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Conserved domains on  [gi|2045450880|gb|QVV70751|]
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LysR family transcriptional regulator [Serratia marcescens]

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];
8-294 2.37e-48

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 161.96  E-value: 2.37e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880   8 IDLKLLRVFVAVAEAQGVSAAQEALLMNQSTISTHLASLETRLGFRLCQRGRSGFRLTPKGERMLIACRSLFNAARDFTR 87
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880  88 VSQSLNGLLTGDLQIGLVDnlvSLPGNPFSQAIKHFQRRHQDVQLQCRICSPNEIEQGLLHRQLDLGIGYFGQQLEALRY 167
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPP---SLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVA 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880 168 QPWLEETQAIYCSADHPLftveepereqienarwvkrgyllaqqlcpiapPHLAAVAHHMESVAHLVLSGTCLGYLPTHY 247
Cdd:COG0583   158 RPLGEERLVLVASPDHPL--------------------------------ARRAPLVNSLEALLAAVAAGLGIALLPRFL 205

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*..
gi 2045450880 248 AARWVEQGLLRQLGGTALSYRATLSLVSRPVQPDEALNALLEDLARA 294
Cdd:COG0583   206 AADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLRE 252
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
8-294 2.37e-48

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 161.96  E-value: 2.37e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880   8 IDLKLLRVFVAVAEAQGVSAAQEALLMNQSTISTHLASLETRLGFRLCQRGRSGFRLTPKGERMLIACRSLFNAARDFTR 87
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880  88 VSQSLNGLLTGDLQIGLVDnlvSLPGNPFSQAIKHFQRRHQDVQLQCRICSPNEIEQGLLHRQLDLGIGYFGQQLEALRY 167
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPP---SLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVA 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880 168 QPWLEETQAIYCSADHPLftveepereqienarwvkrgyllaqqlcpiapPHLAAVAHHMESVAHLVLSGTCLGYLPTHY 247
Cdd:COG0583   158 RPLGEERLVLVASPDHPL--------------------------------ARRAPLVNSLEALLAAVAAGLGIALLPRFL 205

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*..
gi 2045450880 248 AARWVEQGLLRQLGGTALSYRATLSLVSRPVQPDEALNALLEDLARA 294
Cdd:COG0583   206 AADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLRE 252
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 97-294 1.77e-20

LysR substrate binding domain; The structure of this domain is known and is similar to the periplasmic binding proteins. This domain binds a variety of ligands that caries in size and structure, such as amino acids, sugar phosphates, organic acids, metal cations, flavonoids, C6-ring carboxylic acids, H2O2, HOCl, homocysteine, NADPH, ATP, sulphate, muropeptides, acetate, salicylate, citrate, phenol- and quinolone derivatives, acetylserines, fatty acid CoA, shikimate, chorismate, homocysteine, indole-3-acetic acid, Na(I), c-di-GMP, ppGpp and hydrogen peroxide (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 460931 [Multi-domain]  Cd Length: 205  Bit Score: 87.34  E-value: 1.77e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880  97 TGDLQIGLVDnlvSLPGNPFSQAIKHFQRRHQDVQLQCRICSPNEIEQGLLHRQLDLGIGYFGQQLEALRYQPWLEETQA 176
Cdd:pfam03466   1 SGRLRIGAPP---TLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLV 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880 177 IYCSADHPLFTVEEPEREQIENARWV--KRGYLLAQQL-----CPIAPPHLAAVAHHMESVAHLVLSGTCLGYLPTHYAA 249
Cdd:pfam03466  78 LVAPPDHPLARGEPVSLEDLADEPLIllPPGSGLRDLLdralrAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVA 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 2045450880 250 RWVEQGLLRQLGGTALSYRATLSLVSRPVQP-DEALNALLEDLARA 294
Cdd:pfam03466 158 RELADGRLVALPLPEPPLPRELYLVWRKGRPlSPAVRAFIEFLREA 203
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 8-258 2.41e-18

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


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 83.44  E-value: 2.41e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880   8 IDLKLLRVFVAVAEAQGVSAAQEALLMNQSTISTHLASLETRLGFRLCQRGRSGFRLTPKGERMLIACRSLFNAARDFTR 87
Cdd:NF040786    1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880  88 VSQSLNGLLTGDLQIGlvdnLVSLPGNPF-SQAIKHFQRRHQDVQLQCRICSPNEIEQGLLHRQLDLGIgyFGQQLE--A 164
Cdd:NF040786   81 EFDRYGKESKGVLRIG----ASTIPGQYLlPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGF--TGTKLEkkR 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880 165 LRYQPWLEETQAIYCSADHPLFTV--EEPEREQIENARWVKR----------GYLLAQQLCPIAPPHLAAVAHHMESVAH 232
Cdd:NF040786  155 LVYTPFYKDRLVLITPNGTEKYRMlkEEISISELQKEPFIMReegsgtrkeaEKALKSLGISLEDLNVVASLGSTEAIKQ 234

                         250       260
                  ....*....|....*....|....*.
gi 2045450880 233 LVLSGTCLGYLPTHYAARWVEQGLLR 258
Cdd:NF040786  235 SVEAGLGISVISELAAEKEVERGRVL 260
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 116-289 4.91e-14

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


Pssm-ID: 176102 [Multi-domain]  Cd Length: 197  Bit Score: 69.55  E-value: 4.91e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880 116 FSQAIKHFQRRHQDVQLQCRICSPNEIEQGLLHRQLDLGIGYFGQQLEALRYQPWLEETQAIYCSADHPLFTVEEPEREQ 195
Cdd:cd05466    15 LPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPPDHPLAKRKSVTLAD 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880 196 IENARWV--KRGY---LLAQQLC--PIAPPHLAAVAHHMESVAHLVLSGTCLGYLPtHYAARWVEQGLLRQLGGTALSYR 268
Cdd:cd05466    95 LADEPLIlfERGSglrRLLDRAFaeAGFTPNIALEVDSLEAIKALVAAGLGIALLP-ESAVEELADGGLVVLPLEDPPLS 173

                         170       180
                  ....*....|....*....|..
gi 2045450880 269 ATLSLVSRP-VQPDEALNALLE 289
Cdd:cd05466   174 RTIGLVWRKgRYLSPAARAFLE 195
PRK09986 PRK09986
LysR family transcriptional regulator;
5-185 5.75e-14

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 70.91  E-value: 5.75e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880   5 LSDIDLKLLRVFVAVAEAQGVSAAQEALLMNQSTISTHLASLETRLGFRLCQRGRSGFRLTPKGERMLIACRSLF-NAAR 83
Cdd:PRK09986    4 LYRIDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLdNAEQ 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880  84 DFTRVSQSLNGlLTGDLQIGLVDNLV---SLPgnpfsqAIKHFQRRHQDVQLQCRICSPNEIEQGLLHRQLDLGIGYFG- 159
Cdd:PRK09986   84 SLARVEQIGRG-EAGRIEIGIVGTALwgrLRP------AMRHFLKENPNVEWLLRELSPSMQMAALERRELDAGIWRMAd 156

                         170       180
                  ....*....|....*....|....*..
gi 2045450880 160 -QQLEALRYQPWLEETQAIYCSADHPL 185
Cdd:PRK09986  157 lEPNPGFTSRRLHESAFAVAVPEEHPL 183
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
8-294 2.37e-48

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 161.96  E-value: 2.37e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880   8 IDLKLLRVFVAVAEAQGVSAAQEALLMNQSTISTHLASLETRLGFRLCQRGRSGFRLTPKGERMLIACRSLFNAARDFTR 87
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880  88 VSQSLNGLLTGDLQIGLVDnlvSLPGNPFSQAIKHFQRRHQDVQLQCRICSPNEIEQGLLHRQLDLGIGYFGQQLEALRY 167
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPP---SLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVA 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880 168 QPWLEETQAIYCSADHPLftveepereqienarwvkrgyllaqqlcpiapPHLAAVAHHMESVAHLVLSGTCLGYLPTHY 247
Cdd:COG0583   158 RPLGEERLVLVASPDHPL--------------------------------ARRAPLVNSLEALLAAVAAGLGIALLPRFL 205

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*..
gi 2045450880 248 AARWVEQGLLRQLGGTALSYRATLSLVSRPVQPDEALNALLEDLARA 294
Cdd:COG0583   206 AADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLRE 252
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 97-294 1.77e-20

LysR substrate binding domain; The structure of this domain is known and is similar to the periplasmic binding proteins. This domain binds a variety of ligands that caries in size and structure, such as amino acids, sugar phosphates, organic acids, metal cations, flavonoids, C6-ring carboxylic acids, H2O2, HOCl, homocysteine, NADPH, ATP, sulphate, muropeptides, acetate, salicylate, citrate, phenol- and quinolone derivatives, acetylserines, fatty acid CoA, shikimate, chorismate, homocysteine, indole-3-acetic acid, Na(I), c-di-GMP, ppGpp and hydrogen peroxide (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 460931 [Multi-domain]  Cd Length: 205  Bit Score: 87.34  E-value: 1.77e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880  97 TGDLQIGLVDnlvSLPGNPFSQAIKHFQRRHQDVQLQCRICSPNEIEQGLLHRQLDLGIGYFGQQLEALRYQPWLEETQA 176
Cdd:pfam03466   1 SGRLRIGAPP---TLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLV 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880 177 IYCSADHPLFTVEEPEREQIENARWV--KRGYLLAQQL-----CPIAPPHLAAVAHHMESVAHLVLSGTCLGYLPTHYAA 249
Cdd:pfam03466  78 LVAPPDHPLARGEPVSLEDLADEPLIllPPGSGLRDLLdralrAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVA 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 2045450880 250 RWVEQGLLRQLGGTALSYRATLSLVSRPVQP-DEALNALLEDLARA 294
Cdd:pfam03466 158 RELADGRLVALPLPEPPLPRELYLVWRKGRPlSPAVRAFIEFLREA 203
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 8-258 2.41e-18

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


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 83.44  E-value: 2.41e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880   8 IDLKLLRVFVAVAEAQGVSAAQEALLMNQSTISTHLASLETRLGFRLCQRGRSGFRLTPKGERMLIACRSLFNAARDFTR 87
Cdd:NF040786    1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880  88 VSQSLNGLLTGDLQIGlvdnLVSLPGNPF-SQAIKHFQRRHQDVQLQCRICSPNEIEQGLLHRQLDLGIgyFGQQLE--A 164
Cdd:NF040786   81 EFDRYGKESKGVLRIG----ASTIPGQYLlPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGF--TGTKLEkkR 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880 165 LRYQPWLEETQAIYCSADHPLFTV--EEPEREQIENARWVKR----------GYLLAQQLCPIAPPHLAAVAHHMESVAH 232
Cdd:NF040786  155 LVYTPFYKDRLVLITPNGTEKYRMlkEEISISELQKEPFIMReegsgtrkeaEKALKSLGISLEDLNVVASLGSTEAIKQ 234

                         250       260
                  ....*....|....*....|....*.
gi 2045450880 233 LVLSGTCLGYLPTHYAARWVEQGLLR 258
Cdd:NF040786  235 SVEAGLGISVISELAAEKEVERGRVL 260
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
10-69 5.92e-16

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 70.88  E-value: 5.92e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880  10 LKLLRVFVAVAEAQGVSAAQEALLMNQSTISTHLASLETRLGFRLCQRGRSGFRLTPKGE 69
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 116-289 4.91e-14

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


Pssm-ID: 176102 [Multi-domain]  Cd Length: 197  Bit Score: 69.55  E-value: 4.91e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880 116 FSQAIKHFQRRHQDVQLQCRICSPNEIEQGLLHRQLDLGIGYFGQQLEALRYQPWLEETQAIYCSADHPLFTVEEPEREQ 195
Cdd:cd05466    15 LPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPPDHPLAKRKSVTLAD 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880 196 IENARWV--KRGY---LLAQQLC--PIAPPHLAAVAHHMESVAHLVLSGTCLGYLPtHYAARWVEQGLLRQLGGTALSYR 268
Cdd:cd05466    95 LADEPLIlfERGSglrRLLDRAFaeAGFTPNIALEVDSLEAIKALVAAGLGIALLP-ESAVEELADGGLVVLPLEDPPLS 173

                         170       180
                  ....*....|....*....|..
gi 2045450880 269 ATLSLVSRP-VQPDEALNALLE 289
Cdd:cd05466   174 RTIGLVWRKgRYLSPAARAFLE 195
PRK09986 PRK09986
LysR family transcriptional regulator;
5-185 5.75e-14

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 70.91  E-value: 5.75e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880   5 LSDIDLKLLRVFVAVAEAQGVSAAQEALLMNQSTISTHLASLETRLGFRLCQRGRSGFRLTPKGERMLIACRSLF-NAAR 83
Cdd:PRK09986    4 LYRIDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLdNAEQ 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880  84 DFTRVSQSLNGlLTGDLQIGLVDNLV---SLPgnpfsqAIKHFQRRHQDVQLQCRICSPNEIEQGLLHRQLDLGIGYFG- 159
Cdd:PRK09986   84 SLARVEQIGRG-EAGRIEIGIVGTALwgrLRP------AMRHFLKENPNVEWLLRELSPSMQMAALERRELDAGIWRMAd 156

                         170       180
                  ....*....|....*....|....*..
gi 2045450880 160 -QQLEALRYQPWLEETQAIYCSADHPL 185
Cdd:PRK09986  157 lEPNPGFTSRRLHESAFAVAVPEEHPL 183
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 120-277 3.34e-11

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: 61.35  E-value: 3.34e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880 120 IKHFQRRHQDVQLQCRICSPNEIEQGLLHRQLDLGI--GYFGQqlEALRYQPWLEETQAIYCSADHPLFTVEEPEREQIE 197
Cdd:cd08420    19 LARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLveGPVDH--PDLIVEPFAEDELVLVVPPDHPLAGRKEVTAEELA 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880 198 NARWVKR--G--------YLLAQQLCPIAPPHLAAVAHHMESVAHLVLSGTCLGYLPTHYAARWVEQGLLRQLGGTALSY 267
Cdd:cd08420    97 AEPWILRepGsgtrevfeRALAEAGLDGLDLNIVMELGSTEAIKEAVEAGLGISILSRLAVRKELELGRLVALPVEGLRL 176

                         170
                  ....*....|
gi 2045450880 268 RATLSLVSRP 277
Cdd:cd08420   177 TRPFSLIYHK 186
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 10-185 5.79e-11

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 61.90  E-value: 5.79e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880  10 LKLLRVFVAVAEAQGVSAAQEALLMNQSTISTHLASLETRLGFRLCQRGRSGFRLTPKGERMLI----ACRSLFNAARDF 85
Cdd:PRK11242    3 LRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRyarrALQDLEAGRRAI 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880  86 TRVSQslngLLTGDLQIGLVDNLVSLPGNPFsqaIKHFQRRHQDVQLQCRICSPNEIEQGLLHRQLDLGIGYFGQQLEAL 165
Cdd:PRK11242   83 HDVAD----LSRGSLRLAMTPTFTAYLIGPL---IDAFHARYPGITLTIREMSQERIEALLADDELDVGIAFAPVHSPEI 155

                         170       180
                  ....*....|....*....|
gi 2045450880 166 RYQPWLEETQAIYCSADHPL 185
Cdd:PRK11242  156 EAQPLFTETLALVVGRHHPL 175
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 25-201 1.17e-10

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 61.21  E-value: 1.17e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880  25 VSAAQEALLMNQSTISTHLASLETRLGFRLCQRgrSGFRL---TPKGERMLIACRSLFNAARDFTRVSQSLNGLLTGDLQ 101
Cdd:PRK12683   19 LTEVANALYTSQSGVSKQIKDLEDELGVEIFIR--RGKRLtglTEPGKELLQIVERMLLDAENLRRLAEQFADRDSGHLT 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880 102 IGLVDNLV--SLPgnpfsQAIKHFQRRHQDVQLQCRICSPNEIEQGLLHRQLDLGIGYFG----QQLEALRYQPWleeTQ 175
Cdd:PRK12683   97 VATTHTQAryALP-----KVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGIATEAldrePDLVSFPYYSW---HH 168

                         170       180
                  ....*....|....*....|....*.
gi 2045450880 176 AIYCSADHPLFTVEEPEREQIenARW 201
Cdd:PRK12683  169 VVVVPKGHPLTGRENLTLEAI--AEY 192
rbcR CHL00180
LysR transcriptional regulator; Provisional
 10-202 2.95e-09

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 56.95  E-value: 2.95e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880  10 LKLLRVFVAVAEAQGVSAAQEALLMNQSTISTHLASLETRLGFRLCQRGRSGFRLTPKG-------ERMLIACRSLFNAA 82
Cdd:CHL00180    7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGelllrygNRILALCEETCRAL 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880  83 RDftrvsqsLNGLLTGDLQIG--------LVDNLVSLpgnpfsqaikhFQRRHQDVQLQCRICSPNEIEQGLLHRQLDLG 154
Cdd:CHL00180   87 ED-------LKNLQRGTLIIGasqttgtyLMPRLIGL-----------FRQRYPQINVQLQVHSTRRIAWNVANGQIDIA 148

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2045450880 155 I--GYFGQQL-EALRYQPWLEETQAIYCSADHPLFTVEEPEREQIENARWV 202
Cdd:CHL00180  149 IvgGEVPTELkKILEITPYVEDELALIIPKSHPFAKLKKIQKEDLYRLNFI 199
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
8-155 4.14e-09

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 56.56  E-value: 4.14e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880   8 IDLKLLRVFVAVAEAQGVSAAQEALLMNQSTISTHLASLETRLGFRLCQRGRSGFRLTPKGERMLIACRSLFN----AAR 83
Cdd:PRK03601    1 MDTELLKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYAETLMNtwqaAKK 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2045450880  84 DFTRVSQSlnglltGDLQIGLVDNLVSLPGNPFSQAikhFQRRHQDVQLQCRICSPNEIEQGLLHRQLDLGI 155
Cdd:PRK03601   81 EVAHTSQH------NELSIGASASLWECMLTPWLGR---LYQNQEALQFEARIAQRQSLVKQLHERQLDLLI 143
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
8-257 7.06e-09

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 55.97  E-value: 7.06e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880   8 IDLKLLRVFVAVAEAQGVSAAQEALLMNQSTISTHLASLETRLGFRLCQRGRSGFRLTPKGERMLIACRSLFNAARDFTR 87
Cdd:PRK10094    2 FDPETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPS 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880  88 VSQSLNGLLTGDLQIgLVDNLVSLPgnpfsQAIKH----FQRRHQDVQLQCRicspNEIEQG----LLHRQLDLGIGYFG 159
Cdd:PRK10094   82 ELQQVNDGVERQVNI-VINNLLYNP-----QAVAQllawLNERYPFTQFHIS----RQIYMGvwdsLLYEGFSLAIGVTG 151

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880 160 QQ--LEALRYQPWLEETQAIYCSADHPLFTVEEPERE---------QIENA--RWVKR-GYLLAQQLCPIAPPHLAAVAH 225
Cdd:PRK10094  152 TEalANTFSLDPLGSVQWRFVMAADHPLANVEEPLTEaqlrrfpavNIEDSarTLTKRvAWRLPGQKEIIVPDMETKIAA 231

                         250       260       270
                  ....*....|....*....|....*....|..
gi 2045450880 226 HmesvahlvLSGTCLGYLPTHYAARWVEQGLL 257
Cdd:PRK10094  232 H--------LAGVGIGFLPKSLCQSMIDNQQL 255
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 118-276 7.21e-09

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


Pssm-ID: 176126 [Multi-domain]  Cd Length: 201  Bit Score: 54.59  E-value: 7.21e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880 118 QAIKHFQRRHQDVQLQCRICSPNEIEQGLLHRQLDLGIG--YFGQQLEALRYQPWLEETQAIYCSADHPLFTVEEPEREQ 195
Cdd:cd08435    17 PAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAIGrlADDEQPPDLASEELADEPLVVVARPGHPLARRARLTLAD 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880 196 IENARWV--KRGYLLAQQL--------CPiAPPHLAAVAHHMESVAhLVLSGTCLGYLPTHYAARWVEQGLLRQLGGTAL 265
Cdd:cd08435    97 LADYPWVlpPPGTPLRQRLeqlfaaagLP-LPRNVVETASISALLA-LLARSDMLAVLPRSVAEDELRAGVLRELPLPLP 174

                         170
                  ....*....|.
gi 2045450880 266 SYRATLSLVSR 276
Cdd:cd08435   175 TSRRPIGITTR 185
PRK09791 PRK09791
LysR family transcriptional regulator;
6-185 1.35e-08

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 55.15  E-value: 1.35e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880   6 SDIDLKLLRVFVAVAEAQGVSAAQEALLMNQSTISTHLASLETRLGFRLCQRGRSGFRLTPKGERMLIACRSLFNAARDF 85
Cdd:PRK09791    3 FQVKIHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAA 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880  86 TRVSQSLNGLLTGDLQIGLVdnlVSLPGNPFSQAIKHFQRRHQDVQLqcRICSP------NEIEQGllhrQLDLGIG-YF 158
Cdd:PRK09791   83 QEDIRQRQGQLAGQINIGMG---ASIARSLMPAVISRFHQQHPQVKV--RIMEGqlvsmiNELRQG----ELDFTINtYY 153

                         170       180
                  ....*....|....*....|....*...
gi 2045450880 159 GQQLEA-LRYQPWLEETQAIYCSADHPL 185
Cdd:PRK09791  154 QGPYDHeFTFEKLLEKQFAVFCRPGHPA 181
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 100-289 1.51e-08

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: 53.67  E-value: 1.51e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880 100 LQIGLVDnlvSLPGNPFSQAIKHFQRRHQDVQLQCRICSPNEIEQGLLHRQLDLGIGYFGQQLEALRYQPWLEETQAIYC 179
Cdd:cd08414     2 LRIGFVG---SALYGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPPPDPPGLASRPLLREPLVVAL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880 180 SADHPLFTVEEPEREQIENARWV-----KRGYLLAQ--QLCPIA--PPHLAAVAHHMESVAHLVLSGTCLGYLPtHYAAR 250
Cdd:cd08414    79 PADHPLAARESVSLADLADEPFVlfprePGPGLYDQilALCRRAgfTPRIVQEASDLQTLLALVAAGLGVALVP-ASVAR 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 2045450880 251 WVEQGL-LRQLGGTALsyRATLSLVSRPVQPDEALNALLE 289
Cdd:cd08414   158 LQRPGVvYRPLADPPP--RSELALAWRRDNASPALRAFLE 195
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 25-185 1.81e-08

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 54.61  E-value: 1.81e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880  25 VSAAQEALLMNQSTISTHLASLETRLGFRLCQR-GRSGFRLTPKGERMLIACRSLFNAARDFTRVSQSLNGLLTGDLQIG 103
Cdd:PRK12682   19 LTEAAKALHTSQPGVSKAIIELEEELGIEIFIRhGKRLKGLTEPGKAVLDVIERILREVGNIKRIGDDFSNQDSGTLTIA 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880 104 LVDNLV--SLPgnpfsQAIKHFQRRHQDVQLQCRICSPNEIEQGLLHRQLDLGIGyfGQQL---EALRYQPWLEETQAIY 178
Cdd:PRK12682   99 TTHTQAryVLP-----RVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGIA--TESLaddPDLATLPCYDWQHAVI 171


                  ....*..
gi 2045450880 179 CSADHPL 185
Cdd:PRK12682  172 VPPDHPL 178
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
13-183 3.48e-08

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 53.85  E-value: 3.48e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880  13 LRVFVAVAEAQGVSAAQEALLMNQSTISTHLASLETRLGFRLCQRGRSGFRLTPKGERMLIACRSLFN--AARDFTRVSQ 90
Cdd:PRK10086   19 LHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLDtlNQEILDIKNQ 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880  91 SLNGLLTgdlqiglvdnLVSLPGnpFSQ-----AIKHFQRRHQDVQLQCRICSPNEIEQGllhRQLDLGIgYFGQ-QLEA 164
Cdd:PRK10086   99 ELSGTLT----------VYSRPS--IAQcwlvpRLADFTRRYPSISLTILTGNENVNFQR---AGIDLAI-YFDDaPSAQ 162

                         170
                  ....*....|....*....
gi 2045450880 165 LRYQPWLEETQAIYCSADH 183
Cdd:PRK10086  163 LTHHFLMDEEILPVCSPEY 181
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 8-260 8.45e-08

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 52.38  E-value: 8.45e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880   8 IDLKLLRVFVAVAEAQGVSAAQEALLMNQSTISTHLASLETRLGFRLCQrgRSGFRL--TPKGERMLIACRSLFNAARDF 85
Cdd:PRK10837    3 ITLRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFD--RVGKRLvvNEHGRLLYPRALALLEQAVEI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880  86 TRVSQSLNGLL--TGDLQIGlvdNLVsLPGnpfsqAIKHFQRRHQDVQLQCRICSPNEIEQGLLHRQLDLGIGYFGQQLE 163
Cdd:PRK10837   81 EQLFREDNGALriYASSTIG---NYI-LPA-----MIARYRRDYPQLPLELSVGNSQDVINAVLDFRVDIGLIEGPCHSP 151

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880 164 ALRYQPWLEETQAIYCSADHPLFTvEEPEREQIENARWVKR----------GYLLAQQLcpiapPHLAAVAH--HMESVA 231
Cdd:PRK10837  152 ELISEPWLEDELVVFAAPDSPLAR-GPVTLEQLAAAPWILRergsgtreivDYLLLSHL-----PRFELAMElgNSEAIK 225

                         250       260
                  ....*....|....*....|....*....
gi 2045450880 232 HLVLSGTCLGYLPTHYAARWVEQGLLRQL 260
Cdd:PRK10837  226 HAVRHGLGISCLSRRVIADQLQAGTLVEV 254
cbl PRK12679
HTH-type transcriptional regulator Cbl;
31-201 1.63e-07

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 51.73  E-value: 1.63e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880  31 ALLMNQSTISTHLASLETRLGFRL-CQRGRSGFRLTPKGERMLIACRSLFNAARDFTRVSQSLNGLLTGDLQIGLVDNLV 109
Cdd:PRK12679   25 MLFTSQSGVSRHIRELEDELGIEIfIRRGKRLLGMTEPGKALLVIAERILNEASNVRRLADLFTNDTSGVLTIATTHTQA 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880 110 --SLPGnpfsqAIKHFQRRHQDVQLQCRICSPNEIEQGLLHRQLDLGIGyfGQQL---EALRYQPWLEETQAIYCSADHP 184
Cdd:PRK12679  105 rySLPE-----VIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIA--SERLsndPQLVAFPWFRWHHSLLVPHDHP 177

                         170
                  ....*....|....*..
gi 2045450880 185 LFTVEEPEREQIenARW 201
Cdd:PRK12679  178 LTQITPLTLESI--AKW 192
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 120-260 4.73e-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: 49.52  E-value: 4.73e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880 120 IKHFQRRHQDVQLQCRICSPNEIEQGLLHRQLDLGIGYFGQQLEALRYQPWLEETQAIYCSADHPLFTvEEPEREQIENA 199
Cdd:cd08417    19 LARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELPPGLRSQPLFEDRFVCVARKDHPLAG-GPLTLEDYLAA 97

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2045450880 200 RWVK---RG--------YLLAQQLcpiaPPHLAAVAHHMESVAHLVLSGTCLGYLPTHYAARWVEQGLLRQL 260
Cdd:cd08417    98 PHVLvspRGrghglvddALAELGL----SRRVALTVPHFLAAPALVAGTDLIATVPRRLAEALAERLGLRVL 165
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 13-189 8.08e-07

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 49.46  E-value: 8.08e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880  13 LRVFVAVAEAQGVSAAQEALLMNQSTISTHLASLETRLGFRLCQR-GRSgFRLTPKGERMLIACRSLFNAARDFTRVSQS 91
Cdd:PRK11139   11 LRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRrNRS-LLLTEEGQRYFLDIREIFDQLAEATRKLRA 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880  92 LN--GLLTgdlqiglvdnlVSLPgnPfSQAIK-------HFQRRHQDVQLqcRICSPNEIEqGLLHRQLDLGIgYFGQ-Q 161
Cdd:PRK11139   90 RSakGALT-----------VSLL--P-SFAIQwlvprlsSFNEAHPDIDV--RLKAVDRLE-DFLRDDVDVAI-RYGRgN 151

                         170       180       190
                  ....*....|....*....|....*....|...
gi 2045450880 162 LEALRYQPWLEETQAIYCS-----ADHPLFTVE 189
Cdd:PRK11139  152 WPGLRVEKLLDEYLLPVCSpallnGGKPLKTPE 184
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
8-72 9.14e-07

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 49.63  E-value: 9.14e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2045450880   8 IDLKLLRVFVAVAEAQGVSAAQEALLMNQSTISTHLASLETRLGFRLCQRGRSGFRLTPKGERML 72
Cdd:PRK15421    2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILL 66
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 8-262 1.85e-06

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 48.61  E-value: 1.85e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880   8 IDLKLLRVFVAVAEAQGVSAAQEALLMNQSTISTHLASLETRLGFRLCQRGRSGFRLTPKGERMLIACRSLF----NAAR 83
Cdd:PRK09906    1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILeqaeKAKL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880  84 DFTRVSQSlngllTGDLQIGLVDnlvSLPGNPFSQAIKHFQRRHQDVQLQCRICSPNEIEQGLLHRQLDLGIGYFGQQLE 163
Cdd:PRK09906   81 RARKIVQE-----DRQLTIGFVP---SAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPVYSD 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880 164 ALRYQPWLEETQAIYCSADHPLFTVEEPEREQIENARWVKRGYLLAQQLCPI---------APPHLAAVAHHMESVAHLV 234
Cdd:PRK09906  153 EIDYLELLDEPLVVVLPVDHPLAHEKEITAAQLDGVNFISTDPAYSGSLAPIikawfaqhnSQPNIVQVATNILVTMNLV 232

                         250       260
                  ....*....|....*....|....*...
gi 2045450880 235 LSGTCLGYLPTHYAARWVEQGLLRQLGG 262
Cdd:PRK09906  233 GMGLGCTIIPGYMNNFNTGQVVFRPLAG 260
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
10-185 1.94e-06

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 48.43  E-value: 1.94e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880  10 LKLLRvFVAVAEAQG--VSAAQEALLMNQSTISTHLASLETRLG---FRlcqrgRSGFR---LTPKG-------ERMLIA 74
Cdd:PRK12684    3 LHQLR-FVREAVRQNfnLTEAAKALYTSQPGVSKAIIELEDELGveiFT-----RHGKRlrgLTEPGriilasvERILQE 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880  75 CRSLFNAARDFTRVSQslnglltGDLQIGLVDNLV--SLPgnpfsQAIKHFQRRHQDVQLQCRICSPNEIEQGLLHRQLD 152
Cdd:PRK12684   77 VENLKRVGKEFAAQDQ-------GNLTIATTHTQAryALP-----AAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQAD 144

                         170       180       190
                  ....*....|....*....|....*....|....
gi 2045450880 153 LGIGYFG-QQLEALRYQPWLEETQAIYCSADHPL 185
Cdd:PRK12684  145 LAIATEAiADYKELVSLPCYQWNHCVVVPPDHPL 178
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 118-185 3.02e-06

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: 47.13  E-value: 3.02e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2045450880 118 QAIKHFQRRHQDVQLQCRICSPNEIEQGLLHRQLDLGIGYFGQQLEALRYQPWLEETQAIYCSADHPL 185
Cdd:cd08440    17 PVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEADPDLEFEPLLRDPFVLVCPKDHPL 84
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 9-133 3.59e-06

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 47.68  E-value: 3.59e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880   9 DLKLLRVFVAVAEAQGVSAAQEALLMNQSTISTHLASLETRLGFRLCQRGRSGFRLTPKGERMLIACRSLFNAARDFTRV 88
Cdd:PRK14997    3 DLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDA 82

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 2045450880  89 SQSLNGLLTGDLQIGLVDNLVSLPGNPFsqaIKHFQRRHQDVQLQ 133
Cdd:PRK14997   83 IAALQVEPRGIVKLTCPVTLLHVHIGPM---LAKFMARYPDVSLQ 124
PBP2_XapR cd08449
The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved ...
 100-185 2.43e-05

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: 44.18  E-value: 2.43e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880 100 LQIGLVDnlvSLPGNPFSQAIKHFQRRHQDVQLQCRICSPNEIEQGLLHRQLDLGIGYFG--QQLEALRYQPWLEETQAI 177
Cdd:cd08449     2 LNIGMVG---SVLWGGLGPALRRFKRQYPNVTVRFHELSPEAQKAALLSKRIDLGFVRFAdtLNDPPLASELLWREPMVV 78


                  ....*...
gi 2045450880 178 YCSADHPL 185
Cdd:cd08449    79 ALPEEHPL 86
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
8-72 2.84e-05

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 44.96  E-value: 2.84e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2045450880   8 IDLKLLRVFVAVAEAQGVSAAQEALLMNQSTISTHLASLETRLGFRLCQRGRSgFRLTPKGERML 72
Cdd:PRK13348    2 LDYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRGRP-CRPTPAGQRLL 65
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 7-72 2.93e-04

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 41.94  E-value: 2.93e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2045450880   7 DIDLKLLRVFVAVAEAQGVSAAQEALLMNQSTISTHLASLETRLGFRLCQR-GRSGFrLTPKGERML 72
Cdd:PRK15092   10 NLDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARhGRNKL-LTEHGIQLL 75
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
10-103 3.12e-04

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 41.67  E-value: 3.12e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880  10 LKLLRVFVAVAEAQGVSAAQEALLMNQSTISTHLASLETRLGFRLCQRGRSGFRLTPKGERMLIACRSLFNAARDFTRVS 89
Cdd:PRK10632    4 LKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQL 83

                          90
                  ....*....|....
gi 2045450880  90 QSLNGLLTGDLQIG 103
Cdd:PRK10632   84 YAFNNTPIGTLRIG 97
PBP2_CynR cd08425
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, ...
 120-191 4.49e-04

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: 40.39  E-value: 4.49e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2045450880 120 IKHFQRRHQDVQLQCRICSPNEIEQGLLHRQLDLGIGYFGQQLEALRYQPWLEETQAIYCSADHPLFTVEEP 191
Cdd:cd08425    20 IDRFHARYPGIALSLREMPQERIEAALADDRLDLGIAFAPVRSPDIDAQPLFDERLALVVGATHPLAQRRTA 91
PBP2_DntR_NahR_LinR_like cd08459
The C-terminal substrate binding domain of LysR-type transcriptional regulators that are ...
 120-202 5.25e-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: 5.25e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880 120 IKHFQRRHQDVQLQCRICSPNEIEQGLLHRQLDLGIGYFGQQLEALRYQPWLEETQAIYCSADHPLFTvEEPEREQIENA 199
Cdd:cd08459    19 LAALREVAPGVRIETVRLPVDELEEALESGEIDLAIGYLPDLGAGFFQQRLFRERYVCLVRKDHPRIG-STLTLEQFLAA 97


                  ...
gi 2045450880 200 RWV 202
Cdd:cd08459    98 RHV 100
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 118-155 8.56e-04

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: 39.85  E-value: 8.56e-04
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 2045450880 118 QAIKHFQRRHQDVQLQCRICSPNEIEQGLLHRQLDLGI 155
Cdd:cd08415    17 RAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGL 54
cysB PRK12681
HTH-type transcriptional regulator CysB;
10-190 1.57e-03

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 39.50  E-value: 1.57e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880  10 LKLLRVFVAVAEAQ-GVSAAQEALLMNQSTISTHLASLETRLGFRLCqrGRSG---FRLTPKGERMLIACRSLFNAARDF 85
Cdd:PRK12681    3 LQQLRYIVEVVNHNlNVSATAEGLYTSQPGISKQVRMLEDELGIQIF--ARSGkhlTQVTPAGEEIIRIAREILSKVESI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880  86 TRVSQSLNGLLTGDLQIGLVDnlvslpgnpfSQA-------IKHFQRRHQDVQLQCRICSPNEIEQGLLHRQLDLGIGYF 158
Cdd:PRK12681   81 KSVAGEHTWPDKGSLYIATTH----------TQAryalppvIKGFIERYPRVSLHMHQGSPTQIAEAAAKGNADFAIATE 150

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 2045450880 159 GQQL-EALRYQPWLEETQAIYCSADHPL-----FTVEE 190
Cdd:PRK12681  151 ALHLyDDLIMLPCYHWNRSVVVPPDHPLakkkkLTIEE 188
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 5-155 2.12e-03

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 39.20  E-value: 2.12e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880   5 LSDIDLKLLRVFVAVAEAQGVSAAQEALLMNQSTISTHLASLETRLGFRLCQRGRSGFRLTPKGERMLIAC-RSLFNAAR 83
Cdd:PRK11013    1 MAAVSLRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLFEEVqRSYYGLDR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880  84 dFTRVSQSLNGLLTGDLQIglvdnlVSLPgnPFSQAI-----KHFQRRHQDVQLQcriCSPNE---IEQGLLHRQLDLGI 155
Cdd:PRK11013   81 -IVSAAESLREFRQGQLSI------ACLP--VFSQSLlpglcQPFLARYPDVSLN---IVPQEsplLEEWLSAQRHDLGL 148
PBP2_CysB_like cd08413
The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains ...
 110-201 7.40e-03

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


Pssm-ID: 176105 [Multi-domain]  Cd Length: 198  Bit Score: 36.83  E-value: 7.40e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880 110 SLPGnpfsqAIKHFQRRHQDVQLQCRICSPNEIEQGLLHRQLDLGIGY-FGQQLEALRYQPWLEETQAIYCSADHPLFTV 188
Cdd:cd08413    14 VLPP-----VIAAFRKRYPKVKLSLHQGTPSQIAEMVLKGEADIAIATeALDDHPDLVTLPCYRWNHCVIVPPGHPLADL 88

                          90
                  ....*....|...
gi 2045450880 189 EEPEREQIenARW 201
Cdd:cd08413    89 GPLTLEDL--AQY 99
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 109-185 9.53e-03

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


Pssm-ID: 176117 [Multi-domain]  Cd Length: 199  Bit Score: 36.52  E-value: 9.53e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045450880 109 VSLPGNPFSQAIKHFQRRHQDVQLQCRICSPNEIEQGLLHRQLDLGIGYFG---QQLEALRYQPWleETQAIYcSADHPL 185
Cdd:cd08426     8 EGLAAELLPSLIARFRQRYPGVFFTVDVASTADVLEAVLSGEADIGLAFSPppePGIRVHSRQPA--PIGAVV-PPGHPL 84
 
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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