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Conserved domains on  [gi|488997098|ref|WP_002907799|]
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MULTISPECIES: LysR substrate-binding domain-containing protein [Klebsiella]

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
 16-293 1.60e-62

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: 199.30  E-value: 1.60e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098  16 AAARHGNFARAAAELALTEGAISRQIARLEALLDSKLFDRTGSRVRLNPAGARYARQVREILARLERDTHDVSGMPVDGR 95
Cdd:PRK11139  16 AAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEATRKLRARSAKGA 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098  96 sLEIAVLPTFASRWLIPRLGRFAAQHPHIVVNIAARSDPFILPGSGFDAAIHFEHPAWTGMEVTFLFAEYLLPVCHAALL 175
Cdd:PRK11139  96 -LTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDRLEDFLRDDVDVAIRYGRGNWPGLRVEKLLDEYLLPVCSPALL 174

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098 176 TDDDL---PGLLNRLTRIHrRQNPDAWLHYARECGLALDNPAQGPRYDLHEMAIAAVLSQQGVALVPKMYVESELSAGTL 252
Cdd:PRK11139 175 NGGKPlktPEDLARHTLLH-DDSREDWRAWFRAAGLDDLNVQQGPIFSHSSMALQAAIHGQGVALGNRVLAQPEIEAGRL 253

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|.
gi 488997098 253 VAPWPGSPTLAKRFCLIKPGGGEGEPALQMFERWLQTEIAA 293
Cdd:PRK11139 254 VCPFDTVLPSPNAFYLVCPDSQAELPKVAAFRQWLLAEAAQ 294
 
Name Accession Description Interval E-value
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 16-293 1.60e-62

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 199.30  E-value: 1.60e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098  16 AAARHGNFARAAAELALTEGAISRQIARLEALLDSKLFDRTGSRVRLNPAGARYARQVREILARLERDTHDVSGMPVDGR 95
Cdd:PRK11139  16 AAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEATRKLRARSAKGA 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098  96 sLEIAVLPTFASRWLIPRLGRFAAQHPHIVVNIAARSDPFILPGSGFDAAIHFEHPAWTGMEVTFLFAEYLLPVCHAALL 175
Cdd:PRK11139  96 -LTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDRLEDFLRDDVDVAIRYGRGNWPGLRVEKLLDEYLLPVCSPALL 174

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098 176 TDDDL---PGLLNRLTRIHrRQNPDAWLHYARECGLALDNPAQGPRYDLHEMAIAAVLSQQGVALVPKMYVESELSAGTL 252
Cdd:PRK11139 175 NGGKPlktPEDLARHTLLH-DDSREDWRAWFRAAGLDDLNVQQGPIFSHSSMALQAAIHGQGVALGNRVLAQPEIEAGRL 253

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|.
gi 488997098 253 VAPWPGSPTLAKRFCLIKPGGGEGEPALQMFERWLQTEIAA 293
Cdd:PRK11139 254 VCPFDTVLPSPNAFYLVCPDSQAELPKVAAFRQWLLAEAAQ 294
PBP2_GcdR_like cd08481
The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, ...
 96-287 4.67e-61

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: 192.13  E-value: 4.67e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098  96 SLEIAVLPTFASRWLIPRLGRFAAQHPHIVVNIAARSDPFILPGSGFDAAIHFEHPAWTGMEVTFLFAEYLLPVCHAALL 175
Cdd:cd08481    1 TLELAVLPTFGTRWLIPRLPDFLARHPDITVNLVTRDEPFDFSQGSFDAAIHFGDPVWPGAESEYLMDEEVVPVCSPALL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098 176 TDDDL--PGLLNRLTRIHRRQNPDAWLHYARECGLALDNPAQGPRYDLHEMAIAAVLSQQGVALVPKMYVESELSAGTLV 253
Cdd:cd08481   81 AGRALaaPADLAHLPLLQQTTRPEAWRDWFEEVGLEVPTAYRGMRFEQFSMLAQAAVAGLGVALLPRFLIEEELARGRLV 160

                        170       180       190
                 ....*....|....*....|....*....|....
gi 488997098 254 APWPGSPTLAKRFCLIKPGGGEGEPALQMFERWL 287
Cdd:cd08481  161 VPFNLPLTSDKAYYLVYPEDKAESPPVQAFRDWL 194
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
19-293 2.28e-43

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 148.86  E-value: 2.28e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098  19 RHGNFARAAAELALTEGAISRQIARLEALLDSKLFDRTGSRVRLNPAGARYARQVREILARLERDTHDVSGMP-VDGRSL 97
Cdd:COG0583   14 EEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAELRALRgGPRGTL 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098  98 EIAVLPTFASRWLIPRLGRFAAQHPHIVVNIAARSDPFILPG---SGFDAAIHFEHPAWTGMEVTFLFAEYLLPVCHAAl 174
Cdd:COG0583   94 RIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDAlleGELDLAIRLGPPPDPGLVARPLGEERLVLVASPD- 172

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098 175 ltdddlpgllnrltriHRrqnpdawlhyarecgLAldnpAQGPRYDLHEMAIAAVLSQQGVALVPKMYVESELSAGTLVA 254
Cdd:COG0583  173 ----------------HP---------------LA----RRAPLVNSLEALLAAVAAGLGIALLPRFLAADELAAGRLVA 217

                        250       260       270
                 ....*....|....*....|....*....|....*....
gi 488997098 255 PWPGSPTLAKRFCLIKPGGGEGEPALQMFERWLQTEIAA 293
Cdd:COG0583  218 LPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 95-292 2.40e-16

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: 75.79  E-value: 2.40e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098   95 RSLEIAVLPTFASRWLIPRLGRFAAQHPHIVVNIAARSDPFILPG--SG-FDAAIHFEHPAWTGMEVTFLFAEYLLPVCH 171
Cdd:pfam03466   2 GRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLllEGeLDLAIRRGPPDDPGLEARPLGEEPLVLVAP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098  172 AA--LLTDDDL-PGLLNRLTRIHRRQNPDAWLHYARECGLALDNPAQGPRYDLHEMAIAAVLSQQGVALVPKMYVESELS 248
Cdd:pfam03466  82 PDhpLARGEPVsLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARELA 161

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 488997098  249 AGTLVA-PWPGsPTLAKRFCLIKPGGGEGEPALQMFERWLQTEIA 292
Cdd:pfam03466 162 DGRLVAlPLPE-PPLPRELYLVWRKGRPLSPAVRAFIEFLREALA 205
 
Name Accession Description Interval E-value
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 16-293 1.60e-62

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 199.30  E-value: 1.60e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098  16 AAARHGNFARAAAELALTEGAISRQIARLEALLDSKLFDRTGSRVRLNPAGARYARQVREILARLERDTHDVSGMPVDGR 95
Cdd:PRK11139  16 AAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEATRKLRARSAKGA 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098  96 sLEIAVLPTFASRWLIPRLGRFAAQHPHIVVNIAARSDPFILPGSGFDAAIHFEHPAWTGMEVTFLFAEYLLPVCHAALL 175
Cdd:PRK11139  96 -LTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDRLEDFLRDDVDVAIRYGRGNWPGLRVEKLLDEYLLPVCSPALL 174

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098 176 TDDDL---PGLLNRLTRIHrRQNPDAWLHYARECGLALDNPAQGPRYDLHEMAIAAVLSQQGVALVPKMYVESELSAGTL 252
Cdd:PRK11139 175 NGGKPlktPEDLARHTLLH-DDSREDWRAWFRAAGLDDLNVQQGPIFSHSSMALQAAIHGQGVALGNRVLAQPEIEAGRL 253

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|.
gi 488997098 253 VAPWPGSPTLAKRFCLIKPGGGEGEPALQMFERWLQTEIAA 293
Cdd:PRK11139 254 VCPFDTVLPSPNAFYLVCPDSQAELPKVAAFRQWLLAEAAQ 294
PBP2_GcdR_like cd08481
The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, ...
 96-287 4.67e-61

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: 192.13  E-value: 4.67e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098  96 SLEIAVLPTFASRWLIPRLGRFAAQHPHIVVNIAARSDPFILPGSGFDAAIHFEHPAWTGMEVTFLFAEYLLPVCHAALL 175
Cdd:cd08481    1 TLELAVLPTFGTRWLIPRLPDFLARHPDITVNLVTRDEPFDFSQGSFDAAIHFGDPVWPGAESEYLMDEEVVPVCSPALL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098 176 TDDDL--PGLLNRLTRIHRRQNPDAWLHYARECGLALDNPAQGPRYDLHEMAIAAVLSQQGVALVPKMYVESELSAGTLV 253
Cdd:cd08481   81 AGRALaaPADLAHLPLLQQTTRPEAWRDWFEEVGLEVPTAYRGMRFEQFSMLAQAAVAGLGVALLPRFLIEEELARGRLV 160

                        170       180       190
                 ....*....|....*....|....*....|....
gi 488997098 254 APWPGSPTLAKRFCLIKPGGGEGEPALQMFERWL 287
Cdd:cd08481  161 VPFNLPLTSDKAYYLVYPEDKAESPPVQAFRDWL 194
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 97-287 2.20e-52

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: 170.07  E-value: 2.20e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098  97 LEIAVLPTFASRWLIPRLGRFAAQHPHIVVNIAARSDPFILPGSGFDAAIHFEHPAWTGMEVTFLFAEYLLPVCHAALLT 176
Cdd:cd08432    2 LTVSVTPSFAARWLIPRLARFQARHPDIDLRLSTSDRLVDFAREGIDLAIRYGDGDWPGLEAERLMDEELVPVCSPALLA 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098 177 DDDL--PGLLNRLTRIHRRQNPDAWLHYARECGLALDNPAQGPRYDLHEMAIAAVLSQQGVALVPKMYVESELSAGTLVA 254
Cdd:cd08432   82 GLPLlsPADLARHTLLHDATRPEAWQWWLWAAGVADVDARRGPRFDDSSLALQAAVAGLGVALAPRALVADDLAAGRLVR 161

                        170       180       190
                 ....*....|....*....|....*....|...
gi 488997098 255 PWPGSPTLAKRFCLIKPGGGEGEPALQMFERWL 287
Cdd:cd08432  162 PFDLPLPSGGAYYLVYPPGRAESPAVAAFRDWL 194
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
19-293 2.28e-43

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 148.86  E-value: 2.28e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098  19 RHGNFARAAAELALTEGAISRQIARLEALLDSKLFDRTGSRVRLNPAGARYARQVREILARLERDTHDVSGMP-VDGRSL 97
Cdd:COG0583   14 EEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAELRALRgGPRGTL 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098  98 EIAVLPTFASRWLIPRLGRFAAQHPHIVVNIAARSDPFILPG---SGFDAAIHFEHPAWTGMEVTFLFAEYLLPVCHAAl 174
Cdd:COG0583   94 RIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDAlleGELDLAIRLGPPPDPGLVARPLGEERLVLVASPD- 172

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098 175 ltdddlpgllnrltriHRrqnpdawlhyarecgLAldnpAQGPRYDLHEMAIAAVLSQQGVALVPKMYVESELSAGTLVA 254
Cdd:COG0583  173 ----------------HP---------------LA----RRAPLVNSLEALLAAVAAGLGIALLPRFLAADELAAGRLVA 217

                        250       260       270
                 ....*....|....*....|....*....|....*....
gi 488997098 255 PWPGSPTLAKRFCLIKPGGGEGEPALQMFERWLQTEIAA 293
Cdd:COG0583  218 LPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
19-292 2.92e-43

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 150.15  E-value: 2.92e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098  19 RHGNFARAAAELALTEGAISRQIARLEALLDSKLFDRTGSRVRLNPAGARYARQVREILARLERDTHDVSGMPVDGrSLE 98
Cdd:PRK10086  27 RHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLDTLNQEILDIKNQELSG-TLT 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098  99 IAVLPTFASRWLIPRLGRFAAQHPHIVVNIAARSDPFILPGSGFDAAIHFEHPAWTGMEVTFLFAEYLLPVCHAALLTDD 178
Cdd:PRK10086 106 VYSRPSIAQCWLVPRLADFTRRYPSISLTILTGNENVNFQRAGIDLAIYFDDAPSAQLTHHFLMDEEILPVCSPEYAERH 185

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098 179 DLPGLLNRL---TRIHRRQ------NPDAWLHYARECGLALDNPAQGPRYDLHEMAIAAVLSQQGVALVPKMYVESELSA 249
Cdd:PRK10086 186 ALTGNPDNLrhcTLLHDRQawsndsGTDEWHSWAQHFGVNLLPPSSGIGFDRSDLAVIAAMNHIGVAMGRKRLVQKRLAS 265

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|...
gi 488997098 250 GTLVAPWPGSPTLAKRFCLIKPGGGEGEPALQMFERWLQTEIA 292
Cdd:PRK10086 266 GELVAPFGDMEVKCHQHYYVTTLPGRQWPKIEAFIDWLKEQVK 308
PBP2_TrpI cd08482
The C-terminal substrate binding domain of LysR-type transcriptional regulator TrpI, which is ...
 96-287 2.91e-24

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: 97.09  E-value: 2.91e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098  96 SLEIAVLPTFASRWLIPRLGRFAAQHPHIVVNIAARSDPFILPGSGFDAAIHFEHPAW-TGMEVTFLFAEYLLPVC---H 171
Cdd:cd08482    1 PLVLSCSGSLLMRWLIPRLPAFQAALPDIDLQLSASDGPVDSLRDGIDAAIRFNDAPWpAGMQVIELFPERVGPVCspsL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098 172 AALLTD-DDLPGLLNRLTRIHRRQNPDAWLHYARECGLALDNPAQGPRYDLHEMAIAAVLSQQGVALVPKMYVESELSAG 250
Cdd:cd08482   81 APTVPLrQAPAAALLGAPLLHTRSRPQAWPDWAAAQGLAPEKLGTGQSFEHFYYLLEAAVAGLGVAIAPWPLVRDDLASG 160

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 488997098 251 TLVAPWPGSPTLAkRFCLIKPGGGEgEPALQMFERWL 287
Cdd:cd08482  161 RLVAPWGFIETGS-HYVLLRPARLR-DSRAGALADWL 195
PBP2_LTTR_beta_lactamase cd08484
The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase ...
 97-287 1.51e-21

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: 89.35  E-value: 1.51e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098  97 LEIAVLPTFASRWLIPRLGRFAAQHPHIVVNIAARSDPFILPGSGFDAAIHFEHPAWTGMEVTFLFAEYLLPVChaallt 176
Cdd:cd08484    2 LTVGAVGTFAVGWLLPRLAEFRQLHPFIDLRLSTNNNRVDIAAEGLDFAIRFGEGAWPGTDATRLFEAPLSPLC------ 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098 177 dddLPGLLNRLTR--------IHRRQNPDAWLHYARECGLALdNPAQGPRYDLHEMAIAAVLSQQGVALVPKMYVESELS 248
Cdd:cd08484   76 ---TPELARRLSEpadlanetLLRSYRADEWPQWFEAAGVPP-PPINGPVFDSSLLMVEAALQGAGVALAPPSMFSRELA 151

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 488997098 249 AGTLVAPWPGSpTLAKRFCLIKPGGGEGEPALQMFERWL 287
Cdd:cd08484  152 SGALVQPFKIT-VSTGSYWLTRLKSKPETPAMSAFSQWL 189
PBP2_HvrB cd08483
The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an ...
 97-287 5.35e-20

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: 85.47  E-value: 5.35e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098  97 LEIAVLPTFASRWLIPRLGRFAAQHPHIVVNIAARSDPFILPGSGFDAAIHFEHPAWTGMEVTFLFAEYLLPVCHAALLT 176
Cdd:cd08483    2 LTVTLTPSFASNWLMPRLGSFWAKHPEIELSLLPSADLVDLRPDGIDVAIRYGNGDWPGLESEPLTAAPFVVVAAPGLLG 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098 177 DD--DLPGLLNRLTRIHRRQNPDAWLhYARECGLALDNPAqGPRYDLHEMAIAAVLSQQGVALVPKMYVESELSAGTLVA 254
Cdd:cd08483   82 DRkvDSLADLAGLPWLQERGTNEQRV-WLASMGVVPDLER-GVTFLPGQLVLEAARAGLGLSIQARALVEPDIAAGRLTV 159

                        170       180       190
                 ....*....|....*....|....*....|...
gi 488997098 255 PWPGSPTLAKRFCLIKPggGEGEPALQMFERWL 287
Cdd:cd08483  160 LFEEEEEGLGYHIVTRP--GVLRPAAKAFVRWL 190
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 20-166 1.17e-19

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 86.55  E-value: 1.17e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098  20 HGNFARAAAELALTEGAISRQIARLEALLDSKLFDRTGSRVRLNPAGARYARQVREILARLE---RDTHDVSGMpvdGR- 95
Cdd:PRK11242  15 HGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEagrRAIHDVADL---SRg 91

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488997098  96 SLEIAVLPTFASRWLIPRLGRFAAQHPHIVVNIAARSDPFILPGSG---FDAAIHFEHPAWTGMEVTFLFAEYL 166
Cdd:PRK11242  92 SLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMSQERIEALLAddeLDVGIAFAPVHSPEIEAQPLFTETL 165
PBP2_AmpR cd08488
The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in ...
 97-287 5.99e-19

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: 82.58  E-value: 5.99e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098  97 LEIAVLPTFASRWLIPRLGRFAAQHPHIVVNIAARSDPFILPGSGFDAAIHFEHPAWTGMEVTFLFAEYLLPVCHAALLT 176
Cdd:cd08488    2 LHVGAVGTFAVGWLLPRLADFQNRHPFIDLRLSTNNNRVDIAAEGLDYAIRFGSGAWHGIDATRLFEAPLSPLCTPELAR 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098 177 DDDLPGLLNRLTRIhRRQNPDAWLHYARECGLALD-NPAQGPRYDLHEMAIAAVLSQQGVALVPKMYVESELSAGTLVAP 255
Cdd:cd08488   82 QLREPADLARHTLL-RSYRADEWPQWFEAAGVGHPcGLPNSIMFDSSLGMMEAALQGLGVALAPPSMFSRQLASGALVQP 160

                        170       180       190
                 ....*....|....*....|....*....|...
gi 488997098 256 WPgsPTL-AKRFCLIKPGGGEGEPALQMFERWL 287
Cdd:cd08488  161 FA--TTLsTGSYWLTRLQSRPETPAMSAFSAWL 191
PBP2_BlaA cd08487
The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which ...
 97-287 5.71e-18

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: 79.90  E-value: 5.71e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098  97 LEIAVLPTFASRWLIPRLGRFAAQHPHIVVNIAARSDPFILPGSGFDAAIHFEHPAWTGMEVTFLFAEYLLPVCHaallt 176
Cdd:cd08487    2 LTVGAVGTFAVGWLLPRLAEFRQLHPFIELRLRTNNNVVDLATEGLDFAIRFGEGLWPATHNERLLDAPLSVLCS----- 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098 177 dddlPGLLNRLTR--------IHRRQNPDAWLHYARECGLAlDNPAQGPRYDLHEMAIAAVLSQQGVALVPKMYVESELS 248
Cdd:cd08487   77 ----PEIAKRLSHpadlinetLLRSYRTDEWLQWFEAANMP-PIKIRGPVFDSSRLMVEAAMQGAGVALAPAKMFSREIE 151

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 488997098 249 AGTLVAPWPGSpTLAKRFCLIKPGGGEGEPALQMFERWL 287
Cdd:cd08487  152 NGQLVQPFKIE-VETGSYWLTWLKSKPMTPAMELFRQWI 189
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 95-292 2.40e-16

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: 75.79  E-value: 2.40e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098   95 RSLEIAVLPTFASRWLIPRLGRFAAQHPHIVVNIAARSDPFILPG--SG-FDAAIHFEHPAWTGMEVTFLFAEYLLPVCH 171
Cdd:pfam03466   2 GRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLllEGeLDLAIRRGPPDDPGLEARPLGEEPLVLVAP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098  172 AA--LLTDDDL-PGLLNRLTRIHRRQNPDAWLHYARECGLALDNPAQGPRYDLHEMAIAAVLSQQGVALVPKMYVESELS 248
Cdd:pfam03466  82 PDhpLARGEPVsLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARELA 161

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 488997098  249 AGTLVA-PWPGsPTLAKRFCLIKPGGGEGEPALQMFERWLQTEIA 292
Cdd:pfam03466 162 DGRLVAlPLPE-PPLPRELYLVWRKGRPLSPAVRAFIEFLREALA 205
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
19-66 1.17e-14

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 67.02  E-value: 1.17e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 488997098   19 RHGNFARAAAELALTEGAISRQIARLEALLDSKLFDRTGSRVRLNPAG 66
Cdd:pfam00126  12 ETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
rbcR CHL00180
LysR transcriptional regulator; Provisional
 21-133 6.72e-11

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 61.96  E-value: 6.72e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098  21 GNFARAAAELALTEGAISRQIARLEALLDSKLFDRTGSRVRLNPAGARYARQVREILARLERDTHDVsgmpVDGRSLEIA 100
Cdd:CHL00180  20 GSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRAL----EDLKNLQRG 95

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 488997098 101 VLPTFASR----WLIPRL-GRFAAQHPHIVVNIAARSD 133
Cdd:CHL00180  96 TLIIGASQttgtYLMPRLiGLFRQRYPQINVQLQVHST 133
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
21-285 5.49e-09

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 56.18  E-value: 5.49e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098  21 GNFARAAAELALTEGAISRQIARLEALLDSKLFDRTGSRVRLNPAGARYARQVREILARLERDTHDVSgMPVDGRsLEIA 100
Cdd:PRK15421  17 GSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQACN-EPQQTR-LRIA 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098 101 VLPTFASRWLIPRLGRFAAQHPHIVVNIAA--RSDPF---------------ILPGSGFDAAIHFEHpawtgmEVTFLFA 163
Cdd:PRK15421  95 IECHSCIQWLTPALENFHKNWPQVEMDFKSgvTFDPQpalqqgeldlvmtsdILPRSGLHYSPMFDY------EVRLVLA 168

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098 164 EYlLPVCHAALLTDDDLPGlLNRLTRIHRRQNPDAWLHYARECGLAldnpAQGPRYDLHEMAIAAVLSQQGVALVPKMYV 243
Cdd:PRK15421 169 PD-HPLAAKTRITPEDLAS-ETLLIYPVQRSRLDVWRHFLQPAGVS----PSLKSVDNTLLLIQMVAARMGIAALPHWVV 242

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|..
gi 488997098 244 ESELSAGTLVAPWPGSPTLAKRFCLIKpGGGEGEPALQMFER 285
Cdd:PRK15421 243 ESFERQGLVVTKTLGEGLWSRLYAAVR-DGEQRQPVTEAFIR 283
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 99-253 9.11e-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: 54.37  E-value: 9.11e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098  99 IAVLPTFASRWLIPRLGRFAAQHPHIVVNIAArSDPFI-LPGSGFDAAIHFEHPAWTGM------EVTF-LFA--EYLLp 168
Cdd:cd08422    5 ISAPVSFGRLHLAPLLAEFLARYPDVRLELVL-SDRLVdLVEEGFDLAIRIGELPDSSLvarrlgPVRRvLVAspAYLA- 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098 169 vCHAALLTDDDL---PGLLNRLTRIHRR---QNPDAWLHYARECGLALDNPaqgprydlhEMAIAAVLSQQGVALVPKMY 242
Cdd:cd08422   83 -RHGTPQTPEDLarhRCLGYRLPGRPLRwrfRRGGGEVEVRVRGRLVVNDG---------EALRAAALAGLGIALLPDFL 152

                        170
                 ....*....|.
gi 488997098 243 VESELSAGTLV 253
Cdd:cd08422  153 VAEDLASGRLV 163
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 21-136 1.00e-08

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 55.38  E-value: 1.00e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098  21 GNFARAAAELALTEGAISRQIARLEALLDSKLFDRTGSRVRLNPAGARYARQVREILARLERDTHDVSGM-PVDGRSLEI 99
Cdd:PRK11013  19 GSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLFEEVQRSYYGLDRIVSAAESLrEFRQGQLSI 98

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 488997098 100 AVLPTFASRWLIPRLGRFAAQHPHIVVNIAARSDPFI 136
Cdd:PRK11013  99 ACLPVFSQSLLPGLCQPFLARYPDVSLNIVPQESPLL 135
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
19-121 1.61e-08

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 54.59  E-value: 1.61e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098  19 RHGNFARAAAELALTEGAISRQIARLEALLDSKLFDRtGSRVRLNPAG---ARYARQVREILARLERDTHDVSGMPVdgr 95
Cdd:PRK13348  15 ETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGqrlLRHLRQVALLEADLLSTLPAERGSPP--- 90

                         90       100
                 ....*....|....*....|....*.
gi 488997098  96 SLEIAVLPTFASRWLIPRLGRFAAQH 121
Cdd:PRK13348  91 TLAIAVNADSLATWFLPALAAVLAGE 116
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 20-254 4.28e-07

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 50.37  E-value: 4.28e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098  20 HGNFARAAAELALTEGAISRQIARLEALLDSKLFDRTGSRVRLNPAGARYARQVREILARLERDTHDVSGMPVDGRSLEI 99
Cdd:PRK14997  16 EGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDAIAALQVEPRGIVK 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098 100 AVLP-TFASRWLIPRLGRFAAQHPHIVVNIAARSDPFILPGSGFDAAIHFE-HPawtgMEVTFLFAEYLLPVCHAALLTd 177
Cdd:PRK14997  96 LTCPvTLLHVHIGPMLAKFMARYPDVSLQLEATNRRVDVVGEGVDVAIRVRpRP----FEDSDLVMRVLADRGHRLFAS- 170

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098 178 ddlPGLLNRLTRIHRRQNPDAW----------LHYARECGlaldnpAQGPRYDLH--------------EMAIAAVlsqq 233
Cdd:PRK14997 171 ---PDLIARMGIPSAPAELSHWpglslasgkhIHRWELYG------PQGARAEVHftprmittdmlalrEAAMAGV---- 237

                        250       260
                 ....*....|....*....|.
gi 488997098 234 GVALVPKMYVESELSAGTLVA 254
Cdd:PRK14997 238 GLVQLPVLMVKEQLAAGELVA 258
PRK09986 PRK09986
LysR family transcriptional regulator;
22-126 1.09e-06

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 48.95  E-value: 1.09e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098  22 NFARAAAELALTEGAISRQIARLEALLDSKLFDRTGSRVRLNPAGARYARQVREILARLERDTHDVSGMpvdGRS----L 97
Cdd:PRK09986  23 HFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLARVEQI---GRGeagrI 99

                         90       100
                 ....*....|....*....|....*....
gi 488997098  98 EIAVLPTFASRWLIPRLGRFAAQHPHIVV 126
Cdd:PRK09986 100 EIGIVGTALWGRLRPAMRHFLKENPNVEW 128
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
22-170 2.23e-06

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 48.13  E-value: 2.23e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098  22 NFARAAAELALTEGAISRQIARLEALLDSKLFDRTGSRVRLNPAGARYARQVREILARLERDTHDVSGMP---------V 92
Cdd:PRK10082  27 NFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESNLAELRGGSdyaqrkikiA 106

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488997098  93 DGRSLEIAVLPTFASRwlIPRLGRFAAQhphiVVNIAARSDPFILPGSGFDAAIHFEHPAWTGMEVTFLFAEYLLPVC 170
Cdd:PRK10082 107 AAHSLSLGLLPSIISQ--MPPLFTWAIE----AIDVDEAVDKLREGQSDCIFSFHDEDLLEAPFDHIRLFESQLFPVC 178
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 96-260 4.07e-06

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: 46.44  E-value: 4.07e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098  96 SLEIAVLPTFASRWLIPRLGRFAAQHPHIVVNIAARSDPFILPG--SG-FDAAIHFEHPAWTGMEVTFLFAEYLLPVCHA 172
Cdd:cd05466    1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEAllEGeLDLAIVALPVDDPGLESEPLFEEPLVLVVPP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098 173 -------ALLTDDDLPG----LLNRLTRIHRRqnpdaWLHYARECGLALDnpaqgPRY--DLHEMAIAAVLSQQGVALVP 239
Cdd:cd05466   81 dhplakrKSVTLADLADepliLFERGSGLRRL-----LDRAFAEAGFTPN-----IALevDSLEAIKALVAAGLGIALLP 150

                        170       180
                 ....*....|....*....|.
gi 488997098 240 KMYVESELSAGTLVAPWPGSP 260
Cdd:cd05466  151 ESAVEELADGGLVVLPLEDPP 171
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
19-122 8.91e-06

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 46.31  E-value: 8.91e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098  19 RHGNFARAAAELALTEGAISRQIARLEALLDSKLFDRTgSRVRLNPAGA---RYARQVReilaRLERDT-HDVSGMPVDG 94
Cdd:PRK03635  15 REGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVRT-QPCRPTEAGQrllRHARQVR----LLEAELlGELPALDGTP 89

                         90       100       110
                 ....*....|....*....|....*....|..
gi 488997098  95 RSLEIAV----LPTfasrWLIPRLGRFAAQHP 122
Cdd:PRK03635  90 LTLSIAVnadsLAT----WFLPALAPVLARSG 117
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
19-81 1.38e-05

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 45.95  E-value: 1.38e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 488997098  19 RHGNFARAAAELALTEGAISRQIARLEALLDSKLFDRTGSRVRLNPAGARYARQVREILARLE 81
Cdd:PRK10094  15 ETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLE 77
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 22-126 1.48e-05

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 45.53  E-value: 1.48e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098  22 NFARAAAELALTEGAISRQIARLEALLDSKLFDRTGSRVRLNPAGARYARQVREILARLERDTHDVSGMPVDGRSLEIAV 101
Cdd:PRK09906  17 NFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKLRARKIVQEDRQLTIGF 96

                         90       100
                 ....*....|....*....|....*
gi 488997098 102 LPTFASRWLIPRLGRFAAQHPHIVV 126
Cdd:PRK09906  97 VPSAEVNLLPKVLPMFRLRHPDTLI 121
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 19-88 1.60e-05

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 45.70  E-value: 1.60e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 488997098  19 RHGNFARAAAELALTEGAISRQIARLEALLDSKLFDRTGSRVRLNPAGARYARQVREILARLE---RDTHDVS 88
Cdd:PRK11074  15 RTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQetrRQCQQVA 87
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
19-70 4.48e-05

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 44.24  E-value: 4.48e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 488997098  19 RHgnFARAAAELALTEGAISRQIARLEALLDSKLFDRTGSRVRLNPAGAR---YA 70
Cdd:PRK03601  16 RH--FGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERllpYA 68
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
36-124 5.50e-05

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 43.65  E-value: 5.50e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098  36 AISRQIARLEALLDSKLFDRTGSRVRLNPAGARYARQVREILARLERDTHDVSGmpvDGRSL--EIAVlptFAS-----R 108
Cdd:PRK11716   7 TLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQ---QGPSLsgELSL---FCSvtaayS 80

                         90
                 ....*....|....*.
gi 488997098 109 WLIPRLGRFAAQHPHI 124
Cdd:PRK11716  81 HLPPILDRFRAEHPLV 96
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 21-170 7.07e-05

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 43.52  E-value: 7.07e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098  21 GNFARAAAELALTEGAISRQIARLEALLDSKLFDRTGSRVRLNPAGARYARQVREILARLERDTHDV--SGMPVDGrSLE 98
Cdd:PRK11233  16 GSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQLAVhnVGQALSG-QVS 94

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 488997098  99 IAVLP-TFASRWLIPRLGRFAAQHPHIVV----NIAARSDPFILPGSgFDAAIHFEHPAWTGMEVTFLFAEYLLPVC 170
Cdd:PRK11233  95 IGLAPgTAASSLTMPLLQAVRAEFPGIVLylheNSGATLNEKLMNGQ-LDMAVIYEHSPVAGLSSQPLLKEDLFLVG 170
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
21-146 1.42e-04

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 42.83  E-value: 1.42e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098  21 GNFARAAAELALTEGAISRQIARLEALLDSKLFDRTGSRVRLNPAGARYARQVREILARLErDTHD----VSGMPVDgrS 96
Cdd:PRK10632  17 GSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQ-DVHEqlyaFNNTPIG--T 93

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 488997098  97 LEIAVLPTFASRWLIPRLGRFAAQHPHIVVNIAARSDPFILPGSGFDAAI 146
Cdd:PRK10632  94 LRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTGIPAPDLIADGLDVVI 143
PRK09801 PRK09801
LysR family transcriptional regulator;
21-88 1.51e-04

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 42.71  E-value: 1.51e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488997098  21 GNFARAAAELALTEGAISRQIARLEALLDSKLFDRTGSRVRLNPAGARYARQVREILARLERDTHDVS 88
Cdd:PRK09801  21 GSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVT 88
PRK09791 PRK09791
LysR family transcriptional regulator;
17-128 3.79e-04

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 41.29  E-value: 3.79e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098  17 AARHGNFARAAAELALTEGAISRQIARLEALLDSKLFDRTGSRVRLNPAGARYARQVREILARLERDTHDVSG-MPVDGR 95
Cdd:PRK09791  16 VARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQEDIRQrQGQLAG 95

                         90       100       110
                 ....*....|....*....|....*....|....
gi 488997098  96 SLEIAVLPTFAsRWLIPR-LGRFAAQHPHIVVNI 128
Cdd:PRK09791  96 QINIGMGASIA-RSLMPAvISRFHQQHPQVKVRI 128
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 23-136 4.09e-04

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 41.17  E-value: 4.09e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098  23 FARAAAELALTEGAISRQIARLEALLDSKLFDRTGSRVRLNPAGAR---YARQV----REILARLERDthDVSGMPVDGR 95
Cdd:PRK15092  28 FAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQllgYARKIlrfnDEACSSLMYS--NLQGVLTIGA 105

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 488997098  96 SLEIA--VLPTFasrwliprLGRFAAQHPHIVVNIAARSDPFI 136
Cdd:PRK15092 106 SDDTAdtILPFL--------LNRVSSVYPKLALDVRVKRNAFM 140
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 21-66 7.66e-04

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 40.44  E-value: 7.66e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 488997098  21 GNFARAAAELALTEGAISRQIARLEALLDSKLFDRTGSRVRLNPAG 66
Cdd:PRK10837  18 GSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHG 63
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 19-130 1.37e-03

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 39.59  E-value: 1.37e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098  19 RHG-NFARAAAELALTEGAISRQIARLEALLDSKLFDRTGSRV-RLNPAGARYARQVREILA---RLERDTHDVSGMpvD 93
Cdd:PRK12682  14 RRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLkGLTEPGKAVLDVIERILRevgNIKRIGDDFSNQ--D 91

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 488997098  94 GRSLEIAVLPTFAsRWLIPR-LGRFAAQHPHIVVNIAA 130
Cdd:PRK12682  92 SGTLTIATTHTQA-RYVLPRvVAAFRKRYPKVNLSLHQ 128
COG4742 COG4742
Predicted transcriptional regulator, contains HTH domain [Transcription];
27-102 1.97e-03

Predicted transcriptional regulator, contains HTH domain [Transcription];


Pssm-ID: 443776 [Multi-domain]  Cd Length: 267  Bit Score: 39.11  E-value: 1.97e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098  27 AAELALTEGAISRQIARLEallDSKLFDRTGSRVRLNPAGARYARQVREILARLER--------DTHDVSGMPvDGRSLE 98
Cdd:COG4742   36 AESLDVSRSTILRQLKELE---ERGLIERDDGEYELTTLGRLVVEEMEPLLDTLEVleenrdywETHDLSAIP-PELLLR 111


                 ....
gi 488997098  99 IAVL 102
Cdd:COG4742  112 IGEL 115
PBP2_CrgA_like_4 cd08473
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 97-258 3.41e-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 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: 37.92  E-value: 3.41e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098  97 LEIAVLPTFASRWLIPRLGRFAAQHPHIVVNIAARSDPFILPGSGFDAAIHFEHPawtgmevtflfaeyllpvchaaLLT 176
Cdd:cd08473    5 VRVSCPPALAQELLAPLLPRFMAAYPQVRLQLEATNRRVDLIEEGIDVALRVRFP----------------------PLE 62

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488997098 177 DDDL---------------PGLLNRLTRIhrrQNPDAWLHYArecGLALDNPAQGPRYDLH------------------- 222
Cdd:cd08473   63 DSSLvmrvlgqsrqrlvasPALLARLGRP---RSPEDLAGLP---TLSLGDVDGRHSWRLEgpdgesitvrhrprlvtdd 136

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 488997098 223 -EMAIAAVLSQQGVALVPKMYVESELSAGTLVAPWPG 258
Cdd:cd08473  137 lLTLRQAALAGVGIALLPDHLCREALRAGRLVRVLPD 173
PBP2_CrgA_like_9 cd08479
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 105-148 9.67e-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 9. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176168 [Multi-domain]  Cd Length: 198  Bit Score: 36.42  E-value: 9.67e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 488997098 105 FASRWLIPRLGRFAAQHPHIVVNIAARSDPFILPGSGFDAAIHF 148
Cdd:cd08479   11 FGRRHIAPALSDFAKRYPELEVQLELTDRPVDLVEEGFDLDIRV 54
PBP2_CrgA_like_3 cd08472
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-146 9.96e-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: 36.34  E-value: 9.96e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 488997098  94 GRsLEIAVLPTFASRWLIPRLGRFAAQHPHIVVNIAArSDPFI-LPGSGFDAAI 146
Cdd:cd08472    1 GR-LRVDVPGSLARLLLIPALPDFLARYPDIELDLGV-SDRPVdLIREGVDCVI 52
 
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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