NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|518299807|ref|WP_019470015|]
View 

MULTISPECIES: cidABC operon transcriptional activator CidR [Staphylococcus]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 13296482)

LysR family transcriptional regulator, similar to Staphylococcus aureus CidR which positively up-regulates the expression of the cidABC operon in the presence of acetic acid produced by the metabolism of excess glucose

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 92-287 4.32e-89

The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold; This CD includes the substrate binding domain of CidR which positively up-regulates the expression of cidABC operon in the presence of acetic acid produced by the metabolism of excess glucose. The CidR affects the control of murein hydrolase activity by enhancing cidABC expression in the presence of acetic acid. Thus, up-regulation of cidABC expression results in increased murein hydrolase activity. This substrate binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


:

Pssm-ID: 176129 [Multi-domain]  Cd Length: 197  Bit Score: 263.65  E-value: 4.32e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807  92 HISIGLSAVMNMNKFIHILGEFHQQYPNVTYSLVENGGKMIEHQLINDEIDIGITTLPVDQSIFHSLPLYQEELKLVLNK 171
Cdd:cd08438    1 HLRLGLPPLGGSLLFAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVLPVDEEEFDSQPLCNEPLVAVLPR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 172 EHRLAQYEQVKMSMLKDEDFILFNEDFYLNDKIIEAAKNAGYIPNTISKISQWNFIENLLNAHLGVSILPENIVGLLD-S 250
Cdd:cd08438   81 GHPLAGRKTVSLADLADEPFILFNEDFALHDRIIDACQQAGFTPNIAARSSQWDFIAELVAAGLGVALLPRSIAQRLDnA 160

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 518299807 251 DFKNITLEDPGMSWELGVIWKRDKYLSYATRQWIDFM 287
Cdd:cd08438  161 GVKVIPLTDPDLRWQLALIWRKGRYLSHAARAWLALL 197
PRK09791 super family cl32411
LysR family transcriptional regulator;
3-177 3.23e-19

LysR family transcriptional regulator;


The actual alignment was detected with superfamily member PRK09791:

Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 85.58  E-value: 3.23e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807   3 IKHMKYFVEVVNQQGMTNASKSLYIAQPTISKAIKDIENELNMPLFDRSKRQLVLTDAGSVFYYKSKEILSLYKDLPKEI 82
Cdd:PRK09791   7 IHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQEDI 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807  83 NSLLGLETGHISIGLSAVMNMNKFIHILGEFHQQYPNVTYSLVEngGKMIE--HQLINDEIDIGITTL---PVDQSIFHS 157
Cdd:PRK09791  87 RQRQGQLAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRIME--GQLVSmiNELRQGELDFTINTYyqgPYDHEFTFE 164

                        170       180
                 ....*....|....*....|
gi 518299807 158 lPLYQEELKLVLNKEHRLAQ 177
Cdd:PRK09791 165 -KLLEKQFAVFCRPGHPAIG 183
 
Name Accession Description Interval E-value
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 92-287 4.32e-89

The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold; This CD includes the substrate binding domain of CidR which positively up-regulates the expression of cidABC operon in the presence of acetic acid produced by the metabolism of excess glucose. The CidR affects the control of murein hydrolase activity by enhancing cidABC expression in the presence of acetic acid. Thus, up-regulation of cidABC expression results in increased murein hydrolase activity. This substrate binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176129 [Multi-domain]  Cd Length: 197  Bit Score: 263.65  E-value: 4.32e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807  92 HISIGLSAVMNMNKFIHILGEFHQQYPNVTYSLVENGGKMIEHQLINDEIDIGITTLPVDQSIFHSLPLYQEELKLVLNK 171
Cdd:cd08438    1 HLRLGLPPLGGSLLFAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVLPVDEEEFDSQPLCNEPLVAVLPR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 172 EHRLAQYEQVKMSMLKDEDFILFNEDFYLNDKIIEAAKNAGYIPNTISKISQWNFIENLLNAHLGVSILPENIVGLLD-S 250
Cdd:cd08438   81 GHPLAGRKTVSLADLADEPFILFNEDFALHDRIIDACQQAGFTPNIAARSSQWDFIAELVAAGLGVALLPRSIAQRLDnA 160

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 518299807 251 DFKNITLEDPGMSWELGVIWKRDKYLSYATRQWIDFM 287
Cdd:cd08438  161 GVKVIPLTDPDLRWQLALIWRKGRYLSHAARAWLALL 197
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-291 3.62e-59

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 189.31  E-value: 3.62e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807   1 MDIKHMKYFVEVVNQQGMTNASKSLYIAQPTISKAIKDIENELNMPLFDRSKRQLVLTDAGSVFYYKSKEILSLYKDLPK 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807  81 EINSLLGLETGHISIGLSAVMNMNKFIHILGEFHQQYPNVTYSLVENGGKMIEHQLINDEIDIGITTLPVDQSIFHSLPL 160
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 161 YQEELKLVLNKEHRLAQYEQVkmsmlkdedfilfnedfylndkiieaaknagyipntiskISQWNFIENLLNAHLGVSIL 240
Cdd:COG0583  161 GEERLVLVASPDHPLARRAPL---------------------------------------VNSLEALLAAVAAGLGIALL 201

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|...
gi 518299807 241 PENIVG--LLDSDFKNITLEDPGMSWELGVIWKRDKYLSYATRQWIDFMKQRL 291
Cdd:COG0583  202 PRFLAAdeLAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREAL 254
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 90-291 3.82e-43

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: 146.28  E-value: 3.82e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807   90 TGHISIGLSAVMNMNKFIHILGEFHQQYPNVTYSLVENGGKMIEHQLINDEIDIGITTLPVDQSIFHSLPLYQEELKLVL 169
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807  170 NKEHRLAQYEQVKMSMLKDEDFILFNEDFYLNDKIIEAAKNAGYIPNTISKISQWNFIENLLNAHLGVSILPENIVG--L 247
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAreL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 518299807  248 LDSDFKNITLEDPGMSWELGVIWKRDKYLSYATRQWIDFMKQRL 291
Cdd:pfam03466 161 ADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREAL 204
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-193 3.71e-39

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: 138.90  E-value: 3.71e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807   1 MDIKHMKYFVEVVNQQGMTNASKSLYIAQPTISKAIKDIENELNMPLFDRSKRQLVLTDAGSVFYYKSKEILSLYKDLPK 80
Cdd:NF040786   1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807  81 EINSLLGLETGHISIGLSAVMNMNKFIHILGEFHQQYPNVTYSLVENGGKMIEHQLINDEIDIGITTLPVDQSIFHSLPL 160
Cdd:NF040786  81 EFDRYGKESKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKKRLVYTPF 160

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 518299807 161 YQEELKLVLNKEHRLAQY--EQVKMSMLKDEDFIL 193
Cdd:NF040786 161 YKDRLVLITPNGTEKYRMlkEEISISELQKEPFIM 195
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 1-291 8.77e-36

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 129.89  E-value: 8.77e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807   1 MDIKHMKYFVEVVNQQGMTNASKSLYIAQPTISKAIKDIENELNMPLFDRSKRQLVLTDAGSVFYYKSKEILSlYKDLPK 80
Cdd:PRK09906   1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILE-QAEKAK 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807  81 EINSLLGLETGHISIGLSAVMNMNKFIHILGEFHQQYPNVTYSLVENGGKMIEHQLINDEIDIGITTLPVDQSIFHSLPL 160
Cdd:PRK09906  80 LRARKIVQEDRQLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPVYSDEIDYLEL 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 161 YQEELKLVLNKEHRLAQYEQVKMSMLKDEDFILFNEDF--YLNDKIIEAAKNAGYIPNTISKISQWNFIENLLNAHLGVS 238
Cdd:PRK09906 160 LDEPLVVVLPVDHPLAHEKEITAAQLDGVNFISTDPAYsgSLAPIIKAWFAQHNSQPNIVQVATNILVTMNLVGMGLGCT 239

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 518299807 239 ILPENIVGLLDSD--FKNITLEDPgmSWELGVIWKRDKyLSYATRQWIDFMKQRL 291
Cdd:PRK09906 240 IIPGYMNNFNTGQvvFRPLAGNVP--SIALLMAWKKGE-MKPALRDFIAIVQERL 291
PRK09791 PRK09791
LysR family transcriptional regulator;
3-177 3.23e-19

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 85.58  E-value: 3.23e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807   3 IKHMKYFVEVVNQQGMTNASKSLYIAQPTISKAIKDIENELNMPLFDRSKRQLVLTDAGSVFYYKSKEILSLYKDLPKEI 82
Cdd:PRK09791   7 IHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQEDI 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807  83 NSLLGLETGHISIGLSAVMNMNKFIHILGEFHQQYPNVTYSLVEngGKMIE--HQLINDEIDIGITTL---PVDQSIFHS 157
Cdd:PRK09791  87 RQRQGQLAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRIME--GQLVSmiNELRQGELDFTINTYyqgPYDHEFTFE 164

                        170       180
                 ....*....|....*....|
gi 518299807 158 lPLYQEELKLVLNKEHRLAQ 177
Cdd:PRK09791 165 -KLLEKQFAVFCRPGHPAIG 183
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-61 3.85e-19

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 78.97  E-value: 3.85e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 518299807    3 IKHMKYFVEVVNQQGMTNASKSLYIAQPTISKAIKDIENELNMPLFDRSKRQLVLTDAG 61
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
 
Name Accession Description Interval E-value
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 92-287 4.32e-89

The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold; This CD includes the substrate binding domain of CidR which positively up-regulates the expression of cidABC operon in the presence of acetic acid produced by the metabolism of excess glucose. The CidR affects the control of murein hydrolase activity by enhancing cidABC expression in the presence of acetic acid. Thus, up-regulation of cidABC expression results in increased murein hydrolase activity. This substrate binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176129 [Multi-domain]  Cd Length: 197  Bit Score: 263.65  E-value: 4.32e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807  92 HISIGLSAVMNMNKFIHILGEFHQQYPNVTYSLVENGGKMIEHQLINDEIDIGITTLPVDQSIFHSLPLYQEELKLVLNK 171
Cdd:cd08438    1 HLRLGLPPLGGSLLFAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVLPVDEEEFDSQPLCNEPLVAVLPR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 172 EHRLAQYEQVKMSMLKDEDFILFNEDFYLNDKIIEAAKNAGYIPNTISKISQWNFIENLLNAHLGVSILPENIVGLLD-S 250
Cdd:cd08438   81 GHPLAGRKTVSLADLADEPFILFNEDFALHDRIIDACQQAGFTPNIAARSSQWDFIAELVAAGLGVALLPRSIAQRLDnA 160

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 518299807 251 DFKNITLEDPGMSWELGVIWKRDKYLSYATRQWIDFM 287
Cdd:cd08438  161 GVKVIPLTDPDLRWQLALIWRKGRYLSHAARAWLALL 197
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 92-287 2.18e-60

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: 190.50  E-value: 2.18e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807  92 HISIGLSAVMNMNKFIHILGEFHQQYPNVTYSLVENGGKMIEHQLINDEIDIGITTLPVDQSIFHSLPLYQEELKLVLNK 171
Cdd:cd05466    1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 172 EHRLAQYEQVKMSMLKDEDFILFNEDFYLNDKIIEAAKNAGYIPNTISKISQWNFIENLLNAHLGVSILPENIVGLL-DS 250
Cdd:cd05466   81 DHPLAKRKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEELaDG 160

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 518299807 251 DFKNITLEDPGMSWELGVIWKRDKYLSYATRQWIDFM 287
Cdd:cd05466  161 GLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-291 3.62e-59

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 189.31  E-value: 3.62e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807   1 MDIKHMKYFVEVVNQQGMTNASKSLYIAQPTISKAIKDIENELNMPLFDRSKRQLVLTDAGSVFYYKSKEILSLYKDLPK 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807  81 EINSLLGLETGHISIGLSAVMNMNKFIHILGEFHQQYPNVTYSLVENGGKMIEHQLINDEIDIGITTLPVDQSIFHSLPL 160
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 161 YQEELKLVLNKEHRLAQYEQVkmsmlkdedfilfnedfylndkiieaaknagyipntiskISQWNFIENLLNAHLGVSIL 240
Cdd:COG0583  161 GEERLVLVASPDHPLARRAPL---------------------------------------VNSLEALLAAVAAGLGIALL 201

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|...
gi 518299807 241 PENIVG--LLDSDFKNITLEDPGMSWELGVIWKRDKYLSYATRQWIDFMKQRL 291
Cdd:COG0583  202 PRFLAAdeLAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREAL 254
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 90-291 3.82e-43

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: 146.28  E-value: 3.82e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807   90 TGHISIGLSAVMNMNKFIHILGEFHQQYPNVTYSLVENGGKMIEHQLINDEIDIGITTLPVDQSIFHSLPLYQEELKLVL 169
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807  170 NKEHRLAQYEQVKMSMLKDEDFILFNEDFYLNDKIIEAAKNAGYIPNTISKISQWNFIENLLNAHLGVSILPENIVG--L 247
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAreL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 518299807  248 LDSDFKNITLEDPGMSWELGVIWKRDKYLSYATRQWIDFMKQRL 291
Cdd:pfam03466 161 ADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREAL 204
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 92-287 6.67e-40

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: 137.67  E-value: 6.67e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807  92 HISIGlsavmnmnkFIHILG---------EFHQQYPNVTYSLVENGGKMIEHQLINDEIDIGITTLPVDQSIFHSLPLYQ 162
Cdd:cd08434    1 TVRLG---------FLHSLGtslvpdlirAFRKEYPNVTFELHQGSTDELLDDLKNGELDLALCSPVPDEPDIEWIPLFT 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 163 EELKLVLNKEHRLAQYEQVKMSMLKDEDFILFNEDFYLNDKIIEAAKNAGYIPNTISKISQWNFIENLLNAHLGVSILPE 242
Cdd:cd08434   72 EELVLVVPKDHPLAGRDSVDLAELADEPFVLLSPGFGLRPIVDELCAAAGFTPKIAFEGEEDSTIAGLVAAGLGVAILPE 151

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 518299807 243 niVGLLD-SDFKNITLEDPGMSWELGVIWKRDKYLSYATRQWIDFM 287
Cdd:cd08434  152 --MTLLNpPGVKKIPIKDPDAERTIGLAWLKDRYLSPAARRFKDFV 195
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-193 3.71e-39

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: 138.90  E-value: 3.71e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807   1 MDIKHMKYFVEVVNQQGMTNASKSLYIAQPTISKAIKDIENELNMPLFDRSKRQLVLTDAGSVFYYKSKEILSLYKDLPK 80
Cdd:NF040786   1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807  81 EINSLLGLETGHISIGLSAVMNMNKFIHILGEFHQQYPNVTYSLVENGGKMIEHQLINDEIDIGITTLPVDQSIFHSLPL 160
Cdd:NF040786  81 EFDRYGKESKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKKRLVYTPF 160

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 518299807 161 YQEELKLVLNKEHRLAQY--EQVKMSMLKDEDFIL 193
Cdd:NF040786 161 YKDRLVLITPNGTEKYRMlkEEISISELQKEPFIM 195
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 1-291 8.77e-36

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 129.89  E-value: 8.77e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807   1 MDIKHMKYFVEVVNQQGMTNASKSLYIAQPTISKAIKDIENELNMPLFDRSKRQLVLTDAGSVFYYKSKEILSlYKDLPK 80
Cdd:PRK09906   1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILE-QAEKAK 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807  81 EINSLLGLETGHISIGLSAVMNMNKFIHILGEFHQQYPNVTYSLVENGGKMIEHQLINDEIDIGITTLPVDQSIFHSLPL 160
Cdd:PRK09906  80 LRARKIVQEDRQLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPVYSDEIDYLEL 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 161 YQEELKLVLNKEHRLAQYEQVKMSMLKDEDFILFNEDF--YLNDKIIEAAKNAGYIPNTISKISQWNFIENLLNAHLGVS 238
Cdd:PRK09906 160 LDEPLVVVLPVDHPLAHEKEITAAQLDGVNFISTDPAYsgSLAPIIKAWFAQHNSQPNIVQVATNILVTMNLVGMGLGCT 239

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 518299807 239 ILPENIVGLLDSD--FKNITLEDPgmSWELGVIWKRDKyLSYATRQWIDFMKQRL 291
Cdd:PRK09906 240 IIPGYMNNFNTGQvvFRPLAGNVP--SIALLMAWKKGE-MKPALRDFIAIVQERL 291
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 1-291 7.75e-35

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 127.38  E-value: 7.75e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807   1 MDIKHMKYFVEVVNQQGMTNASKSLYIAQPTISKAIKDIENELNMPLFDRSKRQLVLTDAGSVFYYKSKEILslyKDLP- 79
Cdd:PRK11242   1 MLLRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRAL---QDLEa 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807  80 --KEINSLLGLETGHISIGLSAVMNMNKFIHILGEFHQQYPNVTYSLVENGGKMIEHQLINDEIDIGITTLPVDQSIFHS 157
Cdd:PRK11242  78 grRAIHDVADLSRGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMSQERIEALLADDELDVGIAFAPVHSPEIEA 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 158 LPLYQEELKLVLNKEHRLAQYEQ-VKMSMLKDEDFILFNEDFYLNDKIIEAAKNAGYIP------NTISKIsqwnfIENL 230
Cdd:PRK11242 158 QPLFTETLALVVGRHHPLAARRKaLTLDELADEPLVLLSAEFATREQIDRYFRRHGVTPrvaieaNSISAV-----LEIV 232

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 518299807 231 LNAHLGvSILPENIVGlLDSDFKNITLEDPGMSWELGVIWKRDKYLSYATRQWIDFMKQRL 291
Cdd:PRK11242 233 RRGRLA-TLLPAAIAR-EHDGLCAIPLDPPLPQRTAALLRRKGAYRSAAARAFIELALERR 291
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 92-273 8.53e-32

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: 116.84  E-value: 8.53e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807  92 HISIGLSAVMNMNKFIHILGEFHQQYPNVTYSLVENGGKMIEHQLINDEIDIGITTLPVDQSIFHSLPLYQEELKLVLNK 171
Cdd:cd08414    1 RLRIGFVGSALYGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPPPDPPGLASRPLLREPLVVALPA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 172 EHRLAQYEQVKMSMLKDEDFILFNEDF--YLNDKIIEAAKNAGYIPNTISKISQWNFIENLLNAHLGVSILPENIVGLLD 249
Cdd:cd08414   81 DHPLAARESVSLADLADEPFVLFPREPgpGLYDQILALCRRAGFTPRIVQEASDLQTLLALVAAGLGVALVPASVARLQR 160

                        170       180
                 ....*....|....*....|....
gi 518299807 250 SDFKNITLEDPGMSWELGVIWKRD 273
Cdd:cd08414  161 PGVVYRPLADPPPRSELALAWRRD 184
PRK09986 PRK09986
LysR family transcriptional regulator;
1-242 1.73e-27

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 107.89  E-value: 1.73e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807   1 MDIKHMKYFVEVVNQQGMTNASKSLYIAQPTISKAIKDIENELNMPLFDRSKRQLVLTDAGSVFYYKSKEILSLYKDLPK 80
Cdd:PRK09986   7 IDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLA 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807  81 EINSLLGLETGHISIGLSAVMNMNKFIHILGEFHQQYPNVTYSLVENGGKMIEHQLINDEIDIGI--TTLPVDQSIFHSL 158
Cdd:PRK09986  87 RVEQIGRGEAGRIEIGIVGTALWGRLRPAMRHFLKENPNVEWLLRELSPSMQMAALERRELDAGIwrMADLEPNPGFTSR 166

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 159 PLYQEELKLVLNKEHRLAQYEQVKMSMLKDEDFIL--FNE-DFYLNdkIIEAAKNAGYIPNTISKISQWNFIENLLNAHL 235
Cdd:PRK09986 167 RLHESAFAVAVPEEHPLASRSSVPLKALRNEYFITlpFVHsDWGKF--LQRVCQQAGFSPQIIRQVNEPQTVLAMVSMGI 244


                 ....*..
gi 518299807 236 GVSILPE 242
Cdd:PRK09986 245 GITLLPD 251
rbcR CHL00180
LysR transcriptional regulator; Provisional
 12-287 3.83e-26

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 104.33  E-value: 3.83e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807  12 VVNQQGMTNASKSLYIAQPTISKAIKDIENELNMPLFDRSKRQLVLTDAGSVFYYKSKEILSLYKDLPKEINSLLGLETG 91
Cdd:CHL00180  16 IATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRALEDLKNLQRG 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807  92 HISIGLSAVMNMNKFIHILGEFHQQYPNVTYSLVENGGKMIEHQLINDEIDIGIT--TLPVD-QSIFHSLPLYQEELKLV 168
Cdd:CHL00180  96 TLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVggEVPTElKKILEITPYVEDELALI 175

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 169 LNKEHRLAQYEQVKMSMLKDEDFILFNEDFYLNDKIIEAAKNAGYIPNTISKISQWNFIENLLNA---HLGVS------I 239
Cdd:CHL00180 176 IPKSHPFAKLKKIQKEDLYRLNFITLDSNSTIRKVIDNILIQNGIDSKRFKIEMELNSIEAIKNAvqsGLGAAfvsvsaI 255

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*...
gi 518299807 240 LPENIVGLLDSdfknITLEDPGMSWELGVIWKRDKYLSYATRQWIDFM 287
Cdd:CHL00180 256 EKELELGLLHW----IKIENITIKRMLSIITNPNRYKSKASETFYNEI 299
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 1-242 8.43e-23

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 95.48  E-value: 8.43e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807   1 MDIKHMKYFVEVVNQQGMTNASKSLYIAQPTISKAIKDIENELNMPLFDRSKRQLVLTDAGSVFYYKSKEILSLYKDLpK 80
Cdd:PRK11151   1 MNIRDLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVL-K 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807  81 EINSLLGLE-TGHISIGLSAVMNMNKFIHILGEFHQQYPNVTYSLVENGGKMIEHQLINDEIDIGITTLPVDQSIFHSLP 159
Cdd:PRK11151  80 EMASQQGETmSGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCAILALVKESEAFIEVP 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 160 LYQEELKLVLNKEHRLAQYEQVKMSMLKDEDFILFNEDFYLNDKIIEAAKNAGYIPNTISKISQWNFIENLLNAHLGVSI 239
Cdd:PRK11151 160 LFDEPMLLAVYEDHPWANRDRVPMSDLAGEKLLMLEDGHCLRDQAMGFCFEAGADEDTHFRATSLETLRNMVAAGSGITL 239


                 ...
gi 518299807 240 LPE 242
Cdd:PRK11151 240 LPA 242
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 1-242 4.41e-22

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 93.59  E-value: 4.41e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807   1 MDIKHMKYFVEVVNQQGMTNASKSLYIAQPTISKAIKDIENELNMPLFDRSKRQLVLTDAGSVFYYKSKEILSLYKDLPK 80
Cdd:PRK11233   1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807  81 EINSLLGLETGHISIGL---SAVMNMNkfIHILGEFHQQYPNVTYSLVENGGKMIEHQLINDEIDIGITTLPVDQSIFHS 157
Cdd:PRK11233  81 AVHNVGQALSGQVSIGLapgTAASSLT--MPLLQAVRAEFPGIVLYLHENSGATLNEKLMNGQLDMAVIYEHSPVAGLSS 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 158 LPLYQEELKLVLNkehRLAQYEQVKMSMLKDEDFILFNEDFYLNDKIIEAAKNAGYIPNTISKISQWNFIENLLNAHLGV 237
Cdd:PRK11233 159 QPLLKEDLFLVGT---QDCPGQSVDLAAVAQMNLFLPRDYSAVRLRVDEAFSLRRLTAKVIGEIESIATLTAAIASGMGV 235


                 ....*
gi 518299807 238 SILPE 242
Cdd:PRK11233 236 TVLPE 240
PBP2_BudR cd08451
The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is ...
 92-273 2.95e-21

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: 88.77  E-value: 2.95e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807  92 HISIGLSAVMNMNKFI-HILGEFHQQYPNVTYSLVENGGKMIEHQLINDEIDIGITTLPVDQSI-FHSLPLYQEELKLVL 169
Cdd:cd08451    1 RLRVGFTSSAAFHPLVpGLIRRFREAYPDVELTLEEANTAELLEALREGRLDAAFVRPPVARSDgLVLELLLEEPMLVAL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 170 NKEHRLAQYEQVKMSMLKDEDFILFNEDF--YLNDKIIEAAKNAGYIPNTISKISQWNFIENLLNAHLGVSILPENIVGL 247
Cdd:cd08451   81 PAGHPLARERSIPLAALADEPFILFPRPVgpGLYDAIIAACRRAGFTPRIGQEAPQMASAINLVAAGLGVSIVPASMRQL 160

                        170       180
                 ....*....|....*....|....*.
gi 518299807 248 LDSDFKNITLEDPGMSWELGVIWKRD 273
Cdd:cd08451  161 QAPGVVYRPLAGAPLTAPLALAYRRG 186
PRK10341 PRK10341
transcriptional regulator TdcA;
4-289 7.56e-21

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 90.31  E-value: 7.56e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807   4 KHMKYFVEVVNQQGMTNASKSLYIAQPTISKAIKDIENELNMPLFDRSKRQLVLTDAGSVFYYKSKEILSLYKDLPKEIN 83
Cdd:PRK10341  10 QHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEIN 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807  84 SLLGLETGHISIGLSAVMNMNKFIHILGEFHQQYPNVTYSlvenggkMIEHQL------IND-EIDIGITTLPVDQSI-- 154
Cdd:PRK10341  90 GMSSEAVVDVSFGFPSLIGFTFMSDMINKFKEVFPKAQVS-------MYEAQLssflpaIRDgRLDFAIGTLSNEMKLqd 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 155 FHSLPLYQEELKLVLNKEHRLAQyeQVKMSMLKDEDFILFNEDFYLNDKIIEAAKNAGYIPNTISKISQWNFIENL-LNA 233
Cdd:PRK10341 163 LHVEPLFESEFVLVASKSRTCTG--TTTLESLKNEQWVLPQTNMGYYSELLTTLQRNGISIENIVKTDSVVTIYNLvLNA 240

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 518299807 234 HLgVSILPENIVGLLDSD-FKNITLEDPGMSWELGVIWKRDKYLSYATRQWIDFMKQ 289
Cdd:PRK10341 241 DF-LTVIPCDMTSPFGSNqFITIPIEETLPVAQYAAVWSKNYRIKKAASVLVELAKE 296
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 1-216 7.95e-21

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 90.10  E-value: 7.95e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807   1 MDIKHMKYFVEVVNQQ-GMTNASKSLYIAQPTISKAIKDIENELNMPLFDRS-KRQLVLTDAGsvfyyksKEILSLYKDL 78
Cdd:PRK12683   1 MNFQQLRIIREAVRQNfNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRgKRLTGLTEPG-------KELLQIVERM 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807  79 PKEINSL-------LGLETGHISIGLSAVMNMNKFIHILGEFHQQYPNVTYSLVENGGKMIEHQLINDEIDIGITTLPVD 151
Cdd:PRK12683  74 LLDAENLrrlaeqfADRDSGHLTVATTHTQARYALPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGIATEALD 153

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 518299807 152 QSI-FHSLPLYQEELKLVLNKEHRLAQYEQVKMSMLKDEDFILFNEDFYLNDKIIEAAKNAGYIPN 216
Cdd:PRK12683 154 REPdLVSFPYYSWHHVVVVPKGHPLTGRENLTLEAIAEYPIITYDQGFTGRSRIDQAFAEAGLVPD 219
PBP2_XapR cd08449
The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved ...
 92-244 1.57e-20

The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved in xanthosine catabolism, contains the type 2 periplasmic binding fold; In Escherichia coli, XapR is a positive regulator for the expression of xapA gene, encoding xanthosine phosphorylase, and xapB gene, encoding a polypeptide similar to the nucleotide transport protein NupG. As an operon, the expression of both xapA and xapB is fully dependent on the presence of both XapR and the inducer xanthosine. Expression of the xapR is constitutive but not auto-regulated, unlike many other LysR family proteins. 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: 176140 [Multi-domain]  Cd Length: 197  Bit Score: 86.94  E-value: 1.57e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807  92 HISIGL-SAVMNMnKFIHILGEFHQQYPNVTYSLVENGGKMIEHQLINDEIDIGITTLPVDQSI--FHSLPLYQEELKLV 168
Cdd:cd08449    1 HLNIGMvGSVLWG-GLGPALRRFKRQYPNVTVRFHELSPEAQKAALLSKRIDLGFVRFADTLNDppLASELLWREPMVVA 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 518299807 169 LNKEHRLAQYEQVKMSMLKDEDFILFN-EDFYLNDKIIEAAKNAGYIPNTISKISQWNFIENLLNAHLGVSILPENI 244
Cdd:cd08449   80 LPEEHPLAGRKSLTLADLRDEPFVFLRlANSRFADFLINCCLQAGFTPQITQEVVEPQTLMALVAAGFGVALVPESY 156
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 108-286 4.39e-20

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


Pssm-ID: 176131 [Multi-domain]  Cd Length: 197  Bit Score: 85.65  E-value: 4.39e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 108 HILGEFHQQYPNVTYSLVE-NGGKMIEHqLINDEIDIGITTLPVDQSIFHSLPLYQEELKLVLNKEHRLAQYEQVKMSML 186
Cdd:cd08440   17 PVLAAFRRRHPGIRVRLRDvSAEQVIEA-VRSGEVDFGIGSEPEADPDLEFEPLLRDPFVLVCPKDHPLARRRSVTWAEL 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 187 KDEDFILFNEDFYLNDKIIEAAKNAGYIPNTISKISQWNFIENLLNAHLGVSILPENIVGLLD-SDFKNITLEDPGMSWE 265
Cdd:cd08440   96 AGYPLIALGRGSGVRALIDRALAAAGLTLRPAYEVSHMSTALGMVAAGLGVAVLPALALPLADhPGLVARPLTEPVVTRT 175

                        170       180
                 ....*....|....*....|.
gi 518299807 266 LGVIWKRDKYLSYATRQWIDF 286
Cdd:cd08440  176 VGLIRRRGRSLSPAAQAFLDL 196
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
1-240 4.76e-20

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 88.11  E-value: 4.76e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807   1 MDIKHMKYFVEVVNQQ-GMTNASKSLYIAQPTISKAIKDIENELNMPLFDR-SKRQLVLTDAGsvfyyksKEILSLYKDL 78
Cdd:PRK12684   1 MNLHQLRFVREAVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRhGKRLRGLTEPG-------RIILASVERI 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807  79 PKEINSL--LGLE-----TGHISIGLSAVMNMNKFIHILGEFHQQYPNVTYSLVENGGKMIEHQLINDEIDIGITTlpvd 151
Cdd:PRK12684  74 LQEVENLkrVGKEfaaqdQGNLTIATTHTQARYALPAAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAIAT---- 149

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 152 QSIFH-----SLPLYQEELKLVLNKEHRLAQYEQVKMSMLKDEDFILFNEDFYLNDKIIEAAKNAGYIPNTISKISQWNF 226
Cdd:PRK12684 150 EAIADykelvSLPCYQWNHCVVVPPDHPLLERKPLTLEDLAQYPLITYDFAFAGRSKINKAFALRGLKPDIVLEAIDADV 229

                        250
                 ....*....|....
gi 518299807 227 IENLLNAHLGVSIL 240
Cdd:PRK12684 230 IKTYVELGLGVGIV 243
PRK09791 PRK09791
LysR family transcriptional regulator;
3-177 3.23e-19

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 85.58  E-value: 3.23e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807   3 IKHMKYFVEVVNQQGMTNASKSLYIAQPTISKAIKDIENELNMPLFDRSKRQLVLTDAGSVFYYKSKEILSLYKDLPKEI 82
Cdd:PRK09791   7 IHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQEDI 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807  83 NSLLGLETGHISIGLSAVMNMNKFIHILGEFHQQYPNVTYSLVEngGKMIE--HQLINDEIDIGITTL---PVDQSIFHS 157
Cdd:PRK09791  87 RQRQGQLAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRIME--GQLVSmiNELRQGELDFTINTYyqgPYDHEFTFE 164

                        170       180
                 ....*....|....*....|
gi 518299807 158 lPLYQEELKLVLNKEHRLAQ 177
Cdd:PRK09791 165 -KLLEKQFAVFCRPGHPAIG 183
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-61 3.85e-19

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 78.97  E-value: 3.85e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 518299807    3 IKHMKYFVEVVNQQGMTNASKSLYIAQPTISKAIKDIENELNMPLFDRSKRQLVLTDAG 61
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 108-272 2.36e-18

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: 81.03  E-value: 2.36e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 108 HILGEFHQQYPNVTYSLVENGGKMIEHQLINDEIDIGITTLPVDQSIFHSLPLYQEELKLVLNKEHRLAQYEQVKMSMLK 187
Cdd:cd08411   18 RLLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAALLALPVDEPGLEEEPLFDEPFLLAVPKDHPLAKRKSVTPEDLA 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 188 DEDFILFNEDFYLNDKIIEAAKNAGYIPNTISKISQWNFIENLLNAHLGVSILPE---NIVGLLDSDFKNITLEDPGMSW 264
Cdd:cd08411   98 GERLLLLEEGHCLRDQALELCRLAGAREQTDFEATSLETLRQMVAAGLGITLLPElavPSEELRGDRLVVRPFAEPAPSR 177


                 ....*...
gi 518299807 265 ELGVIWKR 272
Cdd:cd08411  178 TIGLVWRR 185
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 1-291 4.15e-18

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 82.35  E-value: 4.15e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807   1 MDIKHMKYFVEVVNQQ-GMTNASKSLYIAQPTISKAIKDIENELNMPLFDRS-KRQLVLTDAGsvfyyksKEILSLYKDL 78
Cdd:PRK12682   1 MNLQQLRFVREAVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHgKRLKGLTEPG-------KAVLDVIERI 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807  79 PKEINSL--LGLE-----TGHISIGLSAVMNMNKFIHILGEFHQQYPNVTYSLVENGGKMIEHQLINDEIDIGITTLPVD 151
Cdd:PRK12682  74 LREVGNIkrIGDDfsnqdSGTLTIATTHTQARYVLPRVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGIATESLA 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 152 Q-SIFHSLPLYQEELKLVLNKEHRLAQYEQVKMSMLKDEDFILFNEDFYLNDKIIEAAKNAGYIPNTISKISQWNFIENL 230
Cdd:PRK12682 154 DdPDLATLPCYDWQHAVIVPPDHPLAQEERITLEDLAEYPLITYHPGFTGRSRIDRAFAAAGLQPDIVLEAIDSDVIKTY 233

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 518299807 231 LNAHLGVSILPEniVGLLDSDFKNITLEDPGMSWELGVIW---KRDKYLSYATRQWIDFMKQRL 291
Cdd:PRK12682 234 VRLGLGVGIVAE--MAYRPDRDGDLVALPAGHLFGPNTAWvalKRGAYLRNYVYKFIELCAPHL 295
PBP2_LTTR_aromatics_like_2 cd08448
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-273 5.47e-18

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type regulator similar to CbnR which is involved in the regulation of chlorocatechol breakdown. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176139 [Multi-domain]  Cd Length: 197  Bit Score: 80.00  E-value: 5.47e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807  92 HISIGLSAVMNMNKFIHILGEFHQQYPNVTYSLVENGGKMIEHQLINDEIDIGITTLPVDQSIFHSLPLYQEELKLVLNK 171
Cdd:cd08448    1 RLRIGFVGSMLYRGLPRILRAFRAEYPGIEVALHEMSSAEQIEALLRGELDLGFVHSRRLPAGLSARLLHREPFVCCLPA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 172 EHRLAQYEQVKMSMLKDEDFILFNEDF--YLNDKIIEAAKNAGYIPNTISKISQWNFIENLLNAHLGVSILPENI--VGL 247
Cdd:cd08448   81 GHPLAARRRIDLRELAGEPFVLFSREVspDYYDQIIALCMDAGFHPKIRHEVRHWLTVVALVAAGMGVALVPRSLarAGL 160

                        170       180
                 ....*....|....*....|....*.
gi 518299807 248 LDSDFknITLEDPGMSWELGVIWKRD 273
Cdd:cd08448  161 AGVRF--LPLKGATQRSELYAAWKAS 184
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 108-286 1.01e-17

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: 79.46  E-value: 1.01e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 108 HILGEFHQQYPNVTYSL-VENGGKmIEHQLINDEIDIGITTLPVDQSIFHSLPLYQEELKLVLNKEHRLAQYEQVKMSML 186
Cdd:cd08420   17 RLLARFRKRYPEVRVSLtIGNTEE-IAERVLDGEIDLGLVEGPVDHPDLIVEPFAEDELVLVVPPDHPLAGRKEVTAEEL 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 187 KDEDFIL----------FNEdfYLNDKII--------------EAAKNAgyipntiskisqwnfIEnllnAHLGVSILPE 242
Cdd:cd08420   96 AAEPWILrepgsgtrevFER--ALAEAGLdgldlnivmelgstEAIKEA---------------VE----AGLGISILSR 154

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 518299807 243 NIVG--LLDSDFKNITLEDPGMSWELGVIWKRDKYLSYATRQWIDF 286
Cdd:cd08420  155 LAVRkeLELGRLVALPVEGLRLTRPFSLIYHKDKYLSPAAEAFLEF 200
PBP2_AlsR cd08452
The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which ...
 92-287 6.58e-16

The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which regulates acetoin formation under stationary phase growth conditions; contains the type 2 periplasmic binding fold; AlsR is responsible for activating the expression of the acetoin operon (alsSD) in response to inducing signals such as glucose and acetate. Like many other LysR family proteins, AlsR is transcribed divergently from the alsSD operon. The alsS gene encodes acetolactate synthase, an enzyme involved in the production of acetoin in cells of stationary-phase. AlsS catalyzes the conversion of two pyruvate molecules to acetolactate and carbon dioxide. Acetolactate is then converted to acetoin at low pH by acetolactate decarboxylase which encoded by the alsD gene. Acetoin is an important physiological metabolite excreted by many microorganisms grown on glucose or other fermentable carbon sources. 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: 176143 [Multi-domain]  Cd Length: 197  Bit Score: 74.46  E-value: 6.58e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807  92 HISIGLSAVMNMNKFIHILGEFHQQYPNVTYSLVENGGKMIEHQLINDEIDIGITTLPVDQSIFHSLPLYQEELKLVLNK 171
Cdd:cd08452    1 LLVIGFVGAAIYEFLPPIVREYRKKFPSVKVELRELSSPDQVEELLKGRIDIGFLHPPIQHTALHIETVQSSPCVLALPK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 172 EHRLAQYEQVKMSMLKDEDFILFNEDFY--LNDKIIEAAKNAGYIPNTISKISQWNFIENLLNAHLGVSILPENIVGLLD 249
Cdd:cd08452   81 QHPLASKEEITIEDLRDEPIITVAREAWptLYDEIIQLCEQAGFRPKIVQEATEYQTVIGLVSAGIGVTFVPSSAKKLFN 160

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 518299807 250 SDFKNITLEDPGMSWELGVIWKRDKyLSYATRQWIDFM 287
Cdd:cd08452  161 LEVAYRKIDQINLNAEWSIAYRKDN-HNPLLKHFIHIS 197
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 108-287 2.56e-15

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


Pssm-ID: 176127 [Multi-domain]  Cd Length: 194  Bit Score: 72.63  E-value: 2.56e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 108 HILGEFHQQYPNVTYSLVENGGKMIEHQLINDEIDIGITTLPVDQ-SIFHSLPLYQEELKLVLNKEHRLAQYEQVKMSML 186
Cdd:cd08436   17 ELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAFVGLPERRpPGLASRELAREPLVAVVAPDHPLAGRRRVALADL 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 187 KDEDFILFNEDFYLNDKIIEAAKNAGYIPNTISKISQWNFIENLLNAHLGVSILPENIVGLLDsDFKNITLEdPGMSWEL 266
Cdd:cd08436   97 ADEPFVDFPPGTGARRQVDRAFAAAGVRRRVAFEVSDVDLLLDLVARGLGVALLPASVAARLP-GLAALPLE-PAPRRRL 174

                        170       180
                 ....*....|....*....|.
gi 518299807 267 GVIWkRDKYLSYATRQWIDFM 287
Cdd:cd08436  175 YLAW-SAPPPSPAARAFLELL 194
PBP2_MleR cd08437
The substrate binding domain of LysR-type transcriptional regulator MleR which required for ...
 92-287 4.82e-14

The substrate binding domain of LysR-type transcriptional regulator MleR which required for malolactic fermentation, contains type 2 periplasmic binidning fold; MleR, a transcription activator of malolactic fermentation system, is found in gram-positive bacteria and belongs to the lysR family of bacterial transcriptional regulators. The mleR gene is required for the expression and induction of malolactic fermentation. 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: 176128  Cd Length: 198  Bit Score: 69.28  E-value: 4.82e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807  92 HISIGLSAVMNMNKFIHILGEFHQQYPNVTYSLVENGGKMIEHQLINDEIDIG--ITTLPVDQSIFHSLPLYQEELKLVL 169
Cdd:cd08437    1 KLRFGLPPIIGNYYFPKLAKDLIKTGLMIQIDTYEGGSAELLEQLLQGDLDIAllGSLTPLENSALHSKIIKTQHFMIIV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 170 NKEHRLAQYEQVKMSMLKDEDFILFNEDFYLNDKIIEAAKNAGYIPNTISKISQWNFIENLLNAHLGVSILPEnIVGLLD 249
Cdd:cd08437   81 SKDHPLAKAKKVNFADLKKENFILLNEHFVHPKAFDSLCQQANFQPNIVYRTNDIHILKSMVRENVGIGFLTD-IAVKPD 159

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 518299807 250 SDFKNITL-EDPGMSWELGVIWKRDKYLSYATRQWIDFM 287
Cdd:cd08437  160 DHLVAIPLlDNEQPTFYISLAHRKDQLLTPAQKKLLDLL 198
PBP2_CynR cd08425
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, ...
 108-281 4.84e-14

The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, contains the type 2 periplasmic binding fold; CynR is a LysR-like transcriptional regulator of the cyn operon, which encodes genes that allow cyanate to be used as a sole source of nitrogen. The operon includes three genes in the following order: cynT (cyanate permease), cynS (cyanase), and cynX (a protein of unknown function). CynR negatively regulates its own expression independently of cyanate. CynR binds to DNA and induces bending of DNA in the presence or absence of cyanate, but the amount of bending is decreased by cyanate. The CynR 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 (PBP2). The PBP2 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: 176116  Cd Length: 197  Bit Score: 69.28  E-value: 4.84e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 108 HILGEFHQQYPNVTYSLVENGGKMIEHQLINDEIDIGITTLPVDQSIFHSLPLYQEELKLVLNKEHRLAQYEQV-KMSML 186
Cdd:cd08425   18 PLIDRFHARYPGIALSLREMPQERIEAALADDRLDLGIAFAPVRSPDIDAQPLFDERLALVVGATHPLAQRRTAlTLDDL 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 187 KDEDFILFNEDFYLNDKIIEAAKNAGYIP------NTISKIsqwnfIENLLNAHLGvSILPENIVgLLDSDFKNITLEDP 260
Cdd:cd08425   98 AAEPLALLSPDFATRQHIDRYFQKQGIKPriaieaNSISAV-----LEVVRRGRLA-TILPDAIA-REQPGLCAVALEPP 170

                        170       180
                 ....*....|....*....|.
gi 518299807 261 GMSWELGVIWKRDKYLSYATR 281
Cdd:cd08425  171 LPGRTAALLRRKGAYRSAAAR 191
cbl PRK12679
HTH-type transcriptional regulator Cbl;
1-247 1.08e-13

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 69.84  E-value: 1.08e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807   1 MDIKHMKYFVEVVNQQ-GMTNASKSLYIAQPTISKAIKDIENELNMPLF-DRSKRQLVLTDAGSVFYYKSKEILSLYKDL 78
Cdd:PRK12679   1 MNFQQLKIIREAARQDyNLTEVANMLFTSQSGVSRHIRELEDELGIEIFiRRGKRLLGMTEPGKALLVIAERILNEASNV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807  79 PKEINSLLGLETGHISIGLSAVMNMNKFIHILGEFHQQYPNVTYSLVENGGKMIEHQLINDEIDIGITT-LPVDQSIFHS 157
Cdd:PRK12679  81 RRLADLFTNDTSGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASeRLSNDPQLVA 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 158 LPLYQEELKLVLNKEHRLAQYEQVKMSMLKDEDFILFNEDFYLNDKIIEAAKNAGYIPNTISKISQWNFIENLLNAHLGV 237
Cdd:PRK12679 161 FPWFRWHHSLLVPHDHPLTQITPLTLESIAKWPLITYRQGITGRSRIDDAFARKGLLADIVLSAQDSDVIKTYVALGLGI 240

                        250
                 ....*....|
gi 518299807 238 SILPENIVGL 247
Cdd:PRK12679 241 GLVAEQSSGE 250
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 108-287 1.15e-13

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: 67.95  E-value: 1.15e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 108 HILGEFHQQYPNVTYSLVENGGKMIEHQLINDEIDIGIT---TLPVDqsiFHSLPLYQEELKLVLNKEHRLAQYEQVKMS 184
Cdd:cd08412   17 GLLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALTydlDLPED---IAFEPLARLPPYVWLPADHPLAGKDEVSLA 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 185 MLKDEDFILFNEDFyLNDKIIEAAKNAGYIPNTISKISQWNFIENLLNAHLGVSILPENIVGLLDSDFKNI---TLEDPG 261
Cdd:cd08412   94 DLAAEPLILLDLPH-SREYFLSLFAAAGLTPRIAYRTSSFEAVRSLVANGLGYSLLNDRPYRPWSYDGKRLvrrPLADPV 172

                        170       180
                 ....*....|....*....|....*.
gi 518299807 262 MSWELGVIWKRDKYLSYATRQWIDFM 287
Cdd:cd08412  173 PPLRLGLAWRRGARLTRAARAFVDFA 198
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
3-155 1.56e-13

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 69.40  E-value: 1.56e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807   3 IKHMKYFVEVVNQQGMTNASKSLYIAQPTISKAIKDIENELNMPLFDRSKRQLVLTDAGSVFYYKSKEILSLYKDLPKEI 82
Cdd:PRK10632   4 LKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQL 83

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 518299807  83 NSLLGLETGHISIGLSAVMNMNKFIHILGEFHQQYPNVTYSLVENggkMIEHQLINDEIDIGITTLPV-DQSIF 155
Cdd:PRK10632  84 YAFNNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTG---IPAPDLIADGLDVVIRVGALqDSSLF 154
PBP2_LTTR_aromatics_like_1 cd08447
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 108-273 2.10e-13

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type regulator similar to CbnR which is involved in the regulation of chlorocatechol breakdown. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176138 [Multi-domain]  Cd Length: 198  Bit Score: 67.29  E-value: 2.10e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 108 HILGEFHQQYPNVTYSLVEnggkMIE----HQLINDEIDIGITTLPVDQSIFHSLPLYQEELKLVLNKEHRLAQYEQVKM 183
Cdd:cd08447   17 RLLAAARAALPDVDLVLRE----MVTtdqiEALESGRIDLGLLRPPFARPGLETRPLVREPLVAAVPAGHPLAGAERLTL 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 184 SMLKDEDFILF--NEDFYLNDKIIEAAKNAGYIPNTISKISQWNFIENLLNAHLGVSILPENIVGLLDSD--FKNITLED 259
Cdd:cd08447   93 EDLDGQPFIMYspTEARYFHDLVVRLFASAGVQPRYVQYLSQIHTMLALVRAGLGVALVPASASRLRFEGvvFRPLDLPR 172

                        170
                 ....*....|....
gi 518299807 260 PGMSwELGVIWKRD 273
Cdd:cd08447  173 DVPV-ELHLAWRRD 185
PBP2_LTTR_like_1 cd08421
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 108-286 6.34e-13

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


Pssm-ID: 176113  Cd Length: 198  Bit Score: 66.01  E-value: 6.34e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 108 HILGEFHQQYPNVTYSLVENGGKMIEHQLINDEIDIGITTLPVDQSIFHSLPLYQEELKLVLNKEHRLAQYEQVKMSMLK 187
Cdd:cd08421   17 EDLASFLAAHPDVRIDLEERLSADIVRAVAEGRADLGIVAGNVDAAGLETRPYRTDRLVVVVPRDHPLAGRASVAFADTL 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 188 DEDFILFNEDFYLNDKIIEAAKNAGYIPNTISKISQWNFIENLLNAHLGVSILPENIVGLLDS--DFKNITLEDPGMSWE 265
Cdd:cd08421   97 DHDFVGLPAGSALHTFLREAAARLGRRLRLRVQVSSFDAVCRMVAAGLGIGIVPESAARRYARalGLRVVPLDDAWARRR 176

                        170       180
                 ....*....|....*....|.
gi 518299807 266 LGVIWKRDKYLSYATRQWIDF 286
Cdd:cd08421  177 LLLCVRSFDALPPAARALVDH 197
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 92-281 1.43e-11

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: 62.23  E-value: 1.43e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807  92 HISIGL----SAVMnmnkFIHILGEFHQQYPNVTYSLVEN-GGKMIEhQLINDEIDIGITTLPVDQSIFHSLPLYQEELK 166
Cdd:cd08433    1 RVSVGLppsaASVL----AVPLLRAVRRRYPGIRLRIVEGlSGHLLE-WLLNGRLDLALLYGPPPIPGLSTEPLLEEDLF 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 167 LVLNKEHRLAQYEQVKMSMLKDEDFILFNEDFYLNDKIIEAAKNAGYIPNTISKISQWNFIENLLNAHLGVSILPENIV- 245
Cdd:cd08433   76 LVGPADAPLPRGAPVPLAELARLPLILPSRGHGLRRLVDEAAARAGLTLNVVVEIDSVATLKALVAAGLGYTILPASAVa 155

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 518299807 246 -GLLDSDFKNITLEDPGMSWELGVIWKRDKYLSYATR 281
Cdd:cd08433  156 aEVAAGRLVAAPIVDPALTRTLSLATPRDRPLSPAAL 192
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 9-193 2.19e-11

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 63.17  E-value: 2.19e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807   9 FVEVVNQQGMTNASKSLYIAQPTISKAIKDIENELNMPLFDRSKRQLVLTDAGSVFYYKSKEILslykDLPKEINSLLGL 88
Cdd:PRK10837  11 FAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALL----EQAVEIEQLFRE 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807  89 ETGHISIGLSAVMNMNKFIHILGEFHQQYPNVTYSL-VENGGKMIEhQLINDEIDIGITTLPVDQSIFHSLPLYQEELKL 167
Cdd:PRK10837  87 DNGALRIYASSTIGNYILPAMIARYRRDYPQLPLELsVGNSQDVIN-AVLDFRVDIGLIEGPCHSPELISEPWLEDELVV 165

                        170       180
                 ....*....|....*....|....*.
gi 518299807 168 VLNKEHRLAQyEQVKMSMLKDEDFIL 193
Cdd:PRK10837 166 FAAPDSPLAR-GPVTLEQLAAAPWIL 190
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
1-181 2.60e-11

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 62.90  E-value: 2.60e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807   1 MDIKHMKYFVEVVNQQGMTNASKSLYIAQPTISKAIKDIENELNMPLFDRSKRQLVLTDAGSVFYYKSKEILSLYKDLPK 80
Cdd:PRK10094   2 FDPETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPS 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807  81 EINSL-LGLETG-HISIGlSAVMNMNKFIHILGEFHQQYPNVTYSLVENGGKMIEHQLINDE--IDIGIT-TLPVDQSiF 155
Cdd:PRK10094  82 ELQQVnDGVERQvNIVIN-NLLYNPQAVAQLLAWLNERYPFTQFHISRQIYMGVWDSLLYEGfsLAIGVTgTEALANT-F 159

                        170       180
                 ....*....|....*....|....*.
gi 518299807 156 HSLPLYQEELKLVLNKEHRLAQYEQV 181
Cdd:PRK10094 160 SLDPLGSVQWRFVMAADHPLANVEEP 185
cysB PRK12681
HTH-type transcriptional regulator CysB;
1-216 1.38e-10

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 61.07  E-value: 1.38e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807   1 MDIKHMKYFVEVVNQQ-GMTNASKSLYIAQPTISKAIKDIENELNMPLFDRSKRQLV-LTDAGSVFYYKSKEILSLYKDL 78
Cdd:PRK12681   1 MKLQQLRYIVEVVNHNlNVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTqVTPAGEEIIRIAREILSKVESI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807  79 PKEINSLLGLETGHISIGLSAVMNMNKFIHILGEFHQQYPNVtySL-VENGGKM-IEHQLINDEIDIGITTLPvdQSIFH 156
Cdd:PRK12681  81 KSVAGEHTWPDKGSLYIATTHTQARYALPPVIKGFIERYPRV--SLhMHQGSPTqIAEAAAKGNADFAIATEA--LHLYD 156

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 518299807 157 S---LPLYQEELKLVLNKEHRLAQYEQVKMSMLKDEDFILFNEDFYLNDKIIEAAKNAGYIPN 216
Cdd:PRK12681 157 DlimLPCYHWNRSVVVPPDHPLAKKKKLTIEELAQYPLVTYVFGFTGRSELDTAFNRAGLTPR 219
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 113-240 1.78e-10

The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the catabolism of opines and that of related regulators, contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulators, OccR and NocR, involved in the catabolism of opines and that of LysR for lysine biosynthesis which clustered together in phylogenetic trees. Opines, such as octopine and nopaline, are low molecular weight compounds found in plant crown gall tumors that are produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. NocR and OccR belong to the family of LysR-type transcriptional regulators that positively regulates the catabolism of nopaline and octopine, respectively. Both nopaline and octopalin are arginine derivatives. In Agrobacterium tumefaciens, NocR regulates expression of the divergently transcribed nocB and nocR genes of the nopaline catabolism (noc) region. OccR protein activates the occQ operon of the Ti plasmid in response to octopine. This operon encodes proteins required for the uptake and catabolism of octopine. The occ operon also encodes the TraR protein, which is a quorum-sensing transcriptional regulator of the Ti plasmid tra regulon. LysR is the transcriptional activator of lysA gene encoding diaminopimelate decarboxylase, an enzyme that catalyses the decarboxylation of diaminopimelate to produce lysine. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176107 [Multi-domain]  Cd Length: 196  Bit Score: 59.11  E-value: 1.78e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 113 FHQQYPNVTYSLVENGGKMIEHQLINDEIDIGITTLPVDQSIFHSLPLYQEELKLVLNKEHRLAQYEQVKMSMLKDEDFI 192
Cdd:cd08415   22 FRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPLDHPGLESEPLASGRAVCVLPPGHPLARKDVVTPADLAGEPLI 101

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 518299807 193 LFNEDFYLNDKIIEAAKNAGYIPNTISKISQWNFIENLLNAHLGVSIL 240
Cdd:cd08415  102 SLGRGDPLRQRVDAAFERAGVEPRIVIETQLSHTACALVAAGLGVAIV 149
PBP2_TdcA cd08418
The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is ...
 92-290 1.92e-10

The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is involved in the degradation of L-serine and L-threonine, contains the type 2 periplasmic binding fold; TdcA, a member of the LysR family, activates the expression of the anaerobically-regulated tdcABCDEFG operon which is involved in the degradation of L-serine and L-threonine to acetate and propionate, respectively. The tdc operon is comprised of one regulatory gene tdcA and six structural genes, tdcB to tdcG. The expression of the tdc operon is affected by several transcription factors including the cAMP receptor protein (CRP), integration host factor (IHF), histone-like protein (HU), and the operon specific regulators TdcA and TcdR. TcdR is divergently transcribed from the operon and encodes a small protein that is required for efficient expression of the Escherichia coli tdc operon. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176110 [Multi-domain]  Cd Length: 201  Bit Score: 59.29  E-value: 1.92e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807  92 HISIGLS---AVMNMNKFIHilgEFHQQYPNVTYSLVENGGKMIEHQLINDEIDIGITTLPVDQSI--FHSLPLYQEELK 166
Cdd:cd08418    1 KVSIGVSsliAHTLMPAVIN---RFKEQFPDVQISIYEGQLSSLLPELRDGRLDFAIGTLPDEMYLkeLISEPLFESDFV 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 167 LVLNKEHRLAQYEQVKmsMLKDEDFILFNEDFYLNDKIIEAAKNAGYIPNTISKISQWNFIENLLNAHLGVSILPENIV- 245
Cdd:cd08418   78 VVARKDHPLQGARSLE--ELLDASWVLPGTRMGYYNNLLEALRRLGYNPRVAVRTDSIVSIINLVEKADFLTILSRDMGr 155

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 518299807 246 GLLDS-DFKNITLEDPGMSWELGVIWKRDKYLSYATRQWIDFMKQR 290
Cdd:cd08418  156 GPLDSfRLITIPVEEPLPSADYYLIYRKKSRLTPLAEQLVELFRRY 201
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
1-245 2.09e-10

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 60.42  E-value: 2.09e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807   1 MDIKHMKYFVEVVNQQGMTNASKSLYIAQPTISKAIKDIENELNMPLFDRSKRQLVLTDAGSVFYYKSKEILSlykDLPK 80
Cdd:PRK15421   2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLP---QISQ 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807  81 EINSLLGLETGHISIGLSAVMNMNKFIHILGEFHQQYPNVTYSLveNGGKMIEHQ--LINDEIDIGITTLPVDQSIFHSL 158
Cdd:PRK15421  79 ALQACNEPQQTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDF--KSGVTFDPQpaLQQGELDLVMTSDILPRSGLHYS 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 159 PLYQEELKLVLNKEHRLAQYEQVKMSMLKDEDFILFNEDFYLNDKIIEAAKNAGYIPNTISKISQWNFIEnLLNAHLGVS 238
Cdd:PRK15421 157 PMFDYEVRLVLAPDHPLAAKTRITPEDLASETLLIYPVQRSRLDVWRHFLQPAGVSPSLKSVDNTLLLIQ-MVAARMGIA 235


                 ....*..
gi 518299807 239 ILPENIV 245
Cdd:PRK15421 236 ALPHWVV 242
PBP2_MdcR cd08416
The C-terminal substrate-binding domian of LysR-type transcriptional regulator MdcR, which ...
 92-274 4.81e-10

The C-terminal substrate-binding domian of LysR-type transcriptional regulator MdcR, which involved in the malonate catabolism contains the type 2 periplasmic binding fold; This family includes the C-terminal substrate binding domain of LysR-type transcriptional regulator (LTTR) MdcR that controls the expression of the malonate decarboxylase (mdc) genes. Like other members of the LTTRs, MdcR is a positive regulatory protein for its target promoter and 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 (PBP2). The PBP2 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: 176108  Cd Length: 199  Bit Score: 58.13  E-value: 4.81e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807  92 HISIGLSAVMNMNKFIHILGEFHQQYPNVTYSLVENGGKMIEHQLINDEIDIGITTLP---VDQSiFHSLPLYQEELKLV 168
Cdd:cd08416    1 RLRLGSLYSLTVNTVPRIIMGLKLRRPELDIELTLGSNKDLLKKLKDGELDAILVATPeglNDPD-FEVVPLFEDDIFLA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 169 LNKEHRLAQYEQVKMSMLKDEDFILFNEDFYLNDKIIEAAKNAGYIPNTISKISQWNFIENLLNAHLGVSILPENIVGLL 248
Cdd:cd08416   80 VPATSPLAASSEIDLRDLKDEKFVTLSEGFATYRGFDEAFEIAGFEPNVVMRVNDIFSLMSMVSGGVGYALLPGRIADVY 159

                        170       180
                 ....*....|....*....|....*..
gi 518299807 249 DSDFKNITLEDP-GMSWELGVIWKRDK 274
Cdd:cd08416  160 EDKVQLIPLAEPyQIRQTIGLVFLRSR 186
PBP2_IlvR cd08453
The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved ...
 108-273 6.96e-10

The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved in the biosynthesis of isoleucine, leucine and valine; contains type 2 periplasmic binding fold; The IlvR is an activator of the upstream and divergently transcribed ilvD gene, which encodes dihydroxy acid dehydratase that participates in isoleucine, leucine, and valine biosynthesis. As in the case of other members of the LysR family, the expression of ilvR gene is repressed in the presence of its own gene product. 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: 176144 [Multi-domain]  Cd Length: 200  Bit Score: 57.37  E-value: 6.96e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 108 HILGEFHQQYPNVTYSLVENGGKMIEHQLINDEIDIGITTLPVDQSIFHSL---PLYQEELKLVLNKEHRLAQYEQVKMS 184
Cdd:cd08453   17 ELVRRFREAYPDVELQLREATSDVQLEALLAGEIDAGIVIPPPGASAPPALayrPLLSEPLVLAVPAAWAAEGGAPLALA 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 185 MLKDEDFILFNE----DFYlnDKIIEAAKNAGYIPNTISKISQWNFIENLLNAHLGVSILPENIVGLLDSDFKNITLEDP 260
Cdd:cd08453   97 AVAAEPLVIFPRriapAFH--DAVTGYYRAAGQTPRIAQEAIQMQTIISLVSAGMGVALVPASLRNLARPGVVYRELADP 174

                        170
                 ....*....|...
gi 518299807 261 GMSWELGVIWKRD 273
Cdd:cd08453  175 APVLETGLVWRRD 187
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
 97-287 2.46e-09

The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO operon, which is involved in the carbon dioxide fixation, contains the type 2 periplasmic binding fold; CbbR, a LysR-type transcriptional regulator, is required to activate expression of RubisCO, one of two unique enzymes in the Calvin-Benson-Bassham (CBB) cycle pathway. All plants, cyanobacteria, and many autotrophic bacteria use the CBB cycle to fix carbon dioxide. Thus, this cycle plays an essential role in assimilating CO2 into organic carbon on earth. The key CBB cycle enzyme is ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO), which catalyzes the actual CO2 fixation reaction. The CO2 concentration affects the expression of RubisCO genes. It has also shown that NADPH enhances the DNA-binding ability of the CbbR. RubisCO is composed of eight large (CbbL) and eight small subunits (CbbS). The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176111  Cd Length: 197  Bit Score: 55.98  E-value: 2.46e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807  97 LSAVMNMNKFI-HILGEFHQQYPNVTYSL-VENGGKMIEhQLINDEIDIGITTLPVDQSIFHSLPLYQEELKLVLNKEHR 174
Cdd:cd08419    4 LAVVSTAKYFApRLLGAFCRRHPGVEVSLrVGNREQVLE-RLADNEDDLAIMGRPPEDLDLVAEPFLDNPLVVIAPPDHP 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 175 LAQYEQVKMSMLKDEDFIL---------FNEDFYlndkiieaaKNAGYIPNTISKISQWNFIENLLNAHLGVSILPENIV 245
Cdd:cd08419   83 LAGQKRIPLERLAREPFLLrepgsgtrlAMERFF---------AEHGVTLRVRMELGSNEAIKQAVMAGLGLSVLSLHTL 153

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 518299807 246 GLLDSDFKNITLEDPGM----SWElgVIWKRDKYLSYATRQWIDFM 287
Cdd:cd08419  154 ALELATGRLAVLDVEGFpirrQWY--VVHRKGKRLSPAAQAFLDFL 197
PRK09801 PRK09801
LysR family transcriptional regulator;
4-161 5.82e-09

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 56.20  E-value: 5.82e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807   4 KHMKYFVEVVNQQGMTNASKSLYIAQPTISKAIKDIENELNMPLFDRSKRQLVLTDAGSVFYYKSKEILSLYKDLPKEIN 83
Cdd:PRK09801   9 KDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVT 88

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 518299807  84 SLLGLETGHISIGLSAVMNMNKFIHILGEFHQQYPNVtyslvenggkMIEHQLINDEIDIGITTLPVDQSIFHSLPLY 161
Cdd:PRK09801  89 QIKTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPEL----------QVHFELFDRQIDLVQDNIDLDIRINDEIPDY 156
PRK12680 PRK12680
LysR family transcriptional regulator;
1-253 7.17e-09

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 55.78  E-value: 7.17e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807   1 MDIKHMKYFVEVVNQQ-GMTNASKSLYIAQPTISKAIKDIENELNMPLFDRSKRQL-VLTDAGSVFYYKSKEILSLYKDL 78
Cdd:PRK12680   1 MTLTQLRYLVAIADAElNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLeSVTPAGVEVIERARAVLSEANNI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807  79 -------PKEINSLLGLETGHisiglsavmNMNKFI--HILGEFHQQYPNVTYSLVENGGKMIEHQLINDEIDIGI-TTL 148
Cdd:PRK12680  81 rtyaanqRRESQGQLTLTTTH---------TQARFVlpPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIvSTA 151

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 149 PVDQSIFHSLPLYQEELKLVLNKEHRLAQYEQV-KMSMLKDEDFILFNEDFYLNDKIIEAAKNAGYIPNTISKISQWNFI 227
Cdd:PRK12680 152 GGEPSAGIAVPLYRWRRLVVVPRGHALDTPRRApDMAALAEHPLISYESSTRPGSSLQRAFAQLGLEPSIALTALDADLI 231

                        250       260
                 ....*....|....*....|....*.
gi 518299807 228 ENLLNAHLGVSILPENIVGLLDSDFK 253
Cdd:PRK12680 232 KTYVRAGLGVGLLAEMAVNANDEDLR 257
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 110-242 1.03e-08

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: 176115 [Multi-domain]  Cd Length: 200  Bit Score: 54.14  E-value: 1.03e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 110 LGEFHQQYPNVTYSLVEnggkMIEHQLIND----EIDIGITT------LPVDQSiFHSLPLYQEELKLVLNKEHRLAQYE 179
Cdd:cd08423   19 LAALRARHPGLEVRLRE----AEPPESLDAlragELDLAVVFdypvtpPPDDPG-LTRVPLLDDPLDLVLPADHPLAGRE 93

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 518299807 180 QVKMSMLKDEDFILFNEDFYLNDKIIEAAKNAGYIPNTISKISQWNFIENLLNAHLGVSILPE 242
Cdd:cd08423   94 EVALADLADEPWIAGCPGSPCHRWLVRACRAAGFTPRIAHEADDYATVLALVAAGLGVALVPR 156
PBP2_YofA_SoxR_like cd08442
The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, ...
 109-287 1.58e-08

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: 53.38  E-value: 1.58e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 109 ILGEFHQQYPNVTYSLVEN-GGKMIEhQLINDEIDIGITTLPVDQSIFHSLPLYQEELKLVLNKEHRLAQYEQVkmsmLK 187
Cdd:cd08442   18 LLAAYHARYPKVDLSLSTGtTGALIQ-AVLEGRLDGAFVAGPVEHPRLEQEPVFQEELVLVSPKGHPPVSRAED----LA 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 188 DEDFILFNEDFYLNDKIIEAAKNAGYIPNTISKISQWNFIENLLNAHLGVSILPENIVGL-----------LDSDFKNIT 256
Cdd:cd08442   93 GSTLLAFRAGCSYRRRLEDWLAEEGVSPGKIMEFGSYHAILGCVAAGMGIALLPRSVLDSlqgrgsvsihpLPEPFADVT 172

                        170       180       190
                 ....*....|....*....|....*....|.
gi 518299807 257 ledpgmSWelgVIWKRDkYLSYATRQWIDFM 287
Cdd:cd08442  173 ------TW---LVWRKD-SFTAALQAFLDLL 193
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 1-149 1.99e-08

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 54.23  E-value: 1.99e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807   1 MDIKHMKYFVEVVNQQGMTNASKSLYIAQPTISKAIKDIENELNMPLFDRSKRQLVLTDAGSVFYYKSKEILSLYKDLPK 80
Cdd:PRK14997   2 TDLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQD 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 518299807  81 EINSLLGLETGHISIGLSAVMnmnKFIHI---LGEFHQQYPNVTYSLvENGGKMIEhqLINDEIDIGITTLP 149
Cdd:PRK14997  82 AIAALQVEPRGIVKLTCPVTL---LHVHIgpmLAKFMARYPDVSLQL-EATNRRVD--VVGEGVDVAIRVRP 147
PBP2_HcaR cd08450
The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in ...
 94-248 9.94e-08

The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in involved in 3-phenylpropionic acid catabolism, contains the type2 periplasmic binding fold; HcaR, a member of the LysR family of transcriptional regulators, controls the expression of the hcA1, A2, B, C, and D operon, encoding for the 3-phenylpropionate dioxygenase complex and 3-phenylpropionate-2',3'-dihydrodiol dehydrogenase, that oxidizes 3-phenylpropionate to 3-(2,3-dihydroxyphenyl) propionate. Dioxygenases play an important role in protecting the cell against the toxic effects of dioxygen. The expression of hcaR is negatively auto-regulated, as for other members of the LysR family, and is strongly repressed in the presence of glucose. 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: 176141 [Multi-domain]  Cd Length: 196  Bit Score: 51.22  E-value: 9.94e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807  94 SIGLSAVMNMNKFIHILGEFHQQYPNVTYSLVENGGKMIEHQLINDEIDIGITTLPVDQSIFHSLPLYQEELKLVLNKEH 173
Cdd:cd08450    3 TIGFLPGAEVQWLPEVLPILREEHPDLDVELSSLFSPQLAEALMRGKLDVAFMRPEIQSDGIDYQLLLKEPLIVVLPADH 82

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 518299807 174 RLAQYEQVKMSMLKDEDFILFNEDF-YLNDKIIEAAKNAGYIPNTISKISQWNFIENLLNAHLGVSILPENIVGLL 248
Cdd:cd08450   83 RLAGREKIPPQDLAGENFISPAPTApVLQQVIENYAAQHNIQPNIIQEADNLLSAMSLVASTLGCALLPLYANNLL 158
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 92-177 2.02e-07

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: 50.29  E-value: 2.02e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807  92 HISIGLSAVMNMNKFIHILGEFHQQYPNVTYSLVENGGKMIEHQLINDEIDIGITTLPVDQSIFHSLPLYQEELKLVLNK 171
Cdd:cd08417    1 TFRIAASDYLEALLLPPLLARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELPPGLRSQPLFEDRFVCVARK 80


                 ....*.
gi 518299807 172 EHRLAQ 177
Cdd:cd08417   81 DHPLAG 86
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
31-149 4.84e-07

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 49.82  E-value: 4.84e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807  31 TISKAIKDIENELNMPLFDRSKRQLVLTDAGSVFYYKSKEILSLYKDLPKEINSLLGLETGHISIGLSAVMNMNKFIHIL 110
Cdd:PRK11716   7 TLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSLFCSVTAAYSHLPPIL 86

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 518299807 111 GEFHQQYPNVTYSLvENG--GKMIEhQLINDEIDIGITTLP 149
Cdd:PRK11716  87 DRFRAEHPLVEIKL-TTGdaADAVE-KVQSGEADLAIAAKP 125
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 19-190 7.84e-07

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 49.46  E-value: 7.84e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807  19 TNASKSLYIAQPTISKAIKDIENELNMPLFDRSKRQLVLTDAGSVFYYKSKEILSLYKDLPKEInsLLGLETGHISIGLS 98
Cdd:PRK11139  24 TRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEATRKL--RARSAKGALTVSLL 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807  99 AVMNMNKFIHILGEFHQQYPNVTYSLVenGGKMIEHQLiNDEIDIGITTLPVDQSIFHSLPLYQEELKLV-----LNKEH 173
Cdd:PRK11139 102 PSFAIQWLVPRLSSFNEAHPDIDVRLK--AVDRLEDFL-RDDVDVAIRYGRGNWPGLRVEKLLDEYLLPVcspalLNGGK 178

                        170
                 ....*....|....*...
gi 518299807 174 RLAQYEQ-VKMSMLKDED 190
Cdd:PRK11139 179 PLKTPEDlARHTLLHDDS 196
PBP2_MetR cd08441
The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which ...
 109-192 2.58e-06

The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which regulates the expression of methionine biosynthetic genes, contains type 2 periplasmic binding fold; MetR, a member of the LysR family, is a positive regulator for the metA, metE, metF, and metH genes. The sulfur-containing amino acid methionine is the universal initiator of protein synthesis in all known organisms and its derivative S-adenosylmethionine (SAM) and autoinducer-2 (AI-2) are involved in various cellular processes. SAM plays a central role as methyl donor in methylation reactions, which are essential for the biosynthesis of phospholipids, proteins, DNA and RNA. The interspecies signaling molecule AI-2 is involved in cell-cell communication process (quorum sensing) and gene regulation in bacteria. Although methionine biosynthetic enzymes and metabolic pathways are well conserved in bacteria, the regulation of methionine biosynthesis involves various regulatory mechanisms. In Escherichia coli and Salmonella enterica serovar Typhimurium, MetJ and MetR regulate the expression of methionine biosynthetic genes. The MetJ repressor negatively regulates the E. coli met genes, except for metH. Several of these genes are also under the positive control of MetR with homocysteine as a co-inducer. In Bacillus subtilis, the met genes are controlled by S-box termination-antitermination system. 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: 176132  Cd Length: 198  Bit Score: 47.18  E-value: 2.58e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 109 ILGEFHQQYPNVTYSLVEnggkmiEHQ------LINDEIDIGITTLPVDQSIFHSLPLYQEELKLVLNKEHRLAQYEQVK 182
Cdd:cd08441   18 VLDQFRERWPDVELDLSS------GFHfdplpaLLRGELDLVITSDPLPLPGIAYEPLFDYEVVLVVAPDHPLAAKEFIT 91

                         90
                 ....*....|
gi 518299807 183 MSMLKDEDFI 192
Cdd:cd08441   92 PEDLADETLI 101
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 110-285 2.64e-06

The C-terminal substrate binding domain of galactose-binding protein regulator contains the type 2 periplasmic binding fold; Galactose-binding protein regulator (GbpR), a member of the LysR family of bacterial transcriptional regulators, regulates the expression of chromosomal virulence gene chvE. The chvE gene is involved in the uptake of specific sugars, in chemotaxis to these sugars, and in the VirA-VirG two-component signal transduction system. In the presence of an inducing sugar such as L-arabinose, D-fucose, or D-galactose, GbpR activates chvE expression, while in the absence of an inducing sugar, GbpR represses expression. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176126 [Multi-domain]  Cd Length: 201  Bit Score: 47.27  E-value: 2.64e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 110 LGEFHQQYPNVTYSLVENGGKMIEHQLINDEID--IGITTLPVDQSIFHSLPLYQEELKLVLNKEHRLAQYEQVKMSMLK 187
Cdd:cd08435   19 IARLLARHPRLTVRVVEGTSDELLEGLRAGELDlaIGRLADDEQPPDLASEELADEPLVVVARPGHPLARRARLTLADLA 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 188 DEDFILfnedfylndkiieaaknagyiPNTISKISQWnfIENLLNAHlGVSiLPENIV---------GLLD-SDF----- 252
Cdd:cd08435   99 DYPWVL---------------------PPPGTPLRQR--LEQLFAAA-GLP-LPRNVVetasisallALLArSDMlavlp 153

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 518299807 253 -------------KNITLEDPGMSWELGVIWKRDKYLSYATRQWID 285
Cdd:cd08435  154 rsvaedelragvlRELPLPLPTSRRPIGITTRRGGPLSPAARALLD 199
PBP2_CysB_like cd08413
The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains ...
 112-216 4.89e-06

The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; CysB is a transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the regulation of transcription in response to sulfur source is attributed to two transcriptional regulators, CysB and Cbl. CysB, in association with Cbl, downregulates the expression of ssuEADCB operon which is required for the utilization of sulfur from aliphatic sulfonates, in the presence of cysteine. Also, Cbl and CysB together directly function as transcriptional activators of tauABCD genes, which are required for utilization of taurine as sulfur source for growth. Like many other members of the LTTR family, CysB is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 176105 [Multi-domain]  Cd Length: 198  Bit Score: 46.08  E-value: 4.89e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 112 EFHQQYPNVTYSLVENGGKMIEHQLINDEIDIGITTLPVDQSI-FHSLPLYQEELKLVLNKEHRLAQYEQVKMSMLKDED 190
Cdd:cd08413   21 AFRKRYPKVKLSLHQGTPSQIAEMVLKGEADIAIATEALDDHPdLVTLPCYRWNHCVIVPPGHPLADLGPLTLEDLAQYP 100

                         90       100
                 ....*....|....*....|....*.
gi 518299807 191 FILFNEDFYLNDKIIEAAKNAGYIPN 216
Cdd:cd08413  101 LITYDFGFTGRSSIDRAFARAGLEPN 126
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 10-181 9.42e-06

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 46.09  E-value: 9.42e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807  10 VEVVNQQG-MTNASKSLYIAQPTISKAIKDIENELNMPLFDRSKRQLVLTDAGSVFyykSKEILSLYKDLpkeinsllgL 88
Cdd:PRK11074  10 VDAVARTGsFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWF---VKEARSVIKKM---------Q 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807  89 ET------------GHISIGLSAVMNMNKFIHILGEFHQQYPNV---TYSLVENGgkmIEHQLINDEIDIGI---TTLPV 150
Cdd:PRK11074  78 ETrrqcqqvangwrGQLSIAVDNIVRPDRTRQLIVDFYRHFDDVeliIRQEVFNG---VWDALADGRVDIAIgatRAIPV 154

                        170       180       190
                 ....*....|....*....|....*....|.
gi 518299807 151 DQSiFHSLPLYQEELKLVLNKEHRLAQYEQV 181
Cdd:PRK11074 155 GGR-FAFRDMGMLSWACVVSSDHPLASMDGP 184
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 4-192 1.47e-05

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 45.75  E-value: 1.47e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807   4 KHMKYFVEVVNQQGMTNASKSLYIAQPTISKAIKDIENELNMPLFDRSKRQLVLTDAG-SVF------YYKSKEILSLYK 76
Cdd:PRK11013   7 RHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGlRLFeevqrsYYGLDRIVSAAE 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807  77 DLPKeinsllgLETGHISIGLSAVMNMNKFIHILGEFHQQYPNVTYSLVENGGKMIEHQLINDEIDIGITTLPVDQSIFH 156
Cdd:PRK11013  87 SLRE-------FRQGQLSIACLPVFSQSLLPGLCQPFLARYPDVSLNIVPQESPLLEEWLSAQRHDLGLTETLHTPAGTE 159

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 518299807 157 SLPLYQEELKLVLNKEHRLAQYEQVKMSMLKDEDFI 192
Cdd:PRK11013 160 RTELLTLDEVCVLPAGHPLAAKKVLTPDDFAGENFI 195
PBP2_OccR cd08457
The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the ...
 110-269 2.53e-05

The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the catabolism of octopine, contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulator OccR, which is involved in the catabolism of octopine. Opines are low molecular weight compounds found in plant crown gall tumors 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. In Agrobacterium tumefaciens, 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, an arginine derivative. The occ operon also encodes the TraR protein, which is a quorum-sensing transcriptional regulator of the Ti plasmid tra regulon. 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: 176146 [Multi-domain]  Cd Length: 196  Bit Score: 44.02  E-value: 2.53e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 110 LGEFHQQYPNVTYSLVENGGKMIEHQLINDEIDIGITTLPVDQSIFHSLPLYQEELKLVLNKEHRLAQYEQVKMSMLKDE 189
Cdd:cd08457   19 LAAFLRLRPNLHLSLMGLSSSQVLEAVASGRADLGIADGPLEERQGFLIETRSLPAVVAVPMGHPLAQLDVVSPQDLAGE 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 190 DFILFNEDFYLNDKIIEAAKNAGYIPNTISKISQWNFIENLLNAHLGVSIL-PENIVGL-LDSdfknITLE--DPGMSWE 265
Cdd:cd08457   99 RIITLENGYLFRMRVEVALGKIGVKRRPIIEVNLSHTALSLVREGLGIAIIdPATAIGLpLDG----IVIRpfDTFIDAG 174


                 ....
gi 518299807 266 LGVI 269
Cdd:cd08457  175 FLVV 178
leuO PRK09508
leucine transcriptional activator; Reviewed
 9-173 2.97e-05

leucine transcriptional activator; Reviewed


Pssm-ID: 181918 [Multi-domain]  Cd Length: 314  Bit Score: 44.63  E-value: 2.97e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807   9 FVEVVNQQGMTNASKSLYIAQPTISKAIKDIENELNMPLFDRSKR-------------------QLVLTD-AGSVFYYKS 68
Cdd:PRK09508  30 FDAVMQEQNITRAAHNLGMSQPAVSNAVARLKVMFNDELFVRYGRgiqptararqlfgpvrqalQLVQNElPGSGFEPES 109

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807  69 KE-ILSLykdlpkEINSLLgletghiSIGLSAVmnmnkfihILGEFHQQYPNVTYSLVENGGKMIEHQLINDEIDIGITT 147
Cdd:PRK09508 110 SErVFNL------CICSPL-------DIRLTSQ--------IYNRIEQIAPNIHVVFKSSLNQNIEHQLRYQETEFVISY 168

                        170       180
                 ....*....|....*....|....*.
gi 518299807 148 LPVDQSIFHSLPLYQEELKLVLNKEH 173
Cdd:PRK09508 169 EEFDRPEFTSVPLFKDELVLVASKNH 194
PBP2_LysR cd08456
The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine ...
 113-240 3.09e-05

The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine biosynthesis, contains the type 2 periplasmic binding fold; LysR, the transcriptional activator of lysA encoding diaminopimelate decarboxylase, catalyses the decarboxylation of diaminopimelate to produce lysine. The 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: 176145 [Multi-domain]  Cd Length: 196  Bit Score: 43.95  E-value: 3.09e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 113 FHQQYPNVTYSLVENGGKMIEHQLINDEIDIGITTLPVDQSIFHSLPLYQEELKLVLNKEHRLAQYEQVKMSMLKDEDFI 192
Cdd:cd08456   22 FLQRHPDVTISIHTRDSPTVEQWLSAQQCDLGLVSTLHEPPGIERERLLRIDGVCVLPPGHRLAVKKVLTPSDLEGEPFI 101

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 518299807 193 LFNEDFYLNDKIIEAAKNAGYIPNTISKISQWNFIENLLNAHLGVSIL 240
Cdd:cd08456  102 SLARTDGTRQRVDALFEQAGVKRRIVVETSYAATICALVAAGVGVSVV 149
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 109-287 3.84e-05

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


Pssm-ID: 176117 [Multi-domain]  Cd Length: 199  Bit Score: 43.45  E-value: 3.84e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 109 ILGEFHQQYPNVTYSL-VENGGKMIEhQLINDEIDIGITTLPVDQSIFHSLPLYQEELKLVLNKEHRLAQYEQVKMSMLK 187
Cdd:cd08426   18 LIARFRQRYPGVFFTVdVASTADVLE-AVLSGEADIGLAFSPPPEPGIRVHSRQPAPIGAVVPPGHPLARQPSVTLAQLA 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 188 DEDFILFNEDFYLNDKIIEAAKNAGYIPNTISKISQWNFIENLLNAHLGVSILPENIVG--LLDSDFKNITLEDPGMSW- 264
Cdd:cd08426   97 GYPLALPPPSFSLRQILDAAFARAGVQLEPVLISNSIETLKQLVAAGGGISLLTELAVRreIRRGQLVAVPLADPHMNHr 176

                        170       180
                 ....*....|....*....|...
gi 518299807 265 ELGVIWKRDKYLSYATRQWIDFM 287
Cdd:cd08426  177 QLELQTRAGRQLPAAASAFLQLL 199
PBP2_Cbl cd08444
The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is ...
 113-242 5.35e-05

The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is required for expression of sulfate starvation-inducible (ssi) genes, contains the type 2 periplasmic binding fold; Cbl is a member of the LysR transcriptional regulators that comprise the largest family of prokaryotic transcription factor. Cbl shows high sequence similarity to CysB, the LysR-type transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the function of Cbl is required for expression of sulfate starvation-inducible (ssi) genes, coupled with the biosynthesis of cysteine from the organic sulfur sources (sulfonates). The ssi genes include the ssuEADCB and tauABCD operons encoding uptake systems for organosulfur compounds, aliphatic sulfonates, and taurine. The genes in these operons encode an ABC-type transport system required for uptake of aliphatic sulfonates and a desulfonation enzyme. Both Cbl and CysB require expression of the tau and ssu genes. Like many other members of the LTTR family, the Cbl is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176135  Cd Length: 198  Bit Score: 43.26  E-value: 5.35e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 113 FHQQYPNVTYSLVENGGKMIEHQLINDEIDIGITTLPVDQSI-FHSLPLYQEELKLVLNKEHRLAQYEQVKMSMLKDEDF 191
Cdd:cd08444   22 FKEQFPNVHLVLHQGSPEEIASMLANGQADIGIATEALENHPeLVSFPYYDWHHHIIVPVGHPLESITPLTIETIAKWPI 101

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 518299807 192 ILFNEDFYLNDKIIEAAKNAGYIPNTISKISQWNFIENLLNAHLGVSILPE 242
Cdd:cd08444  102 ITYHGGFTGRSRIDRAFSRAELTPNIVLSALDADVIKTYVGLGMGIGIVAE 152
PBP2_Chlorocatechol cd08446
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 109-274 7.46e-05

The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the chlorocatechol catabolism, contains the type 2 periplasmic binding fold; This CD includes the substrate binding domain of LysR-type regulators CbnR, ClcR and TfdR, which are involved in the regulation of chlorocatechol breakdown. The chlorocatechol-degradative pathway is often found in bacteria that can use chlorinated aromatic compounds as carbon and energy sources. CbnR is found in the 3-chlorobenzoate degradative bacterium Ralstonia eutropha NH9 and forms a tetramer. CbnR activates the expression of the cbnABCD genes, which are responsible for the degradation of chlorocatechol converted from 3-chlorobenzoate and are transcribed divergently from cbnR. In soil bacterium Pseudomonas putida, the 3-chlorocatechol-degradative pathway is encoded by clcABD operon, which requires the divergently transcribed clcR for activation. TfdR is involved in the activation of tfdA and tfdB gene expression. These genes encode enzymes for the conversion of 2,4-dichlorophenoxyacetic acid and 2,4-dichlorophenol. 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: 176137 [Multi-domain]  Cd Length: 198  Bit Score: 42.65  E-value: 7.46e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 109 ILGEFHQQYPNVTYSLvenggkmieHQLINDE---------IDIGITTL-PVDQSIFHSLpLYQEELKLVLNKEHRLAQY 178
Cdd:cd08446   19 LLRAFLTARPDVTVSL---------HNMTKDEqiealragrIHIGFGRFyPVEPDIAVEN-VAQERLYLAVPKSHPLAAR 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 179 EQVKMSMLKDEDFILF-NEDF-YLNDKIIEAAKNAGYIPNTISKISQWNFIENLLNAHLGVSILPENIVGLLDSDFKNIT 256
Cdd:cd08446   89 PAVSLADLRNEPLILFpRGGRpSFADEVLGLFRRAGVEPRVAQEVEDVVAALALVAAGFGVCIVPESVAALRWPGVVFRP 168

                        170
                 ....*....|....*...
gi 518299807 257 LEDPGMSWELGVIWKRDK 274
Cdd:cd08446  169 LADAEAKVPLSCIYRKDD 186
nhaR PRK11062
transcriptional activator NhaR; Provisional
 5-69 9.83e-05

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 43.07  E-value: 9.83e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 518299807   5 HMKYFVEVVNQQGMTNASKSLYIAQPTISKAIKDIENELNMPLFDRSKRQLVLTDAGS-VFYYKSK 69
Cdd:PRK11062   8 HLYYFWMVCKEGSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGElVFRYADK 73
PBP2_ClcR cd08485
The C-terminal substrate binding domain of LysR-type transcriptional regulator ClcR involved ...
 118-273 1.02e-04

The C-terminal substrate binding domain of LysR-type transcriptional regulator ClcR involved in the chlorocatechol catabolism, contains type 2 periplasmic binding fold; In soil bacterium Pseudomonas putida, the ortho-pathways of catechol and 3-chlorocatechol are central catabolic pathways that convert aromatic and chloroaromaric compounds to tricarboxylic acid (TCA) cycle intermediates. The 3-chlorocatechol-degradative pathway is encoded by clcABD operon, which requires the divergently transcribed clcR and an intermediate of the pathway, 2-chloromuconate, as an inducer for activation. 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: 176174 [Multi-domain]  Cd Length: 198  Bit Score: 42.37  E-value: 1.02e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 118 PNVTYSLVENGGKMIEHQLINDEIDIGITTLPVDQSIFHSLPLYQEELKLVLNKEHRLAQYEQVKMSMLKDEDFILFNED 197
Cdd:cd08485   28 PSATVSLTQMSKNRQIEALDAGTIDIGFGRFYPYQEGVVVRNVTNERLFLGAQKSRARSFGEQVHCSALRNEPLILFPRE 107

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 518299807 198 FY--LNDKIIEAAKNAGYIPNTISKISQWNFIENLLNAHLGVSILPENIVGLLDSDFKNITLEDPGMSWELGVIWKRD 273
Cdd:cd08485  108 GRpsFADEVIGVFKNARVEPKVVAIVEDVNAAMALALAGVGVTIVPETVAMISWPDFGFTELVGSKATVPVSCIYRHD 185
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
1-61 1.75e-04

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 42.31  E-value: 1.75e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 518299807   1 MDIKHMKYFVEVVNQQGMTNASKSLYIAQPTISKAIKDIENELNMPLFDRSKRQLVLTDAG 61
Cdd:PRK03601   1 MDTELLKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAG 61
PBP2_BenM_CatM_CatR cd08445
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 112-261 2.13e-04

The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in benzoate catabolism; contains the type 2 periplasmic binding fold; This CD includes the C-terminal of LysR-type transcription regulators, BenM, CatM, and CatR, which are involved in the benzoate catabolism. The BenM and CatM are paralogs with overlapping functions. BenM responds synergistically to two effectors, benzoate and cis,cis-muconate, to activate expression of the benABCDE operon which is involved in benzoate catabolism, while CatM responses only to muconate. BenM and CatM share high protein sequence identity and bind to the operator-promoter regions that have similar DNA sequences. In Pseudomonas species, phenolic compounds are converted by different enzymes to central intermediates, such as protocatechuate and catechols. Generally, unsubstituted compounds, such as benzoate, are metabolized by an ortho-cleavage pathway. The catBCA operon encodes three enzymes of the ortho-pathway required for benzoate catabolism: muconate lactonizing enzyme I, muconolactone isomerase, and catechol 1,2-dioxygenase. CatR normally responds to benzoate and cis,cis-muconate, an inducer molecule, to activate transcription of the catBCA operon, whose gene products convert benzoate to catechol. 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: 176136  Cd Length: 203  Bit Score: 41.44  E-value: 2.13e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 112 EFHQQYPNVTYSLVE-NGGKMIEhQLINDEIDIGITTLPVDQSIFHSLPLYQEELKLVLNKEHRLAQY-EQVKMSMLKDE 189
Cdd:cd08445   22 RFRQAAPDVEIELIEmTTVQQIE-ALKEGRIDVGFGRLRIEDPAIRRIVLREEPLVVALPAGHPLAQEkAPLTLAQLADE 100

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 518299807 190 DFILFNEDFYLN--DKIIEAAKNAGYIPNTISKISQWNFIENLLNAHLGVSILPENIVGLLDSDFKNITLEDPG 261
Cdd:cd08445  101 PLILYPASPRPSfaDQVLSLFRDHGLRPRVIQEVRELQTALGLVAAGEGVTLVPASVQRLRRDDVVYRPLLDPD 174
PRK15243 PRK15243
virulence genes transcriptional activator SpvR;
4-82 5.19e-04

virulence genes transcriptional activator SpvR;


Pssm-ID: 185155 [Multi-domain]  Cd Length: 297  Bit Score: 40.81  E-value: 5.19e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 518299807   4 KHMKYFVEVVNQQGMTNASKSLYIAQPTISKAIKDIENELNMPLFDRSKRQLVLTDAGSVFYYKSKEILSLYKDLPKEI 82
Cdd:PRK15243   7 KKLKIFITLMETGSFSIATSVLYITRTPLSRVISDLERELKQRLFIRKNGTLIPTEFAQTIYRKVKSHYIFLHALEQEI 85
PBP2_CrgA cd08478
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains ...
 109-210 5.88e-04

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


Pssm-ID: 176167 [Multi-domain]  Cd Length: 199  Bit Score: 40.01  E-value: 5.88e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 109 ILGEFHQQYPNVTYSLVENGGkMIEhqLINDEIDIGITTLPVDQSIFHSLPLYQEELKLVLNKEHrLAQY-EQVKMSMLK 187
Cdd:cd08478   21 LIAKFRERYPDIELELVSNEG-IID--LIERKTDVAIRIGELTDSTLHARPLGKSRLRILASPDY-LARHgTPQSIEDLA 96

                         90       100
                 ....*....|....*....|...
gi 518299807 188 DEDFILFNEDFYLNDKIIEAAKN 210
Cdd:cd08478   97 QHQLLGFTEPASLNTWPIKDADG 119
PBP2_LeuO cd08466
The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an ...
 131-206 1.09e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an activator of leucine synthesis operon, contains the type 2 periplasmic binding fold; LeuO, a LysR-type transcriptional regulator, was originally identified as an activator of the leucine synthesis operon (leuABCD). Subsequently, LeuO was found to be not a specific regulator of the leu gene but a global regulator of unrelated various genes. LeuO activates bglGFB (utilization of beta-D-glucoside) and represses cadCBA (lysine decarboxylation) and dsrA (encoding a regulatory small RNA for translational control of rpoS and hns). LeuO also regulates the yjjQ-bglJ operon which coding for a LuxR-type transcription factor. In Salmonella enterica serovar Typhi, LeuO is a positive regulator of ompS1 (encoding an outer membrane), ompS2 (encoding a pathogenicity determinant), and assT, while LeuO represses the expression of OmpX and Tpx. Both osmS1 and osmS2 influence virulence in the mouse model of Salmonella. In Vibrio cholerae, LeuO is involved in control of biofilm formation and in the stringent response. 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: 176155 [Multi-domain]  Cd Length: 200  Bit Score: 39.16  E-value: 1.09e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518299807 131 MIEHQLINDEIDIGITTLPVDQSIFHSLPLYQEELKLVLNKEH-------RLAQYEQVKMSMLKDEDFILFNEDFYLNDK 203
Cdd:cd08466   40 DLFEDLRLQEVDLVIDYVPFRDPSFKSELLFEDELVCVARKDHpriqgslSLEQYLAEKHVVLSLRRGNLSALDLLTEEV 119


                 ...
gi 518299807 204 IIE 206
Cdd:cd08466  120 LPQ 122
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH