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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490212083  94 TVTLSCIPTAVFYFLPRAIVQFNQSYPNIKVRIYEQGIETCMDSVRKGDVDFGINMNFITHPDIDFIPLVNEPFVLACRQ 173
Cdd:cd08440    1 RVRVAALPSLAATLLPPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEADPDLEFEPLLRDPFVLVCPK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490212083 174 DHPLATRKLVEWRELVSQTLIGVRKSSGNRQLIEKCLADKPWQLSWFYEVRHLSTSLGLVEAGLGVSALPCLAMPHGESA 253
Cdd:cd08440   81 DHPLARRRSVTWAELAGYPLIALGRGSGVRALIDRALAAAGLTLRPAYEVSHMSTALGMVAAGLGVAVLPALALPLADHP 160

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 490212083 254 -VVSVPLVEPVIRRTLGMIRVKNRPLSAAAERLASLL 289
Cdd:cd08440  161 gLVARPLTEPVVTRTVGLIRRRGRSLSPAAQAFLDLL 197

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490212083  94 TVTLSCIPTAVFYFLPRAIVQFNQSYPNIKVRIYEQGIETCMDSVRKGDVDFGINMNFITHPDIDFIPLVNEPFVLACRQ 173
Cdd:cd08440    1 RVRVAALPSLAATLLPPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEADPDLEFEPLLRDPFVLVCPK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490212083 174 DHPLATRKLVEWRELVSQTLIGVRKSSGNRQLIEKCLADKPWQLSWFYEVRHLSTSLGLVEAGLGVSALPCLAMPHGESA 253
Cdd:cd08440   81 DHPLARRRSVTWAELAGYPLIALGRGSGVRALIDRALAAAGLTLRPAYEVSHMSTALGMVAAGLGVAVLPALALPLADHP 160

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 490212083 254 -VVSVPLVEPVIRRTLGMIRVKNRPLSAAAERLASLL 289
Cdd:cd08440  161 gLVARPLTEPVVTRTVGLIRRRGRSLSPAAQAFLDLL 197

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).

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490212083   94 TVTLSCIPTAVFYFLPRAIVQFNQSYPNIKVRIYEQGIETCMDSVRKGDVDFGINMNFITHPDIDFIPLVNEPFVLACRQ 173
Cdd:pfam03466   3 RLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVAPP 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490212083  174 DHPLATRKLVEWRELVSQTLIGVRKSSGNRQLIEKCLADKPWQLSWFYEVRHLSTSLGLVEAGLGVSALPCLAMPH--GE 251
Cdd:pfam03466  83 DHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARelAD 162

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 490212083  252 SAVVSVPLVEPVIRRTLGMIRVKNRPLSAAAERLASLLL 290
Cdd:pfam03466 163 GRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLR 201

aminoethylphosphonate catabolism associated LysR family transcriptional regulator; This group of sequences represents a number of related clades with numerous examples of members adjacent to operons for the degradation of 2-aminoethylphosphonate (AEP) in Pseudomonas, Ralstonia, Bordetella and Burkholderia species. These are transcriptional regulators of the LysR family which contain a helix-turn-helix (HTH) domain (pfam00126) and a periplasmic substrate-binding protein-like domain (pfam03466). [Regulatory functions, DNA interactions]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490212083    8 MKAFVTVAELGSFSKAAEQLNLTQPALTKKIKKIESNLDIALFERTTRKIALTQAGKMLLPKAKSLISgLDAAIFDLNDL 87
Cdd:TIGR03339   2 LKAFHAVARCGSFTRAAERLGLSQPTVTDQVRKLEERYGVELFHRNGRRLELTDAGHRLLPIVERLFQ-QEAEAEFLLRE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490212083   88 TSQLHdTVTLSCIPTAVFYFLPrAIVQFNQSYPNIKVRIYEQGIETCMDSVRKGDVDFGINMNFITHPDIDFIPLVNEPF 167
Cdd:TIGR03339  81 SGALR-EGSLRIAATAPYYVLD-LVARFRQRYPGIEVSVRIGNSQEVLQALQSYRVDVAVSSEVVDDPRLDRVVLGNDPL 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490212083  168 VLACRQDHPLATRKLVEWRELVSQTLIGVRKSSGNRQLIEKCLADKPWQLSWFYEVRHLSTSLGLVEAGLGVSALPCLAM 247
Cdd:TIGR03339 159 VAVVHRQHPLAERESVTLEELAGQPLLMREPGSVTRQTTEEALAAAGVAPRPALEIGSREAIREAVLAGLGVSVVSAAEV 238

                         250       260       270
                  ....*....|....*....|....*....|....*.
gi 490212083  248 P-HGESAVVSVPLVEPVIRRTLGMIRV-KNRPLSAA 281
Cdd:TIGR03339 239 GrDPRLRVLPIVGAEPTMDEYLYCLKErRGARLIAA 274

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

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 490212083    8 MKAFVTVAELGSFSKAAEQLNLTQPALTKKIKKIESNLDIALFERTTRKIALTQAGK 64
Cdd:pfam00126   4 LRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60

HTH-type transcriptional activator AaeR;

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 490212083   4 ELSGMKAFVTVAELGSFSKAAEQLNLTQPALTKKIKKIESNLDIALFERTTRKIALTQAGKM 65
Cdd:PRK10632   3 RLKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRI 64

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490212083  94 TVTLSCIPTAVFYFLPRAIVQFNQSYPNIKVRIYEQGIETCMDSVRKGDVDFGINMNFITHPDIDFIPLVNEPFVLACRQ 173
Cdd:cd08440    1 RVRVAALPSLAATLLPPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEADPDLEFEPLLRDPFVLVCPK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490212083 174 DHPLATRKLVEWRELVSQTLIGVRKSSGNRQLIEKCLADKPWQLSWFYEVRHLSTSLGLVEAGLGVSALPCLAMPHGESA 253
Cdd:cd08440   81 DHPLARRRSVTWAELAGYPLIALGRGSGVRALIDRALAAAGLTLRPAYEVSHMSTALGMVAAGLGVAVLPALALPLADHP 160

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 490212083 254 -VVSVPLVEPVIRRTLGMIRVKNRPLSAAAERLASLL 289
Cdd:cd08440  161 gLVARPLTEPVVTRTVGLIRRRGRSLSPAAQAFLDLL 197

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490212083  94 TVTLSCIPTAVFYFLPRAIVQFNQSYPNIKVRIYEQGIETCMDSVRKGDVDFGINMNFITHPDIDFIPLVNEPFVLACRQ 173
Cdd:cd05466    1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490212083 174 DHPLATRKLVEWRELVSQTLIGVRKSSGNRQLIEKCLADKPWQLSWFYEVRHLSTSLGLVEAGLGVSALPCLAMPHGESA 253
Cdd:cd05466   81 DHPLAKRKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEELADG 160

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 490212083 254 -VVSVPLVEPVIRRTLGMIRVKNRPLSAAAERLASLL 289
Cdd:cd05466  161 gLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490212083   9 KAFVTVAELGSFSKAAEQLNLTQPALTKKIKKIESNLDIALFERTTRKIALTQAGKMLLPKAKSLISGLDAAIFDLNDLT 88
Cdd:NF040786   7 EAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEEEFDRYG 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490212083  89 SQLHDTVTL--SCIPTAvfYFLPRAIVQFNQSYPNIKVRIYEQGIETCMDSVRKGDVDFGINMNFITHPDIDFIPLVNEP 166
Cdd:NF040786  87 KESKGVLRIgaSTIPGQ--YLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKKRLVYTPFYKDR 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490212083 167 FVLACRQDHPLATRKLVEWR--ELVSQTLIGVRKSSGNRQLIEKCLAdkpwqlSWFYEVRHLSTS---------LGLVEA 235
Cdd:NF040786 165 LVLITPNGTEKYRMLKEEISisELQKEPFIMREEGSGTRKEAEKALK------SLGISLEDLNVVaslgsteaiKQSVEA 238

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|..
gi 490212083 236 GLGVSALPCLAMP--HGESAVVSVPLVEPVIRRTLGMIRVKNRPLSAAAERL 285
Cdd:NF040786 239 GLGISVISELAAEkeVERGRVLIFPIPGLPKNRDFYLVYNKNRQLSPTAEAF 290

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490212083 106 YFLPRAIVQFNQSYPNIKVRIYEQGIETCMDSVRKGDVDFGINMNFITHPDIDFIPLVNEPFVLACRQDHPLATRKLVEW 185
Cdd:cd08434   13 SLVPDLIRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLALCSPVPDEPDIEWIPLFTEELVLVVPKDHPLAGRDSVDL 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490212083 186 RELVSQTLIGVRKSSGNRQLIEKCLADKPWQLSWFYEVRHLSTSLGLVEAGLGVSALPCLAmPHGESAVVSVPLVEPVIR 265
Cdd:cd08434   93 AELADEPFVLLSPGFGLRPIVDELCAAAGFTPKIAFEGEEDSTIAGLVAAGLGVAILPEMT-LLNPPGVKKIPIKDPDAE 171

                        170
                 ....*....|....*....
gi 490212083 266 RTLGMIRVKNRPLSAAAER 284
Cdd:cd08434  172 RTIGLAWLKDRYLSPAARR 190

LysR family transcriptional regulator;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490212083  11 FVTVAELGSFSKAAEQLNLTQPALTKKIKKIESNLDIALFERTTRKIALTQAGKMLLPKAKSLISGLDAAIFDLNDLTSQ 90
Cdd:PRK09986  15 FLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLARVEQIGRG 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490212083  91 LHDTVTLSCIPTAVFYFLPRAIVQFNQSYPNIKVRIYEQGIETCMDSVRKGDVDFGINMNFITHPDIDFIP--LVNEPFV 168
Cdd:PRK09986  95 EAGRIEIGIVGTALWGRLRPAMRHFLKENPNVEWLLRELSPSMQMAALERRELDAGIWRMADLEPNPGFTSrrLHESAFA 174

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490212083 169 LACRQDHPLATRKLVEWRELVSQTLIGV--RKSSGNRQLIEKCLAD--KPWQLswfYEVRHLSTSLGLVEAGLGVSALP- 243
Cdd:PRK09986 175 VAVPEEHPLASRSSVPLKALRNEYFITLpfVHSDWGKFLQRVCQQAgfSPQII---RQVNEPQTVLAMVSMGIGITLLPd 251

                        250       260
                 ....*....|....*....|.
gi 490212083 244 -CLAMPHgeSAVVSVPLVEPV 263
Cdd:PRK09986 252 sYAQIPW--PGVVFRPLKERI 270

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490212083  94 TVTLSCIPTAVFYFLPRAIVQFNQSYPNIKVRIYEQGIETCMDSVRKGDVDFGINMNFITHPDIDFIPLVNEPFVLACRQ 173
Cdd:cd08415    1 TLRIAALPALALSLLPRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPLDHPGLESEPLASGRAVCVLPP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490212083 174 DHPLATRKLVEWRELVSQTLIGVRKSSGNRQLIEKCLADKPWQLSWFYEVRHLSTSLGLVEAGLGVSAL-PCLAMPHGES 252
Cdd:cd08415   81 GHPLARKDVVTPADLAGEPLISLGRGDPLRQRVDAAFERAGVEPRIVIETQLSHTACALVAAGLGVAIVdPLTAAGYAGA 160

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 490212083 253 AVVSVPLvEPVIRRTLGMIRVKNRPLSAAAERLASLL 289
Cdd:cd08415  161 GLVVRPF-RPAIPFEFALVRPAGRPLSRLAQAFIDLL 196

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490212083 107 FLPRAIVQFNQSYPNIKVRIYEQGIETCMDSVRKGDVDFGINMNFITHPDIDFIPLVNEPFVLACRQDHPLATRKLVEWR 186
Cdd:cd08438   14 LFAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVLPVDEEEFDSQPLCNEPLVAVLPRGHPLAGRKTVSLA 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490212083 187 ELVSQTLIGVRKS-SGNRQLIEKCladkpwQLSWF-----YEVRHLSTSLGLVEAGLGVSALP-CLAMPHGESAVVSVPL 259
Cdd:cd08438   94 DLADEPFILFNEDfALHDRIIDAC------QQAGFtpniaARSSQWDFIAELVAAGLGVALLPrSIAQRLDNAGVKVIPL 167

                        170       180       190
                 ....*....|....*....|....*....|
gi 490212083 260 VEPVIRRTLGMIRVKNRPLSAAAERLASLL 289
Cdd:cd08438  168 TDPDLRWQLALIWRKGRYLSHAARAWLALL 197

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490212083  94 TVTLSCIPTAVFYFLPRAIVQFNQSYPNIKVRIYEQGIETCMDSVRKGDVDF--GINMNFITHPDIDFIPLVNEPFVLAC 171
Cdd:cd08435    1 TVRVGAVPAAAPVLLPPAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLaiGRLADDEQPPDLASEELADEPLVVVA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490212083 172 RQDHPLATRKLVEWRELVSQTLIGVRKSSGNRQLIEKCLADKPWQLSWF-YEVRHLSTSLGLVEAGLGVSALPCLAMPHG 250
Cdd:cd08435   81 RPGHPLARRARLTLADLADYPWVLPPPGTPLRQRLEQLFAAAGLPLPRNvVETASISALLALLARSDMLAVLPRSVAEDE 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 490212083 251 ESA--VVSVPLVEPVIRRTLGMIRVKNRPLSAAAERLASLL 289
Cdd:cd08435  161 LRAgvLRELPLPLPTSRRPIGITTRRGGPLSPAARALLDAL 201

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490212083  94 TVTLSCIPTAVFYFLPRAIVQFNQSYPNIKVRIYEQGIETCMDSVRKGDVDFGINMNF-----ITHPDIDFIPLVNEPFV 168
Cdd:cd08423    1 TLRVGAFPTAAAALLPPALAALRARHPGLEVRLREAEPPESLDALRAGELDLAVVFDYpvtppPDDPGLTRVPLLDDPLD 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490212083 169 LACRQDHPLATRKLVEWRELVSQTLI-GVRKSSGNRQLIEKCLAD--KPwqlswfyEVRHLS----TSLGLVEAGLGVSA 241
Cdd:cd08423   81 LVLPADHPLAGREEVALADLADEPWIaGCPGSPCHRWLVRACRAAgfTP-------RIAHEAddyaTVLALVAAGLGVAL 153

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 490212083 242 LPCLAMPHGESAVVSVPLVEPVIRRTLGMIRVKNRPLSAAAERLASL 288
Cdd:cd08423  154 VPRLALGARPPGVVVRPLRPPPTRRIYAAVRAGAARRPAVAAALEAL 200

DNA-binding transcriptional regulator HcaR; Provisional

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490212083   4 ELSGMKAFVTVAELGSFSKAAEQLNLTQPALTKKIKKIESNLDIALFERTTRKIALTQAGKMLLPKAKSLISGLDAAIFd 83
Cdd:PRK09906   2 ELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKL- 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490212083  84 LNDLTSQLHDTVTLSCIPTAVFYFLPRAIVQFNQSYPNIKVRIYEQGIETCMDSVRKGDVDFGINMNFITHPDIDFIPLV 163
Cdd:PRK09906  81 RARKIVQEDRQLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPVYSDEIDYLELL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490212083 164 NEPFVLACRQDHPLATRKLVEWRELVSQTLI--GVRKSSGNRQLIEKCLADKPWQLSWFYEVRHLSTSLGLVEAGLGVSA 241
Cdd:PRK09906 161 DEPLVVVLPVDHPLAHEKEITAAQLDGVNFIstDPAYSGSLAPIIKAWFAQHNSQPNIVQVATNILVTMNLVGMGLGCTI 240

                        250
                 ....*....|....*...
gi 490212083 242 LPCLAMPHGESAVVSVPL 259
Cdd:PRK09906 241 IPGYMNNFNTGQVVFRPL 258

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490212083  94 TVTLSCIPTAVFYFLPRAIVQFNQSYPNIKVRIYEQGIETCMDSVRKGDVDFGINMNFITHPDIDFIPLVNEPFVLACRQ 173
Cdd:cd08426    1 RVRVATGEGLAAELLPSLIARFRQRYPGVFFTVDVASTADVLEAVLSGEADIGLAFSPPPEPGIRVHSRQPAPIGAVVPP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490212083 174 DHPLATRKLVEWRELVSQTLIGVRKSSGNRQLIEKCLADKPWQLSWFYEVRHLSTSLGLVEAGLGVSALPCLAMPH--GE 251
Cdd:cd08426   81 GHPLARQPSVTLAQLAGYPLALPPPSFSLRQILDAAFARAGVQLEPVLISNSIETLKQLVAAGGGISLLTELAVRReiRR 160

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 490212083 252 SAVVSVPLVEPVIR-RTLGMIRVKNRPLSAAAERLASLL 289
Cdd:cd08426  161 GQLVAVPLADPHMNhRQLELQTRAGRQLPAAASAFLQLL 199