFRQWLLAEAAQ 294
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
7-295 4.72e-45

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 153.48  E-value: 4.72e-45
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486   7 PLYALRAFEAAARHASFTRAGEELAITQSAVSRHIRTLEEHFGCRLFERHGRQLQLTEPARLLLPGLRDGFDALERACTA 86
Cdd:COG0583   2 DLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAE 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486  87 LRVDDA----TLRLKAPSTLTLRWLLPRLSRFRHLNPDIEVQLTSAWMDVDSVDFQREPFDCAVLLGSGQfSPEWETAAL 162
Cdd:COG0583  82 LRALRGgprgTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPP-DPGLVARPL 160

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486 163 FAEWLVPVCDPDeavepwtlqrlrdsellHPTPDRRdwrrwlqrtglgeevslkggQVFDTLELGIVAAARGYGVSIGDL 242
Cdd:COG0583 161 GEERLVLVASPD-----------------HPLARRA--------------------PLVNSLEALLAAVAAGLGIALLPR 203

                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|...
gi 15600486 243 VMVAEDVAQGRIGLPWPVAVASGESYHLVWPRARRGQERFQRLRDFLLAEVAA 295
Cdd:COG0583 204 FLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 93-289 1.76e-41

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: 142.33  E-value: 1.76e-41
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486  93 TLRLKAPSTLTLRWLLPRLSRFRHLNPDIEVQLTSAWmdvDSVDFQREPFDCAVLLGSGQFsPEWETAALFAEWLVPVCD 172
Cdd:cd08432   1 VLTVSVTPSFAARWLIPRLARFQARHPDIDLRLSTSD---RLVDFAREGIDLAIRYGDGDW-PGLEAERLMDEELVPVCS 76

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486 173 PD--EAVEPWTLQRLRDSELLHPTpDRRDWRRWLQRTGLGEEVSLKGGQVFDTLELGIVAAARGYGVSIGDLVMVAEDVA 250
Cdd:cd08432  77 PAllAGLPLLSPADLARHTLLHDA-TRPEAWQWWLWAAGVADVDARRGPRFDDSSLALQAAVAGLGVALAPRALVADDLA 155

                       170       180       190
                ....*....|....*....|....*....|....*....
gi 15600486 251 QGRIGLPWPVAVASGESYHLVWPRARRGQERFQRLRDFL 289
Cdd:cd08432 156 AGRLVRPFDLPLPSGGAYYLVYPPGRAESPAVAAFRDWL 194
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
11-294 1.50e-39

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 140.52  E-value: 1.50e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486   11 LRAFEAAARHASFTRAGEELAITQSAVSRHIRTLEEHFGCRLFERHGRQLQLTEPARLLLPGLRDGFDALERACTALRVD 90
Cdd:PRK10086  19 LHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLDTLNQEILDIKNQ 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486   91 D--ATLRLKAPSTLTLRWLLPRLSRFRHLNPDIEVQLTSAwmdVDSVDFQREPFDCAVLLGSGQfSPEWETAALFAEWLV 168
Cdd:PRK10086  99 ElsGTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTILTG---NENVNFQRAGIDLAIYFDDAP-SAQLTHHFLMDEEIL 174

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486  169 PVCDPDEAVE---PWTLQRLRDSELLHptpDRRDWRR---------WLQRTGLGEEVSLKgGQVFDTLELGIVAAARGYG 236
Cdd:PRK10086 175 PVCSPEYAERhalTGNPDNLRHCTLLH---DRQAWSNdsgtdewhsWAQHFGVNLLPPSS-GIGFDRSDLAVIAAMNHIG 250

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 15600486  237 VSIGDLVMVAEDVAQGRIGLPWP-VAVASGESYHLVWPRARRGQeRFQRLRDFLLAEVA 294
Cdd:PRK10086 251 VAMGRKRLVQKRLASGELVAPFGdMEVKCHQHYYVTTLPGRQWP-KIEAFIDWLKEQVK 308
PBP2_TrpI cd08482
The C-terminal substrate binding domain of LysR-type transcriptional regulator TrpI, which is ...
 94-289 1.54e-26

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: 103.25  E-value: 1.54e-26
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486  94 LRLKAPSTLTLRWLLPRLSRFRHLNPDIEVQLTSawmDVDSVDFQREPFDCAVLLGSGQFSPEWETAALFAEWLVPVCDP 173
Cdd:cd08482   2 LVLSCSGSLLMRWLIPRLPAFQAALPDIDLQLSA---SDGPVDSLRDGIDAAIRFNDAPWPAGMQVIELFPERVGPVCSP 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486 174 DEAVEpWTL-----QRLRDSELLHPTPDRRDWRRWLQRTGLGEEvSLKGGQVFDTLELGIVAAARGYGVSIGDLVMVAED 248
Cdd:cd08482  79 SLAPT-VPLrqapaAALLGAPLLHTRSRPQAWPDWAAAQGLAPE-KLGTGQSFEHFYYLLEAAVAGLGVAIAPWPLVRDD 156

                       170       180       190       200
                ....*....|....*....|....*....|....*....|.
gi 15600486 249 VAQGRIGLPWPVaVASGESYHLvWPRARRGQERFQRLRDFL 289
Cdd:cd08482 157 LASGRLVAPWGF-IETGSHYVL-LRPARLRDSRAGALADWL 195
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 93-294 8.65e-23

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: 93.51  E-value: 8.65e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486    93 TLRLKAPSTLTLRWLLPRLSRFRHLNPDIEVQLTSAWMDvDSVDFQREP-FDCAVLLGSGQfSPEWETAALFAEWLVPVC 171
Cdd:pfam03466   3 RLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSE-ELLDLLLEGeLDLAIRRGPPD-DPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486   172 DPD---EAVEPWTLQRLRDSELLHPTPD---RRDWRRWLQRTGlgeeVSLKGGQVFDTLELGIVAAARGYGVSIGDLVMV 245
Cdd:pfam03466  81 PPDhplARGEPVSLEDLADEPLILLPPGsglRDLLDRALRAAG----LRPRVVLEVNSLEALLQLVAAGLGIALLPRSAV 156

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 15600486   246 AEDVAQGRI-GLPWPVAVASGEsYHLVWPRARRGQERFQRLRDFLLAEVA 294
Cdd:pfam03466 157 ARELADGRLvALPLPEPPLPRE-LYLVWRKGRPLSPAVRAFIEFLREALA 205
PBP2_GcdR_like cd08481
The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, ...
 101-289 2.67e-22

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: 91.97  E-value: 2.67e-22
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486 101 TLTLRWLLPRLSRFRHLNPDIEVQLTSawmDVDSVDFQREPFDCAVLLGSGQFsPEWETAALFAEWLVPVCDPD--EAVE 178
Cdd:cd08481   9 TFGTRWLIPRLPDFLARHPDITVNLVT---RDEPFDFSQGSFDAAIHFGDPVW-PGAESEYLMDEEVVPVCSPAllAGRA 84

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486 179 PWTLQRLRDSELLHPTPDRRDWRRWLQRTGLGEEVSLKGGQvFDTLELGIVAAARGYGVSIGDLVMVAEDVAQGRIGLPW 258
Cdd:cd08481  85 LAAPADLAHLPLLQQTTRPEAWRDWFEEVGLEVPTAYRGMR-FEQFSMLAQAAVAGLGVALLPRFLIEEELARGRLVVPF 163

                       170       180       190
                ....*....|....*....|....*....|.
gi 15600486 259 PVAVASGESYHLVWPRARRGQERFQRLRDFL 289
Cdd:cd08481 164 NLPLTSDKAYYLVYPEDKAESPPVQAFRDWL 194
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
8-67 3.69e-21

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 84.74  E-value: 3.69e-21
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486     8 LYALRAFEAAARHASFTRAGEELAITQSAVSRHIRTLEEHFGCRLFERHGRQLQLTEPAR 67
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PBP2_LTTR_beta_lactamase cd08484
The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase ...
 94-276 2.35e-18

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: 81.26  E-value: 2.35e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486  94 LRLKAPSTLTLRWLLPRLSRFRHLNPDIEVQLTSawmDVDSVDFQREPFDCAVLLGSGQFsPEWETAALFAEWLVPVCDP 173
Cdd:cd08484   2 LTVGAVGTFAVGWLLPRLAEFRQLHPFIDLRLST---NNNRVDIAAEGLDFAIRFGEGAW-PGTDATRLFEAPLSPLCTP 77

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486 174 DEAvepwtlQRLRD-SELLHPTPDRR----DWRRWLQRTGLGeeVSLKGGQVFDTLELGIVAAARGYGVSIGDLVMVAED 248
Cdd:cd08484  78 ELA------RRLSEpADLANETLLRSyradEWPQWFEAAGVP--PPPINGPVFDSSLLMVEAALQGAGVALAPPSMFSRE 149

                       170       180
                ....*....|....*....|....*...
gi 15600486 249 VAQGRIGLPWPVAVASGeSYHLVWPRAR 276
Cdd:cd08484 150 LASGALVQPFKITVSTG-SYWLTRLKSK 176
PBP2_AmpR cd08488
The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in ...
 94-289 7.68e-17

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: 77.19  E-value: 7.68e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486  94 LRLKAPSTLTLRWLLPRLSRFRHLNPDIEVQLTSawmDVDSVDFQREPFDCAVLLGSGQFsPEWETAALFAEWLVPVCDP 173
Cdd:cd08488   2 LHVGAVGTFAVGWLLPRLADFQNRHPFIDLRLST---NNNRVDIAAEGLDYAIRFGSGAW-HGIDATRLFEAPLSPLCTP 77

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486 174 DEAvepwtlQRLRD-SELLHPTPDRR----DWRRWLQRTGLGEEVSLKGGQVFDTlELGIVAAAR-GYGVSIGDLVMVAE 247
Cdd:cd08488  78 ELA------RQLREpADLARHTLLRSyradEWPQWFEAAGVGHPCGLPNSIMFDS-SLGMMEAALqGLGVALAPPSMFSR 150

                       170       180       190       200
                ....*....|....*....|....*....|....*....|..
gi 15600486 248 DVAQGRIGLPWPVAVASGeSYHLVWPRARRGQERFQRLRDFL 289
Cdd:cd08488 151 QLASGALVQPFATTLSTG-SYWLTRLQSRPETPAMSAFSAWL 191
PBP2_BlaA cd08487
The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which ...
 94-289 3.86e-15

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: 72.19  E-value: 3.86e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486  94 LRLKAPSTLTLRWLLPRLSRFRHLNPDIEVQLTSawmDVDSVDFQREPFDCAVLLGSGQFsPEWETAALFAEWLVPVCDP 173
Cdd:cd08487   2 LTVGAVGTFAVGWLLPRLAEFRQLHPFIELRLRT---NNNVVDLATEGLDFAIRFGEGLW-PATHNERLLDAPLSVLCSP 77

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486 174 DEAVEpwtLQRLRD--SELLHPTPDRRDWRRWLQRTGLgeEVSLKGGQVFDTLELGIVAAARGYGVSIGDLVMVAEDVAQ 251
Cdd:cd08487  78 EIAKR---LSHPADliNETLLRSYRTDEWLQWFEAANM--PPIKIRGPVFDSSRLMVEAAMQGAGVALAPAKMFSREIEN 152

                       170       180       190
                ....*....|....*....|....*....|....*...
gi 15600486 252 GRIGLPWPVAVASGeSYHLVWPRARRGQERFQRLRDFL 289
Cdd:cd08487 153 GQLVQPFKIEVETG-SYWLTWLKSKPMTPAMELFRQWI 189
rbcR CHL00180
LysR transcriptional regulator; Provisional
 11-125 3.14e-14

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 71.59  E-value: 3.14e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486   11 LRAFEAAARHASFTRAGEELAITQSAVSRHIRTLEEHFGCRLFERHGRQLQLTEPARLLlpgLRDGFDAL---ERACTAL 87
Cdd:CHL00180  10 LRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELL---LRYGNRILalcEETCRAL 86

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 15600486   88 ----RVDDATLRLKAPSTlTLRWLLPRL-SRFRHLNPDIEVQL 125
Cdd:CHL00180  87 edlkNLQRGTLIIGASQT-TGTYLMPRLiGLFRQRYPQINVQL 128
PRK09986 PRK09986
LysR family transcriptional regulator;
8-125 3.16e-12

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 65.90  E-value: 3.16e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486    8 LYALRAFEAAARHASFTRAGEELAITQSAVSRHIRTLEEHFGCRLFERHGRQLQLTEPARLLLPGLRDGFDALERACTAL 87
Cdd:PRK09986   9 LKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLARV 88

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 15600486   88 ----RVDDATLRLKAPSTLTLRWLLPRLSRFRHLNPDIEVQL 125
Cdd:PRK09986  89 eqigRGEAGRIEIGIVGTALWGRLRPAMRHFLKENPNVEWLL 130
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 8-125 1.67e-11

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 63.55  E-value: 1.67e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486    8 LYALRAFEAAARHASFTRAGEELAITQSAVSRHIRTLEEHFGCRLFERHGRQLQLTEPARLLLPGLRdgfDALERACTA- 86
Cdd:PRK10837   5 LRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRAL---ALLEQAVEIe 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 15600486   87 --LRVDDATLRLKAPSTLTLRWLLPRLSRFRHLNPDIEVQL 125
Cdd:PRK10837  82 qlFREDNGALRIYASSTIGNYILPAMIARYRRDYPQLPLEL 122
PBP2_HvrB cd08483
The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an ...
 94-271 1.98e-11

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: 61.98  E-value: 1.98e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486  94 LRLKAPSTLTLRWLLPRLSRFRHLNPDIEVQLTSAwMDVdsVDFQREPFDCAVLLGSGQFsPEWETAALFAEWLVPVCDP 173
Cdd:cd08483   2 LTVTLTPSFASNWLMPRLGSFWAKHPEIELSLLPS-ADL--VDLRPDGIDVAIRYGNGDW-PGLESEPLTAAPFVVVAAP 77

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486 174 DeavepWTLQRLRDS-ELLHPTP-----DRRDWRRWLQRTGLgeEVSLKGGQVFDTLELGIVAAARGYGVSIGDLVMVAE 247
Cdd:cd08483  78 G-----LLGDRKVDSlADLAGLPwlqerGTNEQRVWLASMGV--VPDLERGVTFLPGQLVLEAARAGLGLSIQARALVEP 150

                       170       180
                ....*....|....*....|....
gi 15600486 248 DVAQGRIGLPWPvAVASGESYHLV 271
Cdd:cd08483 151 DIAAGRLTVLFE-EEEEGLGYHIV 173
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 11-167 2.37e-11

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 63.05  E-value: 2.37e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486   11 LRAFEAAARHASFTRAGEELAITQSAVSRHIRTLEEHFGCRLFERHGRQLQLTEPARLLLPGLRDGFDALERACTALR-V 89
Cdd:PRK11242   6 IRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRRAIHdV 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486   90 DDAT---LRLKAPSTLTLRWLLPRLSRFRHLNPDIEVQLTSAWMDVDSVDFQREPFDCAVLLgSGQFSPEWETAALFAEW 166
Cdd:PRK11242  86 ADLSrgsLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMSQERIEALLADDELDVGIAF-APVHSPEIEAQPLFTET 164


                 .
gi 15600486  167 L 167
Cdd:PRK11242 165 L 165
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 15-125 3.41e-10

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 60.01  E-value: 3.41e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486   15 EAAARHASFTRAGEELAITQSAVSRHIRTLEEHFGCRLFERHGRQLQ-LTEPARLLLPG----LRDgFDALER-ACTALR 88
Cdd:PRK12682  11 EAVRRNLNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKgLTEPGKAVLDVieriLRE-VGNIKRiGDDFSN 89

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 15600486   89 VDDATLRLKAPSTLTlRWLLPR-LSRFRHLNPDIEVQL 125
Cdd:PRK12682  90 QDSGTLTIATTHTQA-RYVLPRvVAAFRKRYPKVNLSL 126
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 93-289 2.45e-09

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: 55.91  E-value: 2.45e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486  93 TLRLKAPSTLTLRWLLPRLSRFRHLNPDIEVQLTsawMDVDSVDFQREPFDCAVLLGSGQFSpewETAA--LFAEWLVPV 170
Cdd:cd08422   2 RLRISAPVSFGRLHLAPLLAEFLARYPDVRLELV---LSDRLVDLVEEGFDLAIRIGELPDS---SLVArrLGPVRRVLV 75

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486 171 CDPD---EAVEPWTLQRLRDSELLHPTPDRRDWRRWLQRTGLGEEVSLKGGQVFDTLELGIVAAARGYGVSIGDLVMVAE 247
Cdd:cd08422  76 ASPAylaRHGTPQTPEDLARHRCLGYRLPGRPLRWRFRRGGGEVEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAE 155

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*..
gi 15600486 248 DVAQGRIglpwpVAV-----ASGESYHLVWPRARRGQERFQRLRDFL 289
Cdd:cd08422 156 DLASGRL-----VRVlpdwrPPPLPIYAVYPSRRHLPAKVRAFIDFL 197
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
10-81 2.75e-09

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 57.12  E-value: 2.75e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15600486   10 ALRAFEAAARHASFTRAGEELAITQSAVSRHIRTLEEHFGCRLFERHGRQLQLTEPARLLLPGLRDGFDALE 81
Cdd:PRK10094   6 TLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLE 77
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 11-131 5.15e-09

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 56.19  E-value: 5.15e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486   11 LRAFEAAARHASFTRAGEELAITQSAVSRHIRTLEEHFGCRLFERHGRQLQLTEPARLLLPGLRDGFDALERACTALRVD 90
Cdd:PRK15092  16 LRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEACSSLMYS 95

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 15600486   91 DA--TLRLKAPSTlTLRWLLP-RLSRFRHLNP----DIEVQLTSAWMD 131
Cdd:PRK15092  96 NLqgVLTIGASDD-TADTILPfLLNRVSSVYPklalDVRVKRNAFMME 142
cbl PRK12679
HTH-type transcriptional regulator Cbl;
15-125 6.28e-09

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 55.97  E-value: 6.28e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486   15 EAAARHASFTRAGEELAITQSAVSRHIRTLEEHFGCRLFERHG-RQLQLTEPARLLLPGLRDGFDALE--RACTALRVDD 91
Cdd:PRK12679  11 EAARQDYNLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGkRLLGMTEPGKALLVIAERILNEASnvRRLADLFTND 90

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 15600486   92 ATLRLKAPSTLT-LRWLLPRLSR-FRHLNPDIEVQL 125
Cdd:PRK12679  91 TSGVLTIATTHTqARYSLPEVIKaFRELFPEVRLEL 126
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 8-239 1.51e-08

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 54.78  E-value: 1.51e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486    8 LYALRAFEAAARHASFTRAGEELAITQSAVSRHIRTLEEHFGCRLFERHGRQLQLTEPARLLLPGLRDGFDALERA-CTA 86
Cdd:PRK09906   3 LRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAkLRA 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486   87 LRVDDATLRLK---APST--LTLRWLLPRLsRFRHlnPDIEVQLTSAWM----------DVDsVDFQREPFDcavllgsg 151
Cdd:PRK09906  83 RKIVQEDRQLTigfVPSAevNLLPKVLPMF-RLRH--PDTLIELVSLITtqqeeklrrgELD-VGFMRHPVY-------- 150

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486  152 qfSPEWETAALFAEWLV---PVCDPDEAVEPWTLQRLRDSELLHPTPDRrdwRRWLQRTGLG----EEVSLKGGQVFDTL 224
Cdd:PRK09906 151 --SDEIDYLELLDEPLVvvlPVDHPLAHEKEITAAQLDGVNFISTDPAY---SGSLAPIIKAwfaqHNSQPNIVQVATNI 225

                        250
                 ....*....|....*
gi 15600486  225 ELGIVAAARGYGVSI 239
Cdd:PRK09906 226 LVTMNLVGMGLGCTI 240
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 15-71 2.05e-08

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 54.66  E-value: 2.05e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 15600486   15 EAAARHASFTRAGEELAITQSAVSRHIRTLEEHFGCRLFERHG-RQLQLTEPARLLLP 71
Cdd:PRK12683  11 EAVRQNFNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGkRLTGLTEPGKELLQ 68
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
11-233 2.37e-08

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 54.25  E-value: 2.37e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486   11 LRAFEAAARHASFTRAGEELAITQSAVSRHIRTLEEHFGCRLFERHGRQLQLTEPARLLLPGLRDGFDALERACTALRVD 90
Cdd:PRK15421   7 LKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQACNEP 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486   91 DAT-LRLKAPSTLTLRWLLPRLSRFRHLNPDIEVQLTSAWMDVDSVDFQREPFDCA----VLLGSG-QFSPewetaaLFA 164
Cdd:PRK15421  87 QQTrLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVmtsdILPRSGlHYSP------MFD 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15600486  165 EWLVPVCDPDEAVEPWTLQRLRD--SELLHPTPDRRD----WRRWLQRTGLGEevSLKggQVFDTLELGIVAAAR 233
Cdd:PRK15421 161 YEVRLVLAPDHPLAAKTRITPEDlaSETLLIYPVQRSrldvWRHFLQPAGVSP--SLK--SVDNTLLLIQMVAAR 231
PBP2_CrgA_like_8 cd08477
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-289 2.77e-08

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: 53.00  E-value: 2.77e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486  93 TLRLKAPSTLTLRWLLPRLSRFRHLNPDIEVQLTsawMDVDSVDFQREPFDCAVLLGsgqfspEWETAALFAEWLVP--- 169
Cdd:cd08477   2 KLRISAPVTFGSHVLTPALAEYLARYPDVRVDLV---LSDRLVDLVEEGFDAAFRIG------ELADSSLVARPLAPyrm 72

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486 170 -VC-DPD---EAVEPWTLQRLRDSELL--HPTPDRRDWRrwLQRTGLGEEVSLKGGQVFDTLELGIVAAARGYGVSIGDL 242
Cdd:cd08477  73 vLCaSPDylaRHGTPTTPEDLARHECLgfSYWRARNRWR--LEGPGGEVKVPVSGRLTVNSGQALRVAALAGLGIVLQPE 150

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*..
gi 15600486 243 VMVAEDVAQGRIGLPWPVAVASGESYHLVWPRARRGQERFQRLRDFL 289
Cdd:cd08477 151 ALLAEDLASGRLVELLPDYLPPPRPMHLLYPPDRRPTPKLRSFIDFL 197
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 14-135 2.96e-08

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 53.84  E-value: 2.96e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486   14 FEAAARHASFTRAGEELAITQSAVSRHIRTLEEHFGCRLFERHGRQLQLTEPARLLLPGLRDGF---DALERACTALRVD 90
Cdd:PRK14997  10 FVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLveaQAAQDAIAALQVE 89

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 15600486   91 D-ATLRLKAPSTLTLRWLLPRLSRFRHLNPDIEVQLTSAWMDVDSV 135
Cdd:PRK14997  90 PrGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLEATNRRVDVV 135
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 9-64 4.17e-08

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 53.41  E-value: 4.17e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 15600486    9 YALRAFEAAARHASFTRAGEELAITQSAVSRHIRTLEEHFGCRLFERHGRQLQLTE 64
Cdd:PRK11074   5 YSLEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTP 60
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
19-71 4.78e-08

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 53.10  E-value: 4.78e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 15600486   19 RHasFTRAGEELAITQSAVSRHIRTLEEHFGCRLFERHGRQLQLTEPARLLLP 71
Cdd:PRK03601  16 RH--FGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLP 66
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 10-70 5.37e-08

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: 53.00  E-value: 5.37e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15600486    10 ALRAFEAAARHASFTRAGEELAITQSAVSRHIRTLEEHFGCRLFERhGRQLQLTEPARLLL 70
Cdd:TIGR03298   5 QLAALAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVR-TQPCRATEAGQRLL 64
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
10-70 7.54e-08

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 52.85  E-value: 7.54e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15600486   10 ALRAFEAAARHASFTRAGEELAITQSAVSRHIRTLEEHFGCRLFERhGRQLQLTEPARLLL 70
Cdd:PRK03635   6 QLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRLL 65
PRK10341 PRK10341
transcriptional regulator TdcA;
5-128 1.03e-07

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 52.56  E-value: 1.03e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486    5 LPPLYALRAFEAAARHASFTRAGEELAITQSAVSRHIRTLEEHFGCRLFERHGRQLQLTEPARLLLPGLRDGFDALERAC 84
Cdd:PRK10341   6 LPKTQHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMV 85

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 15600486   85 TALRV----DDATLRLKAPSTLTLRWLLPRLSRFRHLNPDIEVQLTSA 128
Cdd:PRK10341  86 NEINGmsseAVVDVSFGFPSLIGFTFMSDMINKFKEVFPKAQVSMYEA 133
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
22-179 1.09e-07

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 52.36  E-value: 1.09e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486   22 SFTRAGEELAITQSAVSRHIRTLEEHFGCRLFERHGRQLQLTEPARLLLPGLRDGFDALERACTALR-VDDATLR---LK 97
Cdd:PRK10082  27 NFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESNLAELRgGSDYAQRkikIA 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486   98 APSTLTLRwLLPrlSRFRHLNPDIEVQLTSawMDVD-SVDFQRE-PFDCAVLLGSGQF-SPEWETAALFAEWLVPVCDPD 174
Cdd:PRK10082 107 AAHSLSLG-LLP--SIISQMPPLFTWAIEA--IDVDeAVDKLREgQSDCIFSFHDEDLlEAPFDHIRLFESQLFPVCASD 181


                 ....*
gi 15600486  175 EAVEP 179
Cdd:PRK10082 182 EHGEA 186
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
32-126 2.34e-07

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 50.97  E-value: 2.34e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486   32 ITQSAVSRHIRTLEEHFGCRLFERHGRQLQLTEPARLLLPGLRDGFDALERACTALRVDDA----TLRLKAPSTLTLRWL 107
Cdd:PRK11716   3 VSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPslsgELSLFCSVTAAYSHL 82

                         90
                 ....*....|....*....
gi 15600486  108 LPRLSRFRHLNPDIEVQLT 126
Cdd:PRK11716  83 PPILDRFRAEHPLVEIKLT 101
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
11-70 2.53e-07

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 51.13  E-value: 2.53e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486   11 LRAFEAAARHASFTRAGEELAITQSAVSRHIRTLEEHFGCRLFERhGRQLQLTEPARLLL 70
Cdd:PRK13348   7 LEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQRLL 65
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 93-289 3.56e-07

The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; This model and hierarchy represent the the substrate-binding domain of the LysR-type transcriptional regulators that form the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, oxidative stress responses, nodule formation of nitrogen-fixing bacteria, synthesis of virulence factors, toxin production, attachment and secretion, to name a few. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 176102 [Multi-domain]  Cd Length: 197  Bit Score: 49.52  E-value: 3.56e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486  93 TLRLKAPSTLTLRWLLPRLSRFRHLNPDIEVQLTSAwmdvDSVDFQRE----PFDCAVLLGSGQfSPEWETAALFAEWLV 168
Cdd:cd05466   1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEG----GSSELLEAllegELDLAIVALPVD-DPGLESEPLFEEPLV 75

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486 169 PVCDPD---EAVEPWTLQRLRDSELLHPTPD---RRDWRRWLQRTGLGEEVSLKggqvFDTLELGIVAAARGYGVSIGDL 242
Cdd:cd05466  76 LVVPPDhplAKRKSVTLADLADEPLILFERGsglRRLLDRAFAEAGFTPNIALE----VDSLEAIKALVAAGLGIALLPE 151

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*..
gi 15600486 243 VMVAEDVAQGRIGLPWPVAVASgESYHLVWPRARRGQERFQRLRDFL 289
Cdd:cd05466 152 SAVEELADGGLVVLPLEDPPLS-RTIGLVWRKGRYLSPAARAFLELL 197
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
15-70 3.78e-07

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 50.75  E-value: 3.78e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 15600486   15 EAAARHASFTRAGEELAITQSAVSRHIRTLEEHFGCRLFERHGRQLQ-LTEPARLLL 70
Cdd:PRK12684  11 EAVRQNFNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRgLTEPGRIIL 67
PRK09791 PRK09791
LysR family transcriptional regulator;
8-74 7.87e-07

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 49.76  E-value: 7.87e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15600486    8 LYALRAFEAAARHASFTRAGEELAITQSAVSRHIRTLEEHFGCRLFERHGRQLQLTE-------PARLLLPGLR 74
Cdd:PRK09791   7 IHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDagesfyqHASLILEELR 80
nhaR PRK11062
transcriptional activator NhaR; Provisional
 22-64 4.67e-04

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 41.15  E-value: 4.67e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 15600486   22 SFTRAGEELAITQSAVSRHIRTLEEHFGCRLFERHGRQLQLTE 64
Cdd:PRK11062  20 SVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTE 62
PRK11886 PRK11886
bifunctional biotin--[acetyl-CoA-carboxylase] ligase/biotin operon repressor BirA;
27-71 5.73e-04

bifunctional biotin--[acetyl-CoA-carboxylase] ligase/biotin operon repressor BirA;


Pssm-ID: 237010 [Multi-domain]  Cd Length: 319  Bit Score: 40.93  E-value: 5.73e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 15600486   27 GEELAITQSAVSRHIRTLEEHfGCRLFERHGRQLQLTEPARLLLP 71
Cdd:PRK11886  25 GEELGISRAAIWKHIQTLEEW-GLDIFSVKGKGYRLAEPLDLLDP 68
leuO PRK09508
leucine transcriptional activator; Reviewed
 11-74 6.29e-04

leucine transcriptional activator; Reviewed


Pssm-ID: 181918 [Multi-domain]  Cd Length: 314  Bit Score: 40.78  E-value: 6.29e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15600486   11 LRAFEAAARHASFTRAGEELAITQSAVSRHIRTLEEHFGCRLFERHGRQLQLTEPARLLLPGLR 74
Cdd:PRK09508  27 LTVFDAVMQEQNITRAAHNLGMSQPAVSNAVARLKVMFNDELFVRYGRGIQPTARARQLFGPVR 90
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 11-70 9.86e-04

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 40.01  E-value: 9.86e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486   11 LRAFE---AAARHASFTRAGEELAITQSAVSRHIRTLEEHFGCRLFERHGRQ-------LQLTEPARLLL 70
Cdd:PRK11151   3 IRDLEylvALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKvlftqagLLLVDQARTVL 72
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-253 1.33e-03

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: 38.98  E-value: 1.33e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486  93 TLRLKAPSTLTLRWLLPRLSRFRHLNPDIEVQLTsawMDVDSVDFQREPFDCAVLLGSG--------QFSPEWETAAlfa 164
Cdd:cd08474   4 TLRINAPRVAARLLLAPLLARFLARYPDIRLELV---VDDGLVDIVAEGFDAGIRLGESvekdmvavPLGPPLRMAV--- 77

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486 165 ewlvpVCDPDeavepwTLQRlrdsellHPTPDR-RD--------WR--------RW-LQRTGLGEEVSLKGGQVFDTLEL 226
Cdd:cd08474  78 -----VASPA------YLAR-------HGTPEHpRDllnhrcirYRfptsgalyRWeFERGGRELEVDVEGPLILNDSDL 139

                       170       180
                ....*....|....*....|....*..
gi 15600486 227 GIVAAARGYGVSIGDLVMVAEDVAQGR 253
Cdd:cd08474 140 MLDAALDGLGIAYLFEDLVAEHLASGR 166
PBP2_CrgA_like_3 cd08472
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-149 1.74e-03

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: 38.65  E-value: 1.74e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 15600486  93 TLRLKAPSTLTLRWLLPRLSRFRHLNPDIEVQLTSAwmdvD-SVDFQREPFDCAVLLG 149
Cdd:cd08472   2 RLRVDVPGSLARLLLIPALPDFLARYPDIELDLGVS----DrPVDLIREGVDCVIRVG 55
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
22-74 3.40e-03

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 38.59  E-value: 3.40e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 15600486   22 SFTRAGEELAITQSAVSRHIRTLEEHFGCRLFERHGRQLQLTEPARLLLPGLR 74
Cdd:PRK10632  18 SFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCR 70
PRK12680 PRK12680
LysR family transcriptional regulator;
24-128 5.26e-03

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 38.06  E-value: 5.26e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600486   24 TRAGEELAITQSAVSRHIRTLEEHFGCRLFERHGRQLQLTEPArlllpglrdGFDALERACTAL------RVDDATLRLK 97
Cdd:PRK12680  20 TLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLESVTPA---------GVEVIERARAVLseanniRTYAANQRRE 90

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 15600486   98 APSTLTL-------RWLL-PRLSRFRHLNPDIEVQLTSA 128
Cdd:PRK12680  91 SQGQLTLttthtqaRFVLpPAVAQIKQAYPQVSVHLQQA 129
 
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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