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Conserved domains on  [gi|1242933732|ref|WP_095870843|]
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LysR family transcriptional regulator [Rhodococcus sp. ACPA1]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 11426520)

LysR family transcriptional regulator negatively or positively regulates the transcription of specific genes; contains 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 proteins

CATH:  3.40.190.10
Gene Ontology:  GO:0003700|GO:0006355|GO:0003677
PubMed:  8257110|19047729
SCOP:  3000083|4000316

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-279 1.09e-37

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 134.22  E-value: 1.09e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732   1 MELRVLRYFLTIVETGSVTKAAEEVRVAQPSLSRQLRGLEASLGMTLFDRGGRQLILTAAGRRFLPLARDLVARADAAEA 80
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732  81 AVGALASGRAMRITVAAPPTTITDVIAPFLSTWGPEDPLVTVQ--AESPARAYQAL-GRGADVAISTAPPRR-RFAGLPV 156
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLElrEGNSDRLVDALlEGELDLAIRLGPPPDpGLVARPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732 157 ARLPLWAYVRADHAWANRDGVtigelaaaplivltpahgtrrvldhavqdadasydivleCDTPHVAQAMAASGHGIAVV 236
Cdd:COG0583   161 GEERLVLVASPDHPLARRAPL---------------------------------------VNSLEALLAAVAAGLGIALL 201

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*.
gi 1242933732 237 SD---DPRFDLHPLLILDGAGEPLQIHLHAAWDPSHYALRSIEIFA 279
Cdd:COG0583   202 PRflaADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFL 247
Periplasmic_Binding_Protein_Type_2 super family cl21456
Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent ...
 165-237 1.44e-09

Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent the ligand-binding domains found in solute binding proteins that serve as initial receptors in the transport, signal transduction and channel gating. The PBP2 proteins share the same architecture as periplasmic binding proteins type 1 (PBP1), but have a different topology. They are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The origin of PBP module can be traced across the distant phyla, including eukaryotes, archebacteria, and prokaryotes. The majority of PBP2 proteins are involved in the uptake of a variety of soluble substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. 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 family includes ionotropic glutamate receptors and unorthodox sensor proteins involved in signal transduction. The substrate binding domain of the LysR transcriptional regulators and the oligopeptide-like transport systems also contain the type 2 periplasmic binding fold and thus they are significantly homologous to that of the PBP2; however, these two families are grouped into a separate hierarchy of the PBP2 superfamily due to the large number of protein sequences.


The actual alignment was detected with superfamily member cd08420:

Pssm-ID: 473866 [Multi-domain]  Cd Length: 201  Bit Score: 56.73  E-value: 1.44e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1242933732 165 VRADHAWANRDGVTIGELAAAPLIVLTPAHGTRRVLDHAVQDADAS---YDIVLECDTPHVAQAMAASGHGIAVVS 237
Cdd:cd08420    78 VPPDHPLAGRKEVTAEELAAEPWILREPGSGTREVFERALAEAGLDgldLNIVMELGSTEAIKEAVEAGLGISILS 153
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-279 1.09e-37

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 134.22  E-value: 1.09e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732   1 MELRVLRYFLTIVETGSVTKAAEEVRVAQPSLSRQLRGLEASLGMTLFDRGGRQLILTAAGRRFLPLARDLVARADAAEA 80
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732  81 AVGALASGRAMRITVAAPPTTITDVIAPFLSTWGPEDPLVTVQ--AESPARAYQAL-GRGADVAISTAPPRR-RFAGLPV 156
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLElrEGNSDRLVDALlEGELDLAIRLGPPPDpGLVARPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732 157 ARLPLWAYVRADHAWANRDGVtigelaaaplivltpahgtrrvldhavqdadasydivleCDTPHVAQAMAASGHGIAVV 236
Cdd:COG0583   161 GEERLVLVASPDHPLARRAPL---------------------------------------VNSLEALLAAVAAGLGIALL 201

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*.
gi 1242933732 237 SD---DPRFDLHPLLILDGAGEPLQIHLHAAWDPSHYALRSIEIFA 279
Cdd:COG0583   202 PRflaADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFL 247
PRK09986 PRK09986
LysR family transcriptional regulator;
3-238 1.30e-23

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 97.49  E-value: 1.30e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732   3 LRVLRYFLTIVETGSVTKAAEEVRVAQPSLSRQLRGLEASLGMTLFDRGGRQLILTAAGRRFLPLARDLVARADAAEAAV 82
Cdd:PRK09986    9 LKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLARV 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732  83 GALASGRAMRITVAAPPTTITDVIAPFLSTWGPEDPLVTVQ--AESPARAYQAL-GRGADVAI---STAPPRRRFAGLPV 156
Cdd:PRK09986   89 EQIGRGEAGRIEIGIVGTALWGRLRPAMRHFLKENPNVEWLlrELSPSMQMAALeRRELDAGIwrmADLEPNPGFTSRRL 168

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732 157 ARLPLWAYVRADHAWANRDGVTIGELAAAPLIVLTPAHGTRRVLDHAV-QDADASYDIVLECDTPHVAQAMAASGHGIAV 235
Cdd:PRK09986  169 HESAFAVAVPEEHPLASRSSVPLKALRNEYFITLPFVHSDWGKFLQRVcQQAGFSPQIIRQVNEPQTVLAMVSMGIGITL 248


                  ...
gi 1242933732 236 VSD 238
Cdd:PRK09986  249 LPD 251
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 92-278 6.26e-23

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: 93.43  E-value: 6.26e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732  92 RITVAAPPTTITDVIAPFLSTWGPEDPLVTVQ--AESPARAYQALGRG-ADVAISTAPPRR-RFAGLPVARLPLWAYVRA 167
Cdd:cd05466     1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSlvEGGSSELLEALLEGeLDLAIVALPVDDpGLESEPLFEEPLVLVVPP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732 168 DHAWANRDGVTIGELAAAPLIVLTPAHGTRRVLDHAVQDADASYDIVLECDTPHVAQAMAASGHGIAVVSDD--PRFDLH 245
Cdd:cd05466    81 DHPLAKRKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESavEELADG 160

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1242933732 246 PLLILDGAGEPLQIHLHAAWDPSHYALRSIEIF 278
Cdd:cd05466   161 GLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAF 193
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 92-278 3.91e-21

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: 88.89  E-value: 3.91e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732  92 RITVAAPPTTITDVIAPFLSTWGPEDPLVTVQ--AESPARAYQALGRG-ADVAISTAPPRR-RFAGLPVARLPLWAYVRA 167
Cdd:pfam03466   3 RLRIGAPPTLASYLLPPLLARFRERYPDVELEltEGNSEELLDLLLEGeLDLAIRRGPPDDpGLEARPLGEEPLVLVAPP 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732 168 DHAWANRDGVTIGELAAAPLIVLTPAHGTRRVLDHAVQDADASYDIVLECDTPHVAQAMAASGHGIAVVSD---DPRFDL 244
Cdd:pfam03466  83 DHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRsavARELAD 162

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1242933732 245 HPLLILDGAGEPLQIHLHAAWDPSHYALRSIEIF 278
Cdd:pfam03466 163 GRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAF 196
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-237 7.47e-15

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: 73.42  E-value: 7.47e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732   1 MELRVLRYFLTIVETGSVTKAAEEVRVAQPSLSRQLRGLEASLGMTLFDRGGRQLILTAAGRRFLPLARDLVARADAAEA 80
Cdd:NF040786    1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732  81 AVGALASGRAMRITVAA---PPTTI-TDVIAPFLSTWgPEDPLVTVQAESPARAYQALGRGADVAIS-TAPPRRRFAGLP 155
Cdd:NF040786   81 EFDRYGKESKGVLRIGAstiPGQYLlPELLKKFKEKY-PNVRFKLMISDSIKVIELLLEGEVDIGFTgTKLEKKRLVYTP 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732 156 VARLPLWAYVRADHAWANR--DGVTIGELAAAPLIVLTPAHGTRRVLDHAVQDADAS---YDIVLECDTPHVAQAMAASG 230
Cdd:NF040786  160 FYKDRLVLITPNGTEKYRMlkEEISISELQKEPFIMREEGSGTRKEAEKALKSLGISledLNVVASLGSTEAIKQSVEAG 239


                  ....*..
gi 1242933732 231 HGIAVVS 237
Cdd:NF040786  240 LGISVIS 246
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 165-237 1.44e-09

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: 56.73  E-value: 1.44e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1242933732 165 VRADHAWANRDGVTIGELAAAPLIVLTPAHGTRRVLDHAVQDADAS---YDIVLECDTPHVAQAMAASGHGIAVVS 237
Cdd:cd08420    78 VPPDHPLAGRKEVTAEELAAEPWILREPGSGTREVFERALAEAGLDgldLNIVMELGSTEAIKEAVEAGLGISILS 153
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-279 1.09e-37

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 134.22  E-value: 1.09e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732   1 MELRVLRYFLTIVETGSVTKAAEEVRVAQPSLSRQLRGLEASLGMTLFDRGGRQLILTAAGRRFLPLARDLVARADAAEA 80
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732  81 AVGALASGRAMRITVAAPPTTITDVIAPFLSTWGPEDPLVTVQ--AESPARAYQAL-GRGADVAISTAPPRR-RFAGLPV 156
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLElrEGNSDRLVDALlEGELDLAIRLGPPPDpGLVARPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732 157 ARLPLWAYVRADHAWANRDGVtigelaaaplivltpahgtrrvldhavqdadasydivleCDTPHVAQAMAASGHGIAVV 236
Cdd:COG0583   161 GEERLVLVASPDHPLARRAPL---------------------------------------VNSLEALLAAVAAGLGIALL 201

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*.
gi 1242933732 237 SD---DPRFDLHPLLILDGAGEPLQIHLHAAWDPSHYALRSIEIFA 279
Cdd:COG0583   202 PRflaADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFL 247
PRK09986 PRK09986
LysR family transcriptional regulator;
3-238 1.30e-23

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 97.49  E-value: 1.30e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732   3 LRVLRYFLTIVETGSVTKAAEEVRVAQPSLSRQLRGLEASLGMTLFDRGGRQLILTAAGRRFLPLARDLVARADAAEAAV 82
Cdd:PRK09986    9 LKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLARV 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732  83 GALASGRAMRITVAAPPTTITDVIAPFLSTWGPEDPLVTVQ--AESPARAYQAL-GRGADVAI---STAPPRRRFAGLPV 156
Cdd:PRK09986   89 EQIGRGEAGRIEIGIVGTALWGRLRPAMRHFLKENPNVEWLlrELSPSMQMAALeRRELDAGIwrmADLEPNPGFTSRRL 168

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732 157 ARLPLWAYVRADHAWANRDGVTIGELAAAPLIVLTPAHGTRRVLDHAV-QDADASYDIVLECDTPHVAQAMAASGHGIAV 235
Cdd:PRK09986  169 HESAFAVAVPEEHPLASRSSVPLKALRNEYFITLPFVHSDWGKFLQRVcQQAGFSPQIIRQVNEPQTVLAMVSMGIGITL 248


                  ...
gi 1242933732 236 VSD 238
Cdd:PRK09986  249 LPD 251
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 92-278 6.26e-23

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: 93.43  E-value: 6.26e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732  92 RITVAAPPTTITDVIAPFLSTWGPEDPLVTVQ--AESPARAYQALGRG-ADVAISTAPPRR-RFAGLPVARLPLWAYVRA 167
Cdd:cd05466     1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSlvEGGSSELLEALLEGeLDLAIVALPVDDpGLESEPLFEEPLVLVVPP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732 168 DHAWANRDGVTIGELAAAPLIVLTPAHGTRRVLDHAVQDADASYDIVLECDTPHVAQAMAASGHGIAVVSDD--PRFDLH 245
Cdd:cd05466    81 DHPLAKRKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESavEELADG 160

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1242933732 246 PLLILDGAGEPLQIHLHAAWDPSHYALRSIEIF 278
Cdd:cd05466   161 GLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAF 193
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 92-278 3.91e-21

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: 88.89  E-value: 3.91e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732  92 RITVAAPPTTITDVIAPFLSTWGPEDPLVTVQ--AESPARAYQALGRG-ADVAISTAPPRR-RFAGLPVARLPLWAYVRA 167
Cdd:pfam03466   3 RLRIGAPPTLASYLLPPLLARFRERYPDVELEltEGNSEELLDLLLEGeLDLAIRRGPPDDpGLEARPLGEEPLVLVAPP 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732 168 DHAWANRDGVTIGELAAAPLIVLTPAHGTRRVLDHAVQDADASYDIVLECDTPHVAQAMAASGHGIAVVSD---DPRFDL 244
Cdd:pfam03466  83 DHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRsavARELAD 162

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1242933732 245 HPLLILDGAGEPLQIHLHAAWDPSHYALRSIEIF 278
Cdd:pfam03466 163 GRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAF 196
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-62 5.87e-21

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 83.97  E-value: 5.87e-21
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732   3 LRVLRYFLTIVETGSVTKAAEEVRVAQPSLSRQLRGLEASLGMTLFDRGGRQLILTAAGR 62
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 1-219 1.52e-19

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 86.55  E-value: 1.52e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732   1 MELRVLRYFLTIVETGSVTKAAEEVRVAQPSLSRQLRGLEASLGMTLFDRGGRQLILTAAGRRFLPLAR----DLVARAd 76
Cdd:PRK11242    1 MLLRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARralqDLEAGR- 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732  77 aaeaavgalasgRAM---------RITVAAPPTTITDVIAPFLSTWGPEDPLVT--VQAESPARAYQALGRGA-DVAIST 144
Cdd:PRK11242   80 ------------RAIhdvadlsrgSLRLAMTPTFTAYLIGPLIDAFHARYPGITltIREMSQERIEALLADDElDVGIAF 147

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1242933732 145 APPR-RRFAGLPVARLPLWAYVRADHAWAN-RDGVTIGELAAAPLIVLTPAHGTRRVLDHAVQDADASYDIVLECDT 219
Cdd:PRK11242  148 APVHsPEIEAQPLFTETLALVVGRHHPLAArRKALTLDELADEPLVLLSAEFATREQIDRYFRRHGVTPRVAIEANS 224
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 1-69 1.16e-15

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 75.58  E-value: 1.16e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1242933732   1 MELRVLRYFLTIVETGSVTKAAEEVRVAQPSLSRQLRGLEASLGMTLFDRGGRQLILTAAGRRFLPLAR 69
Cdd:PRK09906    1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDAR 69
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-237 7.47e-15

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: 73.42  E-value: 7.47e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732   1 MELRVLRYFLTIVETGSVTKAAEEVRVAQPSLSRQLRGLEASLGMTLFDRGGRQLILTAAGRRFLPLARDLVARADAAEA 80
Cdd:NF040786    1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732  81 AVGALASGRAMRITVAA---PPTTI-TDVIAPFLSTWgPEDPLVTVQAESPARAYQALGRGADVAIS-TAPPRRRFAGLP 155
Cdd:NF040786   81 EFDRYGKESKGVLRIGAstiPGQYLlPELLKKFKEKY-PNVRFKLMISDSIKVIELLLEGEVDIGFTgTKLEKKRLVYTP 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732 156 VARLPLWAYVRADHAWANR--DGVTIGELAAAPLIVLTPAHGTRRVLDHAVQDADAS---YDIVLECDTPHVAQAMAASG 230
Cdd:NF040786  160 FYKDRLVLITPNGTEKYRMlkEEISISELQKEPFIMREEGSGTRKEAEKALKSLGISledLNVVASLGSTEAIKQSVEAG 239


                  ....*..
gi 1242933732 231 HGIAVVS 237
Cdd:NF040786  240 LGISVIS 246
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 138-278 2.94e-14

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: 69.87  E-value: 2.94e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732 138 ADVAISTAPPRRR-FAGLPVARLPLWAYVRADHAWANRDGVTIGELAAAPLIVLTPAHGTRRVLDHAVQDADASYDIVLE 216
Cdd:cd08434    50 LDLALCSPVPDEPdIEWIPLFTEELVLVVPKDHPLAGRDSVDLAELADEPFVLLSPGFGLRPIVDELCAAAGFTPKIAFE 129

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1242933732 217 CDTPHVAQAMAASGHGIAVVSDDPRFDLHPLLI--LDGAGEPLQIHLhaAWDPSHYALRSIEIF 278
Cdd:cd08434   130 GEEDSTIAGLVAAGLGVAILPEMTLLNPPGVKKipIKDPDAERTIGL--AWLKDRYLSPAARRF 191
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 1-284 2.83e-13

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 68.92  E-value: 2.83e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732   1 MELRVLRYFLTIVETG-SVTKAAEEVRVAQPSLSRQLRGLEASLGMTLFDRGGRQLI-LTAAGRRFLPLARDLVARADAA 78
Cdd:PRK12683    1 MNFQQLRIIREAVRQNfNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTgLTEPGKELLQIVERMLLDAENL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732  79 EAAVGALASGRAMRITVAAPPT----TITDVIAPFLSTWgPEDPLVTVQAeSPARAYQALGRG-ADVAISTApPRRRFAG 153
Cdd:PRK12683   81 RRLAEQFADRDSGHLTVATTHTqaryALPKVVRQFKEVF-PKVHLALRQG-SPQEIAEMLLNGeADIGIATE-ALDREPD 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732 154 LpvARLPLWAY-----VRADHAWANRDGVTIGELAAAPLIVLTPAHGTRRVLDHAVQDADASYDIVLECDTPHVAQAMAA 228
Cdd:PRK12683  158 L--VSFPYYSWhhvvvVPKGHPLTGRENLTLEAIAEYPIITYDQGFTGRSRIDQAFAEAGLVPDIVLTALDADVIKTYVE 235

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1242933732 229 SGHGIAVVSD---DPRFDlHPLLILDGAgeplqiHL------HAAWDPSH----YALRSIEIFATGLSR 284
Cdd:PRK12683  236 LGMGVGIVAAmayDPQRD-TGLVALDTD------HLfeanttRVGLRRGAylrgYAYRFIELFAPHLSE 297
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-236 7.69e-13

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: 66.01  E-value: 7.69e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732  92 RITVAAPPTTITDVIAPFLSTWGPEDPLVTVQ--AESPARAYQALGRG-ADVAISTAP-PRRRFAGLPVARLPLWAYVRA 167
Cdd:cd08440     1 RVRVAALPSLAATLLPPVLAAFRRRHPGIRVRlrDVSAEQVIEAVRSGeVDFGIGSEPeADPDLEFEPLLRDPFVLVCPK 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1242933732 168 DHAWANRDGVTIGELAAAPLIVLTPAHGTRRVLDHAVQDADASYDIVLECDTPHVAQAMAASGHGIAVV 236
Cdd:cd08440    81 DHPLARRRSVTWAELAGYPLIALGRGSGVRALIDRALAAAGLTLRPAYEVSHMSTALGMVAAGLGVAVL 149
rbcR CHL00180
LysR transcriptional regulator; Provisional
 3-65 2.25e-12

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 66.20  E-value: 2.25e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1242933732   3 LRVLRYFLTIVETGSVTKAAEEVRVAQPSLSRQLRGLEASLGMTLFDRGGRQLILTAAGRRFL 65
Cdd:CHL00180    7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLL 69
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
1-289 1.77e-11

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 63.46  E-value: 1.77e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732   1 MELRVLRYFLTIVETG-SVTKAAEEVRVAQPSLSRQLRGLEASLGMTLFDRGGRQLI-LTAAGRRFLPLARDLVARADAA 78
Cdd:PRK12684    1 MNLHQLRFVREAVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRgLTEPGRIILASVERILQEVENL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732  79 EAAVGALASGRAMRITVAappTTIT-------DVIAPFLSTWgpedPLV--TVQAESPAR-AYQALGRGADVAISTappr 148
Cdd:PRK12684   81 KRVGKEFAAQDQGNLTIA---TTHTqaryalpAAIKEFKKRY----PKVrlSILQGSPTQiAEMVLHGQADLAIAT---- 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732 149 RRFAGLP-VARLPLWAYVRA-----DHAWANRDGVTIGELAAAPLIVLTPAHGTRRVLDHAVQDADASYDIVLECDTPHV 222
Cdd:PRK12684  150 EAIADYKeLVSLPCYQWNHCvvvppDHPLLERKPLTLEDLAQYPLITYDFAFAGRSKINKAFALRGLKPDIVLEAIDADV 229

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1242933732 223 AQAMAASGHGIAVVSD---DPRFDlHPLLILDGAG--EPLQIHL---HAAWdPSHYALRSIEIFATGLSRFCVEQ 289
Cdd:PRK12684  230 IKTYVELGLGVGIVADmafDPERD-RNLRAIDAGHlfGSSTTRLglrRGAY-LRGYVYTFIELFAPTLNRKLVEQ 302
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 1-62 1.80e-11

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 63.55  E-value: 1.80e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1242933732   1 MELRVLRYFLTIVETGSVTKAAEEVRVAQPSLSRQLRGLEASLGMTLFDRGGRQLILTAAGR 62
Cdd:PRK11233    1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGK 62
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 92-235 8.50e-11

The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) protein, contains the type 2 periplasmic binding fold; The NAC is a LysR-type transcription regulator that activates expression of operons such as hut (histidine utilization) and ure (urea utilization), allowing use of non-preferred (poor) nitrogen sources, and represses expression of operons, such as glutamate dehydrogenase (gdh), allowing assimilation of the preferred nitrogen source. The expression of the nac gene is fully dependent on the nitrogen regulatory system (NTR) and the sigma54-containing RNA polymerase (sigma54-RNAP). In response to nitrogen starvation, NTR system activates the expression of nac, and NAC activates the expression of hut, ure, and put (proline utilization). NAC is not involved in the transcription of Sigma70-RNAP operons such as glnA, which directly respond by the NTR system, but activates the transcription of sigma70-RNAP dependent operons such as hut. Hence, NAC allows the coupling of sigma70-RNAP dependent operons to the sigma54-RNAP dependent NTR system. This substrate-binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176124  Cd Length: 198  Bit Score: 60.30  E-value: 8.50e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732  92 RITVAAPPTTITDVIAPFLSTWGPEDPLVTVQ-AESPARAYQA-LGRG-ADVAI-STAPPRRRFAGLPVARLPLWAYVRA 167
Cdd:cd08433     1 RVSVGLPPSAASVLAVPLLRAVRRRYPGIRLRiVEGLSGHLLEwLLNGrLDLALlYGPPPIPGLSTEPLLEEDLFLVGPA 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1242933732 168 DHAWANRDGVTIGELAAAPLIVLTPAHGTRRVLDHAVQDADASYDIVLECDTPHVAQAMAASGHGIAV 235
Cdd:cd08433    81 DAPLPRGAPVPLAELARLPLILPSRGHGLRRLVDEAAARAGLTLNVVVEIDSVATLKALVAAGLGYTI 148
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 17-100 1.06e-10

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 61.01  E-value: 1.06e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732  17 SVTKAAEEVRVAQPSLSRQLRGLEASLGMTLFDRGGRQLILTAAGRRFLPLARDLVarADAAEAAVGALASGRAMRITVA 96
Cdd:PRK11139   22 SFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIF--DQLAEATRKLRARSAKGALTVS 99


                  ....
gi 1242933732  97 APPT 100
Cdd:PRK11139  100 LLPS 103
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 92-236 1.37e-10

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


Pssm-ID: 176107 [Multi-domain]  Cd Length: 196  Bit Score: 59.50  E-value: 1.37e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732  92 RITVAAPPTT----ITDVIAPFLSTwgPEDPLVTVQAESPARAYQALGRG-ADVAISTAPPRRR-FAGLPVARLPLWAYV 165
Cdd:cd08415     1 TLRIAALPALalslLPRAIARFRAR--HPDVRISLHTLSSSTVVEAVLSGqADLGLASLPLDHPgLESEPLASGRAVCVL 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1242933732 166 RADHAWANRDGVTIGELAAAPLIVLTPAHGTRRVLDHAVQDADASYDIVLECDTPHVAQAMAASGHGIAVV 236
Cdd:cd08415    79 PPGHPLARKDVVTPADLAGEPLISLGRGDPLRQRVDAAFERAGVEPRIVIETQLSHTACALVAAGLGVAIV 149
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 122-269 1.41e-10

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: 59.54  E-value: 1.41e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732 122 VQAESPARAYQALGRGADVAISTAPPRR--RFAGLPVARLPLWAYVRADHAWANRDGVTIGELAAAPLIVLTPAHGTRRV 199
Cdd:cd08436    34 RQAGSDDLLAAVREGRLDLAFVGLPERRppGLASRELAREPLVAVVAPDHPLAGRRRVALADLADEPFVDFPPGTGARRQ 113

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732 200 LDHAVQDADASYDIVLECDTPHVAQAMAASGHGIAVVSDDPRFDLHPLLILDGAGEPlQIHLHAAWDPSH 269
Cdd:cd08436   114 VDRAFAAAGVRRRVAFEVSDVDLLLDLVARGLGVALLPASVAARLPGLAALPLEPAP-RRRLYLAWSAPP 182
cysB PRK12681
HTH-type transcriptional regulator CysB;
1-215 1.90e-10

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 60.68  E-value: 1.90e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732   1 MELRVLRYFLTIVETG-SVTKAAEEVRVAQPSLSRQLRGLEASLGMTLFDRGGRQLI-LTAAGRRFLPLARDLVARADAA 78
Cdd:PRK12681    1 MKLQQLRYIVEVVNHNlNVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTqVTPAGEEIIRIAREILSKVESI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732  79 EAAVGALASGRAMRITVAappTTIT-------DVIAPFLSTWgPEDPLVTVQAeSPARAYQALGRG-ADVAISTAPPrRR 150
Cdd:PRK12681   81 KSVAGEHTWPDKGSLYIA---TTHTqaryalpPVIKGFIERY-PRVSLHMHQG-SPTQIAEAAAKGnADFAIATEAL-HL 154

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732 151 FAGLPVarLP--LW---AYVRADHAWANRDGVTIGELAAAPLIVLTPAHGTRRVLDHAVQDADASYDIVL 215
Cdd:PRK12681  155 YDDLIM--LPcyHWnrsVVVPPDHPLAKKKKLTIEELAQYPLVTYVFGFTGRSELDTAFNRAGLTPRIVF 222
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-247 4.45e-10

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: 57.99  E-value: 4.45e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732  92 RITVAAPPTTITDVIAPFLSTWGPEDPLVTVQAES--PARAYQALGRG-ADVAI----STAPPR--RRFAGLPVARLPLW 162
Cdd:cd08423     1 TLRVGAFPTAAAALLPPALAALRARHPGLEVRLREaePPESLDALRAGeLDLAVvfdyPVTPPPddPGLTRVPLLDDPLD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732 163 AYVRADHAWANRDGVTIGELAAAPLIVLTPAHGTRRVLDHAVQDADASYDIVLECDTPHVAQAMAASGHGIAVVsddPRF 242
Cdd:cd08423    81 LVLPADHPLAGREEVALADLADEPWIAGCPGSPCHRWLVRACRAAGFTPRIAHEADDYATVLALVAAGLGVALV---PRL 157


                  ....*
gi 1242933732 243 DLHPL 247
Cdd:cd08423   158 ALGAR 162
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 1-284 4.85e-10

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 59.23  E-value: 4.85e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732   1 MELRVLRYFLTIVETG-SVTKAAEEVRVAQPSLSRQLRGLEASLGMTLFDRGGRQLI-LTAAGRRFLPLARDLVARADAA 78
Cdd:PRK12682    1 MNLQQLRFVREAVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKgLTEPGKAVLDVIERILREVGNI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732  79 EAAVGALASGRAMRITVAappTTIT-------DVIAPFLSTWgpedPLVTV--QAESPARAYQALGRG-ADVAISTAPPR 148
Cdd:PRK12682   81 KRIGDDFSNQDSGTLTIA---TTHTqaryvlpRVVAAFRKRY----PKVNLslHQGSPDEIARMVISGeADIGIATESLA 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732 149 R--RFAGLPVARLPLWAYVRADHAWANRDGVTIGELAAAPLIVLTPAHGTRRVLDHAVQDADASYDIVLECDTPHVAQAM 226
Cdd:PRK12682  154 DdpDLATLPCYDWQHAVIVPPDHPLAQEERITLEDLAEYPLITYHPGFTGRSRIDRAFAAAGLQPDIVLEAIDSDVIKTY 233

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1242933732 227 AASGHGIAVVSD---DPRFDlHPLLILDGAgeplqiHL---HAAW-------DPSHYALRSIEIFATGLSR 284
Cdd:PRK12682  234 VRLGLGVGIVAEmayRPDRD-GDLVALPAG------HLfgpNTAWvalkrgaYLRNYVYKFIELCAPHLSR 297
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 92-269 8.41e-10

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: 57.13  E-value: 8.41e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732  92 RITVAAPPTTITDVIAPFLSTWGPEDPLVTVQAE--SPARAYQALGRG-ADVAISTAPPRR-RFAGLPVARLPLWAYVRA 167
Cdd:cd08414     1 RLRIGFVGSALYGLLPRLLRRFRARYPDVELELRemTTAEQLEALRAGrLDVGFVRPPPDPpGLASRPLLREPLVVALPA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732 168 DHAWANRDGVTIGELAAAPLIVLTPAHGT--RRVLDHAVQDADASYDIVLECDTPHVAQAMAASGHGIAVVSDD------ 239
Cdd:cd08414    81 DHPLAARESVSLADLADEPFVLFPREPGPglYDQILALCRRAGFTPRIVQEASDLQTLLALVAAGLGVALVPASvarlqr 160

                         170       180       190
                  ....*....|....*....|....*....|
gi 1242933732 240 PRFDLHPLlildgAGEPLQIHLHAAWDPSH 269
Cdd:cd08414   161 PGVVYRPL-----ADPPPRSELALAWRRDN 185
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 165-237 1.44e-09

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: 56.73  E-value: 1.44e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1242933732 165 VRADHAWANRDGVTIGELAAAPLIVLTPAHGTRRVLDHAVQDADAS---YDIVLECDTPHVAQAMAASGHGIAVVS 237
Cdd:cd08420    78 VPPDHPLAGRKEVTAEELAAEPWILREPGSGTREVFERALAEAGLDgldLNIVMELGSTEAIKEAVEAGLGISILS 153
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-235 3.79e-09

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: 55.39  E-value: 3.79e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732  92 RITVAAPPTTITDVIAPFLSTWGPEDPLVTVQAE--SPARAYQALGRG-ADVAIS-TAPPRRRFAGLPVARLPLWAYVRA 167
Cdd:cd08426     1 RVRVATGEGLAAELLPSLIARFRQRYPGVFFTVDvaSTADVLEAVLSGeADIGLAfSPPPEPGIRVHSRQPAPIGAVVPP 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1242933732 168 DHAWANRDGVTIGELAAAPLIVLTPAHGTRRVLDHAVQDADASYDIVLECDTPHVAQAMAASGHGIAV 235
Cdd:cd08426    81 GHPLARQPSVTLAQLAGYPLALPPPSFSLRQILDAAFARAGVQLEPVLISNSIETLKQLVAAGGGISL 148
PRK12680 PRK12680
LysR family transcriptional regulator;
1-166 4.83e-09

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 56.55  E-value: 4.83e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732   1 MELRVLRYFLTIVETG-SVTKAAEEVRVAQPSLSRQLRGLEASLGMTLFDRGGRQL-ILTAAGRRFLPLARDLVARADAA 78
Cdd:PRK12680    1 MTLTQLRYLVAIADAElNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLeSVTPAGVEVIERARAVLSEANNI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732  79 EAAVGALASGRAMRITVAAPPTTITDVIAPFLSTWGPEDPLVTV--QAESPARAYQALGRG-ADVAISTAPPRRRFAGLP 155
Cdd:PRK12680   81 RTYAANQRRESQGQLTLTTTHTQARFVLPPAVAQIKQAYPQVSVhlQQAAESAALDLLGQGdADIAIVSTAGGEPSAGIA 160

                         170
                  ....*....|.
gi 1242933732 156 VarlPLWAYVR 166
Cdd:PRK12680  161 V---PLYRWRR 168
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 3-202 5.45e-09

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 55.85  E-value: 5.45e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732   3 LRVLRYFLTIVETGSVTKAAEEVRVAQPSLSRQLRGLEASLGMTLFDRGGRQLILTAAGRRFLPLARDLVARADAAEAAV 82
Cdd:PRK10837    5 LRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQAVEIEQLF 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732  83 GALASgrAMRItvaAPPTTITD-----VIAPFLSTWgPEDPLV--------TVQAESPARAYQALGRGA--DVAISTAPP 147
Cdd:PRK10837   85 REDNG--ALRI---YASSTIGNyilpaMIARYRRDY-PQLPLElsvgnsqdVINAVLDFRVDIGLIEGPchSPELISEPW 158

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1242933732 148 RRRfaglpvarlPLWAYVRADHAWANRDgVTIGELAAAPLIVLTPAHGTRRVLDH 202
Cdd:PRK10837  159 LED---------ELVVFAAPDSPLARGP-VTLEQLAAAPWILRERGSGTREIVDY 203
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 92-270 5.67e-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: 54.87  E-value: 5.67e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732  92 RITVAAPPTTITDVIAPFLSTWGPEDPLVTVQ-AESPARAY-QALGRGA-DVAISTAPP-RRRFAGLPVARLPLWAYVRA 167
Cdd:cd08438     1 HLRLGLPPLGGSLLFAPLLAAFRQRYPNIELElVEYGGKKVeQAVLNGElDVGITVLPVdEEEFDSQPLCNEPLVAVLPR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732 168 DHAWANRDGVTIGELAAAPLIVLTPAHGTRRVLDHAVQDADASYDIVLECDTPHVAQAMAASGHGIAVVS-------DDP 240
Cdd:cd08438    81 GHPLAGRKTVSLADLADEPFILFNEDFALHDRIIDACQQAGFTPNIAARSSQWDFIAELVAAGLGVALLPrsiaqrlDNA 160

                         170       180       190
                  ....*....|....*....|....*....|
gi 1242933732 241 RFDLHPLlildgAGEPLQIHLHAAWDPSHY 270
Cdd:cd08438   161 GVKVIPL-----TDPDLRWQLALIWRKGRY 185
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 1-197 6.13e-09

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 55.81  E-value: 6.13e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732   1 MELRVLRYFLTIVETGSVTKAAEEVRVAQPSLSRQLRGLEASLGMTLFDRGGRQLILTAAGRRFLPLARDLVarADAAEA 80
Cdd:PRK11151    1 MNIRDLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVL--REVKVL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732  81 AVGALASGRAMritvAAP------PTT---ITDVIAPFLSTWGPEDPLVTVQAESPARAYQaLGRGA-DVAI-----STA 145
Cdd:PRK11151   79 KEMASQQGETM----SGPlhigliPTVgpyLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQ-LDSGKlDCAIlalvkESE 153

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1242933732 146 PprrrFAGLPVARLPLWAYVRADHAWANRDGVTIGELAAAPLIVLTPAHGTR 197
Cdd:PRK11151  154 A----FIEVPLFDEPMLLAVYEDHPWANRDRVPMSDLAGEKLLMLEDGHCLR 201
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 1-146 9.32e-08

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 52.30  E-value: 9.32e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732   1 MELRVLRYFLTIVETGSVTKAAEEVRVAQPSLSRQLRGLEASLGMTLFDRGGRQLILTAAGRRFLPLARDLVARADAAEA 80
Cdd:PRK14997    2 TDLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQD 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1242933732  81 AVGALASGRAMRITVAAPPTTITDVIAPFLSTWGPEDPLVTVQAESPARAYQALGRGADVAISTAP 146
Cdd:PRK14997   82 AIAALQVEPRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLEATNRRVDVVGEGVDVAIRVRP 147
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
6-70 1.98e-07

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 51.35  E-value: 1.98e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1242933732   6 LRYFLTIVETGSVTKAAEEVRVAQPSLSRQLRGLEASLGMTLFDRGGRQLILTAAGRRFLPLARD 70
Cdd:PRK10094    7 LRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARD 71
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 3-63 3.28e-07

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 50.76  E-value: 3.28e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1242933732   3 LRVLRYFLTIVETGSVTKAAEEVRVAQPSLSRQLRGLEASLGMTLFDRGGRQLILTAAGRR 63
Cdd:PRK11013    6 LRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLR 66
cbl PRK12679
HTH-type transcriptional regulator Cbl;
17-238 8.80e-07

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 49.42  E-value: 8.80e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732  17 SVTKAAEEVRVAQPSLSRQLRGLEASLGMTLFDRGGRQLI-LTAAGRRFLPLARDLVARADAAEAAVGALASGRAMRITV 95
Cdd:PRK12679   18 NLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRLLgMTEPGKALLVIAERILNEASNVRRLADLFTNDTSGVLTI 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732  96 AAPPT----TITDVIAPFLSTWgPEDPLVTVQAeSPARAYQALGRG-ADVAISTapprRRFAGLP-VARLPLWAY----- 164
Cdd:PRK12679   98 ATTHTqarySLPEVIKAFRELF-PEVRLELIQG-TPQEIATLLQNGeADIGIAS----ERLSNDPqLVAFPWFRWhhsll 171

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1242933732 165 VRADHAWANRDGVTIGELAAAPLIVLTPAHGTRRVLDHAVQDADASYDIVLECDTPHVAQAMAASGHGIAVVSD 238
Cdd:PRK12679  172 VPHDHPLTQITPLTLESIAKWPLITYRQGITGRSRIDDAFARKGLLADIVLSAQDSDVIKTYVALGLGIGLVAE 245
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
30-70 1.02e-06

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 49.05  E-value: 1.02e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1242933732  30 PS-LSRQLRGLEASLGMTLFDRGGRQLILTAAGRRFLPLARD 70
Cdd:PRK11716    5 PStLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQ 46
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
1-116 5.02e-06

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 47.36  E-value: 5.02e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732   1 MELRVLRYFLTIVETGSVTKAAEEVRVAQPSLSRQLRGLEASLGMTLFDRGGRQLILTAAGRRFLPLARDLVARADAAEA 80
Cdd:PRK10082   11 IETKWLYDFLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESNLA 90

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1242933732  81 AVGALASGRAMRITVAAP--------PTTITDViaPFLSTWGPE 116
Cdd:PRK10082   91 ELRGGSDYAQRKIKIAAAhslslgllPSIISQM--PPLFTWAIE 132
nhaR PRK11062
transcriptional activator NhaR; Provisional
 6-61 5.55e-06

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 46.93  E-value: 5.55e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1242933732   6 LRYFLTIVETGSVTKAAEEVRVAQPSLSRQLRGLEASLGMTLFDRGGRQLILTAAG 61
Cdd:PRK11062    9 LYYFWMVCKEGSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELG 64
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
1-71 8.29e-06

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 46.16  E-value: 8.29e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1242933732   1 MELRVLRYFLTIVETGSVTKAAEEVRVAQPSLSRQLRGLEASLGMTLFDRGGRQLILTAAGRRFLPLARDL 71
Cdd:PRK03601    1 MDTELLKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYAETL 71
PBP2_XapR cd08449
The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved ...
 126-238 2.09e-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: 44.57  E-value: 2.09e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732 126 SPARAYQALGRG-ADVAISTAPPRRRFAGL---PVARLPLWAYVRADHAWANRDGVTIGELAAAPLIVLTPAHGT-RRVL 200
Cdd:cd08449    37 SPEAQKAALLSKrIDLGFVRFADTLNDPPLaseLLWREPMVVALPEEHPLAGRKSLTLADLRDEPFVFLRLANSRfADFL 116

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1242933732 201 DHAVQDADASYDIVLECDTPHVAQAMAASGHGIAVVSD 238
Cdd:cd08449   117 INCCLQAGFTPQITQEVVEPQTLMALVAAGFGVALVPE 154
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 132-280 2.09e-05

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: 44.46  E-value: 2.09e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732 132 QALGRG-ADVAI---STAPPRrrFAGLPVARLPLWAYVRADHAWANRDGVTIGELAAAPLIVLTPAHGTRRVLDhAVQDA 207
Cdd:cd08412    43 EGLRSGeLDLALtydLDLPED--IAFEPLARLPPYVWLPADHPLAGKDEVSLADLAAEPLILLDLPHSREYFLS-LFAAA 119

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1242933732 208 DASYDIVLECDTPHVAQAMAASGHGIAVVSDDPR----FDLHPLLILDGAGEPLQIHLHAAWDPSHYALRSIEIFAT 280
Cdd:cd08412   120 GLTPRIAYRTSSFEAVRSLVANGLGYSLLNDRPYrpwsYDGKRLVRRPLADPVPPLRLGLAWRRGARLTRAARAFVD 196
PRK09791 PRK09791
LysR family transcriptional regulator;
1-69 3.02e-05

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 44.75  E-value: 3.02e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1242933732   1 MELRVLRYFLTIVETGSVTKAAEEVRVAQPSLSRQLRGLEASLGMTLFDRGGRQLILTAAGRRFLPLAR 69
Cdd:PRK09791    5 VKIHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHAS 73
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
1-264 3.43e-05

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 44.62  E-value: 3.43e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732   1 MELRVLRYFLTIVETGSVTKAAEEVRVAQPSLSRQLRGLEASLGMTLFDRGGRQLILTAAGRRFLPLARDLVARADAAEA 80
Cdd:PRK15421    2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQ 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732  81 AVGALasgRAMRITVAAPPTTITDVIAPFLSTWGPEDPLVTVQAES-----PARAYQAlGRGADVAISTAPPRRRFAGLP 155
Cdd:PRK15421   82 ACNEP---QQTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSgvtfdPQPALQQ-GELDLVMTSDILPRSGLHYSP 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732 156 VARLPLWAYVRADHAWANRDGVTIGELAAAPLIVLTPAHGTRRVLDHAVQDADASYDIVLECDTPHVAQaMAASGHGIA- 234
Cdd:PRK15421  158 MFDYEVRLVLAPDHPLAAKTRITPEDLASETLLIYPVQRSRLDVWRHFLQPAGVSPSLKSVDNTLLLIQ-MVAARMGIAa 236

                         250       260       270
                  ....*....|....*....|....*....|....
gi 1242933732 235 ----VVSDdprFDLHPLLILDGAGEPLQIHLHAA 264
Cdd:PRK15421  237 lphwVVES---FERQGLVVTKTLGEGLWSRLYAA 267
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 15-72 5.15e-05

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 44.16  E-value: 5.15e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732  15 TGSVTKAAEEV-RVaqPS-LSRQLRGLEASLGMTLFDRGGRQLILTAAGRRFLPLARDLV 72
Cdd:PRK11074   16 TGSFSAAAQELhRV--PSaVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVI 73
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 1-69 5.27e-05

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 43.86  E-value: 5.27e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1242933732   1 MELRVLRYFLTIVETGSVTKAAEEVRVAQPSLSRQLRGLEASLGMTLFDRGGRQLILTAAGRRFLPLAR 69
Cdd:PRK15092   11 LDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYAR 79
PRK10341 PRK10341
transcriptional regulator TdcA;
6-65 5.66e-05

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 44.08  E-value: 5.66e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732   6 LRYFLTIVETGSVTKAAEEVRVAQPSLSRQLRGLEASLGMTLFDRGGRQLILTAAGRRFL 65
Cdd:PRK10341   12 LVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLL 71
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
 139-265 7.67e-05

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: 42.88  E-value: 7.67e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732 139 DVAISTAPPRrrfaGLPV-----ARLPLWAYVRADHAWANRDGVTIGELAAAPLIVLTPAHGTRRVLDHAVQDADASYDI 213
Cdd:cd08419    50 DLAIMGRPPE----DLDLvaepfLDNPLVVIAPPDHPLAGQKRIPLERLAREPFLLREPGSGTRLAMERFFAEHGVTLRV 125

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1242933732 214 VLECDTPH-VAQAMAAsGHGIAVVSDD---PRFDLHPLLILDGAGEPLQIHLHAAW 265
Cdd:cd08419   126 RMELGSNEaIKQAVMA-GLGLSVLSLHtlaLELATGRLAVLDVEGFPIRRQWYVVH 180
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
6-69 1.34e-04

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 42.65  E-value: 1.34e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1242933732   6 LRYFLTIVETGSVTKAAEEVRVAQPSLSRQLRGLEASLGMTLFDRgGRQLILTAAGRRFLPLAR 69
Cdd:PRK13348    7 LEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQRLLRHLR 69
PBP2_OccR cd08457
The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the ...
 92-236 2.90e-04

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: 40.94  E-value: 2.90e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732  92 RITVAAPPTTITDVIAPFLSTWGPEDPL--VTVQAESPARAYQALGRG-ADVAISTAP-PRRRFAGLPVARLPLWAYVRA 167
Cdd:cd08457     1 TLRIAAMPALANGFLPRFLAAFLRLRPNlhLSLMGLSSSQVLEAVASGrADLGIADGPlEERQGFLIETRSLPAVVAVPM 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1242933732 168 DHAWANRDGVTIGELAAAPLIVLTPAHGTRRVLDHAVQDADASYDIVLECDTPHVAQAMAASGHGIAVV 236
Cdd:cd08457    81 GHPLAQLDVVSPQDLAGERIITLENGYLFRMRVEVALGKIGVKRRPIIEVNLSHTALSLVREGLGIAII 149
PBP2_CysB cd08443
The C-terminal substrate domain of LysR-type transcriptional regulator CysB contains type 2 ...
 92-254 4.68e-04

The C-terminal substrate domain of LysR-type transcriptional regulator CysB 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.


Pssm-ID: 176134  Cd Length: 198  Bit Score: 40.62  E-value: 4.68e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732  92 RITVAAPPTTITDVIAPFLSTWGPEDPLVTVQAE--SPARAYQALGRG-ADVAISTAPPRRRFA--GLPVARLPLWAYVR 166
Cdd:cd08443     1 SLYVATTHTQARYVLPPVIKGFIERYPRVSLQMHqgSPTQIAEMVSKGlVDFAIATEALHDYDDliTLPCYHWNRCVVVK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732 167 ADHAWANRDGVTIGELAAAPLIVLTPAHGTRRVLDHAVQDADASYDIVLECDTPHVAQAMAASGHG---IAVVSDDPRFD 243
Cdd:cd08443    81 RDHPLADKQSISIEELATYPIVTYTFGFTGRSELDTAFNRAGLTPNIVLTATDADVIKTYVRLGLGvgvIASMAYDPVDD 160

                         170
                  ....*....|.
gi 1242933732 244 LHpLLILDGAG 254
Cdd:cd08443   161 PD-LVIRDARD 170
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 132-236 1.15e-03

The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a member of the type 2 periplasmic binding fold protein superfamily; OxyR senses hydrogen peroxide and is activated through the formation of an intramolecular disulfide bond. The OxyR activation induces the transcription of genes necessary for the bacterial defense against oxidative stress. The OxyR of LysR-type transcriptional regulator family is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The C-terminal domain also contains the redox-active cysteines that mediate the redox-dependent conformational switch. Thus, the interaction between the OxyR-tetramer and DNA is notably different between the oxidized and reduced forms. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176103 [Multi-domain]  Cd Length: 200  Bit Score: 39.43  E-value: 1.15e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732 132 QALGRGA-DVAISTAPPRRrfAGLPVARL---PLWAYVRADHAWANRDGVTIGELAAAPLIVLTPAHGTRrvldhavqda 207
Cdd:cd08411    44 EKLRSGElDAALLALPVDE--PGLEEEPLfdePFLLAVPKDHPLAKRKSVTPEDLAGERLLLLEEGHCLR---------- 111

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1242933732 208 dasyDIVLE-CDTPHVAQA-------------MAASGHGIAVV 236
Cdd:cd08411   112 ----DQALElCRLAGAREQtdfeatsletlrqMVAAGLGITLL 150
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
17-63 1.90e-03

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 39.21  E-value: 1.90e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1242933732  17 SVTKAAEEVRVAQPSLSRQLRGLEASLGMTLFDRGGRQLILTAAGRR 63
Cdd:PRK10086   30 SFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKR 76
PRK09801 PRK09801
LysR family transcriptional regulator;
6-63 4.55e-03

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 38.09  E-value: 4.55e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1242933732   6 LRYFLTIVETGSVTKAAEEVRVAQPSLSRQLRGLEASLGMTLFDRGGRQLILTAAGRR 63
Cdd:PRK09801   11 LQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQR 68
PBP2_IlvR cd08453
The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved ...
 132-236 5.79e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved in the biosynthesis of isoleucine, leucine and valine; contains type 2 periplasmic binding fold; The IlvR is an activator of the upstream and divergently transcribed ilvD gene, which encodes dihydroxy acid dehydratase that participates in isoleucine, leucine, and valine biosynthesis. As in the case of other members of the LysR family, the expression of ilvR gene is repressed in the presence of its own gene product. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176144 [Multi-domain]  Cd Length: 200  Bit Score: 37.34  E-value: 5.79e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242933732 132 QALGRGA-DVAISTAPPRRR----FAGLPVARLPLWAYVRADHAWANRDGVTIGELAAAPLIVLtpahgTRRVldhavqd 206
Cdd:cd08453    43 EALLAGEiDAGIVIPPPGASappaLAYRPLLSEPLVLAVPAAWAAEGGAPLALAAVAAEPLVIF-----PRRI------- 110

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1242933732 207 ADASYDIVLEC-----DTPHVAQ---------AMAASGHGIAVV 236
Cdd:cd08453   111 APAFHDAVTGYyraagQTPRIAQeaiqmqtiiSLVSAGMGVALV 154
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
6-69 7.06e-03

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 37.45  E-value: 7.06e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1242933732   6 LRYFLTIVETGSVTKAAEEVRVAQPSLSRQLRGLEASLGMTLFDRgGRQLILTAAGRRFLPLAR 69
Cdd:PRK03635    7 LEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRLLRHAR 69
 
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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