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Conserved domains on  [gi|520793718|ref|WP_020292271|]
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LysR family transcriptional regulator [Pseudomonas sp. CFII64]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 11426483)

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

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
22-316 1.44e-47

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 160.42  E-value: 1.44e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718  22 LDWNLLRTFLVIGQEGSISRAAARLHLSQPAISQALKRLEEQLASELVVRRGPRITLSKAGEEVMQIAADLYGTVSRLGP 101
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 102 ALDAPAESVTGKIRLLSISRIQSRSYDDFLAQFHTEFPQVELEIDVLRSSDVISALLQKTASFGLSLCRTPQPRLEQRVM 181
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 182 LEQRYAFFCGKRHRLFGRKNLalsdlqsenfvsftsdqiggnlspltvfrdqqgftgrivasSPSLDEILRLVGAGYGIG 261
Cdd:COG0583  161 GEERLVLVASPDHPLARRAPL-----------------------------------------VNSLEALLAAVAAGLGIA 199

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 520793718 262 CLPEHIVAADVQADDIWRLPPWEGVSDVNVYLLWNREQKMTRAESVFLERFQQML 316
Cdd:COG0583  200 LLPRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREAL 254
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
22-316 1.44e-47

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 160.42  E-value: 1.44e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718  22 LDWNLLRTFLVIGQEGSISRAAARLHLSQPAISQALKRLEEQLASELVVRRGPRITLSKAGEEVMQIAADLYGTVSRLGP 101
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 102 ALDAPAESVTGKIRLLSISRIQSRSYDDFLAQFHTEFPQVELEIDVLRSSDVISALLQKTASFGLSLCRTPQPRLEQRVM 181
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 182 LEQRYAFFCGKRHRLFGRKNLalsdlqsenfvsftsdqiggnlspltvfrdqqgftgrivasSPSLDEILRLVGAGYGIG 261
Cdd:COG0583  161 GEERLVLVASPDHPLARRAPL-----------------------------------------VNSLEALLAAVAAGLGIA 199

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 520793718 262 CLPEHIVAADVQADDIWRLPPWEGVSDVNVYLLWNREQKMTRAESVFLERFQQML 316
Cdd:COG0583  200 LLPRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREAL 254
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 129-310 4.60e-27

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: 104.99  E-value: 4.60e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 129 DFLAQFHTEFPQVELEIDVLRSSDVISALLQKTASFGLSLCRTPQPRLEQRVMLEQRYAFFCGKRHRLFGRKNLALSDLQ 208
Cdd:cd05466   17 PLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPPDHPLAKRKSVTLADLA 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 209 SENFVSFTSDQIGGNLSpLTVFRdQQGFTGRIVASSPSLDEILRLVGAGYGIGCLPEHIVaADVQADDIWRLPPWEGVSD 288
Cdd:cd05466   97 DEPLILFERGSGLRRLL-DRAFA-EAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAV-EELADGGLVVLPLEDPPLS 173

                        170       180
                 ....*....|....*....|..
gi 520793718 289 VNVYLLWNREQKMTRAESVFLE 310
Cdd:cd05466  174 RTIGLVWRKGRYLSPAARAFLE 195
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 131-316 3.09e-25

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: 100.44  E-value: 3.09e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718  131 LAQFHTEFPQVELEIDVLRSSDVISALLQKTASFGLSLCRTPQPRLEQRVMLEQRYAFFCGKRHRLFGRKNLALSDLQSE 210
Cdd:pfam03466  21 LARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVAPPDHPLARGEPVSLEDLADE 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718  211 NFVSFTSDqiGGNLSPLTVFRDQQGFTGRIVASSPSLDEILRLVGAGYGIGCLPEHIVAADVQADDI--WRLPPWEgvSD 288
Cdd:pfam03466 101 PLILLPPG--SGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARELADGRLvaLPLPEPP--LP 176

                         170       180
                  ....*....|....*....|....*...
gi 520793718  289 VNVYLLWNREQKMTRAESVFLERFQQML 316
Cdd:pfam03466 177 RELYLVWRKGRPLSPAVRAFIEFLREAL 204
PRK09986 PRK09986
LysR family transcriptional regulator;
18-299 1.27e-22

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 95.56  E-value: 1.27e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718  18 LNDRLDWNLLRTFLVIGQEGSISRAAARLHLSQPAISQALKRLEEQLASELVVRRGPRITLSKAGEEVMQIAADLYgtvS 97
Cdd:PRK09986   3 RLYRIDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLL---D 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718  98 RLGPALDAPAESVTGKIRLLSISRIQSRSYDDF---LAQFHTEFPQVELEIDVLRSSDVISALLQKTASFGLSLCRTPQP 174
Cdd:PRK09986  80 NAEQSLARVEQIGRGEAGRIEIGIVGTALWGRLrpaMRHFLKENPNVEWLLRELSPSMQMAALERRELDAGIWRMADLEP 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 175 R--LEQRVMLEQRYAFFCGKRHRLFGRKNLALSDLQSENFVSFTSDQ--IGGNLSPLTVfrdQQGFTGRIVASSPSLDEI 250
Cdd:PRK09986 160 NpgFTSRRLHESAFAVAVPEEHPLASRSSVPLKALRNEYFITLPFVHsdWGKFLQRVCQ---QAGFSPQIIRQVNEPQTV 236

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 520793718 251 LRLVGAGYGIGCLPehivaadvqadDIWRLPPWEGVSDV--------NVYLLWNREQ 299
Cdd:PRK09986 237 LAMVSMGIGITLLP-----------DSYAQIPWPGVVFRplkeripaDLYAVYHPDQ 282
HTH_MARR smart00347
helix_turn_helix multiple antibiotic resistance protein;
20-87 3.27e-03

helix_turn_helix multiple antibiotic resistance protein;


Pssm-ID: 197670 [Multi-domain]  Cd Length: 101  Bit Score: 36.42  E-value: 3.27e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 520793718    20 DRLDWNL--LRTFLVIGQEGSISRA--AARLHLSQPAISQALKRLEEQlasELVVR-------RGPRITLSKAGEEVMQ 87
Cdd:smart00347   4 KPLGLTPtqFLVLRILYEEGPLSVSelAKRLGVSPSTVTRVLDRLEKK---GLVRRepspedrRSVLVSLTEEGRELIE 79
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
22-316 1.44e-47

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 160.42  E-value: 1.44e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718  22 LDWNLLRTFLVIGQEGSISRAAARLHLSQPAISQALKRLEEQLASELVVRRGPRITLSKAGEEVMQIAADLYGTVSRLGP 101
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 102 ALDAPAESVTGKIRLLSISRIQSRSYDDFLAQFHTEFPQVELEIDVLRSSDVISALLQKTASFGLSLCRTPQPRLEQRVM 181
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 182 LEQRYAFFCGKRHRLFGRKNLalsdlqsenfvsftsdqiggnlspltvfrdqqgftgrivasSPSLDEILRLVGAGYGIG 261
Cdd:COG0583  161 GEERLVLVASPDHPLARRAPL-----------------------------------------VNSLEALLAAVAAGLGIA 199

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 520793718 262 CLPEHIVAADVQADDIWRLPPWEGVSDVNVYLLWNREQKMTRAESVFLERFQQML 316
Cdd:COG0583  200 LLPRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREAL 254
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 129-310 4.60e-27

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: 104.99  E-value: 4.60e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 129 DFLAQFHTEFPQVELEIDVLRSSDVISALLQKTASFGLSLCRTPQPRLEQRVMLEQRYAFFCGKRHRLFGRKNLALSDLQ 208
Cdd:cd05466   17 PLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPPDHPLAKRKSVTLADLA 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 209 SENFVSFTSDQIGGNLSpLTVFRdQQGFTGRIVASSPSLDEILRLVGAGYGIGCLPEHIVaADVQADDIWRLPPWEGVSD 288
Cdd:cd05466   97 DEPLILFERGSGLRRLL-DRAFA-EAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAV-EELADGGLVVLPLEDPPLS 173

                        170       180
                 ....*....|....*....|..
gi 520793718 289 VNVYLLWNREQKMTRAESVFLE 310
Cdd:cd05466  174 RTIGLVWRKGRYLSPAARAFLE 195
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 131-316 3.09e-25

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: 100.44  E-value: 3.09e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718  131 LAQFHTEFPQVELEIDVLRSSDVISALLQKTASFGLSLCRTPQPRLEQRVMLEQRYAFFCGKRHRLFGRKNLALSDLQSE 210
Cdd:pfam03466  21 LARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVAPPDHPLARGEPVSLEDLADE 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718  211 NFVSFTSDqiGGNLSPLTVFRDQQGFTGRIVASSPSLDEILRLVGAGYGIGCLPEHIVAADVQADDI--WRLPPWEgvSD 288
Cdd:pfam03466 101 PLILLPPG--SGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARELADGRLvaLPLPEPP--LP 176

                         170       180
                  ....*....|....*....|....*...
gi 520793718  289 VNVYLLWNREQKMTRAESVFLERFQQML 316
Cdd:pfam03466 177 RELYLVWRKGRPLSPAVRAFIEFLREAL 204
PRK09986 PRK09986
LysR family transcriptional regulator;
18-299 1.27e-22

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 95.56  E-value: 1.27e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718  18 LNDRLDWNLLRTFLVIGQEGSISRAAARLHLSQPAISQALKRLEEQLASELVVRRGPRITLSKAGEEVMQIAADLYgtvS 97
Cdd:PRK09986   3 RLYRIDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLL---D 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718  98 RLGPALDAPAESVTGKIRLLSISRIQSRSYDDF---LAQFHTEFPQVELEIDVLRSSDVISALLQKTASFGLSLCRTPQP 174
Cdd:PRK09986  80 NAEQSLARVEQIGRGEAGRIEIGIVGTALWGRLrpaMRHFLKENPNVEWLLRELSPSMQMAALERRELDAGIWRMADLEP 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 175 R--LEQRVMLEQRYAFFCGKRHRLFGRKNLALSDLQSENFVSFTSDQ--IGGNLSPLTVfrdQQGFTGRIVASSPSLDEI 250
Cdd:PRK09986 160 NpgFTSRRLHESAFAVAVPEEHPLASRSSVPLKALRNEYFITLPFVHsdWGKFLQRVCQ---QAGFSPQIIRQVNEPQTV 236

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 520793718 251 LRLVGAGYGIGCLPehivaadvqadDIWRLPPWEGVSDV--------NVYLLWNREQ 299
Cdd:PRK09986 237 LAMVSMGIGITLLP-----------DSYAQIPWPGVVFRplkeripaDLYAVYHPDQ 282
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
24-83 1.31e-19

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 80.89  E-value: 1.31e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718   24 WNLLRTFLVIGQEGSISRAAARLHLSQPAISQALKRLEEQLASELVVRRGPRITLSKAGE 83
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 129-316 2.19e-15

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: 73.31  E-value: 2.19e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 129 DFLAQFHTEFPQVELEIDVLRSSDVISALLQKTASFGLSLCRTPQPRLEQRVMLEQRYAFFCGKRHRLFGRKNLALSDLQ 208
Cdd:cd08414   17 RLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPPPDPPGLASRPLLREPLVVALPADHPLAARESVSLADLA 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 209 SENFVSFTSDQIGGNLSPLTVFRDQQGFTGRIVASSPSLDEILRLVGAGYGIGCLPEhiVAADVQADDI------WRLPP 282
Cdd:cd08414   97 DEPFVLFPREPGPGLYDQILALCRRAGFTPRIVQEASDLQTLLALVAAGLGVALVPA--SVARLQRPGVvyrplaDPPPR 174

                        170       180       190
                 ....*....|....*....|....*....|....
gi 520793718 283 WEgvsdvnVYLLWNReqkmtRAESVFLERFQQML 316
Cdd:cd08414  175 SE------LALAWRR-----DNASPALRAFLELA 197
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 27-267 2.70e-15

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 74.81  E-value: 2.70e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718  27 LRTFLVIGQEGSISRAAARLHLSQPAISQALKRLEEQLASELVVRRGPRITLSKAGEEVMQIAAdlygtvsrlgpALDAP 106
Cdd:PRK09906   6 LRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDAR-----------AILEQ 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 107 AESVTGKIRLLSISRIQSR----------SYDDFLAQFHTEFPQVELEIDVLRSSDVISALLQKTASFGLSLCRTPQPRL 176
Cdd:PRK09906  75 AEKAKLRARKIVQEDRQLTigfvpsaevnLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPVYSDEI 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 177 EQRVMLEQRYAFFCGKRHRLFGRKNLALSDLQSENFVSFTSDQIGGNLSPLTVFRDQQGFTGRIVASSPSLDEILRLVGA 256
Cdd:PRK09906 155 DYLELLDEPLVVVLPVDHPLAHEKEITAAQLDGVNFISTDPAYSGSLAPIIKAWFAQHNSQPNIVQVATNILVTMNLVGM 234

                        250
                 ....*....|.
gi 520793718 257 GYGIGCLPEHI 267
Cdd:PRK09906 235 GLGCTIIPGYM 245
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 129-311 1.42e-14

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: 71.09  E-value: 1.42e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 129 DFLAQFHTEFPQVELEIDVLRSSDVISALLQKT--ASFgLSLCRTPQPRLEQRVMLEQRYAFFCGKRHRLFGRKNLALSD 206
Cdd:cd08436   17 ELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRldLAF-VGLPERRPPGLASRELAREPLVAVVAPDHPLAGRRRVALAD 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 207 LQSENFVSFTSdqiGGNLSPLT--VFRDqQGFTGRIVASSPSLDEILRLVGAGYGIGCLPEHIVAA--DVQADDIWRLPP 282
Cdd:cd08436   96 LADEPFVDFPP---GTGARRQVdrAFAA-AGVRRRVAFEVSDVDLLLDLVARGLGVALLPASVAARlpGLAALPLEPAPR 171

                        170       180
                 ....*....|....*....|....*....
gi 520793718 283 WEgvsdvnVYLLWnREQKMTRAESVFLER 311
Cdd:cd08436  172 RR------LYLAW-SAPPPSPAARAFLEL 193
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 27-271 6.46e-14

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 70.76  E-value: 6.46e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718  27 LRTFLVIGQEGSISRAAARLHLSQPAISQALKRLEEQLASELVVRRGPRITLSKAGEEVMQIAadlygtvSRLGPALDAP 106
Cdd:PRK11242   6 IRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYA-------RRALQDLEAG 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 107 AESV-------TGKIRLLSISRIQSRSYDDFLAQFHTEFPQVELEIDVLRSSDVISALLQKTASFGLSLCRTPQPRLEQR 179
Cdd:PRK11242  79 RRAIhdvadlsRGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMSQERIEALLADDELDVGIAFAPVHSPEIEAQ 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 180 VMLEQRYAFFCGKRHRLFG-RKNLALSDLQSENFVSFTSD-----QIGGnlspltVFRdQQGFTGRIVASSPSLDEILRL 253
Cdd:PRK11242 159 PLFTETLALVVGRHHPLAArRKALTLDELADEPLVLLSAEfatreQIDR------YFR-RHGVTPRVAIEANSISAVLEI 231

                        250
                 ....*....|....*...
gi 520793718 254 VGAGYGIGCLPEHIVAAD 271
Cdd:PRK11242 232 VRRGRLATLLPAAIAREH 249
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 129-310 7.48e-14

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: 69.06  E-value: 7.48e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 129 DFLAQFHTEFPQVELEIDVLRSSDVISALLQKTASFGLSLCRTPQPRLEQRVMLEQRYAFFCGKRHRLFGRKNLALSDLQ 208
Cdd:cd08420   17 RLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLVEGPVDHPDLIVEPFAEDELVLVVPPDHPLAGRKEVTAEELA 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 209 SENFV-----SFTSDQI-------GGNLSPLtvfrdqqgftgRIVASSPSLDEILRLVGAGYGIGCLPEHIVAADVQADD 276
Cdd:cd08420   97 AEPWIlrepgSGTREVFeralaeaGLDGLDL-----------NIVMELGSTEAIKEAVEAGLGISILSRLAVRKELELGR 165

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 520793718 277 IWRLPpwegVSDVNV----YLLWNREQKMTRAESVFLE 310
Cdd:cd08420  166 LVALP----VEGLRLtrpfSLIYHKDKYLSPAAEAFLE 199
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
22-87 1.55e-13

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 69.61  E-value: 1.55e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 520793718  22 LDWNLLRTFLVIGQEGSISRAAARLHLSQPAISQALKRLEEQLASELVVRRGPrITLSKAGEEVMQ 87
Cdd:PRK13348   2 LDYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRGRP-CRPTPAGQRLLR 66
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 27-310 7.19e-13

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 67.79  E-value: 7.19e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718  27 LRTFLVIGQEGSISRAAARLHLSQPAISQALKRLEEQLASELVVRRGPRITLSKAGEEVMQIAADLygtvsrlgpaLDAP 106
Cdd:PRK10837   8 LEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALAL----------LEQA 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 107 AE------SVTGKIRLLSISRIQSRSYDDFLAQFHTEFPQVELEIDVLRSSDVISALLQKTASFGL--SLCRTP----QP 174
Cdd:PRK10837  78 VEieqlfrEDNGALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNSQDVINAVLDFRVDIGLieGPCHSPelisEP 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 175 RLEQRVMLeqryafFCGKRHRLFGRKnLALSDLQSENFV-----SFTSDQIGGNL-SPLTVFrdqqgftgRIVASSPSLD 248
Cdd:PRK10837 158 WLEDELVV------FAAPDSPLARGP-VTLEQLAAAPWIlrergSGTREIVDYLLlSHLPRF--------ELAMELGNSE 222

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 520793718 249 EILRLVGAGYGIGCLPEHIVAADVQADDIWRLPPWEGVSDVNVYLLWNREQKMTRAESVFLE 310
Cdd:PRK10837 223 AIKHAVRHGLGISCLSRRVIADQLQAGTLVEVAVPLPRLMRTLYRIHHRQKHLSNALQRFLS 284
PBP2_LTTR_like_1 cd08421
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 131-283 1.01e-12

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: 1.01e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 131 LAQFHTEFPQVELEIDVLRSSDVISALLQKTASFGLSLCRTPQPRLEQRVMLEQRYAFFCGKRHRLFGRKNLALSDLQSE 210
Cdd:cd08421   19 LASFLAAHPDVRIDLEERLSADIVRAVAEGRADLGIVAGNVDAAGLETRPYRTDRLVVVVPRDHPLAGRASVAFADTLDH 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 211 NFVSFTSDqiggnlSPLTVFRDQQ----GFTGRIVASSPSLDEILRLVGAGYGIGCLPEHIVAADVQADDIWRLP---PW 283
Cdd:cd08421   99 DFVGLPAG------SALHTFLREAaarlGRRLRLRVQVSSFDAVCRMVAAGLGIGIVPESAARRYARALGLRVVPlddAW 172
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
27-268 1.82e-12

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 66.96  E-value: 1.82e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718  27 LRTFLVIGQEGSISRAAARLHLSQPAISQALKRLEEQLASELVVRRGPRITLSKAGEEVMQIAADLYGTVSRlgpALDAP 106
Cdd:PRK15421   7 LKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQ---ALQAC 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 107 AESVTGKIRLlsisRIQSRSYDDFLA----QFHTEFPQVELEIDVLRSSDVISALLQKTASFGLSLCRTPQPRLEQRVML 182
Cdd:PRK15421  84 NEPQQTRLRI----AIECHSCIQWLTpaleNFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLHYSPMF 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 183 EQRYAFFCGKRHRLFGRKNLALSDLQSENFVSFTSDQiggnlSPLTVFRDQQGFTGrivaSSPSLDEI------LRLVGA 256
Cdd:PRK15421 160 DYEVRLVLAPDHPLAAKTRITPEDLASETLLIYPVQR-----SRLDVWRHFLQPAG----VSPSLKSVdntlllIQMVAA 230

                        250
                 ....*....|..
gi 520793718 257 GYGIGCLPEHIV 268
Cdd:PRK15421 231 RMGIAALPHWVV 242
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
21-87 3.52e-11

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 62.87  E-value: 3.52e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 520793718  21 RLDWNLLRTFLVIGQEGSISRAAARLHLSQPAISQALKRLEEQLASELVVRRGPrITLSKAGEEVMQ 87
Cdd:PRK03635   1 MLDYKQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVRTQP-CRPTEAGQRLLR 66
PRK12680 PRK12680
LysR family transcriptional regulator;
27-281 1.51e-10

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 61.18  E-value: 1.51e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718  27 LRTFLVIGQ-EGSISRAAARLHLSQPAISQALKRLEEQLASELVVRRGPRI-TLSKAGEEVMQIAADLYGTVSRLGPALD 104
Cdd:PRK12680   6 LRYLVAIADaELNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLeSVTPAGVEVIERARAVLSEANNIRTYAA 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 105 APAESVTGKIrLLSISRIQSR-SYDDFLAQFHTEFPQVELEIDVLRSSDVISALLQKTASFGLSLCRTPQPRLEQRVMLE 183
Cdd:PRK12680  86 NQRRESQGQL-TLTTTHTQARfVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVSTAGGEPSAGIAVPLY 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 184 Q-RYAFFCGKRHRL-FGRKNLALSDLQSENFVSFTSDQIGGnlSPLTVFRDQQGFTGRIVASSPSLDEILRLVGAGYGIG 261
Cdd:PRK12680 165 RwRRLVVVPRGHALdTPRRAPDMAALAEHPLISYESSTRPG--SSLQRAFAQLGLEPSIALTALDADLIKTYVRAGLGVG 242

                        250       260
                 ....*....|....*....|
gi 520793718 262 CLPEHIVAADVQADDIWRLP 281
Cdd:PRK12680 243 LLAEMAVNANDEDLRAWPAP 262
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 39-281 2.47e-10

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 60.39  E-value: 2.47e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718  39 ISRAAARLHLSQPAISQALKRLEEQLASELVVRRGPRIT-LSKAGEEVMQIA----ADLyGTVSRLGPALDAPaESVTgk 113
Cdd:PRK12682  19 LTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKgLTEPGKAVLDVIerilREV-GNIKRIGDDFSNQ-DSGT-- 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 114 irlLSI--SRIQSR-SYDDFLAQFHTEFPQVELEIDVLRSSDVISALLQKTASFGL---------SLCRTPQPRLEQRVM 181
Cdd:PRK12682  95 ---LTIatTHTQARyVLPRVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGIatesladdpDLATLPCYDWQHAVI 171

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 182 LEqryaffcgKRHRLFGRKNLALSDLQSENFVSFTSdQIGGNLSPLTVFRDqQGFTGRIVASSPSLDEILRLVGAGYGIG 261
Cdd:PRK12682 172 VP--------PDHPLAQEERITLEDLAEYPLITYHP-GFTGRSRIDRAFAA-AGLQPDIVLEAIDSDVIKTYVRLGLGVG 241

                        250       260
                 ....*....|....*....|.
gi 520793718 262 CLPEhiVAADVQAD-DIWRLP 281
Cdd:PRK12682 242 IVAE--MAYRPDRDgDLVALP 260
PRK09791 PRK09791
LysR family transcriptional regulator;
27-302 3.95e-10

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 59.78  E-value: 3.95e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718  27 LRTFLVIGQEGSIsRAAAR-LHLSQPAISQALKRLEEQLASELVVRRGPRITLSKAGEEVMQIAADLYGTV--------S 97
Cdd:PRK09791  10 IRAFVEVARQGSI-RGASRmLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELraaqedirQ 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718  98 RLGPAldapaesvTGKIRLLSISRIQSRSYDDFLAQFHTEFPQVELEIDVLRSSDVISALLQKTASFGLSlCRTPQP--- 174
Cdd:PRK09791  89 RQGQL--------AGQINIGMGASIARSLMPAVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDFTIN-TYYQGPydh 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 175 RLEQRVMLEQRYAFFCGKRHRLFGRKNLAlsDLQSENFVSFTSDqiGGNLSPLTVFRDQQGFTGRIVASSPSLDEILRLV 254
Cdd:PRK09791 160 EFTFEKLLEKQFAVFCRPGHPAIGARSLK--QLLDYSWTMPTPH--GSYYKQLSELLDDQAQTPQVGVVCETFSACISLV 235

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*...
gi 520793718 255 GAGYGIGCLPEHIVAADVQADDIWRLPPWEGVSDVNVYLLWNREQKMT 302
Cdd:PRK09791 236 AKSDFLSILPEEMGCDPLHGQGLVMLPVSEILPKATYYLIQRRDTRQT 283
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 129-310 9.57e-10

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: 57.16  E-value: 9.57e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 129 DFLAQFHTEFPQV--ELEIDVlrSSDVISALLQKTASFGLSLCRTPQPRLEQRVMLEQRYAFFCGKRHRLFGRKNLALSD 206
Cdd:cd08434   17 DLIRAFRKEYPNVtfELHQGS--TDELLDDLKNGELDLALCSPVPDEPDIEWIPLFTEELVLVVPKDHPLAGRDSVDLAE 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 207 LQSENFVSFtSDQIGGNLSPLTVFRdQQGFTGRIVASSPSLDEILRLVGAGYGIGCLPEhivAADVQADDIWRLPpwegV 286
Cdd:cd08434   95 LADEPFVLL-SPGFGLRPIVDELCA-AAGFTPKIAFEGEEDSTIAGLVAAGLGVAILPE---MTLLNPPGVKKIP----I 165

                        170       180
                 ....*....|....*....|....*...
gi 520793718 287 SDVN----VYLLWNREQKMTRAESVFLE 310
Cdd:cd08434  166 KDPDaertIGLAWLKDRYLSPAARRFKD 193
rbcR CHL00180
LysR transcriptional regulator; Provisional
 27-89 2.91e-09

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 57.34  E-value: 2.91e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 520793718  27 LRTFLVIGQEGSISRAAARLHLSQPAISQALKRLEEQLASELVVRRGPRITLSKAGEEVMQIA 89
Cdd:CHL00180  10 LRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYG 72
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 131-310 2.94e-09

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: 56.03  E-value: 2.94e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 131 LAQFHTEFPQVELEIDVLRSSDVISALLQKTASFGLSLCRTPQPRLEQRVMLEQRYAFFCGKRHRLFGRKNLALSDLQSE 210
Cdd:cd08438   19 LAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVLPVDEEEFDSQPLCNEPLVAVLPRGHPLAGRKTVSLADLADE 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 211 NFVSFTSD-----QIggnlspLTVFRdQQGFTGRIVASSPSLDEILRLVGAGYGIGCLPEHI---------VAADVQADD 276
Cdd:cd08438   99 PFILFNEDfalhdRI------IDACQ-QAGFTPNIAARSSQWDFIAELVAAGLGVALLPRSIaqrldnagvKVIPLTDPD 171

                        170       180       190
                 ....*....|....*....|....*....|....
gi 520793718 277 IwrlpPWEGVsdvnvyLLWNREQKMTRAESVFLE 310
Cdd:cd08438  172 L----RWQLA------LIWRKGRYLSHAARAWLA 195
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 129-270 3.16e-09

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: 55.99  E-value: 3.16e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 129 DFLAQFHTEFPQVELEIDVLRSSDVISALLQKTASFGLSLCRTPQPRLEQRVMLEQRYAFFCGKRHRLFGRKNLALSDLQ 208
Cdd:cd08440   17 PVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEADPDLEFEPLLRDPFVLVCPKDHPLARRRSVTWAELA 96

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 520793718 209 SENFVSFTSDqiggnlSPLTVFRDQQGFTGRIVASSP----SLDEILRLVGAGYGIGCLPEHIVAA 270
Cdd:cd08440   97 GYPLIALGRG------SGVRALIDRALAAAGLTLRPAyevsHMSTALGMVAAGLGVAVLPALALPL 156
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 35-270 5.82e-09

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 56.20  E-value: 5.82e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718  35 QEGSISRAAARLHLSQPAISQALKRLEEQLASELVVRRGPRIT-LSKAGEEVMQIAADLY---GTVSRLGpalDAPAESV 110
Cdd:PRK12683  15 QNFNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTgLTEPGKELLQIVERMLldaENLRRLA---EQFADRD 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 111 TGKIrLLSISRIQSR-SYDDFLAQFHTEFPQVELEIDVLRSSDVISALLQKTASFGLS---LCRTPqprleQRVMLEQ-- 184
Cdd:PRK12683  92 SGHL-TVATTHTQARyALPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGIAteaLDREP-----DLVSFPYys 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 185 -RYAFFCGKRHRLFGRKNLALSDLQSENFVSFtsdqiggnlspltvfrdQQGFTGR---------------IVASSPSLD 248
Cdd:PRK12683 166 wHHVVVVPKGHPLTGRENLTLEAIAEYPIITY-----------------DQGFTGRsridqafaeaglvpdIVLTALDAD 228

                        250       260
                 ....*....|....*....|..
gi 520793718 249 EILRLVGAGYGIGclpehIVAA 270
Cdd:PRK12683 229 VIKTYVELGMGVG-----IVAA 245
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
21-94 1.02e-08

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 55.58  E-value: 1.02e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 520793718  21 RLDWNLLRTFLVIGQEGSISRAAARLHLSQPAISQALKRLEEQLASELVVRRGPRITLSKAGEEVMQIAADLYG 94
Cdd:PRK10094   1 MFDPETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLS 74
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 130-310 1.52e-08

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: 53.72  E-value: 1.52e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 130 FLAQFHTEFPQVELEIDVLRSSDVISALLQKTASFGLSLCRTPQPRLEQRVMLEQRYAFFCGKRHRLFGRKNLALSDLQS 209
Cdd:cd08415   18 AIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPLDHPGLESEPLASGRAVCVLPPGHPLARKDVVTPADLAG 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 210 ENFVSftsdqiggnLSPLTVFRDQ-------QGFTGRIVASSPSLDEILRLVGAGYGIGcLPEHIVAADVQADDIwRLPP 282
Cdd:cd08415   98 EPLIS---------LGRGDPLRQRvdaaferAGVEPRIVIETQLSHTACALVAAGLGVA-IVDPLTAAGYAGAGL-VVRP 166

                        170       180
                 ....*....|....*....|....*...
gi 520793718 283 WEGVSDVNVYLLWNREQKMTRAESVFLE 310
Cdd:cd08415  167 FRPAIPFEFALVRPAGRPLSRLAQAFID 194
PBP2_LTTR_aromatics_like_2 cd08448
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 128-265 4.56e-08

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: 52.27  E-value: 4.56e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 128 DDFLAQFHTEFPQVELEIDVLRSSDVISALLQKTASFGLSLCRTPQPRLEQRVMLEQryAFFC--GKRHRLFGRKNLALS 205
Cdd:cd08448   16 PRILRAFRAEYPGIEVALHEMSSAEQIEALLRGELDLGFVHSRRLPAGLSARLLHRE--PFVCclPAGHPLAARRRIDLR 93

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 206 DLQSENFVSFTSDQIGGNLSPLTVFRDQQGFTGRIVASSPSLDEILRLVGAGYGIGCLPE 265
Cdd:cd08448   94 ELAGEPFVLFSREVSPDYYDQIIALCMDAGFHPKIRHEVRHWLTVVALVAAGMGVALVPR 153
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 131-312 4.88e-08

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: 52.55  E-value: 4.88e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 131 LAQFHTEFPQVELEIDVLRSSDVISALLQKTASFGLSLCRTPQPRLEQRVMLE-QRYAFFcGKRHRLFGRKNLALSDLQS 209
Cdd:cd08412   19 LRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALTYDLDLPEDIAFEPLARlPPYVWL-PADHPLAGKDEVSLADLAA 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 210 ENFVSFTSDQIGGNLspLTVFRdQQGFTGRIVASSPSLDEILRLVGAGYGIGCLPEHiVAADVQAD--DIWRLPPWEGVS 287
Cdd:cd08412   98 EPLILLDLPHSREYF--LSLFA-AAGLTPRIAYRTSSFEAVRSLVANGLGYSLLNDR-PYRPWSYDgkRLVRRPLADPVP 173

                        170       180
                 ....*....|....*....|....*
gi 520793718 288 DVNVYLLWNREQKMTRAESVFLERF 312
Cdd:cd08412  174 PLRLGLAWRRGARLTRAARAFVDFA 198
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 131-281 7.67e-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: 51.83  E-value: 7.67e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 131 LAQFHTEFPQVELE---------IDVLRSSDVISALLQKTASFGLSLCrtpqPRLEQRVMLEQRYAFFCGKRHRLFGRKN 201
Cdd:cd08423   19 LAALRARHPGLEVRlreaeppesLDALRAGELDLAVVFDYPVTPPPDD----PGLTRVPLLDDPLDLVLPADHPLAGREE 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 202 LALSDLQSENFVSFTSDQIGGNLspLTVFRDQQGFTGRIVASSPSLDEILRLVGAGYGIGCLPEhiVAADVQADDIWRLP 281
Cdd:cd08423   95 VALADLADEPWIAGCPGSPCHRW--LVRACRAAGFTPRIAHEADDYATVLALVAAGLGVALVPR--LALGARPPGVVVRP 170
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
32-145 1.85e-07

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 51.90  E-value: 1.85e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718  32 VIGQEGSISRAAARLHLSQPAISQALKRLEEQLASELVVRRGPRIT-LSKAGEEVMQIAADLYGTVSRLGPALDAPAESV 110
Cdd:PRK12684  12 AVRQNFNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRgLTEPGRIILASVERILQEVENLKRVGKEFAAQD 91

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 520793718 111 TGKirlLSI--SRIQSR-SYDDFLAQFHTEFPQVELEI 145
Cdd:PRK12684  92 QGN---LTIatTHTQARyALPAAIKEFKKRYPKVRLSI 126
PBP2_XapR cd08449
The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved ...
 131-265 2.79e-07

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: 49.96  E-value: 2.79e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 131 LAQFHTEFPQVELEIDVLRSSDVISALLQKTASFGLSLC-RTPQ-PRLEQRVMLEQRYAFFCGKRHRLFGRKNLALSDLQ 208
Cdd:cd08449   19 LRRFKRQYPNVTVRFHELSPEAQKAALLSKRIDLGFVRFaDTLNdPPLASELLWREPMVVALPEEHPLAGRKSLTLADLR 98

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 520793718 209 SENFVSFTSDQIGgnlspltvFRD-------QQGFTGRIVASSPSLDEILRLVGAGYGIGCLPE 265
Cdd:cd08449   99 DEPFVFLRLANSR--------FADflincclQAGFTPQITQEVVEPQTLMALVAAGFGVALVPE 154
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 129-297 3.96e-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: 49.91  E-value: 3.96e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 129 DFLAQFHTEFPQVELEIDVLRSSDVISALLQKTASFGLSLCRTPQPRLEQRVMLEQRYAFFCGKRHRLFGRkNLALSDLQ 208
Cdd:cd08417   17 PLLARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELPPGLRSQPLFEDRFVCVARKDHPLAGG-PLTLEDYL 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 209 SENFVSFTSDqiGGNLSPLTVFRDQQGFTGRIVASSPSLDEILRLVGAGYGIGCLPEHIVAADVQADDIWRLPPWEGVSD 288
Cdd:cd08417   96 AAPHVLVSPR--GRGHGLVDDALAELGLSRRVALTVPHFLAAPALVAGTDLIATVPRRLAEALAERLGLRVLPLPFELPP 173


                 ....*....
gi 520793718 289 VNVYLLWNR 297
Cdd:cd08417  174 FTVSLYWHP 182
cbl PRK12679
HTH-type transcriptional regulator Cbl;
35-265 5.88e-07

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 50.19  E-value: 5.88e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718  35 QEGSISRAAAR-----------LHLSQPAISQALKRLEEQLASELVVRRGPRIT-LSKAGEEVMQIAA---DLYGTVSRL 99
Cdd:PRK12679   4 QQLKIIREAARqdynltevanmLFTSQSGVSRHIRELEDELGIEIFIRRGKRLLgMTEPGKALLVIAErilNEASNVRRL 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 100 GpalDAPAESVTGKIRlLSISRIQSR-SYDDFLAQFHTEFPQVELEIDVLRSSDVISALLQKTASFGLSLCR-TPQPRLE 177
Cdd:PRK12679  84 A---DLFTNDTSGVLT-IATTHTQARySLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASERlSNDPQLV 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 178 QRVMLEQRYAFFCGKRHRLFGRKNLALSDLQSenfvsftsdqiggnlSPLTVFRdqQGFTGR---------------IVA 242
Cdd:PRK12679 160 AFPWFRWHHSLLVPHDHPLTQITPLTLESIAK---------------WPLITYR--QGITGRsriddafarkglladIVL 222

                        250       260
                 ....*....|....*....|...
gi 520793718 243 SSPSLDEILRLVGAGYGIGCLPE 265
Cdd:PRK12679 223 SAQDSDVIKTYVALGLGIGLVAE 245
PRK10341 PRK10341
transcriptional regulator TdcA;
27-310 6.63e-07

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 50.25  E-value: 6.63e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718  27 LRTFLVIGQEGSISRAAARLHLSQPAISQALKRLEEQLASELVVRRGPRITLSKAGEEVMQIAADLYGTVSRLGPALDAP 106
Cdd:PRK10341  12 LVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEINGM 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 107 AESVTGKIRLLSISRIQSRSYDDFLAQFHTEFPQVELEIDVLRSSDVISALLQKTASFGL-SLCRTPQPR-LEQRVMLEQ 184
Cdd:PRK10341  92 SSEAVVDVSFGFPSLIGFTFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIgTLSNEMKLQdLHVEPLFES 171

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 185 RYAFFCGKRHRLFGRKNLAlsDLQSENFVSFTSDQigGNLSPLTVFRDQQGFTGRIVASSPSLDEILRLVGAGYGIGCLP 264
Cdd:PRK10341 172 EFVLVASKSRTCTGTTTLE--SLKNEQWVLPQTNM--GYYSELLTTLQRNGISIENIVKTDSVVTIYNLVLNADFLTVIP 247

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*.
gi 520793718 265 EHIvAADVQADDIWRLPPWEGVSDVNVYLLWNREQKMTRAESVFLE 310
Cdd:PRK10341 248 CDM-TSPFGSNQFITIPIEETLPVAQYAAVWSKNYRIKKAASVLVE 292
leuO PRK09508
leucine transcriptional activator; Reviewed
 23-73 8.02e-07

leucine transcriptional activator; Reviewed


Pssm-ID: 181918 [Multi-domain]  Cd Length: 314  Bit Score: 50.02  E-value: 8.02e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 520793718  23 DWNLLRTFLVIGQEGSISRAAARLHLSQPAISQALKRLEEQLASELVVRRG 73
Cdd:PRK09508  23 DLNLLTVFDAVMQEQNITRAAHNLGMSQPAVSNAVARLKVMFNDELFVRYG 73
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
19-85 8.58e-07

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 49.62  E-value: 8.58e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718  19 NDRLD-WNL--LRTFLVIGQEGSISRAAARLHLSQPAISQALKRLEEQLASELVVRRGPRITLSKAGEEV 85
Cdd:PRK10086   8 NRLLNgWQLskLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRV 77
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 22-82 8.62e-07

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 49.64  E-value: 8.62e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 520793718  22 LDWNLLRTFLVIGQEGSISRAAARLHLSQPAISQALKRLEEQLASELVVRRGPRITLSKAG 82
Cdd:PRK15092  11 LDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHG 71
PBP2_AlsR cd08452
The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which ...
 116-264 9.88e-07

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: 48.65  E-value: 9.88e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 116 LLSISRIQSRSYD---DFLAQFHTEFPQVELEIDVLRSSDVISALLQKTASFGLSLCRTPQPRLEQRVMLEQRYAFFCGK 192
Cdd:cd08452    1 LLVIGFVGAAIYEflpPIVREYRKKFPSVKVELRELSSPDQVEELLKGRIDIGFLHPPIQHTALHIETVQSSPCVLALPK 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 520793718 193 RHRLFGRKNLALSDLQSENFVSFTSDQIGGNLSPLTVFRDQQGFTGRIVASSPSLDEILRLVGAGYGIGCLP 264
Cdd:cd08452   81 QHPLASKEEITIEDLRDEPIITVAREAWPTLYDEIIQLCEQAGFRPKIVQEATEYQTVIGLVSAGIGVTFVP 152
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 38-145 4.59e-06

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 47.53  E-value: 4.59e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718  38 SISRAAARLHLSQPAISQALKRLEEQLASELVVRRGPRITLSKAGEevmqiaaDLYGTVSrlgPALDAPAESvTGKIRL- 116
Cdd:PRK11139  22 SFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQ-------RYFLDIR---EIFDQLAEA-TRKLRAr 90

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 520793718 117 -----LSISRIQSrsyddF--------LAQFHTEFPQVELEI 145
Cdd:PRK11139  91 sakgaLTVSLLPS-----FaiqwlvprLSSFNEAHPDIDVRL 127
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
47-145 6.48e-06

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 46.74  E-value: 6.48e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718  47 HLSQPAISQALKRLEEQLASELVVRRGPRITLSKAGEEVMQIAADLYGTVSRLGPALDAPAESVTGKIRLL-SISRIQSR 125
Cdd:PRK11716   2 HVSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSLFcSVTAAYSH 81

                         90       100
                 ....*....|....*....|
gi 520793718 126 SYdDFLAQFHTEFPQVELEI 145
Cdd:PRK11716  82 LP-PILDRFRAEHPLVEIKL 100
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
22-95 6.92e-06

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 46.93  E-value: 6.92e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 520793718  22 LDWNLLRTFLVIGQEGSISRAAARLHLSQPAISQALKRLEEQLASELVVRRGPRITLSKAGEEVMQIAADLYGT 95
Cdd:PRK03601   1 MDTELLKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYAETLMNT 74
PBP2_HcaR cd08450
The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in ...
 134-267 1.01e-05

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: 45.45  E-value: 1.01e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 134 FHTEFPQVELEIDVLRSSDVISALLQktASFGLSLCRTP--QPRLEQRVMLEQRYAFFCGKRHRLFGRKNLALSDLQSEN 211
Cdd:cd08450   22 LREEHPDLDVELSSLFSPQLAEALMR--GKLDVAFMRPEiqSDGIDYQLLLKEPLIVVLPADHRLAGREKIPPQDLAGEN 99

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 520793718 212 FVSftSDQIGGNLSPLTV-FRDQQGFTGRIVASSPSLDEILRLVGAGYGIGCLPEHI 267
Cdd:cd08450  100 FIS--PAPTAPVLQQVIEnYAAQHNIQPNIIQEADNLLSAMSLVASTLGCALLPLYA 154
MntR COG1321
Mn-dependent transcriptional regulator MntR, DtxR family [Transcription];
25-93 1.62e-05

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


Pssm-ID: 440932 [Multi-domain]  Cd Length: 135  Bit Score: 44.04  E-value: 1.62e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 520793718  25 NLLRTFLVIGQEG---SISRAAARLHLSQPAISQALKRLEEQlasELVVRRGPR-ITLSKAGEEvmqIAADLY 93
Cdd:COG1321   10 DYLKAIYELSEEGgpvRTSDIAERLGVSPPSVTEMLKKLEEK---GLVEYEPYGgITLTEEGRE---LALRIV 76
PBP2_YofA_SoxR_like cd08442
The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, ...
 130-316 2.17e-05

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: 44.52  E-value: 2.17e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 130 FLAQFHTEFPQVELEIDVLRSSDVISALLQKT--ASFglsLCRTPQ-PRLEQRVMLEQRYAFFCGKRHRLFGRknlaLSD 206
Cdd:cd08442   18 LLAAYHARYPKVDLSLSTGTTGALIQAVLEGRldGAF---VAGPVEhPRLEQEPVFQEELVLVSPKGHPPVSR----AED 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 207 LQSENFVSFTS-----DQIGgnlsplTVFRDQQGFTGRIVASSpSLDEILRLVGAGYGIGCLPEHIVAADVQADDIWRLP 281
Cdd:cd08442   91 LAGSTLLAFRAgcsyrRRLE------DWLAEEGVSPGKIMEFG-SYHAILGCVAAGMGIALLPRSVLDSLQGRGSVSIHP 163

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 520793718 282 PWEGVSDVNVYLLWnREQKMTRAesvfLERFQQML 316
Cdd:cd08442  164 LPEPFADVTTWLVW-RKDSFTAA----LQAFLDLL 193
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 27-82 3.23e-05

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 45.06  E-value: 3.23e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 520793718  27 LRTFLVIGQEGSISRAAARLHLSQPAISQALKRLEEQLASELVVR--RGprITLSKAG 82
Cdd:PRK11233   6 LKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRtkRG--VTPTEAG 61
cysB PRK12681
HTH-type transcriptional regulator CysB;
32-96 4.16e-05

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 44.50  E-value: 4.16e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 520793718  32 VIGQEGSISRAAARLHLSQPAISQALKRLEEQLASELVVRRGPRIT-LSKAGEEVMQIAADLYGTV 96
Cdd:PRK12681  12 VVNHNLNVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTqVTPAGEEIIRIAREILSKV 77
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 37-83 6.69e-05

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 43.78  E-value: 6.69e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 520793718  37 GSISRAAARLHLSQPAISQALKRLEEQLASELVVRRGPRITLSKAGE 83
Cdd:PRK11074  17 GSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGE 63
PBP2_Chlorocatechol cd08446
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 130-265 1.09e-04

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: 1.09e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 130 FLAQFHTEFPQVELEIDVLRSSDVISALLQKTASFGLSLCRTPQPRLEQRVMLEQRYAFFCGKRHRLFGRKNLALSDLQS 209
Cdd:cd08446   19 LLRAFLTARPDVTVSLHNMTKDEQIEALRAGRIHIGFGRFYPVEPDIAVENVAQERLYLAVPKSHPLAARPAVSLADLRN 98

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 210 ENFVSFTSdqiGGNLS----PLTVFRdQQGFTGRIVASSPSLDEILRLVGAGYGIGCLPE 265
Cdd:cd08446   99 EPLILFPR---GGRPSfadeVLGLFR-RAGVEPRVAQEVEDVVAALALVAAGFGVCIVPE 154
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 129-281 1.52e-04

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: 41.91  E-value: 1.52e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 129 DFLAQFHTEFPQVELEIDVLRSSDVISALLQKTASFGLSLCRTPQPRLEQRVMLEQRYAFFCGKRHRLFGRKNLALSDLQ 208
Cdd:cd08426   17 SLIARFRQRYPGVFFTVDVASTADVLEAVLSGEADIGLAFSPPPEPGIRVHSRQPAPIGAVVPPGHPLARQPSVTLAQLA 96

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 520793718 209 SENFV----SFTSDQIGGnlsplTVFRdQQGFTGRIVASSPSLDEILRLVGAGYGIGCLPEHIVAADVQADDIWRLP 281
Cdd:cd08426   97 GYPLAlpppSFSLRQILD-----AAFA-RAGVQLEPVLISNSIETLKQLVAAGGGISLLTELAVRREIRRGQLVAVP 167
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
 131-274 2.81e-04

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: 41.34  E-value: 2.81e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 131 LAQFHTEFPQVELEIDVLRSSDVISALLQKT---ASFGlslcRTPQ-PRLEQRVMLEQRYAFFCGKRHRLFGRKNLALSD 206
Cdd:cd08419   18 LGAFCRRHPGVEVSLRVGNREQVLERLADNEddlAIMG----RPPEdLDLVAEPFLDNPLVVIAPPDHPLAGQKRIPLER 93

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 520793718 207 LQSENFV-----SFTSdqiggnlspLTV--FRDQQGFTGRIVASSPSLDEILRLVGAGYGIGCLPEHIVAADVQA 274
Cdd:cd08419   94 LAREPFLlrepgSGTR---------LAMerFFAEHGVTLRVRMELGSNEAIKQAVMAGLGLSVLSLHTLALELAT 159
PBP2_DntR_NahR_LinR_like cd08459
The C-terminal substrate binding domain of LysR-type transcriptional regulators that are ...
 139-299 6.45e-04

The C-terminal substrate binding domain of LysR-type transcriptional regulators that are involved in the catabolism of dinitrotoluene, naphthalene and gamma-hexachlorohexane; contains the type 2 periplasmic binding fold; This CD includes LysR-like bacterial transcriptional regulators, DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. DntR from Burkholderia species controls genes encoding enzymes for oxidative degradation of the nitro-aromatic compound 2,4-dinitrotoluene. The active form of DntR is homotetrameric, consisting of a dimer of dimers. NahR is a salicylate-dependent transcription activator of the nah and sal operons for naphthalene degradation. Salicylic acid is an intermediate of the oxidative degradation of the aromatic ring in soil bacteria. LinR positively regulates expression of the genes (linD and linE) encoding enzymes for gamma-hexachlorocyclohexane (a haloorganic insecticide) degradation. Expression of linD and linE are induced by their substrates, 2,5-dichlorohydroquinone (2,5-DCHQ) and chlorohydroquinone (CHQ). 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: 176148 [Multi-domain]  Cd Length: 201  Bit Score: 40.25  E-value: 6.45e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 139 PQVELEIDVLRSSDVISALLQKTASFGLSLCRTPQPRLEQRVMLEQRYAFFCGKRHRLFGRKnLALSDLQSENFVSFTSd 218
Cdd:cd08459   27 PGVRIETVRLPVDELEEALESGEIDLAIGYLPDLGAGFFQQRLFRERYVCLVRKDHPRIGST-LTLEQFLAARHVVVSA- 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 219 QIGGNLSPLTVFRDqQGFTGRIVASSPSLDEILRLVGAGYGIGCLPEHIVAADVQADDIWRLPPWEGVSDVNVYLLWNRE 298
Cdd:cd08459  105 SGTGHGLVEQALRE-AGIRRRIALRVPHFLALPLIVAQTDLVATVPERLARLFARAGGLRIVPLPFPLPPFEVKLYWHRR 183


                 .
gi 520793718 299 Q 299
Cdd:cd08459  184 F 184
PBP2_LysR cd08456
The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine ...
 117-260 9.13e-04

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: 39.71  E-value: 9.13e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 117 LSISRIQSRSYDdFLAQ----FHTEFPQVELEIdVLRSSDVISALLQ-KTASFGLSLCRTPQPRLEQRVMLEQRYAFFCG 191
Cdd:cd08456    2 LRIAVLPALSQS-FLPRaikaFLQRHPDVTISI-HTRDSPTVEQWLSaQQCDLGLVSTLHEPPGIERERLLRIDGVCVLP 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 520793718 192 KRHRLFGRKNLALSDLQSENFVSFTSdqigGNLSPLTVFR--DQQGFTGRIVASSPSLDEILRLVGAGYGI 260
Cdd:cd08456   80 PGHRLAVKKVLTPSDLEGEPFISLAR----TDGTRQRVDAlfEQAGVKRRIVVETSYAATICALVAAGVGV 146
PBP2_LTTR_aromatics_like_1 cd08447
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 131-298 9.61e-04

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: 39.55  E-value: 9.61e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 131 LAQFHTEFPQVELEIDVLRSSDVISALLQKTASFGLSLCRTPQPRLEQRVMLEQRYAFFCGKRHRLFGRKNLALSDLQSE 210
Cdd:cd08447   19 LAAARAALPDVDLVLREMVTTDQIEALESGRIDLGLLRPPFARPGLETRPLVREPLVAAVPAGHPLAGAERLTLEDLDGQ 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 211 NFVSFTS-------DQIGGNLSpltvfrdQQGFTGRIVASSPSLDEILRLVGAGYGIGCLPEhiVAADVQADDIwRLPPW 283
Cdd:cd08447   99 PFIMYSPtearyfhDLVVRLFA-------SAGVQPRYVQYLSQIHTMLALVRAGLGVALVPA--SASRLRFEGV-VFRPL 168

                        170
                 ....*....|....*..
gi 520793718 284 EGVSDVNV--YLLWNRE 298
Cdd:cd08447  169 DLPRDVPVelHLAWRRD 185
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
37-82 1.23e-03

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 40.13  E-value: 1.23e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 520793718  37 GSISRAAARLHLSQPAISQALKRLEEQLASELVVRRGPRITLSKAG 82
Cdd:PRK10632  17 GSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAG 62
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 204-310 1.68e-03

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


Pssm-ID: 176114 [Multi-domain]  Cd Length: 197  Bit Score: 38.96  E-value: 1.68e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 204 LSDLQSENFVSFTSdqiGGNLSPLTVFRDQQGFT----GRIVASSPSLdeILRLVGAGYGIGCLPEHIVAADVQA----- 274
Cdd:cd08422   90 PEDLARHRCLGYRL---PGRPLRWRFRRGGGEVEvrvrGRLVVNDGEA--LRAAALAGLGIALLPDFLVAEDLASgrlvr 164

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 520793718 275 --DDiWRLPPWEgvsdvnVYLLWNREQKMTRAESVFLE 310
Cdd:cd08422  165 vlPD-WRPPPLP------IYAVYPSRRHLPAKVRAFID 195
PBP2_CynR cd08425
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, ...
 131-311 1.87e-03

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: 38.85  E-value: 1.87e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 131 LAQFHTEFPQVELEIDVLRSSDVISALLQKTASFGLSLCRTPQPRLEQRVMLEQRYAFFCGKRHRLFGRKN-LALSDLQS 209
Cdd:cd08425   20 IDRFHARYPGIALSLREMPQERIEAALADDRLDLGIAFAPVRSPDIDAQPLFDERLALVVGATHPLAQRRTaLTLDDLAA 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 210 ENFVSFTSDQIggNLSPLTVFRDQQGFTGRIVASSPSLDEILRLVGAGYGIGCLPEHIVAadvQADDIWRLPPWEGVSDV 289
Cdd:cd08425  100 EPLALLSPDFA--TRQHIDRYFQKQGIKPRIAIEANSISAVLEVVRRGRLATILPDAIAR---EQPGLCAVALEPPLPGR 174

                        170       180
                 ....*....|....*....|..
gi 520793718 290 NVYLLWNREQKMTRAESVFLER 311
Cdd:cd08425  175 TAALLRRKGAYRSAAARAFAAL 196
MarR COG1846
DNA-binding transcriptional regulator, MarR family [Transcription];
27-96 2.18e-03

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


Pssm-ID: 441451 [Multi-domain]  Cd Length: 142  Bit Score: 38.03  E-value: 2.18e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 520793718  27 LRTFLVIGQEG--SISRAAARLHLSQPAISQALKRLEEQlasELVVR-------RGPRITLSKAGEEVMQIAADLYGTV 96
Cdd:COG1846   41 FRVLAALAEAGglTQSELAERLGLTKSTVSRLLDRLEEK---GLVERepdpedrRAVLVRLTEKGRALLEEARPALEAL 116
MarR_2 pfam12802
MarR family; The Mar proteins are involved in the multiple antibiotic resistance, a ...
 20-72 2.36e-03

MarR family; The Mar proteins are involved in the multiple antibiotic resistance, a non-specific resistance system. The expression of the mar operon is controlled by a repressor, MarR. A large number of compounds induce transcription of the mar operon. This is thought to be due to the compound binding to MarR, and the resulting complex stops MarR binding to the DNA. With the MarR repression lost, transcription of the operon proceeds. The structure of MarR is known and shows MarR as a dimer with each subunit containing a winged-helix DNA binding motif.


Pssm-ID: 432797 [Multi-domain]  Cd Length: 60  Bit Score: 35.64  E-value: 2.36e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 520793718   20 DRLDWNLLRtFLVIGQEGSISRAAARLHLSQPAISQALKRLEEQlasELVVRR 72
Cdd:pfam12802   4 TPAQFRVLL-ALARNPGLTVAELARRLGISKQTVSRLVKRLEAK---GLVERE 52
PRK10216 PRK10216
HTH-type transcriptional regulator YidZ;
21-60 2.79e-03

HTH-type transcriptional regulator YidZ;


Pssm-ID: 182312 [Multi-domain]  Cd Length: 319  Bit Score: 39.03  E-value: 2.79e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 520793718  21 RLDWNLLRTFLVIGQEGSISRAAARLHLSQPAISQALKRL 60
Cdd:PRK10216   7 TLDLNLLLCLQLLMQERSVTKAAKRMNVTPSAVSKSLAKL 46
HTH_MARR smart00347
helix_turn_helix multiple antibiotic resistance protein;
20-87 3.27e-03

helix_turn_helix multiple antibiotic resistance protein;


Pssm-ID: 197670 [Multi-domain]  Cd Length: 101  Bit Score: 36.42  E-value: 3.27e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 520793718    20 DRLDWNL--LRTFLVIGQEGSISRA--AARLHLSQPAISQALKRLEEQlasELVVR-------RGPRITLSKAGEEVMQ 87
Cdd:smart00347   4 KPLGLTPtqFLVLRILYEEGPLSVSelAKRLGVSPSTVTRVLDRLEKK---GLVRRepspedrRSVLVSLTEEGRELIE 79
PBP2_OccR cd08457
The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the ...
 129-277 3.93e-03

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: 37.85  E-value: 3.93e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 129 DFLAQFHTEFPQVELEIDVLRSSDVISALLQKTASFGLSLCRTPQPRLEQRVMLEQRYAFFCGKRHRLFGRKNLALSDLQ 208
Cdd:cd08457   17 RFLAAFLRLRPNLHLSLMGLSSSQVLEAVASGRADLGIADGPLEERQGFLIETRSLPAVVAVPMGHPLAQLDVVSPQDLA 96

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 520793718 209 SENFVSftsdqiggnLSPLTVFRD--QQGFTGRIVASSPSLD-----EILRLVGAGYGIGCLpEHIVAADVQADDI 277
Cdd:cd08457   97 GERIIT---------LENGYLFRMrvEVALGKIGVKRRPIIEvnlshTALSLVREGLGIAII-DPATAIGLPLDGI 162
PBP2_TdcA cd08418
The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is ...
 129-312 4.28e-03

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: 37.72  E-value: 4.28e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 129 DFLAQFHTEFPQVELEIDVLRSSDVISALLQKTASFGLS-LCRTPQPR-LEQRVMLEQRYAFFCGKRHRLfgRKNLALSD 206
Cdd:cd08418   17 AVINRFKEQFPDVQISIYEGQLSSLLPELRDGRLDFAIGtLPDEMYLKeLISEPLFESDFVVVARKDHPL--QGARSLEE 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 207 LQSENFVSFTSDqiGGNLSPLTVFRDQQGFTGRIVASSPSLDEILRLVGAGYGIGCLPEHIVAADVQADDIWRLPPWEGV 286
Cdd:cd08418   95 LLDASWVLPGTR--MGYYNNLLEALRRLGYNPRVAVRTDSIVSIINLVEKADFLTILSRDMGRGPLDSFRLITIPVEEPL 172

                        170       180
                 ....*....|....*....|....*.
gi 520793718 287 SDVNVYLLWNREQKMTRAESVFLERF 312
Cdd:cd08418  173 PSADYYLIYRKKSRLTPLAEQLVELF 198
Lrp COG1522
DNA-binding transcriptional regulator, Lrp family [Transcription];
20-86 5.15e-03

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


Pssm-ID: 441131 [Multi-domain]  Cd Length: 138  Bit Score: 36.68  E-value: 5.15e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 520793718  20 DRLDWNLLRtflVIGQEGSISRA--AARLHLSQPAISQALKRLEEqlaSELVVRRGPRITLSKAGEEVM 86
Cdd:COG1522    4 DEIDRRILR---LLQEDGRLSFAelAERVGLSESTVLRRVRRLEE---AGVIRGYGAVVDPEKLGLGVT 66
nhaR PRK11062
transcriptional activator NhaR; Provisional
 22-89 7.53e-03

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 37.68  E-value: 7.53e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 520793718  22 LDWNLLRTFLVIGQEGSISRAAARLHLSQPAISQALKRLEEQLASELVVRRGPRITLSKAGEEVMQIA 89
Cdd:PRK11062   4 INYNHLYYFWMVCKEGSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGELVFRYA 71
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 37-260 7.99e-03

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 37.66  E-value: 7.99e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718  37 GSISRAAARLHLSQPAISQALKRLEEQLASELVVRRGPRITLSKAG----EEVmQIAadLYGtVSRLGPALDAPAESVTG 112
Cdd:PRK11013  19 GSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGlrlfEEV-QRS--YYG-LDRIVSAAESLREFRQG 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 113 KirlLSISRIQSRSYD---DFLAQFHTEFPQVELEIDVLRSSDVISALLQKTASFGLSLCRTPQPRLEQRVMLEQRYAFF 189
Cdd:PRK11013  95 Q---LSIACLPVFSQSllpGLCQPFLARYPDVSLNIVPQESPLLEEWLSAQRHDLGLTETLHTPAGTERTELLTLDEVCV 171

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 520793718 190 CGKRHRLFGRKNLALSDLQSENFVSftsdqiggnLSPLTVFRD-------QQGFTGRIVASSPSLDEILRLVGAGYGI 260
Cdd:PRK11013 172 LPAGHPLAAKKVLTPDDFAGENFIS---------LSRTDSYRQlldqlfaEHGVKRRMVVETHSAASVCAMVRAGVGV 240
PBP2_MleR cd08437
The substrate binding domain of LysR-type transcriptional regulator MleR which required for ...
 129-281 8.33e-03

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: 36.93  E-value: 8.33e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 129 DFLAQFHTEFPQVELEIDVLRSSDVISALLQktASFGLSLCRTPQP----RLEQRVMLEQRYAFFCGKRHRLFGRKNLAL 204
Cdd:cd08437   17 KLAKDLIKTGLMIQIDTYEGGSAELLEQLLQ--GDLDIALLGSLTPlensALHSKIIKTQHFMIIVSKDHPLAKAKKVNF 94

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 520793718 205 SDLQSENFVSFTSdqigGNLSP--LTVFRDQQGFTGRIVASSPSLDEILRLVGAGYGIGCLPEHIVaadVQADDIWRLP 281
Cdd:cd08437   95 ADLKKENFILLNE----HFVHPkaFDSLCQQANFQPNIVYRTNDIHILKSMVRENVGIGFLTDIAV---KPDDHLVAIP 166
PBP2_BudR cd08451
The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is ...
 133-265 9.69e-03

The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is responsible for activation of the expression of the butanediol operon genes; contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of BudR regulator, which is responsible for induction of the butanediol formation pathway under fermentative growth conditions. Three enzymes are involved in the production of 1 mol of 2,3 butanediol from the condensation of 2 mol of pyruvate with acetolactate and acetoin as intermediates: acetolactate synthetase, acetolactate decarboxylase, and acetoin reductase. In Klebsiella terrigena, BudR regulates the expression of the budABC operon genes, encoding these three enzymes of the butanediol pathway. In many bacterial species, the use of this pathway can prevent intracellular acidification by diverting metabolism from acid production to the formation of neutral compounds (acetoin and butanediol). This substrate-binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176142 [Multi-domain]  Cd Length: 199  Bit Score: 36.77  E-value: 9.69e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 520793718 133 QFHTEFPQVELEIDVLRSSDVISALLQKT--ASFGLSLCRTPqPRLEQRVMLEQRYAFFCGKRHRLFGRKNLALSDLQSE 210
Cdd:cd08451   22 RFREAYPDVELTLEEANTAELLEALREGRldAAFVRPPVARS-DGLVLELLLEEPMLVALPAGHPLARERSIPLAALADE 100

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 520793718 211 NFVSFTSdQIGGNL--SPLTVFRdQQGFTGRIVASSPSLDEILRLVGAGYGIGCLPE 265
Cdd:cd08451  101 PFILFPR-PVGPGLydAIIAACR-RAGFTPRIGQEAPQMASAINLVAAGLGVSIVPA 155
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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