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Conserved domains on  [gi|489199469|ref|WP_003108721|]
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MULTISPECIES: LysR family transcriptional regulator [Pseudomonas]

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];
1-275 9.58e-49

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 162.34  E-value: 9.58e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469   1 MDIDLARTFLEIARSGSFVAAAERLHLTQTAVTARIQNLEGQLGCRLFVRNRAGARLTADGEHFLGYASQLVQTWDAARR 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469  81 DL-PLPDGFRNLLNLGGEVSLCNPLLLNWMRRLREAIPGHAVRVEIGQGADLLKQLEQGALDAALVYQPEYWPGLQVEQL 159
Cdd:COG0583   81 ELrALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469 160 LEEKLVMvrsVVSAEPYLyvdwgpdfrsqhdaalpdrAKAALACNLGPLALQYIMQNGGSGYFRTRVVSSYLDGGTLQRV 239
Cdd:COG0583  161 GEERLVL---VASPDHPL-------------------ARRAPLVNSLEALLAAVAAGLGIALLPRFLAADELAAGRLVAL 218

                        250       260       270
                 ....*....|....*....|....*....|....*...
gi 489199469 240 E-QAPEFAYPTYLVYSRER-LSPTLRHAFQLLREVVRE 275
Cdd:COG0583  219 PlPDPPPPRPLYLVWRRRRhLSPAVRAFLDFLREALAE 256
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-275 9.58e-49

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 162.34  E-value: 9.58e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469   1 MDIDLARTFLEIARSGSFVAAAERLHLTQTAVTARIQNLEGQLGCRLFVRNRAGARLTADGEHFLGYASQLVQTWDAARR 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469  81 DL-PLPDGFRNLLNLGGEVSLCNPLLLNWMRRLREAIPGHAVRVEIGQGADLLKQLEQGALDAALVYQPEYWPGLQVEQL 159
Cdd:COG0583   81 ELrALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469 160 LEEKLVMvrsVVSAEPYLyvdwgpdfrsqhdaalpdrAKAALACNLGPLALQYIMQNGGSGYFRTRVVSSYLDGGTLQRV 239
Cdd:COG0583  161 GEERLVL---VASPDHPL-------------------ARRAPLVNSLEALLAAVAAGLGIALLPRFLAADELAAGRLVAL 218

                        250       260       270
                 ....*....|....*....|....*....|....*...
gi 489199469 240 E-QAPEFAYPTYLVYSRER-LSPTLRHAFQLLREVVRE 275
Cdd:COG0583  219 PlPDPPPPRPLYLVWRRRRhLSPAVRAFLDFLREALAE 256
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
1-253 1.97e-32

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 120.51  E-value: 1.97e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469   1 MDIDLARTFLEIARSGSFVAAAERLHLTQTAVTARIQNLEGQLGCRLFVRNRAGARLTADGEHFLGYASQLVQTWDAARR 80
Cdd:PRK03601   1 MDTELLKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYAETLMNTWQAAKK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469  81 DLPLPDGfRNLLNLGGEVSLCNPLLLNWMRRLREAIPGHAVRVEIGQGADLLKQLEQGALDAALVYQPEYWPGLQVEQLL 160
Cdd:PRK03601  81 EVAHTSQ-HNELSIGASASLWECMLTPWLGRLYQNQEALQFEARIAQRQSLVKQLHERQLDLLITTEAPKMDEFSSQLLG 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469 161 EEKLVMVRS----VVSAEPYLYVDWGPDFrSQHDAAL--PDRAkAALACNLGPLALQYIMQNGGSGYFRTRVVSSYLDgg 234
Cdd:PRK03601 160 HFTLALYTSapskKKSELNYIRLEWGADF-QQHEAGLigADEV-PILTTSSAELARQLLATLNGCAFLPVHWAKEKGG-- 235

                        250
                 ....*....|....*....
gi 489199469 235 tLQRVEQAPEFAYPTYLVY 253
Cdd:PRK03601 236 -LHTVPDSTTLSRPLYAIW 253
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-167 8.83e-23

selenium metabolism-associated LysR family transcriptional regulator; LysR family transcriptional regulators regularly appear encoded adjacent to selenecysteine incorporation proteins such as SelB. This model represents one especially well-conserved subgroup of such transcription factors from species such as Merdimonas faecis, Sellimonas intestinalis, Syntrophotalea acetylenica, and Hydrogenivirga caldilitoris. Seed alignment members were selected by proximity to selB, but not all family members are expected to have similar genomic locations.


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 94.99  E-value: 8.83e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469   1 MDIDLARTFLEIARSGSFVAAAERLHLTQTAVTARIQNLEGQLGCRLFVRNRAGARLTADGEHFLGYASQLVQTWDAARR 80
Cdd:NF040786   1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469  81 DLplpDGFRN----LLNLGGEVSLCNPLLLNWMRRLREAIPGHAVRVEIGQGADLLKQLEQGALDAALV-YQPEYwPGLQ 155
Cdd:NF040786  81 EF---DRYGKeskgVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTgTKLEK-KRLV 156

                        170
                 ....*....|..
gi 489199469 156 VEQLLEEKLVMV 167
Cdd:NF040786 157 YTPFYKDRLVLI 168
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-62 8.89e-21

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 83.20  E-value: 8.89e-21
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469    3 IDLARTFLEIARSGSFVAAAERLHLTQTAVTARIQNLEGQLGCRLFVRNRAGARLTADGE 62
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 1-266 2.29e-11

multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, including founding member GSU2202 from Geobacter sulfurreducens PCA, are LysR family transcriptional regulators found regularly in the vicinity of multiheme cytochromes such as GSU2203, a decaheme c-type cytochrome.


Pssm-ID: 468965 [Multi-domain]  Cd Length: 301  Bit Score: 63.22  E-value: 2.29e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469   1 MDIDLARTFLEIARSGSFVAAAERLHLTQTAVTARIQNLEGQLGCRLFVRNRAGARLTADGEHFLgyasqlvqtwDAARR 80
Cdd:NF041036   1 METRYLKTLVIVAEEGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVL----------EKARR 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469  81 DLPLPDG-FRNLLNLGGE--VSLCN---------PLLLN-WMrrLREAIPgHAVRVEIGQGADLLKQLEQGALDAAL--- 144
Cdd:NF041036  71 ILDIEDSlMDELKSFKGRqrLSICCtptfgmahlPGVLNrFM--LRNADV-VDLKFLFHSPAQALEGIQNKEFDLAIieh 147

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469 145 ---------------------VYQPEY---WPGLQVEQLLEEKLVMVRSVVSAEPYLYVDWGpdfRSQHDaaLPDRAKAA 200
Cdd:NF041036 148 cadldlgrfhtyplpqdelvfVSAPSLglpTPNVTLERLLELCLITRRDGCSSRDLLRRNLA---EQGRD--LDDFRRVV 222

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489199469 201 LACNLGpLALQYIMQNGGSGYFRTRVVSSYLDGGTL--QRVEQAPEFAYPTyLVYSRERLSPTLRHAF 266
Cdd:NF041036 223 VSDDLR-LTIQTVLDGGGISFVSRSLVCEYLKNGQLreHYVEGFPHVRCRT-VVARKCRENDPLLSAF 288
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 92-269 2.99e-08

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: 52.60  E-value: 2.99e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469  92 LNLGGEVSLCNPLLLNWMRRLREAIPGHAVRVEIGQGADLLKQLEQGALDAALVYQPEYWPGLQVEQLLEEKLVMV---- 167
Cdd:cd05466    2 LRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVvppd 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469 168 -----RSVVSA-----EPYLYVDWGPDFRSQHDAALpDRA----KAALACNLGPLALQYIMQNGGSGyFRTRVVSSYLDG 233
Cdd:cd05466   82 hplakRKSVTLadladEPLILFERGSGLRRLLDRAF-AEAgftpNIALEVDSLEAIKALVAAGLGIA-LLPESAVEELAD 159

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 489199469 234 GTLQRVE-QAPEFAYPTYLVYSRER-LSPTLRHAFQLL 269
Cdd:cd05466  160 GGLVVLPlEDPPLSRTIGLVWRKGRyLSPAARAFLELL 197
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-275 9.58e-49

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 162.34  E-value: 9.58e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469   1 MDIDLARTFLEIARSGSFVAAAERLHLTQTAVTARIQNLEGQLGCRLFVRNRAGARLTADGEHFLGYASQLVQTWDAARR 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469  81 DL-PLPDGFRNLLNLGGEVSLCNPLLLNWMRRLREAIPGHAVRVEIGQGADLLKQLEQGALDAALVYQPEYWPGLQVEQL 159
Cdd:COG0583   81 ELrALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469 160 LEEKLVMvrsVVSAEPYLyvdwgpdfrsqhdaalpdrAKAALACNLGPLALQYIMQNGGSGYFRTRVVSSYLDGGTLQRV 239
Cdd:COG0583  161 GEERLVL---VASPDHPL-------------------ARRAPLVNSLEALLAAVAAGLGIALLPRFLAADELAAGRLVAL 218

                        250       260       270
                 ....*....|....*....|....*....|....*...
gi 489199469 240 E-QAPEFAYPTYLVYSRER-LSPTLRHAFQLLREVVRE 275
Cdd:COG0583  219 PlPDPPPPRPLYLVWRRRRhLSPAVRAFLDFLREALAE 256
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
1-253 1.97e-32

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 120.51  E-value: 1.97e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469   1 MDIDLARTFLEIARSGSFVAAAERLHLTQTAVTARIQNLEGQLGCRLFVRNRAGARLTADGEHFLGYASQLVQTWDAARR 80
Cdd:PRK03601   1 MDTELLKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYAETLMNTWQAAKK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469  81 DLPLPDGfRNLLNLGGEVSLCNPLLLNWMRRLREAIPGHAVRVEIGQGADLLKQLEQGALDAALVYQPEYWPGLQVEQLL 160
Cdd:PRK03601  81 EVAHTSQ-HNELSIGASASLWECMLTPWLGRLYQNQEALQFEARIAQRQSLVKQLHERQLDLLITTEAPKMDEFSSQLLG 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469 161 EEKLVMVRS----VVSAEPYLYVDWGPDFrSQHDAAL--PDRAkAALACNLGPLALQYIMQNGGSGYFRTRVVSSYLDgg 234
Cdd:PRK03601 160 HFTLALYTSapskKKSELNYIRLEWGADF-QQHEAGLigADEV-PILTTSSAELARQLLATLNGCAFLPVHWAKEKGG-- 235

                        250
                 ....*....|....*....
gi 489199469 235 tLQRVEQAPEFAYPTYLVY 253
Cdd:PRK03601 236 -LHTVPDSTTLSRPLYAIW 253
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-167 8.83e-23

selenium metabolism-associated LysR family transcriptional regulator; LysR family transcriptional regulators regularly appear encoded adjacent to selenecysteine incorporation proteins such as SelB. This model represents one especially well-conserved subgroup of such transcription factors from species such as Merdimonas faecis, Sellimonas intestinalis, Syntrophotalea acetylenica, and Hydrogenivirga caldilitoris. Seed alignment members were selected by proximity to selB, but not all family members are expected to have similar genomic locations.


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 94.99  E-value: 8.83e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469   1 MDIDLARTFLEIARSGSFVAAAERLHLTQTAVTARIQNLEGQLGCRLFVRNRAGARLTADGEHFLGYASQLVQTWDAARR 80
Cdd:NF040786   1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469  81 DLplpDGFRN----LLNLGGEVSLCNPLLLNWMRRLREAIPGHAVRVEIGQGADLLKQLEQGALDAALV-YQPEYwPGLQ 155
Cdd:NF040786  81 EF---DRYGKeskgVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTgTKLEK-KRLV 156

                        170
                 ....*....|..
gi 489199469 156 VEQLLEEKLVMV 167
Cdd:NF040786 157 YTPFYKDRLVLI 168
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-62 8.89e-21

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 83.20  E-value: 8.89e-21
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469    3 IDLARTFLEIARSGSFVAAAERLHLTQTAVTARIQNLEGQLGCRLFVRNRAGARLTADGE 62
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 89-274 5.50e-20

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: 85.42  E-value: 5.50e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469   89 RNLLNLGGEVSLCNPLLLNWMRRLREAIPGHAVRVEIGQGADLLKQLEQGALDAALVYQPEYWPGLQVEQLLEEKLVMV- 167
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVa 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469  168 -------------RSVVSAEPYLYVDWGPDFRSQHDAALPD---RAKAALACNLGPLALQYIMQNGGSGYFRTRVVSSYL 231
Cdd:pfam03466  81 ppdhplargepvsLEDLADEPLILLPPGSGLRDLLDRALRAaglRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAREL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 489199469  232 DGGTLQRVE-QAPEFAYPTYLVYSRER-LSPTLRHAFQLLREVVR 274
Cdd:pfam03466 161 ADGRLVALPlPEPPLPRELYLVWRKGRpLSPAVRAFIEFLREALA 205
PRK09791 PRK09791
LysR family transcriptional regulator;
7-168 5.59e-18

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 82.12  E-value: 5.59e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469   7 RTFLEIARSGSFVAAAERLHLTQTAVTARIQNLEGQLGCRLFVRNRAGARLTADGEHFLGYASQLVQTWDAARRDLPLPD 86
Cdd:PRK09791  11 RAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQEDIRQRQ 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469  87 G-FRNLLNLGGEVSLCNPLLLNWMRRLREAIPGHAVRVEIGQGADLLKQLEQGALDAAL--VYQPEYWPGLQVEQLLE-E 162
Cdd:PRK09791  91 GqLAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDFTIntYYQGPYDHEFTFEKLLEkQ 170


                 ....*.
gi 489199469 163 KLVMVR 168
Cdd:PRK09791 171 FAVFCR 176
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 1-144 1.12e-13

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 69.67  E-value: 1.12e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469   1 MDIDLARTFLEIARSGSFVAAAERLHLTQTAVTARIQNLEGQLGCRLFVRNRAGARLTADGEHFLGYASQLVQTWDAARR 80
Cdd:PRK15092  11 LDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEACS 90

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469  81 DLPlpdgFRNL---LNLGGEVSLCN---PLLLNwmrRLREAIPGHAVRVEIGQGADLLKQLEQGALDAAL 144
Cdd:PRK15092  91 SLM----YSNLqgvLTIGASDDTADtilPFLLN---RVSSVYPKLALDVRVKRNAFMMEMLESQEVDLAV 153
PRK10341 PRK10341
transcriptional regulator TdcA;
9-172 2.07e-13

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 69.12  E-value: 2.07e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469   9 FLEIARSGSFVAAAERLHLTQTAVTARIQNLEGQLGCRLFVRNRAGARLTADGEHFLGYASQLVQtwdaarrdlplpdGF 88
Cdd:PRK10341  15 FQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITR-------------EM 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469  89 RNLLN----LGG----EVSLCNPLLLNW------MRRLREAIPGHAVRVEIGQGADLLKQLEQGALDAAL--VYQPEYWP 152
Cdd:PRK10341  82 KNMVNeingMSSeavvDVSFGFPSLIGFtfmsdmINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIgtLSNEMKLQ 161

                        170       180
                 ....*....|....*....|
gi 489199469 153 GLQVEQLLEEKLVMVRSVVS 172
Cdd:PRK10341 162 DLHVEPLFESEFVLVASKSR 181
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
1-70 3.91e-13

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 68.29  E-value: 3.91e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469   1 MDIDLARTFLEIARSGSFVAAAERLHLTQTAVTARIQNLEGQLGCRLFVRNRAGARLTADGEHFLGYASQ 70
Cdd:PRK10094   2 FDPETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARD 71
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
2-83 6.13e-12

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 64.61  E-value: 6.13e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469   2 DIDLARTFLEIARSGSFVAAAERLHLTQTAVTARIQNLEGQLGCRLFVRNRAgARLTADGEHFLGYASQLVQTWDAARRD 81
Cdd:PRK13348   3 DYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRGRP-CRPTPAGQRLLRHLRQVALLEADLLST 81


                 ..
gi 489199469  82 LP 83
Cdd:PRK13348  82 LP 83
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 1-266 2.29e-11

multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, including founding member GSU2202 from Geobacter sulfurreducens PCA, are LysR family transcriptional regulators found regularly in the vicinity of multiheme cytochromes such as GSU2203, a decaheme c-type cytochrome.


Pssm-ID: 468965 [Multi-domain]  Cd Length: 301  Bit Score: 63.22  E-value: 2.29e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469   1 MDIDLARTFLEIARSGSFVAAAERLHLTQTAVTARIQNLEGQLGCRLFVRNRAGARLTADGEHFLgyasqlvqtwDAARR 80
Cdd:NF041036   1 METRYLKTLVIVAEEGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVL----------EKARR 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469  81 DLPLPDG-FRNLLNLGGE--VSLCN---------PLLLN-WMrrLREAIPgHAVRVEIGQGADLLKQLEQGALDAAL--- 144
Cdd:NF041036  71 ILDIEDSlMDELKSFKGRqrLSICCtptfgmahlPGVLNrFM--LRNADV-VDLKFLFHSPAQALEGIQNKEFDLAIieh 147

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469 145 ---------------------VYQPEY---WPGLQVEQLLEEKLVMVRSVVSAEPYLYVDWGpdfRSQHDaaLPDRAKAA 200
Cdd:NF041036 148 cadldlgrfhtyplpqdelvfVSAPSLglpTPNVTLERLLELCLITRRDGCSSRDLLRRNLA---EQGRD--LDDFRRVV 222

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489199469 201 LACNLGpLALQYIMQNGGSGYFRTRVVSSYLDGGTL--QRVEQAPEFAYPTyLVYSRERLSPTLRHAF 266
Cdd:NF041036 223 VSDDLR-LTIQTVLDGGGISFVSRSLVCEYLKNGQLreHYVEGFPHVRCRT-VVARKCRENDPLLSAF 288
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 7-169 5.34e-11

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 61.78  E-value: 5.34e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469   7 RTFLEIARSGSFVAAAERLHLTQTAVTARIQNLEGQLGCRLFVRNRAGARLTADGE-HFLGYASQLVQTWDAARRdlplp 85
Cdd:PRK11139  12 RAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQrYFLDIREIFDQLAEATRK----- 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469  86 dgfrnLLNLGGE----VSLCNPLLLNW-MRRL---REAIPGHAVRVeigQGADLLKQLEQGALDAALVYQPEYWPGLQVE 157
Cdd:PRK11139  87 -----LRARSAKgaltVSLLPSFAIQWlVPRLssfNEAHPDIDVRL---KAVDRLEDFLRDDVDVAIRYGRGNWPGLRVE 158

                        170
                 ....*....|..
gi 489199469 158 QLLEEKLVMVRS 169
Cdd:PRK11139 159 KLLDEYLLPVCS 170
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
8-62 5.47e-11

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 61.94  E-value: 5.47e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 489199469   8 TFLEIARSGSFVAAAERLHLTQTAVTARIQNLEGQLGCRLFVRNRAGARLTADGE 62
Cdd:PRK10086  21 TFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGK 75
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
1-144 1.02e-10

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 61.19  E-value: 1.02e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469   1 MDIDLARTFLEIARSGSFVAAAERLHLTQTAVTARIQNLEGQLGCRLFVRNRAGARLTADGEHFLGYASQLVQTWDAARR 80
Cdd:PRK15421   2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQ 81

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489199469  81 DLPLPDGFRnlLNLGGEVSLCNPLLLNWMRRLREAIPGHAVRVEIGQGADLLKQLEQGALDAAL 144
Cdd:PRK15421  82 ACNEPQQTR--LRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVM 143
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 7-167 1.64e-10

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 60.36  E-value: 1.64e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469   7 RTFLEIARSGSFVAAAERLHLTQTAVTARIQNLEGQLGCRLFVRNRAGARLTADGEHFLGYASQLVQTWDAARRDL-PLP 85
Cdd:PRK11242   7 RYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRRAIhDVA 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469  86 DGFRNLLNLGGEVSLCNPLLLNWMRRLREAIPGHAVRV-EIGQGAdLLKQLEQGALDAALVYQPEYWPGLQVEQLLEEKL 164
Cdd:PRK11242  87 DLSRGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIrEMSQER-IEALLADDELDVGIAFAPVHSPEIEAQPLFTETL 165


                 ...
gi 489199469 165 VMV 167
Cdd:PRK11242 166 ALV 168
rbcR CHL00180
LysR transcriptional regulator; Provisional
 7-71 1.72e-10

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 60.42  E-value: 1.72e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489199469   7 RTFLEIARSGSFVAAAERLHLTQTAVTARIQNLEGQLGCRLFVRNRAGARLTADGEHFLGYASQL 71
Cdd:CHL00180  11 RILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRI 75
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 1-167 1.98e-10

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 60.17  E-value: 1.98e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469   1 MDIDLARTFLEIARSGSFVAAAERLHLTQTAVTARIQNLEGQLGCRLFVRNRAGARLTADGEHFLGYASQLVQTWD---- 76
Cdd:PRK09906   1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEkakl 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469  77 ----AARRDLPLPDGFRNLlnlgGEVSLCNPLLLNwmrrLREAIPGHAVRVEIGQGADLLKQLEQGALDAALVYQPEYWP 152
Cdd:PRK09906  81 rarkIVQEDRQLTIGFVPS----AEVNLLPKVLPM----FRLRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPVYSD 152

                        170
                 ....*....|....*
gi 489199469 153 GLQVEQLLEEKLVMV 167
Cdd:PRK09906 153 EIDYLELLDEPLVVV 167
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
1-89 4.31e-10

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 59.02  E-value: 4.31e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469   1 MDIDLARTFLEIARSGSFVAAAERLHLTQTAVTARIQNLEGQLGCRLFVRNRaGARLTADGEHFLGYASQLVQTWDAARR 80
Cdd:PRK03635   2 LDYKQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVRTQ-PCRPTEAGQRLLRHARQVRLLEAELLG 80


                 ....*....
gi 489199469  81 DLPLPDGFR 89
Cdd:PRK03635  81 ELPALDGTP 89
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
26-149 2.16e-09

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 56.75  E-value: 2.16e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469  26 HLTQTAVTARIQNLEGQLGCRLFVR-NRAgARLTADGEHFLGYASQLVQTWDAARRDLplpDGFRNLLNlgGEVSL-CN- 102
Cdd:PRK11716   2 HVSPSTLSRQIQRLEEELGQPLFVRdNRS-VTLTEAGEELRPFAQQTLLQWQQLRHTL---DQQGPSLS--GELSLfCSv 75

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 489199469 103 -------PLLLnwmRRLREAIPghavRVEI----GQGADLLKQLEQGALDAALVYQPE 149
Cdd:PRK11716  76 taayshlPPIL---DRFRAEHP----LVEIklttGDAADAVEKVQSGEADLAIAAKPE 126
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 12-81 5.65e-09

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 56.10  E-value: 5.65e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469  12 IARSGSFVAAAERLHLTQTAVTARIQNLEGQLGCRLFVRNRAGARLTADGEHFLGYASQLVQTWDAARRD 81
Cdd:PRK11074  13 VARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRRQ 82
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 9-231 5.95e-09

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 55.85  E-value: 5.95e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469   9 FLEIARSGSFVAAAERLHLTQTAVTARIQNLEGQLGCRLFvrNRAGARLTADgEH-------FLGYASQLVQTWDAARRD 81
Cdd:PRK10837  11 FAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLF--DRVGKRLVVN-EHgrllyprALALLEQAVEIEQLFRED 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469  82 LplpdgfrNLLNLGGEVSLCNPLLLNWMRRLREAIPGHAVRVEIGQGADLLKQLEQGALDAALVYQPEYWPGLQVEQLLE 161
Cdd:PRK10837  88 N-------GALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNSQDVINAVLDFRVDIGLIEGPCHSPELISEPWLE 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469 162 EKLVMVRSVVSAepylyvdwgpdfRSQHDAALPDRAKAAlacnlgplalqYIMQNGGSGyfrTRVVSSYL 231
Cdd:PRK10837 161 DELVVFAAPDSP------------LARGPVTLEQLAAAP-----------WILRERGSG---TREIVDYL 204
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 92-269 2.99e-08

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: 52.60  E-value: 2.99e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469  92 LNLGGEVSLCNPLLLNWMRRLREAIPGHAVRVEIGQGADLLKQLEQGALDAALVYQPEYWPGLQVEQLLEEKLVMV---- 167
Cdd:cd05466    2 LRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVvppd 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469 168 -----RSVVSA-----EPYLYVDWGPDFRSQHDAALpDRA----KAALACNLGPLALQYIMQNGGSGyFRTRVVSSYLDG 233
Cdd:cd05466   82 hplakRKSVTLadladEPLILFERGSGLRRLLDRAF-AEAgftpNIALEVDSLEAIKALVAAGLGIA-LLPESAVEELAD 159

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 489199469 234 GTLQRVE-QAPEFAYPTYLVYSRER-LSPTLRHAFQLL 269
Cdd:cd05466  160 GGLVVLPlEDPPLSRTIGLVWRKGRyLSPAARAFLELL 197
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 9-167 1.33e-06

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 48.91  E-value: 1.33e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469   9 FLEIARSGSFVAAAERLHLTQTAVTARIQNLEGQLGCRLFVRNRAGARLTADGEHFLGYASQLVQTWDAARRDLplpdgF 88
Cdd:PRK11233   9 FVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQLAV-----H 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469  89 RNLLNLGGEVSL-------CNPLLLNWMRRLREAIPGHAVRVEIGQGADLLKQLEQGALDAALVYQPEYWPGLQVEQLLE 161
Cdd:PRK11233  84 NVGQALSGQVSIglapgtaASSLTMPLLQAVRAEFPGIVLYLHENSGATLNEKLMNGQLDMAVIYEHSPVAGLSSQPLLK 163


                 ....*.
gi 489199469 162 EKLVMV 167
Cdd:PRK11233 164 EDLFLV 169
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 92-167 5.36e-06

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: 45.96  E-value: 5.36e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489199469  92 LNLGGEVSLCNPLLLNWMRRLREAIPGhaVRVEIGQG--ADLLKQLEQGALDAALVYQPEYWPGLQVEQLLEEKLVMV 167
Cdd:cd08414    2 LRIGFVGSALYGLLPRLLRRFRARYPD--VELELREMttAEQLEALRAGRLDVGFVRPPPDPPGLASRPLLREPLVVA 77
PBP2_BudR cd08451
The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is ...
 101-167 2.13e-05

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: 44.48  E-value: 2.13e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489199469 101 CNPLLLNWMRRLREAIPGHAVRVEIGQGADLLKQLEQGALDAALVYQP-EYWPGLQVEQLLEEKLVMV 167
Cdd:cd08451   12 FHPLVPGLIRRFREAYPDVELTLEEANTAELLEALREGRLDAAFVRPPvARSDGLVLELLLEEPMLVA 79
PBP2_LTTR_like_2 cd08427
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 109-167 2.39e-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: 176118 [Multi-domain]  Cd Length: 195  Bit Score: 44.10  E-value: 2.39e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 489199469 109 MRRLREAIPGHAVRVEIGQGADLLKQLEQGALDAALVYQPEYW--PGLQVEQLLEEKLVMV 167
Cdd:cd08427   19 LARLRRRHPDLEVHIVPGLSAELLARVDAGELDAAIVVEPPFPlpKDLVWTPLVREPLVLI 79
PRK09801 PRK09801
LysR family transcriptional regulator;
7-114 2.67e-05

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 45.03  E-value: 2.67e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469   7 RTFLEIARSGSFVAAAERLHLTQTAVTARIQNLEGQLGCRLFVRNRAGARLTADG----EHFLGYASQLVQTWDAARRDL 82
Cdd:PRK09801  12 QVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGqrcyEHALEILTQYQRLVDDVTQIK 91

                         90       100       110
                 ....*....|....*....|....*....|...
gi 489199469  83 PLPDGF-RNLLNLGGEVSLCNPLLLNWMRRLRE 114
Cdd:PRK09801  92 TRPEGMiRIGCSFGFGRSHIAPAITELMRNYPE 124
PRK09986 PRK09986
LysR family transcriptional regulator;
1-62 2.88e-05

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 44.71  E-value: 2.88e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489199469   1 MDIDLARTFLEIARSGSFVAAAERLHLTQTAVTARIQNLEGQLGCRLFVRNRAGARLTADGE 62
Cdd:PRK09986   7 IDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGK 68
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 109-167 5.79e-05

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: 42.97  E-value: 5.79e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 489199469 109 MRRLREAIPGHAVRVEIGQGADLLKQLEQGALDAALVYQPEYWPGLQVEQLLEEKLVMV 167
Cdd:cd08433   19 LRAVRRRYPGIRLRIVEGLSGHLLEWLLNGRLDLALLYGPPPIPGLSTEPLLEEDLFLV 77
nhaR PRK11062
transcriptional activator NhaR; Provisional
 9-68 1.19e-04

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 42.69  E-value: 1.19e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469   9 FLEIARSGSFVAAAERLHLTQTAVTARIQNLEGQLGCRLFVRNRAGARLTADGEHFLGYA 68
Cdd:PRK11062  12 FWMVCKEGSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGELVFRYA 71
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
11-80 1.57e-04

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 42.66  E-value: 1.57e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489199469  11 EIARSG-SFVAAAERLHLTQTAVTARIQNLEGQLGCRLFVRNraGAR---LTADGEHFLGYASQLVQTWDAARR 80
Cdd:PRK12684  11 EAVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRH--GKRlrgLTEPGRIILASVERILQEVENLKR 82
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 109-193 4.69e-04

The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of dinitrotoluene and similar compounds, such as DntR, NahR, and LinR. 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. Also included are related LysR-type regulators clustered together in phylogenetic trees, including NodD, ToxR, LeuO, SyrM, TdcA, and PnbR. 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: 176109 [Multi-domain]  Cd Length: 200  Bit Score: 40.28  E-value: 4.69e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469 109 MRRLREAIPGHAVRVEIGQGADLLKQLEQGALDAALVYQPEYWPGLQVEQLLEEKLVMV--------RSVVS-----AEP 175
Cdd:cd08417   19 LARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELPPGLRSQPLFEDRFVCVarkdhplaGGPLTledylAAP 98

                         90
                 ....*....|....*...
gi 489199469 176 YLYVDWGPDFRSQHDAAL 193
Cdd:cd08417   99 HVLVSPRGRGHGLVDDAL 116
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 104-167 8.65e-04

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: 39.40  E-value: 8.65e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489199469 104 LLLNWMRRLREAIPGHAVRVEIGQGADLLKQLEQGALDAALVYQPEYWPGLQVEQLLEEKLVMV 167
Cdd:cd08420   14 LLPRLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLVEGPVDHPDLIVEPFAEDELVLV 77
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 103-167 1.36e-03

The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a member of the type 2 periplasmic binding fold protein superfamily; OxyR senses hydrogen peroxide and is activated through the formation of an intramolecular disulfide bond. The OxyR activation induces the transcription of genes necessary for the bacterial defense against oxidative stress. The OxyR of LysR-type transcriptional regulator family 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 C-terminal domain also contains the redox-active cysteines that mediate the redox-dependent conformational switch. Thus, the interaction between the OxyR-tetramer and DNA is notably different between the oxidized and reduced forms. 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: 176103 [Multi-domain]  Cd Length: 200  Bit Score: 39.05  E-value: 1.36e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489199469 103 PLLLnwmRRLREAIPGHAVRVEIGQGADLLKQLEQGALDAALVYQPEYWPGLQVEQLLEEKLVMV 167
Cdd:cd08411   17 PRLL---PALRQAYPKLRLYLREDQTERLLEKLRSGELDAALLALPVDEPGLEEEPLFDEPFLLA 78
PBP2_YofA_SoxR_like cd08442
The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, ...
 123-167 2.19e-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: 38.36  E-value: 2.19e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 489199469 123 VEIGQGADLLKQLEQGALDAALVYQPEYWPGLQVEQLLEEKLVMV 167
Cdd:cd08442   33 LSTGTTGALIQAVLEGRLDGAFVAGPVEHPRLEQEPVFQEELVLV 77
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 7-65 3.31e-03

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 38.43  E-value: 3.31e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 489199469   7 RTFLEIARSG-SFVAAAERLHLTQTAVTARIQNLEGQLGCRLFVRNraGARL---TADGEHFL 65
Cdd:PRK12682   7 RFVREAVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRH--GKRLkglTEPGKAVL 67
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 109-161 4.75e-03

The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator PAO1-like, a member of the type 2 periplasmic binding fold protein superfamily; This family includes the C-terminal substrate domain of a putative LysR-type transcriptional regulator from the plant pathogen Pseudomonas aeruginosa PAO1and its closely related homologs. The LysR-type transcriptional regulators (LTTRs) are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of N2 fixing bacteria, and synthesis of virulence factors, to a name a few. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 176104 [Multi-domain]  Cd Length: 198  Bit Score: 37.52  E-value: 4.75e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 489199469 109 MRRLREAIPGHAVRVEIGQGADLLKQLEQGALDAALVYQPEYWPGLQVEQLLE 161
Cdd:cd08412   19 LRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALTYDLDLPEDIAFEPLAR 71
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 110-167 9.44e-03

The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA expression of glutamate synthase operon, contains type 2 periplasmic binding fold; GltC, a member of the LysR family of bacterial transcriptional factors, activates the expression of gltA gene of glutamate synthase operon and is essential for cell growth in the absence of glutamate. Glutamate synthase is a heterodimeric protein that encoded by gltA and gltB, whose expression is subject to nutritional regulation. GltC also negatively auto-regulates its own expression. This substrate-binding domain has strong homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176125 [Multi-domain]  Cd Length: 195  Bit Score: 36.36  E-value: 9.44e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199469 110 RRLREAIPGhaVRVEIGQGA--DLLKQLEQGALDAALVYQPEYWPGLQVEQLLEEKLVMV 167
Cdd:cd08434   20 RAFRKEYPN--VTFELHQGStdELLDDLKNGELDLALCSPVPDEPDIEWIPLFTEELVLV 77
 
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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