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Conserved domains on  [gi|896545347|ref|WP_049446637|]
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MULTISPECIES: LysR substrate-binding domain-containing protein [Stenotrophomonas]

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
 1-296 2.59e-74

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: 230.50  E-value: 2.59e-74
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347   1 MLLRPSLLPALAVFAVAARHQNFAQAAQELHLTASAVSHHVRRLEEVLEVRLFLRHARGVRLTAEGRQLADAASAAFTDV 80
Cdd:PRK11139   1 MSRRLPPLNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347  81 AAVAHHLQ-PDADSVpLRVTTLRSLSYCWLLPRLPRFTQAYPHIRIELHTGSGLDRYDDNGPEVGIRYGLGQWPGLRAQH 159
Cdd:PRK11139  81 AEATRKLRaRSAKGA-LTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDRLEDFLRDDVDVAIRYGRGNWPGLRVEK 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347 160 LMDDYLFPVASPALA-GVETLVDPARIADLPLLTDLSPQGWRDWFRHAGVRPPSPlPPMHTFADSTDAMRAAVYGMGAVL 238
Cdd:PRK11139 160 LLDEYLLPVCSPALLnGGKPLKTPEDLARHTLLHDDSREDWRAWFRAAGLDDLNV-QQGPIFSHSSMALQAAIHGQGVAL 238

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 896545347 239 ARTHIAQPYMQRYEVVRLPGPALKARYAYHVVHAEGQPPSPAARLFIDWLLEQAQDER 296
Cdd:PRK11139 239 GNRVLAQPEIEAGRLVCPFDTVLPSPNAFYLVCPDSQAELPKVAAFRQWLLAEAAQEQ 296
 
Name Accession Description Interval E-value
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 1-296 2.59e-74

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 230.50  E-value: 2.59e-74
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347   1 MLLRPSLLPALAVFAVAARHQNFAQAAQELHLTASAVSHHVRRLEEVLEVRLFLRHARGVRLTAEGRQLADAASAAFTDV 80
Cdd:PRK11139   1 MSRRLPPLNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347  81 AAVAHHLQ-PDADSVpLRVTTLRSLSYCWLLPRLPRFTQAYPHIRIELHTGSGLDRYDDNGPEVGIRYGLGQWPGLRAQH 159
Cdd:PRK11139  81 AEATRKLRaRSAKGA-LTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDRLEDFLRDDVDVAIRYGRGNWPGLRVEK 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347 160 LMDDYLFPVASPALA-GVETLVDPARIADLPLLTDLSPQGWRDWFRHAGVRPPSPlPPMHTFADSTDAMRAAVYGMGAVL 238
Cdd:PRK11139 160 LLDEYLLPVCSPALLnGGKPLKTPEDLARHTLLHDDSREDWRAWFRAAGLDDLNV-QQGPIFSHSSMALQAAIHGQGVAL 238

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 896545347 239 ARTHIAQPYMQRYEVVRLPGPALKARYAYHVVHAEGQPPSPAARLFIDWLLEQAQDER 296
Cdd:PRK11139 239 GNRVLAQPEIEAGRLVCPFDTVLPSPNAFYLVCPDSQAELPKVAAFRQWLLAEAAQEQ 296
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 95-288 1.46e-53

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: 173.54  E-value: 1.46e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347  95 PLRVTTLRSLSYCWLLPRLPRFTQAYPHIRIELHTGSGLDRYDDNGPEVGIRYGLGQWPGLRAQHLMDDYLFPVASPALA 174
Cdd:cd08432    1 VLTVSVTPSFAARWLIPRLARFQARHPDIDLRLSTSDRLVDFAREGIDLAIRYGDGDWPGLEAERLMDEELVPVCSPALL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347 175 GVETLVDPARIADLPLLTDLS-PQGWRDWFRHAGVRPPSPlPPMHTFADSTDAMRAAVYGMGAVLARTHIAQPYMQRYEV 253
Cdd:cd08432   81 AGLPLLSPADLARHTLLHDATrPEAWQWWLWAAGVADVDA-RRGPRFDDSSLALQAAVAGLGVALAPRALVADDLAAGRL 159

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 896545347 254 VRLPGPALKARYAYHVVHAEGQPPSPAARLFIDWL 288
Cdd:cd08432  160 VRPFDLPLPSGGAYYLVYPPGRAESPAVAAFRDWL 194
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
8-294 2.43e-49

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 164.65  E-value: 2.43e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347   8 LPALAVFAVAARHQNFAQAAQELHLTASAVSHHVRRLEEVLEVRLFLRHARGVRLTAEGRQLADAASAAFTDVAAVAHHL 87
Cdd:COG0583    3 LRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAEL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347  88 QPDADSV--PLRVTTLRSLSYCWLLPRLPRFTQAYPHIRIELHTGSG---LDRYDDNGPEVGIRYGLGQWPGLRAQHLMD 162
Cdd:COG0583   83 RALRGGPrgTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSdrlVDALLEGELDLAIRLGPPPDPGLVARPLGE 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347 163 DYLFPVASPALagvetlvdpariadlplltdlspqgwrdwfrhagvrppsPLPPMHTFADSTDAMRAAV-YGMGAVLART 241
Cdd:COG0583  163 ERLVLVASPDH---------------------------------------PLARRAPLVNSLEALLAAVaAGLGIALLPR 203

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|...
gi 896545347 242 HIAQPYMQRYEVVRLPGPALKARYAYHVVHAEGQPPSPAARLFIDWLLEQAQD 294
Cdd:COG0583  204 FLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 96-293 9.35e-29

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: 109.69  E-value: 9.35e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347   96 LRVTTLRSLSYCWLLPRLPRFTQAYPHIRIELHTGSG---LDRYDDNGPEVGIRYGLGQWPGLRAQHLMDDYLFPVASPA 172
Cdd:pfam03466   4 LRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSeelLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVAPPD 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347  173 --LAGVETlVDPARIADLPLLTDLSPQGWRDWFRHAGVRPPSPLPPMHTFADSTDAMRAAVYGMGAVLARTHIAQPYMQR 250
Cdd:pfam03466  84 hpLARGEP-VSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARELAD 162

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 896545347  251 YEVVRLPGPALKARYAYHVVHAEGQPPSPAARLFIDWLLEQAQ 293
Cdd:pfam03466 163 GRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREALA 205
 
Name Accession Description Interval E-value
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 1-296 2.59e-74

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 230.50  E-value: 2.59e-74
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347   1 MLLRPSLLPALAVFAVAARHQNFAQAAQELHLTASAVSHHVRRLEEVLEVRLFLRHARGVRLTAEGRQLADAASAAFTDV 80
Cdd:PRK11139   1 MSRRLPPLNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347  81 AAVAHHLQ-PDADSVpLRVTTLRSLSYCWLLPRLPRFTQAYPHIRIELHTGSGLDRYDDNGPEVGIRYGLGQWPGLRAQH 159
Cdd:PRK11139  81 AEATRKLRaRSAKGA-LTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDRLEDFLRDDVDVAIRYGRGNWPGLRVEK 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347 160 LMDDYLFPVASPALA-GVETLVDPARIADLPLLTDLSPQGWRDWFRHAGVRPPSPlPPMHTFADSTDAMRAAVYGMGAVL 238
Cdd:PRK11139 160 LLDEYLLPVCSPALLnGGKPLKTPEDLARHTLLHDDSREDWRAWFRAAGLDDLNV-QQGPIFSHSSMALQAAIHGQGVAL 238

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 896545347 239 ARTHIAQPYMQRYEVVRLPGPALKARYAYHVVHAEGQPPSPAARLFIDWLLEQAQDER 296
Cdd:PRK11139 239 GNRVLAQPEIEAGRLVCPFDTVLPSPNAFYLVCPDSQAELPKVAAFRQWLLAEAAQEQ 296
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 95-288 1.46e-53

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: 173.54  E-value: 1.46e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347  95 PLRVTTLRSLSYCWLLPRLPRFTQAYPHIRIELHTGSGLDRYDDNGPEVGIRYGLGQWPGLRAQHLMDDYLFPVASPALA 174
Cdd:cd08432    1 VLTVSVTPSFAARWLIPRLARFQARHPDIDLRLSTSDRLVDFAREGIDLAIRYGDGDWPGLEAERLMDEELVPVCSPALL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347 175 GVETLVDPARIADLPLLTDLS-PQGWRDWFRHAGVRPPSPlPPMHTFADSTDAMRAAVYGMGAVLARTHIAQPYMQRYEV 253
Cdd:cd08432   81 AGLPLLSPADLARHTLLHDATrPEAWQWWLWAAGVADVDA-RRGPRFDDSSLALQAAVAGLGVALAPRALVADDLAAGRL 159

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 896545347 254 VRLPGPALKARYAYHVVHAEGQPPSPAARLFIDWL 288
Cdd:cd08432  160 VRPFDLPLPSGGAYYLVYPPGRAESPAVAAFRDWL 194
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
2-293 1.89e-50

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 169.41  E-value: 1.89e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347   2 LLRPSLLPALAVFAVAARHQNFAQAAQELHLTASAVSHHVRRLEEVLEVRLFLRHARGVRLTAEGRQLADAASAAFTDVA 81
Cdd:PRK10086  10 LLNGWQLSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLDTLN 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347  82 AVAHHLQPDADSVPLRVTTLRSLSYCWLLPRLPRFTQAYPHIRIELHTGSGLDRYDDNGPEVGIRYGLGQWPGLRAQHLM 161
Cdd:PRK10086  90 QEILDIKNQELSGTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTILTGNENVNFQRAGIDLAIYFDDAPSAQLTHHFLM 169

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347 162 DDYLFPVASPALAGVETLV-DPARIADLPLLTDLSPQG-------WRDWFRHAGVRPPSPLPPMhTFADSTDAMRAAVYG 233
Cdd:PRK10086 170 DEEILPVCSPEYAERHALTgNPDNLRHCTLLHDRQAWSndsgtdeWHSWAQHFGVNLLPPSSGI-GFDRSDLAVIAAMNH 248

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 896545347 234 MGAVLARTHIAQPYMQRYE-VVRLPGPALKARYAYHVVHAEgQPPSPAARLFIDWLLEQAQ 293
Cdd:PRK10086 249 IGVAMGRKRLVQKRLASGElVAPFGDMEVKCHQHYYVTTLP-GRQWPKIEAFIDWLKEQVK 308
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
8-294 2.43e-49

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 164.65  E-value: 2.43e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347   8 LPALAVFAVAARHQNFAQAAQELHLTASAVSHHVRRLEEVLEVRLFLRHARGVRLTAEGRQLADAASAAFTDVAAVAHHL 87
Cdd:COG0583    3 LRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAEL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347  88 QPDADSV--PLRVTTLRSLSYCWLLPRLPRFTQAYPHIRIELHTGSG---LDRYDDNGPEVGIRYGLGQWPGLRAQHLMD 162
Cdd:COG0583   83 RALRGGPrgTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSdrlVDALLEGELDLAIRLGPPPDPGLVARPLGE 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347 163 DYLFPVASPALagvetlvdpariadlplltdlspqgwrdwfrhagvrppsPLPPMHTFADSTDAMRAAV-YGMGAVLART 241
Cdd:COG0583  163 ERLVLVASPDH---------------------------------------PLARRAPLVNSLEALLAAVaAGLGIALLPR 203

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|...
gi 896545347 242 HIAQPYMQRYEVVRLPGPALKARYAYHVVHAEGQPPSPAARLFIDWLLEQAQD 294
Cdd:COG0583  204 FLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
PBP2_GcdR_like cd08481
The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, ...
 96-288 2.80e-36

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: 128.95  E-value: 2.80e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347  96 LRVTTLRSLSYCWLLPRLPRFTQAYPHIRIELHTGSGLDRYDDNGPEVGIRYGLGQWPGLRAQHLMDDYLFPVASPALAG 175
Cdd:cd08481    2 LELAVLPTFGTRWLIPRLPDFLARHPDITVNLVTRDEPFDFSQGSFDAAIHFGDPVWPGAESEYLMDEEVVPVCSPALLA 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347 176 VETLVDPARIADLPLLTDLS-PQGWRDWFRHAGVRPPSPLPPMHtFADSTDAMRAAVYGMGAVLARTHIAQPYMQRYEVV 254
Cdd:cd08481   82 GRALAAPADLAHLPLLQQTTrPEAWRDWFEEVGLEVPTAYRGMR-FEQFSMLAQAAVAGLGVALLPRFLIEEELARGRLV 160

                        170       180       190
                 ....*....|....*....|....*....|....
gi 896545347 255 RLPGPALKARYAYHVVHAEGQPPSPAARLFIDWL 288
Cdd:cd08481  161 VPFNLPLTSDKAYYLVYPEDKAESPPVQAFRDWL 194
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 96-293 9.35e-29

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: 109.69  E-value: 9.35e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347   96 LRVTTLRSLSYCWLLPRLPRFTQAYPHIRIELHTGSG---LDRYDDNGPEVGIRYGLGQWPGLRAQHLMDDYLFPVASPA 172
Cdd:pfam03466   4 LRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSeelLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVAPPD 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347  173 --LAGVETlVDPARIADLPLLTDLSPQGWRDWFRHAGVRPPSPLPPMHTFADSTDAMRAAVYGMGAVLARTHIAQPYMQR 250
Cdd:pfam03466  84 hpLARGEP-VSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARELAD 162

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 896545347  251 YEVVRLPGPALKARYAYHVVHAEGQPPSPAARLFIDWLLEQAQ 293
Cdd:pfam03466 163 GRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREALA 205
PBP2_LTTR_beta_lactamase cd08484
The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase ...
 95-288 1.84e-25

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: 100.52  E-value: 1.84e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347  95 PLRVTTLRSLSYCWLLPRLPRFTQAYPHIRIELHTGSGLDRYDDNGPEVGIRYGLGQWPGLRAQHLMDDYLFPVASPALA 174
Cdd:cd08484    1 VLTVGAVGTFAVGWLLPRLAEFRQLHPFIDLRLSTNNNRVDIAAEGLDFAIRFGEGAWPGTDATRLFEAPLSPLCTPELA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347 175 gvETLVDPARIADLPLLTDLSPQGWRDWFRHAGVRPPSPLPPMhtFADSTDAMRAAVYGMGAVLARTHIAQPYMQRYEVV 254
Cdd:cd08484   81 --RRLSEPADLANETLLRSYRADEWPQWFEAAGVPPPPINGPV--FDSSLLMVEAALQGAGVALAPPSMFSRELASGALV 156

                        170       180       190
                 ....*....|....*....|....*....|....
gi 896545347 255 RLPGPALKARyAYHVVHAEGQPPSPAARLFIDWL 288
Cdd:cd08484  157 QPFKITVSTG-SYWLTRLKSKPETPAMSAFSQWL 189
PBP2_AmpR cd08488
The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in ...
 95-288 3.83e-24

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: 96.83  E-value: 3.83e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347  95 PLRVTTLRSLSYCWLLPRLPRFTQAYPHIRIELHTGSGLDRYDDNGPEVGIRYGLGQWPGLRAQHLMDDYLFPVASPALA 174
Cdd:cd08488    1 VLHVGAVGTFAVGWLLPRLADFQNRHPFIDLRLSTNNNRVDIAAEGLDYAIRFGSGAWHGIDATRLFEAPLSPLCTPELA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347 175 gvETLVDPARIADLPLLTDLSPQGWRDWFRHAGVRPPSPLPPMHTFADSTDAMRAAVYGMGAVLARTHIAQPYMQRYEVV 254
Cdd:cd08488   81 --RQLREPADLARHTLLRSYRADEWPQWFEAAGVGHPCGLPNSIMFDSSLGMMEAALQGLGVALAPPSMFSRQLASGALV 158

                        170       180       190
                 ....*....|....*....|....*....|....
gi 896545347 255 RlPGPALKARYAYHVVHAEGQPPSPAARLFIDWL 288
Cdd:cd08488  159 Q-PFATTLSTGSYWLTRLQSRPETPAMSAFSAWL 191
PBP2_HvrB cd08483
The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an ...
 95-288 7.10e-23

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: 93.56  E-value: 7.10e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347  95 PLRVTTLRSLSYCWLLPRLPRFTQAYPHIRIELHTGSGLDRYDDNGPEVGIRYGLGQWPGLRAQHLMDDYLFPVASPALA 174
Cdd:cd08483    1 PLTVTLTPSFASNWLMPRLGSFWAKHPEIELSLLPSADLVDLRPDGIDVAIRYGNGDWPGLESEPLTAAPFVVVAAPGLL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347 175 GVETLVDPARIADLPLLTDLSPQGWRDWFRHAGVRPpsPLPPMHTFADSTDAMRAAVYGMG-AVLARThIAQPYMQRYEV 253
Cdd:cd08483   81 GDRKVDSLADLAGLPWLQERGTNEQRVWLASMGVVP--DLERGVTFLPGQLVLEAARAGLGlSIQARA-LVEPDIAAGRL 157

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 896545347 254 VRLpGPALKARYAYHVVHAEGqPPSPAARLFIDWL 288
Cdd:cd08483  158 TVL-FEEEEEGLGYHIVTRPG-VLRPAAKAFVRWL 190
PBP2_BlaA cd08487
The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which ...
 108-288 2.81e-21

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: 89.14  E-value: 2.81e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347 108 WLLPRLPRFTQAYPHIRIELHTGSGLDRYDDNGPEVGIRYGLGQWPGLRAQHLMDDYLFPVASPALAgvETLVDPARIAD 187
Cdd:cd08487   14 WLLPRLAEFRQLHPFIELRLRTNNNVVDLATEGLDFAIRFGEGLWPATHNERLLDAPLSVLCSPEIA--KRLSHPADLIN 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347 188 LPLLTDLSPQGWRDWFRHAGVRPPSPLPPMHtfaDSTDAM-RAAVYGMGAVLARTHIAQPYMQRYEVVRlPGPALKARYA 266
Cdd:cd08487   92 ETLLRSYRTDEWLQWFEAANMPPIKIRGPVF---DSSRLMvEAAMQGAGVALAPAKMFSREIENGQLVQ-PFKIEVETGS 167

                        170       180
                 ....*....|....*....|..
gi 896545347 267 YHVVHAEGQPPSPAARLFIDWL 288
Cdd:cd08487  168 YWLTWLKSKPMTPAMELFRQWI 189
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
10-67 7.31e-20

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 81.28  E-value: 7.31e-20
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 896545347   10 ALAVFAVAARHQNFAQAAQELHLTASAVSHHVRRLEEVLEVRLFLRHARGVRLTAEGR 67
Cdd:pfam00126   3 QLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 96-288 2.04e-18

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: 81.72  E-value: 2.04e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347  96 LRVTTLRSLSYCWLLPRLPRFTQAYPHIRIELHTGSGL-----DRYDdngpeVGIRYGLGQWPGLRAQHLMDDYLFPVAS 170
Cdd:cd08422    3 LRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLvdlveEGFD-----LAIRIGELPDSSLVARRLGPVRRVLVAS 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347 171 PA-LAGVETLVDPARIADLPLLTDLSPQGWRDW-FRHAGVRPPSPLPPMHTfADSTDAMR-AAVYGMGAVLARTHIAQPY 247
Cdd:cd08422   78 PAyLARHGTPQTPEDLARHRCLGYRLPGRPLRWrFRRGGGEVEVRVRGRLV-VNDGEALRaAALAGLGIALLPDFLVAED 156

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 896545347 248 MQRYEVVR-LPGPALkARYAYHVVHAEGQPPSPAARLFIDWL 288
Cdd:cd08422  157 LASGRLVRvLPDWRP-PPLPIYAVYPSRRHLPAKVRAFIDFL 197
PBP2_TrpI cd08482
The C-terminal substrate binding domain of LysR-type transcriptional regulator TrpI, which is ...
 108-239 1.33e-16

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: 76.67  E-value: 1.33e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347 108 WLLPRLPRFTQAYPHIRIELHTGSGLDRYDDNGPEVGIRYGLGQWP-GLRAQHLMDDYLFPVASPALAGVETLVD--PAR 184
Cdd:cd08482   14 WLIPRLPAFQAALPDIDLQLSASDGPVDSLRDGIDAAIRFNDAPWPaGMQVIELFPERVGPVCSPSLAPTVPLRQapAAA 93

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 896545347 185 IADLPLLTDLS-PQGWRDWFRHAGVrPPSPLPPMHTFADSTDAMRAAVYGMGAVLA 239
Cdd:cd08482   94 LLGAPLLHTRSrPQAWPDWAAAQGL-APEKLGTGQSFEHFYYLLEAAVAGLGVAIA 148
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 96-288 7.19e-15

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: 71.86  E-value: 7.19e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347  96 LRVTTLRSLSYCWLLPRLPRFTQAYPHIRIELHTGSG---LDRYDDNGPEVGIRYGLGQWPGLRAQHLMDDYLFPVASP- 171
Cdd:cd05466    2 LRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSselLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPPd 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347 172 -ALAGVETlVDPARIADLPLLTDLSPQGWRD----WFRHAGVRPPSplppmHTFADSTDAMRAAV-YGMG-AVLARthIA 244
Cdd:cd05466   82 hPLAKRKS-VTLADLADEPLILFERGSGLRRlldrAFAEAGFTPNI-----ALEVDSLEAIKALVaAGLGiALLPE--SA 153

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 896545347 245 QPYMQRYEVVRLPGPALKARYAYHVVHAEGQPPSPAARLFIDWL 288
Cdd:cd05466  154 VEELADGGLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
31-130 1.25e-13

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 69.46  E-value: 1.25e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347  31 HLTASAVSHHVRRLEEVLEVRLFLRHARGVRLTAEGRQLADAASAAFTDVAAVAHHLQPDADSV--PLR----VTTlrsl 104
Cdd:PRK11716   2 HVSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLsgELSlfcsVTA---- 77

                         90       100
                 ....*....|....*....|....*.
gi 896545347 105 SYCWLLPRLPRFTQAYPHIRIELHTG 130
Cdd:PRK11716  78 AYSHLPPILDRFRAEHPLVEIKLTTG 103
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 1-210 4.33e-12

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 65.36  E-value: 4.33e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347   1 MLLRpSLLPALAVfavaARHQNFAQAAQELHLTASAVSHHVRRLEEVLEVRLFLRHARGVRLTAEGRQLADAASAAFTDV 80
Cdd:PRK11242   1 MLLR-HIRYFLAV----AEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDL 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347  81 AAV--AHHLQPDADSVPLRVTTLRSLSyCWLL-PRLPRFTQAYPHIRIELHTGSgLDRYD----DNGPEVGIRYGLGQWP 153
Cdd:PRK11242  76 EAGrrAIHDVADLSRGSLRLAMTPTFT-AYLIgPLIDAFHARYPGITLTIREMS-QERIEallaDDELDVGIAFAPVHSP 153

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 896545347 154 GLRAQHLMDDYLFPVASP--ALAGVETLVDPARIADLPLL---TDLSPQGWRD-WFRHAGVRP 210
Cdd:PRK11242 154 EIEAQPLFTETLALVVGRhhPLAARRKALTLDELADEPLVllsAEFATREQIDrYFRRHGVTP 216
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
19-126 1.54e-10

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 60.80  E-value: 1.54e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347  19 RHqnFAQAAQELHLTASAVSHHVRRLEEVLEVRLFLRHARGVRLTAEG-RQLADAASAAFTDVAA---VAHHLQPDadsv 94
Cdd:PRK03601  16 RH--FGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGeRLLPYAETLMNTWQAAkkeVAHTSQHN---- 89

                         90       100       110
                 ....*....|....*....|....*....|..
gi 896545347  95 PLRVTTLRSLSYCWLLPRLPRFTQAYPHIRIE 126
Cdd:PRK03601  90 ELSIGASASLWECMLTPWLGRLYQNQEALQFE 121
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 10-88 1.67e-10

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 60.73  E-value: 1.67e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 896545347  10 ALAVFAVAARHQNFAQAAQELHLTASAVSHHVRRLEEVLEVRLFLRHARGVRLTAEGRQLADAASAAFTDVAAVAHHLQ 88
Cdd:PRK11074   6 SLEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRRQCQ 84
PRK09986 PRK09986
LysR family transcriptional regulator;
8-128 1.76e-09

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 57.81  E-value: 1.76e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347   8 LPALAVFAVAARHQNFAQAAQELHLTASAVSHHVRRLEEVLEVRLFLRHARGVRLT-------AEGRQLADAASAAFTDV 80
Cdd:PRK09986   9 LKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLThagkilmEESRRLLDNAEQSLARV 88

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 896545347  81 AAVAHHlqpDADSVPLRVTTlrslSYCW--LLPRLPRFTQAYPHIRIELH 128
Cdd:PRK09986  89 EQIGRG---EAGRIEIGIVG----TALWgrLRPAMRHFLKENPNVEWLLR 131
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 17-131 4.41e-09

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 56.54  E-value: 4.41e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347  17 AARHQ-NFAQAAQELHLTASAVSHHVRRLEEVLEVRLFLRHA-RGVRLTAEGRQLADAASAAFTDVaavaHHLQ------ 88
Cdd:PRK12682  12 AVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGkRLKGLTEPGKAVLDVIERILREV----GNIKrigddf 87

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 896545347  89 PDADSVPLRVTTLRSLSYcWLLPR-LPRFTQAYPHIRIELHTGS 131
Cdd:PRK12682  88 SNQDSGTLTIATTHTQAR-YVLPRvVAAFRKRYPKVNLSLHQGS 130
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
22-210 6.98e-09

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 56.18  E-value: 6.98e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347  22 NFAQAAQELHLTASAVSHHVRRLEEVLEVRLFLRHARGVRLTAEGRQLADAASAAFTDVAAVAHHLQpDADSVPLRVTTL 101
Cdd:PRK15421  18 SLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQACN-EPQQTRLRIAIE 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347 102 RSLSYCWLLPRLPRFTQAYPHIRIELHTGSGLDryddngPEVGIRYG---------LGQWPGLRAQHLMDDYLFPVASP- 171
Cdd:PRK15421  97 CHSCIQWLTPALENFHKNWPQVEMDFKSGVTFD------PQPALQQGeldlvmtsdILPRSGLHYSPMFDYEVRLVLAPd 170

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 896545347 172 -ALAGvETLVDPARIADLPLLTDLSPQG----WRDWFRHAGVRP 210
Cdd:PRK15421 171 hPLAA-KTRITPEDLASETLLIYPVQRSrldvWRHFLQPAGVSP 213
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 109-286 1.37e-08

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


Pssm-ID: 176112 [Multi-domain]  Cd Length: 201  Bit Score: 54.03  E-value: 1.37e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347 109 LLPR-LPRFTQAYPHIRIELHTGSG---LDRYDDNGPEVGIRYGLGQWPGLRAQHLMDDYLFPVASPA--LAGVETlVDP 182
Cdd:cd08420   14 LLPRlLARFRKRYPEVRVSLTIGNTeeiAERVLDGEIDLGLVEGPVDHPDLIVEPFAEDELVLVVPPDhpLAGRKE-VTA 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347 183 ARIADLPLLTDLSPQGWRDWFRHA---GVRPPSPLPPMHTFaDSTDAMRAAV-YGMG-AVLARtHIAQPYMQRYEVVRLP 257
Cdd:cd08420   93 EELAAEPWILREPGSGTREVFERAlaeAGLDGLDLNIVMEL-GSTEAIKEAVeAGLGiSILSR-LAVRKELELGRLVALP 170

                        170       180
                 ....*....|....*....|....*....
gi 896545347 258 GPALKARYAYHVVHAEGQPPSPAARLFID 286
Cdd:cd08420  171 VEGLRLTRPFSLIYHKDKYLSPAAEAFLE 199
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
11-70 4.44e-08

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 53.44  E-value: 4.44e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347  11 LAVFAVAARHQNFAQAAQELHLTASAVSHHVRRLEEVLEVRLFLRhARGVRLTAEGRQLA 70
Cdd:PRK13348   7 LEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQRLL 65
PBP2_CrgA_like_3 cd08472
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 95-290 6.25e-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 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: 52.13  E-value: 6.25e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347  95 PLRVTTLRSLSYCWLLPRLPRFTQAYPHIRIELHTGsglDRYDD---NGPEVGIRYGLGQWPGLRAQHLMDDYLFPVASP 171
Cdd:cd08472    2 RLRVDVPGSLARLLLIPALPDFLARYPDIELDLGVS---DRPVDlirEGVDCVIRVGELADSSLVARRLGELRMVTCASP 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347 172 A-LAGVETlvdPARIADL---PLLTDLSPQGWRDW---FRHAGVRPPSPLPPMHTFADSTDAMRAAVYGMGAVLARTHIA 244
Cdd:cd08472   79 AyLARHGT---PRHPEDLerhRAVGYFSARTGRVLpweFQRDGEEREVKLPSRVSVNDSEAYLAAALAGLGIIQVPRFMV 155

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 896545347 245 QPYMQRYEVVRLPGPALKARYAYHVVHAEGQPPSPAARLFIDWLLE 290
Cdd:cd08472  156 RPHLASGRLVEVLPDWRPPPLPVSLLYPHRRHLSPRVRVFVDWVAE 201
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
10-130 8.53e-08

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 52.89  E-value: 8.53e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347  10 ALAVFAVAARHQNFAQAAQELHLTASAVSHHVRRLEEVLEVRLFLRHARGVRLTAEGRQLADAASAAFTDVAAVAHHLQP 89
Cdd:PRK10094   6 TLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPSELQQ 85

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 896545347  90 DADSVPLRV------------TTLRSLSycWLLPRLPrFTQAypHIRIELHTG 130
Cdd:PRK10094  86 VNDGVERQVnivinnllynpqAVAQLLA--WLNERYP-FTQF--HISRQIYMG 133
cbl PRK12679
HTH-type transcriptional regulator Cbl;
17-131 4.28e-07

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 50.58  E-value: 4.28e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347  17 AARHQNFAQAAQELHLTASAVSHHVRRLEEVLEVRLFLRhaRGVRL---TAEGRQLADAASAAFTDVAAV---AHHLQPD 90
Cdd:PRK12679  13 ARQDYNLTEVANMLFTSQSGVSRHIRELEDELGIEIFIR--RGKRLlgmTEPGKALLVIAERILNEASNVrrlADLFTND 90

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 896545347  91 ADSVPLRVTTLRSLSYCwLLPRLPRFTQAYPHIRIELHTGS 131
Cdd:PRK12679  91 TSGVLTIATTHTQARYS-LPEVIKAFRELFPEVRLELIQGT 130
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
 109-288 4.43e-07

The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO operon, which is involved in the carbon dioxide fixation, contains the type 2 periplasmic binding fold; CbbR, a LysR-type transcriptional regulator, is required to activate expression of RubisCO, one of two unique enzymes in the Calvin-Benson-Bassham (CBB) cycle pathway. All plants, cyanobacteria, and many autotrophic bacteria use the CBB cycle to fix carbon dioxide. Thus, this cycle plays an essential role in assimilating CO2 into organic carbon on earth. The key CBB cycle enzyme is ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO), which catalyzes the actual CO2 fixation reaction. The CO2 concentration affects the expression of RubisCO genes. It has also shown that NADPH enhances the DNA-binding ability of the CbbR. RubisCO is composed of eight large (CbbL) and eight small subunits (CbbS). 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: 176111  Cd Length: 197  Bit Score: 49.43  E-value: 4.43e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347 109 LLPR-LPRFTQAYPHIRIELHTG---SGLDRYDDNGPEVGIrygLGQWP---GLRAQHLMDDYLFPVASPA--LAGvETL 179
Cdd:cd08419   13 FAPRlLGAFCRRHPGVEVSLRVGnreQVLERLADNEDDLAI---MGRPPedlDLVAEPFLDNPLVVIAPPDhpLAG-QKR 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347 180 VDPARIADLPLLTDLSPQGWR----DWFRHAGVRPPSPLppmhTFAdSTDAMRAAVY-GMG-AVLARtHIAQPYMQRYEV 253
Cdd:cd08419   89 IPLERLAREPFLLREPGSGTRlameRFFAEHGVTLRVRM----ELG-SNEAIKQAVMaGLGlSVLSL-HTLALELATGRL 162

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 896545347 254 VRLPGPALKARYAYHVVHAEGQPPSPAARLFIDWL 288
Cdd:cd08419  163 AVLDVEGFPIRRQWYVVHRKGKRLSPAAQAFLDFL 197
PBP2_CrgA_like_8 cd08477
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 96-288 5.40e-07

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: 49.15  E-value: 5.40e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347  96 LRVTTLRSLSYCWLLPRLPRFTQAYPHIRIELHTGSGLDRYDDNGPEVGIRYGLGQWPGLRAQHLMDDYLFPVASPA-LA 174
Cdd:cd08477    3 LRISAPVTFGSHVLTPALAEYLARYPDVRVDLVLSDRLVDLVEEGFDAAFRIGELADSSLVARPLAPYRMVLCASPDyLA 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347 175 GVETlvdPARIADLPLLTDLSPQGWR---DW-FRHAGVRPPSPLPPMHTfADSTDAMR-AAVYGMGAVLARTHIAQPYMQ 249
Cdd:cd08477   83 RHGT---PTTPEDLARHECLGFSYWRarnRWrLEGPGGEVKVPVSGRLT-VNSGQALRvAALAGLGIVLQPEALLAEDLA 158

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 896545347 250 RYEVVR-LPGPALKARyAYHVVHAEGQPPSPAARLFIDWL 288
Cdd:cd08477  159 SGRLVElLPDYLPPPR-PMHLLYPPDRRPTPKLRSFIDFL 197
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 8-271 9.86e-07

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 49.30  E-value: 9.86e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347   8 LPALAVFAVAARHQNFAQAAQELHLTASAVSHHVRRLEEVLEVRLFLRHARGVRLTAEGRQLADAASAAFTDVAAVAHHL 87
Cdd:PRK10837   5 LRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQAVEIEQLF 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347  88 QpdADSVPLRVTTLRSLSYCWLLPRLPRFTQAYPHIRIELHTGSGLD--------RYDdngpeVGIRYGLGQWPGLRAQH 159
Cdd:PRK10837  85 R--EDNGALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNSQDvinavldfRVD-----IGLIEGPCHSPELISEP 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347 160 LMDDYLFPVASPALAGVETLVDPARIADLPLLTDLSPQGWRDWFRHAGVrppSPLPPMHTFAD--STDAMRAAV-YGMG- 235
Cdd:PRK10837 158 WLEDELVVFAAPDSPLARGPVTLEQLAAAPWILRERGSGTREIVDYLLL---SHLPRFELAMElgNSEAIKHAVrHGLGi 234

                        250       260       270
                 ....*....|....*....|....*....|....*...
gi 896545347 236 AVLARtHIAQPYMQRYEVVRL--PGPALKaRYAYHVVH 271
Cdd:PRK10837 235 SCLSR-RVIADQLQAGTLVEVavPLPRLM-RTLYRIHH 270
leuO PRK09508
leucine transcriptional activator; Reviewed
 3-69 1.05e-06

leucine transcriptional activator; Reviewed


Pssm-ID: 181918 [Multi-domain]  Cd Length: 314  Bit Score: 49.25  E-value: 1.05e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 896545347   3 LRPSLLPALAVFAVAARHQNFAQAAQELHLTASAVSHHVRRLEEVLEVRLFLRHARGVRLTAEGRQL 69
Cdd:PRK09508  19 LRMVDLNLLTVFDAVMQEQNITRAAHNLGMSQPAVSNAVARLKVMFNDELFVRYGRGIQPTARARQL 85
rbcR CHL00180
LysR transcriptional regulator; Provisional
 5-131 1.17e-06

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 49.25  E-value: 1.17e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347   5 PSLLPALAVFAVAARHQNFAQAAQELHLTASAVSHHVRRLEEVLEVRLFLRHARGVRLTAEG--------RQLA--DAAS 74
Cdd:CHL00180   4 PFTLDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGelllrygnRILAlcEETC 83

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 896545347  75 AAFTDVaavaHHLQPDADSVPLRVTTLRslsycWLLPRL-PRFTQAYPHIRIELHTGS 131
Cdd:CHL00180  84 RALEDL----KNLQRGTLIIGASQTTGT-----YLMPRLiGLFRQRYPQINVQLQVHS 132
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 11-129 6.80e-06

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 46.69  E-value: 6.80e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347  11 LAVFAVAARHQNFAQAAQELHLTASAVSHHVRRLEEVLEVRLFLRHARGVRLTAEGRQLADAASAAFTDV-AAVAHHLQP 89
Cdd:PRK09906   6 LRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAeKAKLRARKI 85

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 896545347  90 DADSVPLRVTTLRSLSYCWLLPRLPRFTQAYPHIRIELHT 129
Cdd:PRK09906  86 VQEDRQLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVS 125
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 8-293 7.87e-06

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 46.52  E-value: 7.87e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347   8 LPALAVFAVAARHQNFAQAAQELHLTASAVSHHVRRLEEVLEVRLFLRHARGVRLTAEGRQLADAASAAFTDVAAVAH-- 85
Cdd:PRK14997   4 LNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDai 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347  86 -HLQPDADSVpLRVTTLRSLSYCWLLPRLPRFTQAYPHIRIELHTGSGLDRYDDNGPEVGIRYGLGQW--PGLRAQHLMD 162
Cdd:PRK14997  84 aALQVEPRGI-VKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLEATNRRVDVVGEGVDVAIRVRPRPFedSDLVMRVLAD 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347 163 DYLFPVASPALagVETLVDPARIADL---PLLTDLSPQGWRDW--FRHAGVRPPSPLPPMHTFADSTDAMRAAVYGMGAV 237
Cdd:PRK14997 163 RGHRLFASPDL--IARMGIPSAPAELshwPGLSLASGKHIHRWelYGPQGARAEVHFTPRMITTDMLALREAAMAGVGLV 240

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 896545347 238 LARTHIAQPYMQRYEVVRLPGPALKARYAYHVVHAEGQPPSPAARLFIDWLLEQAQ 293
Cdd:PRK14997 241 QLPVLMVKEQLAAGELVAVLEEWEPRREVIHAVFPSRRGLLPSVRALVDFLTEEYA 296
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
16-131 8.16e-06

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 46.51  E-value: 8.16e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347  16 VAARHQNFAQAAQELHLTASAVSHHVRRLEEVLEVRLFLRHARGVR-LTAEGRQLADAASAAFTDV-------AAVAHHl 87
Cdd:PRK12684  12 AVRQNFNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRgLTEPGRIILASVERILQEVenlkrvgKEFAAQ- 90

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 896545347  88 qpdaDSVPLRVTTLRSLSYCWLLPRLPRFTQAYPHIRIELHTGS 131
Cdd:PRK12684  91 ----DQGNLTIATTHTQARYALPAAIKEFKKRYPKVRLSILQGS 130
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 4-69 9.26e-06

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 46.56  E-value: 9.26e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 896545347   4 RPSL---LPALAVFAVAARHQNFAQAAQELHLTASAVSHHVRRLEEVLEVRLFLRHARGVRLTAEGRQL 69
Cdd:PRK15092   6 RPIInldLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQL 74
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 96-288 1.06e-05

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: 45.53  E-value: 1.06e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347  96 LRVTTLRSLSYCWLLPRLPRFTQAYPHIRIELHTGSGL-----DRYDdngpeVGIRYGLGQWPGLRAQHLMDDY-LFPVA 169
Cdd:cd08474    5 LRINAPRVAARLLLAPLLARFLARYPDIRLELVVDDGLvdivaEGFD-----AGIRLGESVEKDMVAVPLGPPLrMAVVA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347 170 SPA-LA--GVetlvdPARIADLP--------LLTDLSPQGWRdwFRHAG----VRPPSPLppmhTFADSTDAMRAAVYGM 234
Cdd:cd08474   80 SPAyLArhGT-----PEHPRDLLnhrciryrFPTSGALYRWE--FERGGreleVDVEGPL----ILNDSDLMLDAALDGL 148

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 896545347 235 G-AVLARTHIAqPYMQRYEVVRLPGPALKARYAYHVVHAEGQPPSPAARLFIDWL 288
Cdd:cd08474  149 GiAYLFEDLVA-EHLASGRLVRVLEDWSPPFPGGYLYYPSRRRVPPALRAFIDFL 202
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
8-67 1.19e-05

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 46.29  E-value: 1.19e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347   8 LPALAVFAVAARHQNFAQAAQELHLTASAVSHHVRRLEEVLEVRLFLRHARGVRLTAEGR 67
Cdd:PRK10632   4 LKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGR 63
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 17-131 1.38e-05

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 45.80  E-value: 1.38e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347  17 AARHQ-NFAQAAQELHLTASAVSHHVRRLEEVLEVRLFLRhaRGVRL---TAEGRQLADAASAAFTDVAAVAHHLQ--PD 90
Cdd:PRK12683  12 AVRQNfNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIR--RGKRLtglTEPGKELLQIVERMLLDAENLRRLAEqfAD 89

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 896545347  91 ADSVPLRVTTLRSLSYCWLLPRLPRFTQAYPHIRIELHTGS 131
Cdd:PRK12683  90 RDSGHLTVATTHTQARYALPKVVRQFKEVFPKVHLALRQGS 130
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
9-128 1.72e-05

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 45.53  E-value: 1.72e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347   9 PALAVFAVAARHQNFAQAAQELHLTASAVSHHVRRLEE----VLEVRlflrhARGVRLTAEGRQLAdaasAAFTDVAAVA 84
Cdd:PRK03635   5 KQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEErvgqVLLVR-----TQPCRPTEAGQRLL----RHARQVRLLE 75

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 896545347  85 HHLQPDADSVPLRVTTLR------SLSyCWLLPRLPRFTQAYPhIRIELH 128
Cdd:PRK03635  76 AELLGELPALDGTPLTLSiavnadSLA-TWFLPALAPVLARSG-VLLDLV 123
PBP2_CrgA cd08478
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains ...
 109-288 2.98e-05

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


Pssm-ID: 176167 [Multi-domain]  Cd Length: 199  Bit Score: 44.25  E-value: 2.98e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347 109 LLPRLPRFTQAYPHIRIELHTGSGLDRYDDNGPEVGIRYGLGQWPGLRAQHLMDDYLFPVASPA-LAGVETlvdPARIAD 187
Cdd:cd08478   18 LAPLIAKFRERYPDIELELVSNEGIIDLIERKTDVAIRIGELTDSTLHARPLGKSRLRILASPDyLARHGT---PQSIED 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347 188 LP---LLTDLSPQGWRDW-FRHAGVRPPSPLPpmHTFADSTDAMRA-AVYGMGAVLARTHIAQPYMQRYEVVRLPGP-AL 261
Cdd:cd08478   95 LAqhqLLGFTEPASLNTWpIKDADGNLLKIQP--TITASSGETLRQlALSGCGIACLSDFMTDKDIAEGRLIPLFAEqTS 172

                        170       180
                 ....*....|....*....|....*..
gi 896545347 262 KARYAYHVVHAEGQPPSPAARLFIDWL 288
Cdd:cd08478  173 DVRQPINAVYYRNTALSLRIRCFIDFL 199
PRK09791 PRK09791
LysR family transcriptional regulator;
11-74 7.12e-05

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 43.60  E-value: 7.12e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 896545347  11 LAVFAVAARHQNFAQAAQELHLTASAVSHHVRRLEEVLEVRLFLRHARGVRLTAEGRQLADAAS 74
Cdd:PRK09791  10 IRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHAS 73
PRK12680 PRK12680
LysR family transcriptional regulator;
15-154 2.77e-04

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 41.92  E-value: 2.77e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347  15 AVAARHQNFAQAAQELHLTASAVSHHVRRLEEVLEVRLFLRHARGVR-LTAEGRQLADAASAAFTDVAAVAHHL--QPDA 91
Cdd:PRK12680  11 AIADAELNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLEsVTPAGVEVIERARAVLSEANNIRTYAanQRRE 90

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 896545347  92 DSVPLRVTTLRSLSYCWLLPRLPRFTQAYPHIRIELHTG---SGLDRYDDNGPEVGIRYGLGQWPG 154
Cdd:PRK12680  91 SQGQLTLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQQAaesAALDLLGQGDADIAIVSTAGGEPS 156
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 18-128 3.50e-04

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 41.55  E-value: 3.50e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347  18 ARHQNFAQAAQELHLTASAVSHHVRRLEEVLEVRLFLRHARGVRLTAEGRQLADAASAAFTDVAAVAH--HLQPDADSVP 95
Cdd:PRK11151  13 AEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVLKEmaSQQGETMSGP 92

                         90       100       110
                 ....*....|....*....|....*....|....
gi 896545347  96 LRVTTLRSLSyCWLLPR-LPRFTQAYPHIRIELH 128
Cdd:PRK11151  93 LHIGLIPTVG-PYLLPHiIPMLHQTFPKLEMYLH 125
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 95-288 3.54e-04

The C-terminal substrate binding domain of galactose-binding protein regulator contains the type 2 periplasmic binding fold; Galactose-binding protein regulator (GbpR), a member of the LysR family of bacterial transcriptional regulators, regulates the expression of chromosomal virulence gene chvE. The chvE gene is involved in the uptake of specific sugars, in chemotaxis to these sugars, and in the VirA-VirG two-component signal transduction system. In the presence of an inducing sugar such as L-arabinose, D-fucose, or D-galactose, GbpR activates chvE expression, while in the absence of an inducing sugar, GbpR represses expression. 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: 176126 [Multi-domain]  Cd Length: 201  Bit Score: 41.10  E-value: 3.54e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347  95 PLRVTTLRSLSYCWLLPRLPRFTQAYPHIRIELHTGSGLD-----RYDDNGPEVGIRYGLGQWPGLRAQHLMDDYLFPVA 169
Cdd:cd08435    1 TVRVGAVPAAAPVLLPPAIARLLARHPRLTVRVVEGTSDElleglRAGELDLAIGRLADDEQPPDLASEELADEPLVVVA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347 170 SPAlagvETLVDPARIadlpLLTDLSPQGW---------RDW----FRHAGVRPPSPLppmhTFADSTDAMRAAV--YGM 234
Cdd:cd08435   81 RPG----HPLARRARL----TLADLADYPWvlpppgtplRQRleqlFAAAGLPLPRNV----VETASISALLALLarSDM 148

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 896545347 235 GAVLARtHIAQPYMQRYEVVRLPGPALKARYAYHVVHAEGQPPSPAARLFIDWL 288
Cdd:cd08435  149 LAVLPR-SVAEDELRAGVLRELPLPLPTSRRPIGITTRRGGPLSPAARALLDAL 201
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 96-286 5.16e-04

The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA expression of glutamate synthase operon, contains type 2 periplasmic binding fold; GltC, a member of the LysR family of bacterial transcriptional factors, activates the expression of gltA gene of glutamate synthase operon and is essential for cell growth in the absence of glutamate. Glutamate synthase is a heterodimeric protein that encoded by gltA and gltB, whose expression is subject to nutritional regulation. GltC also negatively auto-regulates its own expression. This substrate-binding domain has strong 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: 176125 [Multi-domain]  Cd Length: 195  Bit Score: 40.21  E-value: 5.16e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347  96 LRVTTLRSLSyCWLLPRLPR-FTQAYPHIRIELHTGSG---LDRYDDNGPEVGIRYGLGQWPGLRAQHLMDDYLFpVASP 171
Cdd:cd08434    2 VRLGFLHSLG-TSLVPDLIRaFRKEYPNVTFELHQGSTdelLDDLKNGELDLALCSPVPDEPDIEWIPLFTEELV-LVVP 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347 172 A---LAGvETLVDPARIADLPLLTdLSPQ-GWR----DWFRHAGVRPPSplppmhTF-ADSTDAMRAAV-YGMG-AVLAR 240
Cdd:cd08434   80 KdhpLAG-RDSVDLAELADEPFVL-LSPGfGLRpivdELCAAAGFTPKI------AFeGEEDSTIAGLVaAGLGvAILPE 151

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 896545347 241 THIAQPymqrYEVVRLPGPALKARYAYHVVHAEGQPPSPAARLFID 286
Cdd:cd08434  152 MTLLNP----PGVKKIPIKDPDAERTIGLAWLKDRYLSPAARRFKD 193
PRK10341 PRK10341
transcriptional regulator TdcA;
7-69 6.23e-04

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 41.00  E-value: 6.23e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 896545347   7 LLP---ALAVFAVAARHQNFAQAAQELHLTASAVSHHVRRLEEVLEVRLFLRHARGVRLTAEGRQL 69
Cdd:PRK10341   5 LLPktqHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVL 70
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 109-286 2.95e-03

The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator PAO1-like, a member of the type 2 periplasmic binding fold protein superfamily; This family includes the C-terminal substrate domain of a putative LysR-type transcriptional regulator from the plant pathogen Pseudomonas aeruginosa PAO1and its closely related homologs. The LysR-type transcriptional regulators (LTTRs) are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of N2 fixing bacteria, and synthesis of virulence factors, to a 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: 176104 [Multi-domain]  Cd Length: 198  Bit Score: 38.29  E-value: 2.95e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347 109 LLPRL-PRFTQAYPHIRIELHTGSG---LDRYDDNGPEVGIRYGLGQWPGLRAQHLMDD--YLFPVASPALAGVETlVDP 182
Cdd:cd08412   14 YLPGLlRRFREAYPGVEVRVVEGNQeelEEGLRSGELDLALTYDLDLPEDIAFEPLARLppYVWLPADHPLAGKDE-VSL 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347 183 ARIADLPL-LTDLsPQGWR---DWFRHAGVRPPsplPPMHTfaDSTDAMRAAV---YGMGAVLARTHIAQPY-MQRYEVV 254
Cdd:cd08412   93 ADLAAEPLiLLDL-PHSREyflSLFAAAGLTPR---IAYRT--SSFEAVRSLVangLGYSLLNDRPYRPWSYdGKRLVRR 166

                        170       180       190
                 ....*....|....*....|....*....|....
gi 896545347 255 RLPG--PALKARYAYHVvhaeGQPPSPAARLFID 286
Cdd:cd08412  167 PLADpvPPLRLGLAWRR----GARLTRAARAFVD 196
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 25-191 5.02e-03

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 38.12  E-value: 5.02e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347  25 QAAQELHLTASAVSHHVRRLEEVLEVRLFLRHARGVRLTAEGRQLADAASA-------AFTDVAAVAHHLQPDAdSVPLR 97
Cdd:PRK11233  20 QAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAilrqceqAQLAVHNVGQALSGQV-SIGLA 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347  98 VTTL-RSLSycwlLPRLPRFTQAYPHIRIELHTGSG--LDRYDDNGP-EVGIRYGLGQWPGLRAQHLMDDYLFPVASPAL 173
Cdd:PRK11233  99 PGTAaSSLT----MPLLQAVRAEFPGIVLYLHENSGatLNEKLMNGQlDMAVIYEHSPVAGLSSQPLLKEDLFLVGTQDC 174

                        170
                 ....*....|....*...
gi 896545347 174 AGVEtlVDPARIADLPLL 191
Cdd:PRK11233 175 PGQS--VDLAAVAQMNLF 190
MntR COG1321
Mn-dependent transcriptional regulator MntR, DtxR family [Transcription];
27-70 7.06e-03

Mn-dependent transcriptional regulator MntR, DtxR family [Transcription];


Pssm-ID: 440932 [Multi-domain]  Cd Length: 135  Bit Score: 36.33  E-value: 7.06e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 896545347  27 AQELHLTASAVSHHVRRLEEvlevRLFLRHA--RGVRLTAEGRQLA 70
Cdd:COG1321   31 AERLGVSPPSVTEMLKKLEE----KGLVEYEpyGGITLTEEGRELA 72
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 96-288 7.83e-03

TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to a name a few. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176131 [Multi-domain]  Cd Length: 197  Bit Score: 36.73  E-value: 7.83e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347  96 LRVTTLRSLSYCWLLPRLPRFTQAYPHIRIELHTGSG---LDRYDDNGPEVGIRYGLGQWPGLRAQHLMDDYLFPVASP- 171
Cdd:cd08440    2 VRVAALPSLAATLLPPVLAAFRRRHPGIRVRLRDVSAeqvIEAVRSGEVDFGIGSEPEADPDLEFEPLLRDPFVLVCPKd 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896545347 172 -ALAGVETlVDPARIADLPLLTDLSPQGWRDWFRHAGVRPPSPLPPMHTFADSTDAMRAAVYGMG-AVLARTHIAQPYMQ 249
Cdd:cd08440   82 hPLARRRS-VTWAELAGYPLIALGRGSGVRALIDRALAAAGLTLRPAYEVSHMSTALGMVAAGLGvAVLPALALPLADHP 160

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 896545347 250 RYEVVRLPGPALKARYAyhVVHAEGQPPSPAARLFIDWL 288
Cdd:cd08440  161 GLVARPLTEPVVTRTVG--LIRRRGRSLSPAAQAFLDLL 197
 
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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