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Conserved domains on  [gi|2084061965|gb|QZD89317|]
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LysR family transcriptional regulator [Qipengyuania aurantiaca]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 11426483)

LysR family transcriptional regulator containing an N-terminal HTH (helix-turn-helix) DNA-binding domain and a C-terminal substrate binding domain, which is structurally homologous to the type 2 periplasmic-binding (PBP2) fold proteins

CATH:  3.40.190.10
Gene Ontology:  GO:0003700|GO:0003677|GO:0006355
PubMed:  19047729|8257110|15808743
SCOP:  4000316

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
7-297 1.85e-54

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 177.75  E-value: 1.85e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965   7 SLDQLRIFLAVAEEGSFGAAARKMGRAVSAVSYGVSQMESQLGVTLFEREGsRRPVLTEEGRGLLTEAKAVADGIDHLLA 86
Cdd:COG0583     2 DLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTG-RGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965  87 KTQSLHAGLESEVSLVVDVMLPGEVTASVLRDFRVMFPTVALRLQVEALGAVAACLLEGGADLGIGGPVLADhPELERQA 166
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPD-PGLVARP 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965 167 IGSVELVPVAAPYHPLARagiepgesrkhlqlvltdRSPLTEgrefsvlspeswrlaDLGAKHALLKEGIGWGNMPRHMV 246
Cdd:COG0583   160 LGEERLVLVASPDHPLAR------------------RAPLVN---------------SLEALLAAVAAGLGIALLPRFLA 206

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2084061965 247 SGDIDEGRLCLLDLPEkPGAHYTLSALWRRDARPGPATSWLIDAMRERIGK 297
Cdd:COG0583   207 ADELAAGRLVALPLPD-PPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
7-297 1.85e-54

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 177.75  E-value: 1.85e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965   7 SLDQLRIFLAVAEEGSFGAAARKMGRAVSAVSYGVSQMESQLGVTLFEREGsRRPVLTEEGRGLLTEAKAVADGIDHLLA 86
Cdd:COG0583     2 DLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTG-RGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965  87 KTQSLHAGLESEVSLVVDVMLPGEVTASVLRDFRVMFPTVALRLQVEALGAVAACLLEGGADLGIGGPVLADhPELERQA 166
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPD-PGLVARP 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965 167 IGSVELVPVAAPYHPLARagiepgesrkhlqlvltdRSPLTEgrefsvlspeswrlaDLGAKHALLKEGIGWGNMPRHMV 246
Cdd:COG0583   160 LGEERLVLVASPDHPLAR------------------RAPLVN---------------SLEALLAAVAAGLGIALLPRFLA 206

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2084061965 247 SGDIDEGRLCLLDLPEkPGAHYTLSALWRRDARPGPATSWLIDAMRERIGK 297
Cdd:COG0583   207 ADELAAGRLVALPLPD-PPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 3-289 7.77e-31

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 117.35  E-value: 7.77e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965   3 LGEPSLDQLRiflAVAEEGSFGAAARKMGRAVSAVSYGVSQMESQLGVTLFEREgSRRPVLTEEGRGLLTEAKAVADGID 82
Cdd:PRK11074    2 WSEYSLEVVD---AVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERR-HRDVELTPAGEWFVKEARSVIKKMQ 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965  83 HLLAKTQSLHAGLESEVSLVVDVMLPGEVTASVLRDFRVMFPTVALRLQVEALGAVAACLLEGGADLGIGG----PVLAD 158
Cdd:PRK11074   78 ETRRQCQQVANGWRGQLSIAVDNIVRPDRTRQLIVDFYRHFDDVELIIRQEVFNGVWDALADGRVDIAIGAtraiPVGGR 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965 159 HpelERQAIGSVELVPVAAPYHPLA-RAG-IEPGESRKHLQLVLTDRS---P------LTEGREFSVlsPESWRLADlga 227
Cdd:PRK11074  158 F---AFRDMGMLSWACVVSSDHPLAsMDGpLSDDELRPYPSLCLEDTSrtlPkritwlLDNQRRLVV--PDWESAIN--- 229

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2084061965 228 khaLLKEGIGWGNMPRHMVSGDIDEGRLCLLDLPE-KPGAHYTLSalWRRDaRPGPATSWLID 289
Cdd:PRK11074  230 ---CLSAGLCVGMVPTHFAKPLINSGKLVELTLENpFPDSPCCLT--WQQN-DMSPALAWLLD 286
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 98-294 5.76e-24

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: 96.59  E-value: 5.76e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965  98 EVSLVVDVMLPGEVTASVLRDFRVMFPTVALRLQVEALGAVAACLLEGGADLGIGGPVLaDHPELERQAIGSVELVPVAA 177
Cdd:pfam03466   3 RLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPP-DDPGLEARPLGEEPLVLVAP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965 178 PYHPLAR-AGIEPGESRKHLQLVLTDRSPLTE-----GREFSVLSPESWRLADLGAKHALLKEGIGWGNMPRHMVSGDID 251
Cdd:pfam03466  82 PDHPLARgEPVSLEDLADEPLILLPPGSGLRDlldraLRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARELA 161

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 2084061965 252 EGRLCLLDLPEkPGAHYTLSALWRRDARPGPATSWLIDAMRER 294
Cdd:pfam03466 162 DGRLVALPLPE-PPLPRELYLVWRKGRPLSPAVRAFIEFLREA 203
PBP2_HupR cd08431
The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which ...
 98-289 6.28e-23

The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which regulates expression of the heme uptake receptor HupA; contains the type 2 periplasmic binding fold; HupR, a member of the LysR family, activates hupA transcription under low-iron conditions in the presence of hemin. The expression of many iron-uptake genes, such as hupA, is regulated at the transcriptional level by iron and an iron-binding repressor protein called Fur (ferric uptake regulation). Under iron-abundant conditions with heme, the active Fur repressor protein represses transcription of the iron-uptake gene hupA, and prevents transcriptional activation via HupR. Under low-iron conditions with heme, the Fur repressor is inactive and transcription of the hupA is allowed. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176122 [Multi-domain]  Cd Length: 195  Bit Score: 93.49  E-value: 6.28e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965  98 EVSLVVDVMLPGEVTASVLRDFRVMFPTVALRLQVEALGAVAACLLEGGADLGIGGPVLADHPELERQAIGSVELVPVAA 177
Cdd:cd08431     1 ELRIAIDTVLPLQPLYPLIAEFYQLNKATRIRLSEEVLGGTWDALASGRADLVIGATGELPPGGVKTRPLGEVEFVFAVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965 178 PYHPLARAG--IEPGESRKHLQLVLTDRSPLTEGREFSVLSPES-WRLADLGAKHALLKEGIGWGNMPRHMVSGDIDEGR 254
Cdd:cd08431    81 PNHPLAKLDgpLDASAIKQYPAIVVADTSRNLPPRSSGLLEGQDrIRVPTMQAKIDAQVLGLGVGYLPRHLAKPELASGE 160

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 2084061965 255 LCLLDLpEKPGAHYTLSALWRRDARpGPATSWLID 289
Cdd:cd08431   161 LVEKAL-EDPRPPQELFLAWRKDQR-GKALAWFVQ 193
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 9-78 1.69e-08

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


Pssm-ID: 274509 [Multi-domain]  Cd Length: 292  Bit Score: 54.54  E-value: 1.69e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965   9 DQLRIFLAVAEEGSFGAAARKMGRAVSAVSYGVSQMESQLGVTLFERegSRRPVLTEEGRGLLTEAKAVA 78
Cdd:TIGR03298   4 RQLAALAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVR--TQPCRATEAGQRLLRHARQVR 71
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
7-297 1.85e-54

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 177.75  E-value: 1.85e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965   7 SLDQLRIFLAVAEEGSFGAAARKMGRAVSAVSYGVSQMESQLGVTLFEREGsRRPVLTEEGRGLLTEAKAVADGIDHLLA 86
Cdd:COG0583     2 DLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTG-RGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965  87 KTQSLHAGLESEVSLVVDVMLPGEVTASVLRDFRVMFPTVALRLQVEALGAVAACLLEGGADLGIGGPVLADhPELERQA 166
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPD-PGLVARP 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965 167 IGSVELVPVAAPYHPLARagiepgesrkhlqlvltdRSPLTEgrefsvlspeswrlaDLGAKHALLKEGIGWGNMPRHMV 246
Cdd:COG0583   160 LGEERLVLVASPDHPLAR------------------RAPLVN---------------SLEALLAAVAAGLGIALLPRFLA 206

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2084061965 247 SGDIDEGRLCLLDLPEkPGAHYTLSALWRRDARPGPATSWLIDAMRERIGK 297
Cdd:COG0583   207 ADELAAGRLVALPLPD-PPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 3-289 7.77e-31

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 117.35  E-value: 7.77e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965   3 LGEPSLDQLRiflAVAEEGSFGAAARKMGRAVSAVSYGVSQMESQLGVTLFEREgSRRPVLTEEGRGLLTEAKAVADGID 82
Cdd:PRK11074    2 WSEYSLEVVD---AVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERR-HRDVELTPAGEWFVKEARSVIKKMQ 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965  83 HLLAKTQSLHAGLESEVSLVVDVMLPGEVTASVLRDFRVMFPTVALRLQVEALGAVAACLLEGGADLGIGG----PVLAD 158
Cdd:PRK11074   78 ETRRQCQQVANGWRGQLSIAVDNIVRPDRTRQLIVDFYRHFDDVELIIRQEVFNGVWDALADGRVDIAIGAtraiPVGGR 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965 159 HpelERQAIGSVELVPVAAPYHPLA-RAG-IEPGESRKHLQLVLTDRS---P------LTEGREFSVlsPESWRLADlga 227
Cdd:PRK11074  158 F---AFRDMGMLSWACVVSSDHPLAsMDGpLSDDELRPYPSLCLEDTSrtlPkritwlLDNQRRLVV--PDWESAIN--- 229

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2084061965 228 khaLLKEGIGWGNMPRHMVSGDIDEGRLCLLDLPE-KPGAHYTLSalWRRDaRPGPATSWLID 289
Cdd:PRK11074  230 ---CLSAGLCVGMVPTHFAKPLINSGKLVELTLENpFPDSPCCLT--WQQN-DMSPALAWLLD 286
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
8-307 5.08e-26

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 104.89  E-value: 5.08e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965   8 LDQ--LRIFLAVAEEGSFGAAARKMGRAVSAVSYGVSQMESQLGVTLFEREgSRRPVLTEEGRGLLTEAKAVADGIDHLL 85
Cdd:PRK10094    2 FDPetLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRT-TRSVTLTAAGEHLLSQARDWLSWLESMP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965  86 AKTQSLHAGLESEVSLVV-DVMLPGEVTASVLRDFRVMFPTVALRLQVEALGAVAACLLEGGADLGIGgpVLADHP---E 161
Cdd:PRK10094   81 SELQQVNDGVERQVNIVInNLLYNPQAVAQLLAWLNERYPFTQFHISRQIYMGVWDSLLYEGFSLAIG--VTGTEAlanT 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965 162 LERQAIGSVELVPVAAPYHPLAragiepgesrkHLQLVLTDrsplTEGREFSVLSPE----------SWRLA-------- 223
Cdd:PRK10094  159 FSLDPLGSVQWRFVMAADHPLA-----------NVEEPLTE----AQLRRFPAVNIEdsartltkrvAWRLPgqkeiivp 223

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965 224 DLGAKHALLKEGIGWGNMPRHMVSGDIDEGRLCLLDLPEkPGAHYTLSALWRRDARpGPATSWLIDAMRERigkcsgvEP 303
Cdd:PRK10094  224 DMETKIAAHLAGVGIGFLPKSLCQSMIDNQQLVSRVIPT-MRPPSPLSLAWRKFGS-GKAVEDIVTLFTQR-------RP 294


                  ....
gi 2084061965 304 SVSG 307
Cdd:PRK10094  295 EISG 298
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 98-294 5.76e-24

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: 96.59  E-value: 5.76e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965  98 EVSLVVDVMLPGEVTASVLRDFRVMFPTVALRLQVEALGAVAACLLEGGADLGIGGPVLaDHPELERQAIGSVELVPVAA 177
Cdd:pfam03466   3 RLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPP-DDPGLEARPLGEEPLVLVAP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965 178 PYHPLAR-AGIEPGESRKHLQLVLTDRSPLTE-----GREFSVLSPESWRLADLGAKHALLKEGIGWGNMPRHMVSGDID 251
Cdd:pfam03466  82 PDHPLARgEPVSLEDLADEPLILLPPGSGLRDlldraLRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARELA 161

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 2084061965 252 EGRLCLLDLPEkPGAHYTLSALWRRDARPGPATSWLIDAMRER 294
Cdd:pfam03466 162 DGRLVALPLPE-PPLPRELYLVWRKGRPLSPAVRAFIEFLREA 203
PBP2_HupR cd08431
The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which ...
 98-289 6.28e-23

The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which regulates expression of the heme uptake receptor HupA; contains the type 2 periplasmic binding fold; HupR, a member of the LysR family, activates hupA transcription under low-iron conditions in the presence of hemin. The expression of many iron-uptake genes, such as hupA, is regulated at the transcriptional level by iron and an iron-binding repressor protein called Fur (ferric uptake regulation). Under iron-abundant conditions with heme, the active Fur repressor protein represses transcription of the iron-uptake gene hupA, and prevents transcriptional activation via HupR. Under low-iron conditions with heme, the Fur repressor is inactive and transcription of the hupA is allowed. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176122 [Multi-domain]  Cd Length: 195  Bit Score: 93.49  E-value: 6.28e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965  98 EVSLVVDVMLPGEVTASVLRDFRVMFPTVALRLQVEALGAVAACLLEGGADLGIGGPVLADHPELERQAIGSVELVPVAA 177
Cdd:cd08431     1 ELRIAIDTVLPLQPLYPLIAEFYQLNKATRIRLSEEVLGGTWDALASGRADLVIGATGELPPGGVKTRPLGEVEFVFAVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965 178 PYHPLARAG--IEPGESRKHLQLVLTDRSPLTEGREFSVLSPES-WRLADLGAKHALLKEGIGWGNMPRHMVSGDIDEGR 254
Cdd:cd08431    81 PNHPLAKLDgpLDASAIKQYPAIVVADTSRNLPPRSSGLLEGQDrIRVPTMQAKIDAQVLGLGVGYLPRHLAKPELASGE 160

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 2084061965 255 LCLLDLpEKPGAHYTLSALWRRDARpGPATSWLID 289
Cdd:cd08431   161 LVEKAL-EDPRPPQELFLAWRKDQR-GKALAWFVQ 193
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
8-68 8.93e-20

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 81.28  E-value: 8.93e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2084061965   8 LDQLRIFLAVAEEGSFGAAARKMGRAVSAVSYGVSQMESQLGVTLFEReGSRRPVLTEEGR 68
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFER-TTRGVRLTEAGE 60
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 7-184 4.19e-15

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 73.95  E-value: 4.19e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965   7 SLDQLRIFLAVAEEGSFGAAARKMGRAVSAVSYGVSQMESQLGVTLFEREGsRRPVLTEEGRGLLTEAKAV---ADGIDH 83
Cdd:PRK10837    4 TLRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVG-KRLVVNEHGRLLYPRALALleqAVEIEQ 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965  84 LLakTQSLHAGLESEVSLVVDVMLPGevtasVLRDFRVMFPTVALRLQVEALGAVAACLLEGGADLG-IGGPvlADHPEL 162
Cdd:PRK10837   83 LF--REDNGALRIYASSTIGNYILPA-----MIARYRRDYPQLPLELSVGNSQDVINAVLDFRVDIGlIEGP--CHSPEL 153

                         170       180
                  ....*....|....*....|..
gi 2084061965 163 ERQAIGSVELVPVAAPYHPLAR 184
Cdd:PRK10837  154 ISEPWLEDELVVFAAPDSPLAR 175
rbcR CHL00180
LysR transcriptional regulator; Provisional
 7-204 7.24e-15

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 73.52  E-value: 7.24e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965   7 SLDQLRIFLAVAEEGSFGAAARKMGRAVSAVSYGVSQMESQLGVTLFEREGsRRPVLTEEGRGLLTEAK---AVADGIDH 83
Cdd:CHL00180    6 TLDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSK-NKASLTEAGELLLRYGNrilALCEETCR 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965  84 LLAKTQSLHAGlesevSLVVDV--MLPGEVTASVLRDFRVMFPTVALRLQVEALGAVAACLLEGGADLGI-GGPVLAD-H 159
Cdd:CHL00180   85 ALEDLKNLQRG-----TLIIGAsqTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIvGGEVPTElK 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 2084061965 160 PELERQAIGSVELVPVAAPYHPLARAGIEPGESRKHLQLVLTDRS 204
Cdd:CHL00180  160 KILEITPYVEDELALIIPKSHPFAKLKKIQKEDLYRLNFITLDSN 204
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 113-291 2.24e-14

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: 70.32  E-value: 2.24e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965 113 ASVLRDFRVMFPTVALRLQVEALGAVAACLLEGGADLGIG-GPVlaDHPELERQAIGSVELVPVAAPYHPLARAGIEPGE 191
Cdd:cd05466    16 PPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVaLPV--DDPGLESEPLFEEPLVLVVPPDHPLAKRKSVTLA 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965 192 SRKHLQLVLTDRSP------LTEGREFSVLSPESWRLADLGAKHALLKEGIGWGNMPRHMVSgDIDEGRLCLLDLpEKPG 265
Cdd:cd05466    94 DLADEPLILFERGSglrrllDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVE-ELADGGLVVLPL-EDPP 171

                         170       180
                  ....*....|....*....|....*.
gi 2084061965 266 AHYTLSALWRRDARPGPATSWLIDAM 291
Cdd:cd05466   172 LSRTIGLVWRKGRYLSPAARAFLELL 197
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 106-289 2.22e-12

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: 64.82  E-value: 2.22e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965 106 MLPgevtaSVLRDFRVMFPTVALRLQVEALGAVAACLLEGGADLG-IGGPVlaDHPELERQAIGSVELVPVAAPYHPLAR 184
Cdd:cd08420    14 LLP-----RLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGlVEGPV--DHPDLIVEPFAEDELVLVVPPDHPLAG 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965 185 AGIEPGESRKHLQLVLTDrspltEG---REF--SVLSPESWRLADL----------GAKHAlLKEGIGWGNMPRHMVSGD 249
Cdd:cd08420    87 RKEVTAEELAAEPWILRE-----PGsgtREVfeRALAEAGLDGLDLnivmelgsteAIKEA-VEAGLGISILSRLAVRKE 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 2084061965 250 IDEGRLCLLDLPEkPGAHYTLSALWRRDARPGPATSWLID 289
Cdd:cd08420   161 LELGRLVALPVEG-LRLTRPFSLIYHKDKYLSPAAEAFLE 199
PRK09986 PRK09986
LysR family transcriptional regulator;
7-135 1.18e-11

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 63.97  E-value: 1.18e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965   7 SLDQLRIFLAVAEEGSFGAAARKMGRAVSAVSYGVSQMESQLGVTLFEREgSRRPVLTEEGRGLLTEAKAVADGIDHLLA 86
Cdd:PRK09986    8 DLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRH-SRSVVLTHAGKILMEESRRLLDNAEQSLA 86

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2084061965  87 KTQSLHAGLESEVSL-VVDVMLPGEVTaSVLRDFRVMFP--TVALR-----LQVEAL 135
Cdd:PRK09986   87 RVEQIGRGEAGRIEIgIVGTALWGRLR-PAMRHFLKENPnvEWLLRelspsMQMAAL 142
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 8-185 5.60e-11

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 62.32  E-value: 5.60e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965   8 LDQLRIFLAVAEEG-SFGAAARKMGRAVSAVSYGVSQMESQLGVTLFEREGSRRPVLTEEGRGLLTEAKAVADGIDHLla 86
Cdd:PRK12682    3 LQQLRFVREAVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKGLTEPGKAVLDVIERILREVGNI-- 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965  87 KTQSLHAGLESEVSLVVDV-------MLPGevtasVLRDFRVMFPTVALRLQVEALGAVAACLLEGGADLGIGGPVLADH 159
Cdd:PRK12682   81 KRIGDDFSNQDSGTLTIATthtqaryVLPR-----VVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGIATESLADD 155

                         170       180
                  ....*....|....*....|....*.
gi 2084061965 160 PELERQAIGSVELVPVAAPYHPLARA 185
Cdd:PRK12682  156 PDLATLPCYDWQHAVIVPPDHPLAQE 181
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 8-271 9.52e-11

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 61.58  E-value: 9.52e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965   8 LDQLRIFLAVAEEGSFGAAARKMGRAVSAVSYGVSQMESQLGVTLFEREGsRRPVLTEEGRGLLTEAKAVADGIDHllAK 87
Cdd:PRK15092   13 LDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHG-RNKLLTEHGIQLLGYARKILRFNDE--AC 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965  88 TQSLHAGLESEVSL-----VVDVMLPgevtaSVLRDFRVMFPTVALRLQVEALGAVAACLLEGGADLGIGGPVLADHPEL 162
Cdd:PRK15092   90 SSLMYSNLQGVLTIgasddTADTILP-----FLLNRVSSVYPKLALDVRVKRNAFMMEMLESQEVDLAVTTHRPSSFPAL 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965 163 ERQAigSVELVPVAAPYHPlaragiEPGESrkhLQLVLTDR-SPLtegREFSVLSPE----SWRLA----DLGAKHALLK 233
Cdd:PRK15092  165 NLRT--SPTLWYCAAEYVL------QKGEP---IPLVLLDEpSPF---RDMALATLNaagiPWRIAyvasTLSAVRAAVK 230

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|..
gi 2084061965 234 EGIGWGNMPRHMVSGDidegrLCLLD----LPEKPGAHYTLS 271
Cdd:PRK15092  231 AGLGVTARPVEMMSPD-----LRVLGesegLPPLPDTEYLLC 267
PRK10341 PRK10341
transcriptional regulator TdcA;
6-152 1.66e-10

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 61.03  E-value: 1.66e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965   6 PSLDQLRIFLAVAEEGSFGAAARKMGRAVSAVSYGVSQMESQLGVTLFEREGSrRPVLTEEGRGLLTEAKAVADGIDHLL 85
Cdd:PRK10341    7 PKTQHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNT-GVTLTPAGQVLLSRSESITREMKNMV 85

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2084061965  86 AKTQSLHAGLESEVSLVVDVMLPGEVTASVLRDFRVMFPTVALRLQVEALGAVAACLLEGGADLGIG 152
Cdd:PRK10341   86 NEINGMSSEAVVDVSFGFPSLIGFTFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIG 152
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 8-185 5.27e-10

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 59.29  E-value: 5.27e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965   8 LDQLRIFLAVAEEG-SFGAAARKMGRAVSAVSYGVSQMESQLGVTLFEREGSRRPVLTEEGRGLLTEAKAV---ADGIDH 83
Cdd:PRK12683    3 FQQLRIIREAVRQNfNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTGLTEPGKELLQIVERMlldAENLRR 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965  84 LLAKTQSLHAGlesevSLVVDV-------MLPgevtaSVLRDFRVMFPTVALRLQVEALGAVAACLLEGGADLGIGGPVL 156
Cdd:PRK12683   83 LAEQFADRDSG-----HLTVATthtqaryALP-----KVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGIATEAL 152

                         170       180
                  ....*....|....*....|....*....
gi 2084061965 157 ADHPELERQAIGSVELVPVAAPYHPLARA 185
Cdd:PRK12683  153 DREPDLVSFPYYSWHHVVVVPKGHPLTGR 181
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 8-184 6.66e-10

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 58.81  E-value: 6.66e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965   8 LDQLRIFLAVAEEGSFGAAARKMGRAVSAVSYGVSQMESQLGVTLFEREGsRRPVLTEEGRGLLTEAKAVadgIDHLLAK 87
Cdd:PRK11242    3 LRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSG-RTVRLTDAGEVYLRYARRA---LQDLEAG 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965  88 TQSLH-AGLESEVSLVVDVM--LPGEVTASVLRDFRVMFPTVALRLQVEALGAVAACLLEGGADLGIG-GPVLAdhPELE 163
Cdd:PRK11242   79 RRAIHdVADLSRGSLRLAMTptFTAYLIGPLIDAFHARYPGITLTIREMSQERIEALLADDELDVGIAfAPVHS--PEIE 156

                         170       180
                  ....*....|....*....|.
gi 2084061965 164 RQAIGSVELVPVAAPYHPLAR 184
Cdd:PRK11242  157 AQPLFTETLALVVGRHHPLAA 177
cbl PRK12679
HTH-type transcriptional regulator Cbl;
35-162 1.56e-09

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 57.90  E-value: 1.56e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965  35 SAVSYGVSQMESQLGVTLFEREGSRRPVLTEEGRGLLTeakaVADGIDHLLAKTQSLHAGLESEVSLVVDVM-------- 106
Cdd:PRK12679   31 SGVSRHIRELEDELGIEIFIRRGKRLLGMTEPGKALLV----IAERILNEASNVRRLADLFTNDTSGVLTIAtthtqary 106

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2084061965 107 -LPGevtasVLRDFRVMFPTVALRLQVEALGAVAACLLEGGADLGIGGPVLADHPEL 162
Cdd:PRK12679  107 sLPE-----VIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASERLSNDPQL 158
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
9-78 2.28e-09

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 57.29  E-value: 2.28e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965   9 DQLRIFLAVAEEGSFGAAARKMGRAVSAVSYGVSQMESQLGVTLFEREGSRRPvlTEEGRGLLTEAKAVA 78
Cdd:PRK13348    5 KQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRGRPCRP--TPAGQRLLRHLRQVA 72
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
8-198 8.31e-09

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 55.75  E-value: 8.31e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965   8 LDQLRIFLAVAEEG-SFGAAARKMGRAVSAVSYGVSQMESQLGVTLFEREGSRRPVLTEEGRGLLTEAKAVADGIDHLla 86
Cdd:PRK12684    3 LHQLRFVREAVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRGLTEPGRIILASVERILQEVENL-- 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965  87 KTQSLHAGLESEVSLVVDV-------MLPgevtaSVLRDFRVMFPTVALRLQVEALGAVAACLLEGGADLGIGGPVLADH 159
Cdd:PRK12684   81 KRVGKEFAAQDQGNLTIATthtqaryALP-----AAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAIATEAIADY 155

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 2084061965 160 PELERQAIGSVELVPVAAPYHPLARagiepgesRKHLQL 198
Cdd:PRK12684  156 KELVSLPCYQWNHCVVVPPDHPLLE--------RKPLTL 186
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
8-258 1.33e-08

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 55.15  E-value: 1.33e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965   8 LDQLRIFLAVAEEGSFGAAARKMGRAVSAVSYGVSQMESQLGVTLFEREgSRRPVLTEEG-------RGLLTEAKAVAdg 80
Cdd:PRK10632    4 LKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRS-TRSIGLTEAGriyyqgcRRMLHEVQDVH-- 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965  81 iDHLLA----KTQSLHAGLESevSLVVDVMLPgeVTASVLRDfrvmFPTVALRLqveALGAVAACLLEGGADLGIGGPVL 156
Cdd:PRK10632   81 -EQLYAfnntPIGTLRIGCSS--TMAQNVLAG--LTAKMLKE----YPGLSVNL---VTGIPAPDLIADGLDVVIRVGAL 148

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965 157 ADhPELERQAIGSVELVpVAAPYHPLARAGI--EPGESRKHLQLVLTDRSplteGREFSVLSPE--SWRLADLGAKHA-- 230
Cdd:PRK10632  149 QD-SSLFSRRLGAMPMV-VCAAKSYLAQYGTpeKPADLSSHSWLEYSVRP----DNEFELIAPEgiSTRLIPQGRFVTnd 222

                         250       260       270
                  ....*....|....*....|....*....|....
gi 2084061965 231 ------LLKEGIGWGNMPRHMVSGDIDEGRLCLL 258
Cdd:PRK10632  223 pqtlvrWLTAGAGIAYVPLMWVIDEINRGELEIL 256
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 9-78 1.69e-08

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


Pssm-ID: 274509 [Multi-domain]  Cd Length: 292  Bit Score: 54.54  E-value: 1.69e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965   9 DQLRIFLAVAEEGSFGAAARKMGRAVSAVSYGVSQMESQLGVTLFERegSRRPVLTEEGRGLLTEAKAVA 78
Cdd:TIGR03298   4 RQLAALAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVR--TQPCRATEAGQRLLRHARQVR 71
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 8-183 3.77e-08

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 53.62  E-value: 3.77e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965   8 LDQLRIFLAVAEEGSFGAAARKMGRAVSAVSYGVSQMESQLGVTLFEREgSRRPVLTEEGRGLLTEAKAVADGIDHllAK 87
Cdd:PRK09906    3 LRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRD-KRKVALTAAGEVFLQDARAILEQAEK--AK 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965  88 TQSLHAGLESEVsLVVDVMLPGEVTA--SVLRDFRVMFPTVALRL-------QVEAlgavaacLLEGGADLGIGGPVLaD 158
Cdd:PRK09906   80 LRARKIVQEDRQ-LTIGFVPSAEVNLlpKVLPMFRLRHPDTLIELvslittqQEEK-------LRRGELDVGFMRHPV-Y 150

                         170       180
                  ....*....|....*....|....*
gi 2084061965 159 HPELERQAIGSVELVPVAAPYHPLA 183
Cdd:PRK09906  151 SDEIDYLELLDEPLVVVLPVDHPLA 175
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
8-83 7.84e-08

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 52.70  E-value: 7.84e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2084061965   8 LDQLRIFLAVAEEGSFGAAARKMGRAVSAVSYGVSQMESQLGVTLFEREgSRRPVLTEEGRGLLTEAKAVADGIDH 83
Cdd:PRK10086   16 LSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRS-HRKVELTEEGKRVFWALKSSLDTLNQ 90
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
9-78 8.43e-08

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 52.47  E-value: 8.43e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965   9 DQLRIFLAVAEEGSFGAAARKMGRAVSAVSYGVSQMESQLGVTLFERegSRRPVLTEEGRGLLTEAKAVA 78
Cdd:PRK03635    5 KQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR--TQPCRPTEAGQRLLRHARQVR 72
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 6-131 3.77e-07

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 50.76  E-value: 3.77e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965   6 PSLDQLRIFLAVAEEGSFGAAARKMGRAVSAVSYGVSQMESQLGVTLFEREgSRRPVLTEEG-------RGLLTEAKAVA 78
Cdd:PRK14997    2 TDLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRT-TRQFNVTEVGqtfyehcKAMLVEAQAAQ 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2084061965  79 DGIDHLLAKTQSLhagleseVSLVVDVMLPGEVTASVLRDFRVMFPTVALRLQ 131
Cdd:PRK14997   81 DAIAALQVEPRGI-------VKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLE 126
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 6-87 1.53e-06

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 48.69  E-value: 1.53e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965   6 PSLDQLRIFLAVAEEGSFGAAARKMGRAVSAVSYGVSQMESQLGVTLFEREGsRRPVLTEEGRGLLTEAKA----VADGI 81
Cdd:PRK11139    6 PPLNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRN-RSLLLTEEGQRYFLDIREifdqLAEAT 84


                  ....*.
gi 2084061965  82 DHLLAK 87
Cdd:PRK11139   85 RKLRAR 90
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
 116-285 2.40e-06

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: 47.12  E-value: 2.40e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965 116 LRDFRVMFPTVALRLQVEALGAVAACLLEGGADLGIGGPVlADHPELERQAIGSVELVPVAAPYHPLARAGI-------- 187
Cdd:cd08419    18 LGAFCRRHPGVEVSLRVGNREQVLERLADNEDDLAIMGRP-PEDLDLVAEPFLDNPLVVIAPPDHPLAGQKRiplerlar 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965 188 ------EPG-ESRKHLQLVLTDRS-PLTEGREFSvlSPESwrladlgAKHALLkEGIGWGNMPRHMVSGDIDEGRLCLLD 259
Cdd:cd08419    97 epfllrEPGsGTRLAMERFFAEHGvTLRVRMELG--SNEA-------IKQAVM-AGLGLSVLSLHTLALELATGRLAVLD 166

                         170       180
                  ....*....|....*....|....*.
gi 2084061965 260 LPEKPgAHYTLSALWRRDARPGPATS 285
Cdd:cd08419   167 VEGFP-IRRQWYVVHRKGKRLSPAAQ 191
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 114-184 3.90e-06

The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the catabolism of opines and that of related regulators, contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulators, OccR and NocR, involved in the catabolism of opines and that of LysR for lysine biosynthesis which clustered together in phylogenetic trees. Opines, such as octopine and nopaline, are low molecular weight compounds found in plant crown gall tumors that are produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. NocR and OccR belong to the family of LysR-type transcriptional regulators that positively regulates the catabolism of nopaline and octopine, respectively. Both nopaline and octopalin are arginine derivatives. In Agrobacterium tumefaciens, NocR regulates expression of the divergently transcribed nocB and nocR genes of the nopaline catabolism (noc) region. OccR protein activates the occQ operon of the Ti plasmid in response to octopine. This operon encodes proteins required for the uptake and catabolism of octopine. The occ operon also encodes the TraR protein, which is a quorum-sensing transcriptional regulator of the Ti plasmid tra regulon. LysR is the transcriptional activator of lysA gene encoding diaminopimelate decarboxylase, an enzyme that catalyses the decarboxylation of diaminopimelate to produce lysine. 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: 176107 [Multi-domain]  Cd Length: 196  Bit Score: 46.79  E-value: 3.90e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2084061965 114 SVLRDFRVMFPTVALRLQVEALGAVAACLLEGGADLGIGGPVLaDHPELERQAIGSVELVPVAAPYHPLAR 184
Cdd:cd08415    17 RAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPL-DHPGLESEPLASGRAVCVLPPGHPLAR 86
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 113-289 7.52e-06

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


Pssm-ID: 176127 [Multi-domain]  Cd Length: 194  Bit Score: 45.67  E-value: 7.52e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965 113 ASVLRDFRVMFPTVALRLQVEALGAVAACLLEGGADLGIGGPVLADHPELERQAIGSVELVPVAAPYHPLA-RAGIEPGE 191
Cdd:cd08436    16 PELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAFVGLPERRPPGLASRELAREPLVAVVAPDHPLAgRRRVALAD 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965 192 SRKHlqlVLTDRSPLTEGRE----------------FSVLSPESwrLADLGAKhallkeGIGWGNMPRHMVSGDideGRL 255
Cdd:cd08436    96 LADE---PFVDFPPGTGARRqvdrafaaagvrrrvaFEVSDVDL--LLDLVAR------GLGVALLPASVAARL---PGL 161

                         170       180       190
                  ....*....|....*....|....*....|....
gi 2084061965 256 CLLDLpeKPGAHYTLSALWRRDArPGPATSWLID 289
Cdd:cd08436   162 AALPL--EPAPRRRLYLAWSAPP-PSPAARAFLE 192
PBP2_TdcA cd08418
The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is ...
 100-294 8.22e-06

The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is involved in the degradation of L-serine and L-threonine, contains the type 2 periplasmic binding fold; TdcA, a member of the LysR family, activates the expression of the anaerobically-regulated tdcABCDEFG operon which is involved in the degradation of L-serine and L-threonine to acetate and propionate, respectively. The tdc operon is comprised of one regulatory gene tdcA and six structural genes, tdcB to tdcG. The expression of the tdc operon is affected by several transcription factors including the cAMP receptor protein (CRP), integration host factor (IHF), histone-like protein (HU), and the operon specific regulators TdcA and TcdR. TcdR is divergently transcribed from the operon and encodes a small protein that is required for efficient expression of the Escherichia coli tdc operon. 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: 176110 [Multi-domain]  Cd Length: 201  Bit Score: 45.81  E-value: 8.22e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965 100 SLVVDVMLPGevtasVLRDFRVMFPTVALRLQVEALGAVAACLLEGGADLGIGgPVLADHP--ELERQAIGSVELVPVAA 177
Cdd:cd08418     8 SLIAHTLMPA-----VINRFKEQFPDVQISIYEGQLSSLLPELRDGRLDFAIG-TLPDEMYlkELISEPLFESDFVVVAR 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965 178 PYHPLARAgiEPGESRKHLQLVL--TDRSP---LTEGREFSVLSPESWRLAD-LGAKHALLKEGIGWGNMPRHMVSGDID 251
Cdd:cd08418    82 KDHPLQGA--RSLEELLDASWVLpgTRMGYynnLLEALRRLGYNPRVAVRTDsIVSIINLVEKADFLTILSRDMGRGPLD 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 2084061965 252 EGRLCLLDLPEK-PGAHYTLsaLWRRDARPGPATSWLIDAMRER 294
Cdd:cd08418   160 SFRLITIPVEEPlPSADYYL--IYRKKSRLTPLAEQLVELFRRY 201
PBP2_CysB_like cd08413
The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains ...
 115-183 9.41e-06

The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; CysB is a transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the regulation of transcription in response to sulfur source is attributed to two transcriptional regulators, CysB and Cbl. CysB, in association with Cbl, downregulates the expression of ssuEADCB operon which is required for the utilization of sulfur from aliphatic sulfonates, in the presence of cysteine. Also, Cbl and CysB together directly function as transcriptional activators of tauABCD genes, which are required for utilization of taurine as sulfur source for growth. Like many other members of the LTTR family, CysB is 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 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: 176105 [Multi-domain]  Cd Length: 198  Bit Score: 45.69  E-value: 9.41e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2084061965 115 VLRDFRVMFPTVALRLQVEALGAVAACLLEGGADLGIGGPVLADHPEL--------ERQAIgsvelVPvaaPYHPLA 183
Cdd:cd08413    18 VIAAFRKRYPKVKLSLHQGTPSQIAEMVLKGEADIAIATEALDDHPDLvtlpcyrwNHCVI-----VP---PGHPLA 86
ModE COG2005
DNA-binding transcriptional regulator ModE (molybdenum-dependent) [Transcription];
4-95 1.15e-05

DNA-binding transcriptional regulator ModE (molybdenum-dependent) [Transcription];


Pssm-ID: 441608 [Multi-domain]  Cd Length: 118  Bit Score: 43.66  E-value: 1.15e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965   4 GEPSLDQLRIFL--AVAEEGSFGAAARKMGravsaVSYG-----VSQMESQLGVTLFERE-------GSRrpvLTEEGRG 69
Cdd:COG2005    15 GGVFLGPGRIELleAIDETGSISAAAKAMG-----MSYKrawdlIDAMNNLLGEPLVERQtggkgggGAR---LTPEGRR 86

                          90       100
                  ....*....|....*....|....*.
gi 2084061965  70 LLTEAKAVADGIDHLLAKTQSLHAGL 95
Cdd:COG2005    87 LLALYRRLEAEAQRALAALFEELFAL 112
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
8-183 1.55e-05

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 45.78  E-value: 1.55e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965   8 LDQLRIFLAVAEEGSFGAAARKMGRAVSAVSYGVSQMESQLGVTLFEREgSRRPVLTEEGRGLLTEAKAVADGIDHLLak 87
Cdd:PRK15421    4 VKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRK-SQPLRFTPQGEILLQLANQVLPQISQAL-- 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965  88 tQSLHAGLESEVSLVVDVMLPGEVTASVLRDFRVMFPTVALRLQVEALGAVAACLLEGGADLGIGGPVLAdHPELERQAI 167
Cdd:PRK15421   81 -QACNEPQQTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILP-RSGLHYSPM 158

                         170
                  ....*....|....*.
gi 2084061965 168 GSVELVPVAAPYHPLA 183
Cdd:PRK15421  159 FDYEVRLVLAPDHPLA 174
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 115-290 1.70e-05

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: 44.82  E-value: 1.70e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965 115 VLRDFRVMFPTVALRLQVEALGAVAACLLEGGADLGIGgPVLADHPELERQAIGSVELVPVAAPYHPLARagiepgesrk 194
Cdd:cd08440    18 VLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIG-SEPEADPDLEFEPLLRDPFVLVCPKDHPLAR---------- 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965 195 hlqlvltdRSPLT----EGREFSVLSPES--WRLADLGAKH------------------ALLKEGIGWGNMPRHMVSGdI 250
Cdd:cd08440    87 --------RRSVTwaelAGYPLIALGRGSgvRALIDRALAAagltlrpayevshmstalGMVAAGLGVAVLPALALPL-A 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 2084061965 251 DEGRLCLLDLPEkPGAHYTLSALWRRDARPGPATSWLIDA 290
Cdd:cd08440   158 DHPGLVARPLTE-PVVTRTVGLIRRRGRSLSPAAQAFLDL 196
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 142-291 1.78e-05

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: 44.74  E-value: 1.78e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965 142 LLEGGADLGIGGPVLADhPELERQAIGSVELVPVAAP-YhpLARAGI--EPGESRKHLQLVLTDRSPLTE------GREF 212
Cdd:cd08422    43 LVEEGFDLAIRIGELPD-SSLVARRLGPVRRVLVASPaY--LARHGTpqTPEDLARHRCLGYRLPGRPLRwrfrrgGGEV 119

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2084061965 213 SVLSPESWRLADLGAKHALLKEGIGWGNMPRHMVSGDIDEGRLCLLdLPEKPGAHYTLSALWRRDARPGPATSWLIDAM 291
Cdd:cd08422   120 EVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAEDLASGRLVRV-LPDWRPPPLPIYAVYPSRRHLPAKVRAFIDFL 197
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 99-290 2.72e-05

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: 44.19  E-value: 2.72e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965  99 VSLVVDVMLPgevtaSVLRDFRVMFPTVALRLQVEALGAVAACLLEGGADLGIGG-PVLADHPELERQAIGSVELVPVAA 177
Cdd:cd08435     7 VPAAAPVLLP-----PAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAIGRlADDEQPPDLASEELADEPLVVVAR 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965 178 PYHPLARAG------------IEPGES---RKHLQLVLTDR-----SPLTEGREFSVLSpeswrladlgakhALLKEG-- 235
Cdd:cd08435    82 PGHPLARRArltladladypwVLPPPGtplRQRLEQLFAAAglplpRNVVETASISALL-------------ALLARSdm 148

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2084061965 236 IGWgnMPRHMVSGDIDEGRLCLLDLPeKPGAHYTLSALWRRDARPGPATSWLIDA 290
Cdd:cd08435   149 LAV--LPRSVAEDELRAGVLRELPLP-LPTSRRPIGITTRRGGPLSPAARALLDA 200
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
35-181 3.65e-05

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 44.42  E-value: 3.65e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965  35 SAVSYGVSQMESQLGVTLFEREgSRRPVLTEEGRGLLTEAKAVADGIDHLLAKTQSLHAGLESEVSLVvdvmlpGEVTAS 114
Cdd:PRK11716    6 STLSRQIQRLEEELGQPLFVRD-NRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSLF------CSVTAA 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965 115 ------VLRDFRVMFPTVALRLQV----EALGAVaaclLEGGADLGIGGpvladHPE-----LERQAIGSVELVpVAAPY 179
Cdd:PRK11716   79 yshlppILDRFRAEHPLVEIKLTTgdaaDAVEKV----QSGEADLAIAA-----KPEtlpasVAFSPIDEIPLV-LIAPA 148


                  ..
gi 2084061965 180 HP 181
Cdd:PRK11716  149 LP 150
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
11-101 3.71e-05

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 44.62  E-value: 3.71e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965  11 LRIFLAVAEEGSFGAAARKMGRAVSAVSYGVSQMESQLGVTLFEREgsRRPV-LTEEGRGLLTEAKAVADgiDHLLAKTQ 89
Cdd:PRK03601    6 LKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRH--RNNIrLTAAGERLLPYAETLMN--TWQAAKKE 81

                          90
                  ....*....|..
gi 2084061965  90 SLHAGLESEVSL 101
Cdd:PRK03601   82 VAHTSQHNELSI 93
PRK09791 PRK09791
LysR family transcriptional regulator;
8-185 3.84e-05

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 44.37  E-value: 3.84e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965   8 LDQLRIFLAVAEEGSFGAAARKMGRAVSAVSYGVSQMESQLGVTLFEREgSRRPVLTEEGRG-------LLTEAKAVADG 80
Cdd:PRK09791    7 IHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRR-SKGVTLTDAGESfyqhaslILEELRAAQED 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965  81 IDhllaKTQSLHAGlesEVSLVVDVMLPGEVTASVLRDFRVMFPTVALRLQVEALGAVAACLLEGGADLGI----GGPVl 156
Cdd:PRK09791   86 IR----QRQGQLAG---QINIGMGASIARSLMPAVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDFTIntyyQGPY- 157

                         170       180
                  ....*....|....*....|....*....
gi 2084061965 157 aDHpELERQAIGSVELVPVAAPYHPLARA 185
Cdd:PRK09791  158 -DH-EFTFEKLLEKQFAVFCRPGHPAIGA 184
PRK12680 PRK12680
LysR family transcriptional regulator;
7-151 4.05e-05

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 44.61  E-value: 4.05e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965   7 SLDQLRIFLAVAE-EGSFGAAARKMGRAVSAVSYGVSQMESQLGVTLFEREGSRRPVLTEEGRGLLTEAKAVADGIDHLl 85
Cdd:PRK12680    2 TLTQLRYLVAIADaELNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLESVTPAGVEVIERARAVLSEANNI- 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2084061965  86 aKTQSLHAGLESEVSLVVDV-------MLPGEVTAsvlrdFRVMFPTVALRLQVEALGAVAACLLEGGADLGI 151
Cdd:PRK12680   81 -RTYAANQRRESQGQLTLTTthtqarfVLPPAVAQ-----IKQAYPQVSVHLQQAAESAALDLLGQGDADIAI 147
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 98-186 8.28e-05

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


Pssm-ID: 176117 [Multi-domain]  Cd Length: 199  Bit Score: 42.68  E-value: 8.28e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965  98 EVSLVVDVMLPGEVTASVLRDFRVMFPTVALRLQVEALGAVAACLLEGGADLGIGGPvLADHPELERQAIGSVELVPVAA 177
Cdd:cd08426     1 RVRVATGEGLAAELLPSLIARFRQRYPGVFFTVDVASTADVLEAVLSGEADIGLAFS-PPPEPGIRVHSRQPAPIGAVVP 79


                  ....*....
gi 2084061965 178 PYHPLARAG 186
Cdd:cd08426    80 PGHPLARQP 88
PBP2_Cbl cd08444
The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is ...
 115-207 1.05e-04

The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is required for expression of sulfate starvation-inducible (ssi) genes, contains the type 2 periplasmic binding fold; Cbl is a member of the LysR transcriptional regulators that comprise the largest family of prokaryotic transcription factor. Cbl shows high sequence similarity to CysB, the LysR-type transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the function of Cbl is required for expression of sulfate starvation-inducible (ssi) genes, coupled with the biosynthesis of cysteine from the organic sulfur sources (sulfonates). The ssi genes include the ssuEADCB and tauABCD operons encoding uptake systems for organosulfur compounds, aliphatic sulfonates, and taurine. The genes in these operons encode an ABC-type transport system required for uptake of aliphatic sulfonates and a desulfonation enzyme. Both Cbl and CysB require expression of the tau and ssu genes. Like many other members of the LTTR family, the Cbl is 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 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: 176135  Cd Length: 198  Bit Score: 42.49  E-value: 1.05e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965 115 VLRDFRVMFPTVALRLQVEALGAVAACLLEGGADLGIGGPVLADHPELerqaigsvelvpVAAPYHPLARAGIEPGESRk 194
Cdd:cd08444    18 VVQAFKEQFPNVHLVLHQGSPEEIASMLANGQADIGIATEALENHPEL------------VSFPYYDWHHHIIVPVGHP- 84

                          90
                  ....*....|...
gi 2084061965 195 hlqlvLTDRSPLT 207
Cdd:cd08444    85 -----LESITPLT 92
PBP2_DntR_like_1 cd08460
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 109-189 4.66e-04

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold; This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. 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: 176149 [Multi-domain]  Cd Length: 200  Bit Score: 40.65  E-value: 4.66e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965 109 GEVTASVLRDFRVMFPTVALRLQVEALGAVAAcLLEGGADLGIGGPVLADhPELERQAIGSVELVPVAAPYHPLARAGIE 188
Cdd:cd08460    12 AAFGPALLAAVAAEAPGVRLRFVPESDKDVDA-LREGRIDLEIGVLGPTG-PEIRVQTLFRDRFVGVVRAGHPLARGPIT 89


                  .
gi 2084061965 189 P 189
Cdd:cd08460    90 P 90
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 106-287 5.34e-04

The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold; This CD includes the substrate binding domain of CidR which positively up-regulates the expression of cidABC operon in the presence of acetic acid produced by the metabolism of excess glucose. The CidR affects the control of murein hydrolase activity by enhancing cidABC expression in the presence of acetic acid. Thus, up-regulation of cidABC expression results in increased murein hydrolase activity. This substrate binding domain has 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: 176129 [Multi-domain]  Cd Length: 197  Bit Score: 40.23  E-value: 5.34e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965 106 MLPGEVTASVLRDFRVMFPTVALRLqVEALG-AVAACLLEGGADLGIGgpVL-ADHPELERQAIGSVELVPVAAPYHPLA 183
Cdd:cd08438     9 LGGSLLFAPLLAAFRQRYPNIELEL-VEYGGkKVEQAVLNGELDVGIT--VLpVDEEEFDSQPLCNEPLVAVLPRGHPLA 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965 184 -RAGIEPgESRKHLQLVLtdrspLTEgrEFSvLSP---ESWRLA-------------DLGAkhALLKEGIGWGNMPRhMV 246
Cdd:cd08438    86 gRKTVSL-ADLADEPFIL-----FNE--DFA-LHDriiDACQQAgftpniaarssqwDFIA--ELVAAGLGVALLPR-SI 153

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 2084061965 247 SGDIDEGRLCLLDLpEKPGAHYTLSALWRRDARPGPATS-WL 287
Cdd:cd08438   154 AQRLDNAGVKVIPL-TDPDLRWQLALIWRKGRYLSHAARaWL 194
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 116-287 5.62e-04

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: 40.26  E-value: 5.62e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965 116 LRDFRVMFPTVALRLQVeALGAVAacLLEGGADLGI-GGPvlADHPELERQAIGSVELVPVAAPYHPLARAGIEPGESRK 194
Cdd:cd08432    19 LARFQARHPDIDLRLST-SDRLVD--FAREGIDLAIrYGD--GDWPGLEAERLMDEELVPVCSPALLAGLPLLSPADLAR 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965 195 HLQLVLTDRS-----PLTEGREFSVLSPESWRLADLG-AKHALLkEGIGWGNMPRHMVSGDIDEGRL-CLLDLPEKPGAH 267
Cdd:cd08432    94 HTLLHDATRPeawqwWLWAAGVADVDARRGPRFDDSSlALQAAV-AGLGVALAPRALVADDLAAGRLvRPFDLPLPSGGA 172

                         170       180
                  ....*....|....*....|....
gi 2084061965 268 YTLsaLWRRDARPGPA----TSWL 287
Cdd:cd08432   173 YYL--VYPPGRAESPAvaafRDWL 194
PBP2_YofA_SoxR_like cd08442
The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, ...
 110-289 1.43e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, contains the type 2 periplasmic binding fold; YofA is a LysR-like transcriptional regulator of cell growth in Bacillus subtillis. YofA controls cell viability and the formation of constrictions during cell division. YofaA positively regulates expression of the cell division gene ftsW, and thus is essential for cell viability during stationary-phase growth of Bacillus substilis. YofA shows significant homology to SoxR from Arthrobacter sp. TE1826. SoxR is a negative regulator for the sarcosine oxidase gene soxA. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine, which is involved in the metabolism of creatine and choline. 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: 176133  Cd Length: 193  Bit Score: 39.13  E-value: 1.43e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965 110 EVTASV-----LRDFRVMFPTVALRLQVEALGAVAACLLEGGADLG-IGGPVlaDHPELERQAIGSVELVPVAAPYHPLA 183
Cdd:cd08442     8 ETTAAVrlpplLAAYHARYPKVDLSLSTGTTGALIQAVLEGRLDGAfVAGPV--EHPRLEQEPVFQEELVLVSPKGHPPV 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965 184 RAGIEPGES-----------RKHLQLVLTDRSpltegrefsvLSPEswRLADLGAKHALLK---EGIGWGNMPRHMVSGD 249
Cdd:cd08442    86 SRAEDLAGStllafragcsyRRRLEDWLAEEG----------VSPG--KIMEFGSYHAILGcvaAGMGIALLPRSVLDSL 153

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 2084061965 250 IDEGRLCLLDLPEkPGAHYTLSALWRRDARpGPATSWLID 289
Cdd:cd08442   154 QGRGSVSIHPLPE-PFADVTTWLVWRKDSF-TAALQAFLD 191
PBP2_BudR cd08451
The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is ...
 111-184 3.32e-03

The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is responsible for activation of the expression of the butanediol operon genes; contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of BudR regulator, which is responsible for induction of the butanediol formation pathway under fermentative growth conditions. Three enzymes are involved in the production of 1 mol of 2,3 butanediol from the condensation of 2 mol of pyruvate with acetolactate and acetoin as intermediates: acetolactate synthetase, acetolactate decarboxylase, and acetoin reductase. In Klebsiella terrigena, BudR regulates the expression of the budABC operon genes, encoding these three enzymes of the butanediol pathway. In many bacterial species, the use of this pathway can prevent intracellular acidification by diverting metabolism from acid production to the formation of neutral compounds (acetoin and butanediol). This substrate-binding domain has 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: 176142 [Multi-domain]  Cd Length: 199  Bit Score: 37.93  E-value: 3.32e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2084061965 111 VTASVLRDFRVMFPTVALRLQVEALGAVAACLLEGGADLGIGGPVLADHPELERQAIGSVELVPVAAPYHPLAR 184
Cdd:cd08451    15 LVPGLIRRFREAYPDVELTLEEANTAELLEALREGRLDAAFVRPPVARSDGLVLELLLEEPMLVALPAGHPLAR 88
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 115-185 3.37e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; This CD includes the C-terminal substrate binding domain of LTTRs involved in degradation of aromatic compounds, such as CbnR, BenM, CatM, ClcR and TfdR, as well as that of other transcriptional regulators clustered together in phylogenetic trees, including XapR, HcaR, MprR, IlvR, BudR, AlsR, LysR, and OccR. 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: 176106 [Multi-domain]  Cd Length: 197  Bit Score: 37.87  E-value: 3.37e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2084061965 115 VLRDFRVMFPTVALRLQVEALGAVAACLLEGGADLGIGGPVLaDHPELERQAIGSVELVPVAAPYHPLARA 185
Cdd:cd08414    18 LLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPPP-DPPGLASRPLLREPLVVALPADHPLAAR 87
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 7-189 4.88e-03

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 38.05  E-value: 4.88e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965   7 SLDQLRIFLAVAEEGSFGAAARKMGRAVSAVSYGVSQMESQLGVTLFEREGSR-RPvlTEEGRGLLTEAKAVADGIDHLL 85
Cdd:PRK11013    5 SLRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRlHP--TVQGLRLFEEVQRSYYGLDRIV 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965  86 AKTQSLHAGLESEVSLVV-----DVMLPGevtasVLRDFRVMFPTVALR-------LQVEALGAVAaclleggADLGigg 153
Cdd:PRK11013   83 SAAESLREFRQGQLSIAClpvfsQSLLPG-----LCQPFLARYPDVSLNivpqespLLEEWLSAQR-------HDLG--- 147

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 2084061965 154 pvLADH----PELERQAIGSVELVPVAAPYHPLA-RAGIEP 189
Cdd:PRK11013  148 --LTETlhtpAGTERTELLTLDEVCVLPAGHPLAaKKVLTP 186
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 111-283 6.33e-03

The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) protein, contains the type 2 periplasmic binding fold; The NAC is a LysR-type transcription regulator that activates expression of operons such as hut (histidine utilization) and ure (urea utilization), allowing use of non-preferred (poor) nitrogen sources, and represses expression of operons, such as glutamate dehydrogenase (gdh), allowing assimilation of the preferred nitrogen source. The expression of the nac gene is fully dependent on the nitrogen regulatory system (NTR) and the sigma54-containing RNA polymerase (sigma54-RNAP). In response to nitrogen starvation, NTR system activates the expression of nac, and NAC activates the expression of hut, ure, and put (proline utilization). NAC is not involved in the transcription of Sigma70-RNAP operons such as glnA, which directly respond by the NTR system, but activates the transcription of sigma70-RNAP dependent operons such as hut. Hence, NAC allows the coupling of sigma70-RNAP dependent operons to the sigma54-RNAP dependent NTR system. This substrate-binding domain has 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: 176124  Cd Length: 198  Bit Score: 37.19  E-value: 6.33e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965 111 VTASVLRDFRVMFPTVALRLqVEAL-GAVAACLLEGGADLGiggpVLADHPE---LERQAIGSVELVPVAAPYHPLARAG 186
Cdd:cd08433    14 LAVPLLRAVRRRYPGIRLRI-VEGLsGHLLEWLLNGRLDLA----LLYGPPPipgLSTEPLLEEDLFLVGPADAPLPRGA 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965 187 ------------IEPgeSRKHLQLVLTDRSPLTEGREFSVlspeSWRLADLGAKHALLKEGIGWGNMPRHMVSGDIDEGR 254
Cdd:cd08433    89 pvplaelarlplILP--SRGHGLRRLVDEAAARAGLTLNV----VVEIDSVATLKALVAAGLGYTILPASAVAAEVAAGR 162

                         170       180
                  ....*....|....*....|....*....
gi 2084061965 255 LCLLDLPEkPGAHYTLSALWRRDARPGPA 283
Cdd:cd08433   163 LVAAPIVD-PALTRTLSLATPRDRPLSPA 190
PBP2_LTTR_like_1 cd08421
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 116-289 6.42e-03

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


Pssm-ID: 176113  Cd Length: 198  Bit Score: 37.12  E-value: 6.42e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965 116 LRDFRVMFPTVALRLQVEALGAVAACLLEGGADLGI-GGPVlaDHPELERQAIGSVELVPVAAPYHPLARA--------- 185
Cdd:cd08421    19 LASFLAAHPDVRIDLEERLSADIVRAVAEGRADLGIvAGNV--DAAGLETRPYRTDRLVVVVPRDHPLAGRasvafadtl 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084061965 186 -----GIEPGESrkhLQLVLTDRSpLTEGREFSVlspeSWRLADLGAKHALLKEGIGWGNMPRHMVSGDIDEGRLCLLDL 260
Cdd:cd08421    97 dhdfvGLPAGSA---LHTFLREAA-ARLGRRLRL----RVQVSSFDAVCRMVAAGLGIGIVPESAARRYARALGLRVVPL 168

                         170       180
                  ....*....|....*....|....*....
gi 2084061965 261 PEkPGAHYTLSALWRRDARPGPATSWLID 289
Cdd:cd08421   169 DD-AWARRRLLLCVRSFDALPPAARALVD 196
 
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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