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Conserved domains on  [gi|498436330|ref|WP_010742009|]
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MULTISPECIES: LysR family transcriptional regulator [Enterococcus]

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];
1-288 2.19e-39

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 138.46  E-value: 2.19e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330   1 MDQQKLQLFLDLTETLNYTETAERNYMTQGNVSKKISALEKELQVPLFDRSNRQIQLTEEGRLLLPDIKRIVRAYQVLTD 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330  81 SLSEYREKKERVLTIHTIPTMPNYRGFDLLTNFLKQHPEIHLNLKES------EAMALGNFEIeknrvyFFRSLREQTEk 154
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGnsdrlvDALLEGELDL------AIRLGPPPDP- 153
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330 155 nSIITEK---DRFVAVLPKRHPLAKNAVIALSdladenflilglaespyysveelcreagfepkityqgtrIDLILRMIE 231
Cdd:COG0583  154 -GLVARPlgeERLVLVASPDHPLARRAPLVNS---------------------------------------LEALLAAVA 193
                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 498436330 232 EGLGVSLIMEKSLGNSL-SDQLVTREIEPTnESFLNFYL---SEDADAPAPKEFFQFLQSE 288
Cdd:COG0583  194 AGLGIALLPRFLAADELaAGRLVALPLPDP-PPPRPLYLvwrRRRHLSPAVRAFLDFLREA 253
Periplasmic_Binding_Protein_Type_2 super family cl21456
Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent ...
166-238 5.98e-10

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 cd08412:

Pssm-ID: 473866 [Multi-domain]  Cd Length: 198  Bit Score: 57.55  E-value: 5.98e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 498436330 166 AVLPKRHPLAKNAVIALSDLADENFLILGLAESPYYSVeELCREAGFEPKITYQGTRIDLILRMIEEGLGVSL 238
Cdd:cd08412   76 VWLPADHPLAGKDEVSLADLAAEPLILLDLPHSREYFL-SLFAAAGLTPRIAYRTSSFEAVRSLVANGLGYSL 147
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-288 2.19e-39

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 138.46  E-value: 2.19e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330   1 MDQQKLQLFLDLTETLNYTETAERNYMTQGNVSKKISALEKELQVPLFDRSNRQIQLTEEGRLLLPDIKRIVRAYQVLTD 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330  81 SLSEYREKKERVLTIHTIPTMPNYRGFDLLTNFLKQHPEIHLNLKES------EAMALGNFEIeknrvyFFRSLREQTEk 154
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGnsdrlvDALLEGELDL------AIRLGPPPDP- 153
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330 155 nSIITEK---DRFVAVLPKRHPLAKNAVIALSdladenflilglaespyysveelcreagfepkityqgtrIDLILRMIE 231
Cdd:COG0583  154 -GLVARPlgeERLVLVASPDHPLARRAPLVNS---------------------------------------LEALLAAVA 193
                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 498436330 232 EGLGVSLIMEKSLGNSL-SDQLVTREIEPTnESFLNFYL---SEDADAPAPKEFFQFLQSE 288
Cdd:COG0583  194 AGLGIALLPRFLAADELaAGRLVALPLPDP-PPPRPLYLvwrRRRHLSPAVRAFLDFLREA 253
PRK09986 PRK09986
LysR family transcriptional regulator;
6-241 1.04e-28

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 111.35  E-value: 1.04e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330   6 LQLFLDLTETLNYTETAERNYMTQGNVSKKISALEKELQVPLFDRSNRQIQLTEEGRLLLPDIKRI-VRAYQVLTDSLSE 84
Cdd:PRK09986  12 LRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLlDNAEQSLARVEQI 91
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330  85 YREKKERvLTIHTIPTMPNYRGFDLLTNFLKQHPEIHLNLKE-SEAMALGNFEIEKNRVYFFRSLREQTEKN--SIITEK 161
Cdd:PRK09986  92 GRGEAGR-IEIGIVGTALWGRLRPAMRHFLKENPNVEWLLRElSPSMQMAALERRELDAGIWRMADLEPNPGftSRRLHE 170
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330 162 DRFVAVLPKRHPLAKNAVIALSDLADENFLILGLAESPY-YSVEELCREAGFEPKITYQGTRIDLILRMIEEGLGVSLIM 240
Cdd:PRK09986 171 SAFAVAVPEEHPLASRSSVPLKALRNEYFITLPFVHSDWgKFLQRVCQQAGFSPQIIRQVNEPQTVLAMVSMGIGITLLP 250

                 .
gi 498436330 241 E 241
Cdd:PRK09986 251 D 251
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
93-285 8.87e-27

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


Pssm-ID: 176102 [Multi-domain]  Cd Length: 197  Bit Score: 103.45  E-value: 8.87e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330  93 LTIHTIPTMPNYRGFDLLTNFLKQHPEIHLNLKESEAMALGNfEIEKNRVYF-FRSLREQTEKNSIIT-EKDRFVAVLPK 170
Cdd:cd05466    2 LRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLE-ALLEGELDLaIVALPVDDPGLESEPlFEEPLVLVVPP 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330 171 RHPLAKNAVIALSDLADENFLILGLAESPYYSVEELCREAGFEPKITYQGTRIDLILRMIEEGLGVSLIMEKSLGNSLSD 250
Cdd:cd05466   81 DHPLAKRKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEELADG 160
                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 498436330 251 QLVTREIEPTNESF-LNF-YLSEDADAPAPKEFFQFL 285
Cdd:cd05466  161 GLVVLPLEDPPLSRtIGLvWRKGRYLSPAARAFLELL 197
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
1-289 1.47e-23

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: 97.30  E-value: 1.47e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330   1 MDQQKLQLFLDLTETLNYTETAERNYMTQGNVSKKISALEKELQVPLFDRSNRQIQLTEEGRLLLPDIKRIVRAYQVLTD 80
Cdd:NF040786   1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330  81 SLSEYREKKERVLTI--HTIPTmpNYRGFDLLTNFLKQHPEIHLNLKESE----AMALGNFEIEknrVYFFRSLREQTEK 154
Cdd:NF040786  81 EFDRYGKESKGVLRIgaSTIPG--QYLLPELLKKFKEKYPNVRFKLMISDsikvIELLLEGEVD---IGFTGTKLEKKRL 155
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330 155 NSIITEKDRFVAVLPKRHPL--AKNAVIALSDLADENFLILGLAESPYYSVEELCREAGFEPK-------ITYQGTridl 225
Cdd:NF040786 156 VYTPFYKDRLVLITPNGTEKyrMLKEEISISELQKEPFIMREEGSGTRKEAEKALKSLGISLEdlnvvasLGSTEA---- 231
                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 498436330 226 ILRMIEEGLGVSLI------MEKSLGN----SLSDQLVTReieptnesflNFYLSEDADA---PAPKEFFQFLQSEY 289
Cdd:NF040786 232 IKQSVEAGLGISVIselaaeKEVERGRvlifPIPGLPKNR----------DFYLVYNKNRqlsPTAEAFLQFVKERY 298
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
90-290 4.57e-23

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: 93.89  E-value: 4.57e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330   90 ERVLTIHTIPTMPNYRGFDLLTNFLKQHPEIHLNLKESEAMALgnFEIEKNRVY--FFRSLREQTEknSIITEK---DRF 164
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEEL--LDLLLEGELdlAIRRGPPDDP--GLEARPlgeEPL 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330  165 VAVLPKRHPLAKNAVIALSDLADENFLILGLAESPYYSVEELCREAGFEPKITYQGTRIDLILRMIEEGLGVSLIMEKSL 244
Cdd:pfam03466  77 VLVAPPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAV 156
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 498436330  245 GNSL-SDQLVTREI---EPTNESFLnFYLSEDADAPAPKEFFQFLQSEYS 290
Cdd:pfam03466 157 ARELaDGRLVALPLpepPLPRELYL-VWRKGRPLSPAVRAFIEFLREALA 205
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
166-238 5.98e-10

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: 57.55  E-value: 5.98e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 498436330 166 AVLPKRHPLAKNAVIALSDLADENFLILGLAESPYYSVeELCREAGFEPKITYQGTRIDLILRMIEEGLGVSL 238
Cdd:cd08412   76 VWLPADHPLAGKDEVSLADLAAEPLILLDLPHSREYFL-SLFAAAGLTPRIAYRTSSFEAVRSLVANGLGYSL 147
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-288 2.19e-39

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 138.46  E-value: 2.19e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330   1 MDQQKLQLFLDLTETLNYTETAERNYMTQGNVSKKISALEKELQVPLFDRSNRQIQLTEEGRLLLPDIKRIVRAYQVLTD 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330  81 SLSEYREKKERVLTIHTIPTMPNYRGFDLLTNFLKQHPEIHLNLKES------EAMALGNFEIeknrvyFFRSLREQTEk 154
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGnsdrlvDALLEGELDL------AIRLGPPPDP- 153
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330 155 nSIITEK---DRFVAVLPKRHPLAKNAVIALSdladenflilglaespyysveelcreagfepkityqgtrIDLILRMIE 231
Cdd:COG0583  154 -GLVARPlgeERLVLVASPDHPLARRAPLVNS---------------------------------------LEALLAAVA 193
                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 498436330 232 EGLGVSLIMEKSLGNSL-SDQLVTREIEPTnESFLNFYL---SEDADAPAPKEFFQFLQSE 288
Cdd:COG0583  194 AGLGIALLPRFLAADELaAGRLVALPLPDP-PPPRPLYLvwrRRRHLSPAVRAFLDFLREA 253
PRK09986 PRK09986
LysR family transcriptional regulator;
6-241 1.04e-28

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 111.35  E-value: 1.04e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330   6 LQLFLDLTETLNYTETAERNYMTQGNVSKKISALEKELQVPLFDRSNRQIQLTEEGRLLLPDIKRI-VRAYQVLTDSLSE 84
Cdd:PRK09986  12 LRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLlDNAEQSLARVEQI 91
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330  85 YREKKERvLTIHTIPTMPNYRGFDLLTNFLKQHPEIHLNLKE-SEAMALGNFEIEKNRVYFFRSLREQTEKN--SIITEK 161
Cdd:PRK09986  92 GRGEAGR-IEIGIVGTALWGRLRPAMRHFLKENPNVEWLLRElSPSMQMAALERRELDAGIWRMADLEPNPGftSRRLHE 170
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330 162 DRFVAVLPKRHPLAKNAVIALSDLADENFLILGLAESPY-YSVEELCREAGFEPKITYQGTRIDLILRMIEEGLGVSLIM 240
Cdd:PRK09986 171 SAFAVAVPEEHPLASRSSVPLKALRNEYFITLPFVHSDWgKFLQRVCQQAGFSPQIIRQVNEPQTVLAMVSMGIGITLLP 250

                 .
gi 498436330 241 E 241
Cdd:PRK09986 251 D 251
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
93-285 8.87e-27

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


Pssm-ID: 176102 [Multi-domain]  Cd Length: 197  Bit Score: 103.45  E-value: 8.87e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330  93 LTIHTIPTMPNYRGFDLLTNFLKQHPEIHLNLKESEAMALGNfEIEKNRVYF-FRSLREQTEKNSIIT-EKDRFVAVLPK 170
Cdd:cd05466    2 LRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLE-ALLEGELDLaIVALPVDDPGLESEPlFEEPLVLVVPP 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330 171 RHPLAKNAVIALSDLADENFLILGLAESPYYSVEELCREAGFEPKITYQGTRIDLILRMIEEGLGVSLIMEKSLGNSLSD 250
Cdd:cd05466   81 DHPLAKRKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEELADG 160
                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 498436330 251 QLVTREIEPTNESF-LNF-YLSEDADAPAPKEFFQFL 285
Cdd:cd05466  161 GLVVLPLEDPPLSRtIGLvWRKGRYLSPAARAFLELL 197
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
108-285 2.07e-24

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: 97.19  E-value: 2.07e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330 108 DLLTNFLKQHPEIHLNLKES------EAMALGNFEIEknrvyFFRSLREQTEKNSIITEKDRFVAVLPKRHPLAKNAVIA 181
Cdd:cd08414   17 RLLRRFRARYPDVELELREMttaeqlEALRAGRLDVG-----FVRPPPDPPGLASRPLLREPLVVALPADHPLAARESVS 91
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330 182 LSDLADENFLILGLAESPYYS--VEELCREAGFEPKITYQGTRIDLILRMIEEGLGVSLIMEkSLGNSLSDQLVTREIEP 259
Cdd:cd08414   92 LADLADEPFVLFPREPGPGLYdqILALCRRAGFTPRIVQEASDLQTLLALVAAGLGVALVPA-SVARLQRPGVVYRPLAD 170
                        170       180
                 ....*....|....*....|....*...
gi 498436330 260 TNESfLNFYL--SEDADAPAPKEFFQFL 285
Cdd:cd08414  171 PPPR-SELALawRRDNASPALRAFLELA 197
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
1-289 1.47e-23

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: 97.30  E-value: 1.47e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330   1 MDQQKLQLFLDLTETLNYTETAERNYMTQGNVSKKISALEKELQVPLFDRSNRQIQLTEEGRLLLPDIKRIVRAYQVLTD 80
Cdd:NF040786   1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330  81 SLSEYREKKERVLTI--HTIPTmpNYRGFDLLTNFLKQHPEIHLNLKESE----AMALGNFEIEknrVYFFRSLREQTEK 154
Cdd:NF040786  81 EFDRYGKESKGVLRIgaSTIPG--QYLLPELLKKFKEKYPNVRFKLMISDsikvIELLLEGEVD---IGFTGTKLEKKRL 155
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330 155 NSIITEKDRFVAVLPKRHPL--AKNAVIALSDLADENFLILGLAESPYYSVEELCREAGFEPK-------ITYQGTridl 225
Cdd:NF040786 156 VYTPFYKDRLVLITPNGTEKyrMLKEEISISELQKEPFIMREEGSGTRKEAEKALKSLGISLEdlnvvasLGSTEA---- 231
                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 498436330 226 ILRMIEEGLGVSLI------MEKSLGN----SLSDQLVTReieptnesflNFYLSEDADA---PAPKEFFQFLQSEY 289
Cdd:NF040786 232 IKQSVEAGLGISVIselaaeKEVERGRvlifPIPGLPKNR----------DFYLVYNKNRqlsPTAEAFLQFVKERY 298
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
90-290 4.57e-23

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: 93.89  E-value: 4.57e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330   90 ERVLTIHTIPTMPNYRGFDLLTNFLKQHPEIHLNLKESEAMALgnFEIEKNRVY--FFRSLREQTEknSIITEK---DRF 164
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEEL--LDLLLEGELdlAIRRGPPDDP--GLEARPlgeEPL 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330  165 VAVLPKRHPLAKNAVIALSDLADENFLILGLAESPYYSVEELCREAGFEPKITYQGTRIDLILRMIEEGLGVSLIMEKSL 244
Cdd:pfam03466  77 VLVAPPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAV 156
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 498436330  245 GNSL-SDQLVTREI---EPTNESFLnFYLSEDADAPAPKEFFQFLQSEYS 290
Cdd:pfam03466 157 ARELaDGRLVALPLpepPLPRELYL-VWRKGRPLSPAVRAFIEFLREALA 205
PBP2_LTTR_aromatics_like_2 cd08448
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
104-285 4.28e-22

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


Pssm-ID: 176139 [Multi-domain]  Cd Length: 197  Bit Score: 91.17  E-value: 4.28e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330 104 YRGF-DLLTNFLKQHPEIHLNLKE----SEAMALGNFEIEKNRVYFfRSLREQTEKNSIITEKdrFVAVLPKRHPLAKNA 178
Cdd:cd08448   12 YRGLpRILRAFRAEYPGIEVALHEmssaEQIEALLRGELDLGFVHS-RRLPAGLSARLLHREP--FVCCLPAGHPLAARR 88
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330 179 VIALSDLADENFLILGLAESPYY--SVEELCREAGFEPKITYQGTRIDLILRMIEEGLGVSLImEKSLGNSLSDQLVTRE 256
Cdd:cd08448   89 RIDLRELAGEPFVLFSREVSPDYydQIIALCMDAGFHPKIRHEVRHWLTVVALVAAGMGVALV-PRSLARAGLAGVRFLP 167
                        170       180       190
                 ....*....|....*....|....*....|
gi 498436330 257 IEP-TNESFLNFYLSEDADAPAPKEFFQFL 285
Cdd:cd08448  168 LKGaTQRSELYAAWKASAPNPALQAFLAAL 197
PBP2_XapR cd08449
The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved ...
108-239 7.53e-20

The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved in xanthosine catabolism, contains the type 2 periplasmic binding fold; In Escherichia coli, XapR is a positive regulator for the expression of xapA gene, encoding xanthosine phosphorylase, and xapB gene, encoding a polypeptide similar to the nucleotide transport protein NupG. As an operon, the expression of both xapA and xapB is fully dependent on the presence of both XapR and the inducer xanthosine. Expression of the xapR is constitutive but not auto-regulated, unlike many other LysR family proteins. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176140 [Multi-domain]  Cd Length: 197  Bit Score: 85.02  E-value: 7.53e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330 108 DLLTNFLKQHPEIHLNLKE-SEAM---ALGNFEIEknrVYFFRSLREQ--TEKNSIITEKDRFVAVLPKRHPLAKNAVIA 181
Cdd:cd08449   17 PALRRFKRQYPNVTVRFHElSPEAqkaALLSKRID---LGFVRFADTLndPPLASELLWREPMVVALPEEHPLAGRKSLT 93
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 498436330 182 LSDLADENFLILGLAESPYYS-VEELCREAGFEPKITYQGTRIDLILRMIEEGLGVSLI 239
Cdd:cd08449   94 LADLRDEPFVFLRLANSRFADfLINCCLQAGFTPQITQEVVEPQTLMALVAAGFGVALV 152
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
1-289 7.57e-20

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 87.13  E-value: 7.57e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330   1 MDQQKLQLFLDLTETLNYTETAERNYMTQGNVSKKISALEKELQVPLFDRSNRQIQLTEEGRLLLPDiKRIVRAYQVLTD 80
Cdd:PRK09906   1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQD-ARAILEQAEKAK 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330  81 SLSEYREKKERVLTIHTIPTMPNYRGFDLLTNFLKQHPEIHLNL------KESEAMALGNFEIEknrvyFFRSLREQTEK 154
Cdd:PRK09906  80 LRARKIVQEDRQLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELvslittQQEEKLRRGELDVG-----FMRHPVYSDEI 154
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330 155 NSIITEKDRFVAVLPKRHPLAKNAVIALSDLADENFLILGLAESPYYS--VEELCREAGFEPKITYQGTRIDLILRMIEE 232
Cdd:PRK09906 155 DYLELLDEPLVVVLPVDHPLAHEKEITAAQLDGVNFISTDPAYSGSLApiIKAWFAQHNSQPNIVQVATNILVTMNLVGM 234
                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330 233 GLGVSlIMEKSLGNSLSDQLVTREIE---PTNESFLNFylSEDADAPAPKEFFQFLQSEY 289
Cdd:PRK09906 235 GLGCT-IIPGYMNNFNTGQVVFRPLAgnvPSIALLMAW--KKGEMKPALRDFIAIVQERL 291
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
93-285 5.44e-19

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: 82.58  E-value: 5.44e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330  93 LTIHTIPtmpnyrgfDLLTNFLKQHPEIHLNLKES------EAMALGNFEIEknrVYFFRSLREQTEKNSIITEkdRFVA 166
Cdd:cd08434   10 LGTSLVP--------DLIRAFRKEYPNVTFELHQGstdellDDLKNGELDLA---LCSPVPDEPDIEWIPLFTE--ELVL 76
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330 167 VLPKRHPLAKNAVIALSDLADENFLIL----GLaespYYSVEELCREAGFEPKITYQGTRIDLILRMIEEGLGVSLIMEK 242
Cdd:cd08434   77 VVPKDHPLAGRDSVDLAELADEPFVLLspgfGL----RPIVDELCAAAGFTPKIAFEGEEDSTIAGLVAAGLGVAILPEM 152
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 498436330 243 SLGN-------SLSDQLVTREIeptnesflnfYLSEDAD---APAPKEFFQFL 285
Cdd:cd08434  153 TLLNppgvkkiPIKDPDAERTI----------GLAWLKDrylSPAARRFKDFV 195
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
109-258 6.28e-18

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: 79.91  E-value: 6.28e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330 109 LLTNFLKQHPEIHLNLKESEA----MALGNFEIEknrVYFFRSLREQTEKNSIITEKDRFVAVLPKRHPLAKNAVIALSD 184
Cdd:cd08438   18 LLAAFRQRYPNIELELVEYGGkkveQAVLNGELD---VGITVLPVDEEEFDSQPLCNEPLVAVLPRGHPLAGRKTVSLAD 94
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 498436330 185 LADENFLILglaESPYY---SVEELCREAGFEPKITYQGTRIDLILRMIEEGLGVSLIMEKSLGNSLSDQLVTREIE 258
Cdd:cd08438   95 LADEPFILF---NEDFAlhdRIIDACQQAGFTPNIAARSSQWDFIAELVAAGLGVALLPRSIAQRLDNAGVKVIPLT 168
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
16-241 1.31e-17

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 81.19  E-value: 1.31e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330  16 LNYTETAERNYMTQGNVSKKISALEKELQVPLFDRSNRQIQ-LTEEGRLLLPDIKRIVRAYQVLTDSLSEYREKKERVLT 94
Cdd:PRK12682  17 LNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKgLTEPGKAVLDVIERILREVGNIKRIGDDFSNQDSGTLT 96
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330  95 IHTIPTMPNYRGFDLLTNFLKQHPEIHLNLKESEAMALGNFEIeknrvyffrslREQTEKnSIITEK-DRF--------- 164
Cdd:PRK12682  97 IATTHTQARYVLPRVVAAFRKRYPKVNLSLHQGSPDEIARMVI-----------SGEADI-GIATESlADDpdlatlpcy 164
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330 165 ----VAVLPKRHPLAKNAVIALSDLADENFLILGLAESPYYSVEELCREAGFEPKITYQGTRIDLILRMIEEGLGVSLIM 240
Cdd:PRK12682 165 dwqhAVIVPPDHPLAQEERITLEDLAEYPLITYHPGFTGRSRIDRAFAAAGLQPDIVLEAIDSDVIKTYVRLGLGVGIVA 244

                 .
gi 498436330 241 E 241
Cdd:PRK12682 245 E 245
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
16-130 1.83e-17

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 80.66  E-value: 1.83e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330  16 LNYTETAERNYMTQGNVSKKISALEKELQVPLFDRSNRQIQLTEEGRLLLPDIKRIVRAYQVLTDSLseyREKK-ERVLT 94
Cdd:PRK11139  21 LSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEATRKL---RARSaKGALT 97
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 498436330  95 IHTIPT------MPNyrgfdlLTNFLKQHPEIHLNLKESEAM 130
Cdd:PRK11139  98 VSLLPSfaiqwlVPR------LSSFNEAHPDIDVRLKAVDRL 133
PBP2_BudR cd08451
The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is ...
107-259 1.35e-16

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


Pssm-ID: 176142 [Multi-domain]  Cd Length: 199  Bit Score: 76.45  E-value: 1.35e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330 107 FDLLTNFLKQHPEIHLNLKESEAMALgnfeIEKNR-----VYFFRSLREQTEK-NSIITEKDRFVAVLPKRHPLAKNAVI 180
Cdd:cd08451   17 PGLIRRFREAYPDVELTLEEANTAEL----LEALRegrldAAFVRPPVARSDGlVLELLLEEPMLVALPAGHPLARERSI 92
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330 181 ALSDLADENFLI------LGLaespYYSVEELCREAGFEPKITYQGTRIDLILRMIEEGLGVSLIMEkSLGNSLSDQLVT 254
Cdd:cd08451   93 PLAALADEPFILfprpvgPGL----YDAIIAACRRAGFTPRIGQEAPQMASAINLVAAGLGVSIVPA-SMRQLQAPGVVY 167

                 ....*
gi 498436330 255 REIEP 259
Cdd:cd08451  168 RPLAG 172
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
6-62 4.28e-16

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 70.88  E-value: 4.28e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 498436330    6 LQLFLDLTETLNYTETAERNYMTQGNVSKKISALEKELQVPLFDRSNRQIQLTEEGR 62
Cdd:pfam00126   4 LRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PBP2_MleR cd08437
The substrate binding domain of LysR-type transcriptional regulator MleR which required for ...
150-270 1.45e-15

The substrate binding domain of LysR-type transcriptional regulator MleR which required for malolactic fermentation, contains type 2 periplasmic binidning fold; MleR, a transcription activator of malolactic fermentation system, is found in gram-positive bacteria and belongs to the lysR family of bacterial transcriptional regulators. The mleR gene is required for the expression and induction of malolactic fermentation. This substrate binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176128  Cd Length: 198  Bit Score: 73.52  E-value: 1.45e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330 150 EQTEKNSIITEKDRFVAVLPKRHPLAKNAVIALSDLADENFLILGLAESPYYSVEELCREAGFEPKITYQGTRIDLILRM 229
Cdd:cd08437   62 ENSALHSKIIKTQHFMIIVSKDHPLAKAKKVNFADLKKENFILLNEHFVHPKAFDSLCQQANFQPNIVYRTNDIHILKSM 141
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 498436330 230 IEEGLGVSLIMEKSLGNslSDQLVTreIEPTNESFLNFYLS 270
Cdd:cd08437  142 VRENVGIGFLTDIAVKP--DDHLVA--IPLLDNEQPTFYIS 178
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
16-239 1.49e-15

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 75.46  E-value: 1.49e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330  16 LNYTETAERNYMTQGNVSKKISALEKELQVPLFDRS-NRQIQLTEEGRLLLPDIKRIVRAYQVLTDSLSEYREKKERVLT 94
Cdd:PRK12683  17 FNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRgKRLTGLTEPGKELLQIVERMLLDAENLRRLAEQFADRDSGHLT 96
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330  95 IHTIPTMPNYRGFDLLTNFLKQHPEIHLNLKE------SEAMALGNFEI----EknrvyffrSLREQTEKNSIITEKDRF 164
Cdd:PRK12683  97 VATTHTQARYALPKVVRQFKEVFPKVHLALRQgspqeiAEMLLNGEADIgiatE--------ALDREPDLVSFPYYSWHH 168
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330 165 VAVLPKRHPLAKNAVIALSDLA-------DENFliLGLAEspyysVEELCREAGFEPKITYQGTRIDLILRMIEEGLGVS 237
Cdd:PRK12683 169 VVVVPKGHPLTGRENLTLEAIAeypiityDQGF--TGRSR-----IDQAFAEAGLVPDIVLTALDADVIKTYVELGMGVG 241

                 ..
gi 498436330 238 LI 239
Cdd:PRK12683 242 IV 243
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
162-239 1.57e-15

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


Pssm-ID: 176115 [Multi-domain]  Cd Length: 200  Bit Score: 73.40  E-value: 1.57e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330 162 DRFVAVLPKRHPLAKNAVIALSDLADENFlILGLAESPYY-SVEELCREAGFEPKITYqgtRID---LILRMIEEGLGVS 237
Cdd:cd08423   77 DPLDLVLPADHPLAGREEVALADLADEPW-IAGCPGSPCHrWLVRACRAAGFTPRIAH---EADdyaTVLALVAAGLGVA 152

                 ..
gi 498436330 238 LI 239
Cdd:cd08423  153 LV 154
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
17-239 5.92e-15

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 73.49  E-value: 5.92e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330  17 NYTETAERNYMTQGNVSKKISALEKELQVPLFDRSNRQIQLTEEGRLLLPDIK-------RIVRAyqvlTDSLSEYREKK 89
Cdd:PRK11013  20 SLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLFEEVQrsyygldRIVSA----AESLREFRQGQ 95
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330  90 ervLTIHTIPT-----MPnyrgfDLLTNFLKQHPEIHLNL--KES----EAMALGNFEIeknrvyffrSLREQ------T 152
Cdd:PRK11013  96 ---LSIACLPVfsqslLP-----GLCQPFLARYPDVSLNIvpQESplleEWLSAQRHDL---------GLTETlhtpagT 158
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330 153 EKNSIITEKDrfVAVLPKRHPLAKNAVIALSDLADENFLILGLAESPYYSVEELCREAGFEPKITYQGTRIDLILRMIEE 232
Cdd:PRK11013 159 ERTELLTLDE--VCVLPAGHPLAAKKVLTPDDFAGENFISLSRTDSYRQLLDQLFAEHGVKRRMVVETHSAASVCAMVRA 236

                 ....*..
gi 498436330 233 GLGVSLI 239
Cdd:PRK11013 237 GVGVSIV 243
rbcR CHL00180
LysR transcriptional regulator; Provisional
17-239 1.40e-14

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 72.36  E-value: 1.40e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330  17 NYTETAERNYMTQGNVSKKISALEKELQVPLFDRSNRQIQLTEEGRLLLPDIKRIVRAYQVLTDSLSEYREKKERVLTIH 96
Cdd:CHL00180  21 SFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRALEDLKNLQRGTLIIG 100
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330  97 TIPTMPNYRGFDLLTNFLKQHPEIHLNLK----ESEAMALGNFEIEKNRVYffRSLREQTEKNSIITE--KDRFVAVLPK 170
Cdd:CHL00180 101 ASQTTGTYLMPRLIGLFRQRYPQINVQLQvhstRRIAWNVANGQIDIAIVG--GEVPTELKKILEITPyvEDELALIIPK 178
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 498436330 171 RHPLAKNAVIALSDLADENFLILGLAESPYYSVEELCREAGFEP---KITYQGTRIDLILRMIEEGLGVSLI 239
Cdd:CHL00180 179 SHPFAKLKKIQKEDLYRLNFITLDSNSTIRKVIDNILIQNGIDSkrfKIEMELNSIEAIKNAVQSGLGAAFV 250
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
5-239 2.84e-14

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 71.55  E-value: 2.84e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330   5 KLQLFLDLTET----LNYTETAERNYMTQGNVSKKISALEKELQVPLFDR-SNRQIQLTEEGRLLLPDIKRIVRAYQVLT 79
Cdd:PRK12684   2 NLHQLRFVREAvrqnFNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRhGKRLRGLTEPGRIILASVERILQEVENLK 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330  80 DSLSEYREKKERVLTIHTIPTMPNYRGFDLLTNFLKQHPEIHLNLKE------SEAMALGNFEIEKnrvyffrslreQTE 153
Cdd:PRK12684  82 RVGKEFAAQDQGNLTIATTHTQARYALPAAIKEFKKRYPKVRLSILQgsptqiAEMVLHGQADLAI-----------ATE 150
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330 154 KnsiITEKDRFVA----------VLPKRHPLAKNAVIALSDLA-------DENFLILGLaespyysVEELCREAGFEPKI 216
Cdd:PRK12684 151 A---IADYKELVSlpcyqwnhcvVVPPDHPLLERKPLTLEDLAqyplityDFAFAGRSK-------INKAFALRGLKPDI 220
                        250       260
                 ....*....|....*....|...
gi 498436330 217 TYQGTRIDLILRMIEEGLGVSLI 239
Cdd:PRK12684 221 VLEAIDADVIKTYVELGLGVGIV 243
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
93-259 7.08e-14

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: 68.74  E-value: 7.08e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330  93 LTIHTIPTMPNyrGF--DLLTNFLKQHPEIHLNLkES-------EAMALGNFEIEknrVYFFRSLREQTEKNSIITEkdR 163
Cdd:cd08415    2 LRIAALPALAL--SLlpRAIARFRARHPDVRISL-HTlssstvvEAVLSGQADLG---LASLPLDHPGLESEPLASG--R 73
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330 164 FVAVLPKRHPLAKNAVIALSDLADENFLILGLAESPYYSVEELCREAGFEPKITYQGTRIDLILRMIEEGLGVSLIMEKS 243
Cdd:cd08415   74 AVCVLPPGHPLARKDVVTPADLAGEPLISLGRGDPLRQRVDAAFERAGVEPRIVIETQLSHTACALVAAGLGVAIVDPLT 153
                        170
                 ....*....|....*.
gi 498436330 244 LGNSLSDQLVTREIEP 259
Cdd:cd08415  154 AAGYAGAGLVVRPFRP 169
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
98-258 8.11e-14

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: 68.71  E-value: 8.11e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330  98 IPT-----MPNyrgfdLLTNFLKQHPEIHLNLKES------EAMALG--------------NFEIEKnrvyFFRslreqt 152
Cdd:cd08411    8 IPTiapylLPR-----LLPALRQAYPKLRLYLREDqterllEKLRSGeldaallalpvdepGLEEEP----LFD------ 72
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330 153 eknsiitekDRFVAVLPKRHPLAKNAVIALSDLADENFLILG----LAEspyySVEELCREAGFEPKITYQGTRIDLILR 228
Cdd:cd08411   73 ---------EPFLLAVPKDHPLAKRKSVTPEDLAGERLLLLEeghcLRD----QALELCRLAGAREQTDFEATSLETLRQ 139
                        170       180       190
                 ....*....|....*....|....*....|..
gi 498436330 229 MIEEGLGVSLIMEKSLGNSLS--DQLVTREIE 258
Cdd:cd08411  140 MVAAGLGITLLPELAVPSEELrgDRLVVRPFA 171
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
6-233 1.71e-13

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 69.21  E-value: 1.71e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330   6 LQLFLDLTETLNYTETAERNYMTQGNVSKKISALEKELQVPLFDRSNRQIQLTEEGRLLLPDIKRIVRAYQVLTDSLSEY 85
Cdd:PRK11242   6 IRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRRAIHDV 85
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330  86 REKKERVLTIHTIPTMPNYRGFDLLTNFLKQHPEIHLNLKE--SEAM--ALGNFEIEKNrVYFFRSLREQTEKNSIITEk 161
Cdd:PRK11242  86 ADLSRGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREmsQERIeaLLADDELDVG-IAFAPVHSPEIEAQPLFTE- 163
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 498436330 162 dRFVAVLPKRHPLA-KNAVIALSDLADENFLILGLAESPYYSVEELCREAGFEPKITYQGTRIDLILRMIEEG 233
Cdd:PRK11242 164 -TLALVVGRHHPLAaRRKALTLDELADEPLVLLSAEFATREQIDRYFRRHGVTPRVAIEANSISAVLEIVRRG 235
cysB PRK12681
HTH-type transcriptional regulator CysB;
16-239 3.29e-12

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 65.69  E-value: 3.29e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330  16 LNYTETAERNYMTQGNVSKKISALEKELQVPLFDRSNRQI-QLTEEGRlllpDIKRIVRAYQVLTDSL----SEYREKKE 90
Cdd:PRK12681  17 LNVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLtQVTPAGE----EIIRIAREILSKVESIksvaGEHTWPDK 92
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330  91 RVLTIHTIPTMPNYRGFDLLTNFLKQHPEIHLNLKE------SEAMALG--NFEIEKNRVYFFRSL---------Reqte 153
Cdd:PRK12681  93 GSLYIATTHTQARYALPPVIKGFIERYPRVSLHMHQgsptqiAEAAAKGnaDFAIATEALHLYDDLimlpcyhwnR---- 168
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330 154 knSIitekdrfvaVLPKRHPLAKNAVIALSDLADEN-----FLILGLAEspyysVEELCREAGFEPKITYQGTRIDLILR 228
Cdd:PRK12681 169 --SV---------VVPPDHPLAKKKKLTIEELAQYPlvtyvFGFTGRSE-----LDTAFNRAGLTPRIVFTATDADVIKT 232
                        250
                 ....*....|.
gi 498436330 229 MIEEGLGVSLI 239
Cdd:PRK12681 233 YVRLGLGVGVI 243
PBP2_AlsR cd08452
The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which ...
165-261 4.77e-12

The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which regulates acetoin formation under stationary phase growth conditions; contains the type 2 periplasmic binding fold; AlsR is responsible for activating the expression of the acetoin operon (alsSD) in response to inducing signals such as glucose and acetate. Like many other LysR family proteins, AlsR is transcribed divergently from the alsSD operon. The alsS gene encodes acetolactate synthase, an enzyme involved in the production of acetoin in cells of stationary-phase. AlsS catalyzes the conversion of two pyruvate molecules to acetolactate and carbon dioxide. Acetolactate is then converted to acetoin at low pH by acetolactate decarboxylase which encoded by the alsD gene. Acetoin is an important physiological metabolite excreted by many microorganisms grown on glucose or other fermentable carbon sources. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176143 [Multi-domain]  Cd Length: 197  Bit Score: 63.67  E-value: 4.77e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330 165 VAVLPKRHPLAKNAVIALSDLADENFLILGLAESP--YYSVEELCREAGFEPKITYQGTRIDLILRMIEEGLGVSLImEK 242
Cdd:cd08452   75 VLALPKQHPLASKEEITIEDLRDEPIITVAREAWPtlYDEIIQLCEQAGFRPKIVQEATEYQTVIGLVSAGIGVTFV-PS 153
                         90
                 ....*....|....*....
gi 498436330 243 SLGNSLSDQLVTREIEPTN 261
Cdd:cd08452  154 SAKKLFNLEVAYRKIDQIN 172
PBP2_LTTR_like_1 cd08421
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
108-239 1.19e-11

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


Pssm-ID: 176113  Cd Length: 198  Bit Score: 62.54  E-value: 1.19e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330 108 DLLTNFLKQHPEIHLNLKESEAMalgnfEIeknrvyfFRSLREQTEKNSIITE-------------KDRFVAVLPKRHPL 174
Cdd:cd08421   17 EDLASFLAAHPDVRIDLEERLSA-----DI-------VRAVAEGRADLGIVAGnvdaagletrpyrTDRLVVVVPRDHPL 84
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 498436330 175 AKNAVIALSDLADENFLILGLAESPYYSVEELCREAGFEPKITYQGTRIDLILRMIEEGLGVSLI 239
Cdd:cd08421   85 AGRASVAFADTLDHDFVGLPAGSALHTFLREAAARLGRRLRLRVQVSSFDAVCRMVAAGLGIGIV 149
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
93-258 1.22e-11

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: 62.54  E-value: 1.22e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330  93 LTIHTIPT-----MPnyrgfDLLTNFLKQHPEIHLNLKES------------EA-MALGNFEIEKNRVYFfRSLREqtek 154
Cdd:cd08440    2 VRVAALPSlaatlLP-----PVLAAFRRRHPGIRVRLRDVsaeqvieavrsgEVdFGIGSEPEADPDLEF-EPLLR---- 71
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330 155 nsiitekDRFVAVLPKRHPLAKNAVIALSDLADENFLILGLAESPYYSVEELCREAGFEPKITYQGTRIDLILRMIEEGL 234
Cdd:cd08440   72 -------DPFVLVCPKDHPLARRRSVTWAELAGYPLIALGRGSGVRALIDRALAAAGLTLRPAYEVSHMSTALGMVAAGL 144
                        170       180
                 ....*....|....*....|....
gi 498436330 235 GVSLIMEKSLGNSLSDQLVTREIE 258
Cdd:cd08440  145 GVAVLPALALPLADHPGLVARPLT 168
PBP2_LTTR_aromatics_like_1 cd08447
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
161-277 7.33e-11

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


Pssm-ID: 176138 [Multi-domain]  Cd Length: 198  Bit Score: 60.35  E-value: 7.33e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330 161 KDRFVAVLPKRHPLAKNAVIALSDLADENFLILGLAESPYYS--VEELCREAGFEPKITYQGTRIDLILRMIEEGLGVSL 238
Cdd:cd08447   71 REPLVAAVPAGHPLAGAERLTLEDLDGQPFIMYSPTEARYFHdlVVRLFASAGVQPRYVQYLSQIHTMLALVRAGLGVAL 150
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 498436330 239 IMEKSLGNSLSDqLVTREIE--PTNESFLNFYLSEDADAPA 277
Cdd:cd08447  151 VPASASRLRFEG-VVFRPLDlpRDVPVELHLAWRRDNDNPA 190
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
5-124 7.66e-11

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 61.56  E-value: 7.66e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330   5 KLQLFLDLTETLNYTETAERNYMTQGNVSKKISALEKELQVPLFDRSNRQIQLTEEGrlllpdiKRIvraYQVLTDSLS- 83
Cdd:PRK10086  18 KLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEG-------KRV---FWALKSSLDt 87
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 498436330  84 ---EYREKKER----VLTIHTIPT------MPNyrgfdlLTNFLKQHPEIHLNL 124
Cdd:PRK10086  88 lnqEILDIKNQelsgTLTVYSRPSiaqcwlVPR------LADFTRRYPSISLTI 135
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
166-238 5.98e-10

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: 57.55  E-value: 5.98e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 498436330 166 AVLPKRHPLAKNAVIALSDLADENFLILGLAESPYYSVeELCREAGFEPKITYQGTRIDLILRMIEEGLGVSL 238
Cdd:cd08412   76 VWLPADHPLAGKDEVSLADLAAEPLILLDLPHSREYFL-SLFAAAGLTPRIAYRTSSFEAVRSLVANGLGYSL 147
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
93-285 8.15e-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: 57.23  E-value: 8.15e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330  93 LTIHTIPTMPNYRGFDLLTNFLKQHPEIHLNLKES------EAMALGNFEIEknrvyfFRSLREQ--TEKNSIITEKDRF 164
Cdd:cd08436    2 LAIGTITSLAAVDLPELLARFHRRHPGVDIRLRQAgsddllAAVREGRLDLA------FVGLPERrpPGLASRELAREPL 75
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330 165 VAVLPKRHPLAKNAVIALSDLADENFLILglaesPYYS-----VEELCREAGFEPKITYQGTRIDLILRMIEEGLGVSLI 239
Cdd:cd08436   76 VAVVAPDHPLAGRRRVALADLADEPFVDF-----PPGTgarrqVDRAFAAAGVRRRVAFEVSDVDLLLDLVARGLGVALL 150
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 498436330 240 MEKSLGNslSDQLVTREIEPTNESFLNFYLSEDADAPAPKEFFQFL 285
Cdd:cd08436  151 PASVAAR--LPGLAALPLEPAPRRRLYLAWSAPPPSPAARAFLELL 194
PBP2_OccR cd08457
The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the ...
93-259 2.45e-09

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: 55.96  E-value: 2.45e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330  93 LTIHTIPTMPNyrGF--DLLTNFLKQHPEIHLNLKES------EAMALGNFEIEknrvyfFRSLREQTEKNSII-TEKDR 163
Cdd:cd08457    2 LRIAAMPALAN--GFlpRFLAAFLRLRPNLHLSLMGLsssqvlEAVASGRADLG------IADGPLEERQGFLIeTRSLP 73
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330 164 FVAVLPKRHPLAKNAVIALSDLADENFLILglaESPY---YSVEELCREAGFEPKITYQGTRIDLILRMIEEGLGVSLIM 240
Cdd:cd08457   74 AVVAVPMGHPLAQLDVVSPQDLAGERIITL---ENGYlfrMRVEVALGKIGVKRRPIIEVNLSHTALSLVREGLGIAIID 150
                        170
                 ....*....|....*....
gi 498436330 241 EKSLGNSLSDQLVTREIEP 259
Cdd:cd08457  151 PATAIGLPLDGIVIRPFDT 169
cbl PRK12679
HTH-type transcriptional regulator Cbl;
17-265 2.46e-09

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 57.13  E-value: 2.46e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330  17 NYTETAERNYMTQGNVSKKISALEKELQVPLF-DRSNRQIQLTEEGRLLLPDIKRIV-------RAYQVLTDSLSEyrek 88
Cdd:PRK12679  18 NLTEVANMLFTSQSGVSRHIRELEDELGIEIFiRRGKRLLGMTEPGKALLVIAERILneasnvrRLADLFTNDTSG---- 93
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330  89 kerVLTIHTIPTMPNYRGFDLLTNFLKQHPEIHLNL-----KESEAMaLGNFEIEKNRVyffrslREQTEKNSIITEKDR 163
Cdd:PRK12679  94 ---VLTIATTHTQARYSLPEVIKAFRELFPEVRLELiqgtpQEIATL-LQNGEADIGIA------SERLSNDPQLVAFPW 163
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330 164 F----VAVLPKRHPLAKNAVIALSDLADENFLILGLAESPYYSVEELCREAGFEPKITYQGTRIDLILRMIEEGLGVSLI 239
Cdd:PRK12679 164 FrwhhSLLVPHDHPLTQITPLTLESIAKWPLITYRQGITGRSRIDDAFARKGLLADIVLSAQDSDVIKTYVALGLGIGLV 243
                        250       260
                 ....*....|....*....|....*....
gi 498436330 240 MEKSLG---NSLSDQLVTREIEPTNESFL 265
Cdd:PRK12679 244 AEQSSGeqeESNLIRLDTRHLFDANTVWL 272
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
1-95 5.47e-09

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 55.97  E-value: 5.47e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330   1 MDQQKLQLFLDLTETLNYTETAERNYMTQGNVSKKISALEKELQVPLFDRSNRQIQLTEEGRLLLPDIKRIVRAYQVLTD 80
Cdd:PRK10094   2 FDPETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPS 81
                         90
                 ....*....|....*
gi 498436330  81 SLSEYREKKERVLTI 95
Cdd:PRK10094  82 ELQQVNDGVERQVNI 96
PBP2_LysR cd08456
The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine ...
93-259 6.49e-09

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


Pssm-ID: 176145 [Multi-domain]  Cd Length: 196  Bit Score: 54.73  E-value: 6.49e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330  93 LTIHTIPTMPNyrGF--DLLTNFLKQHPEIHLNLKE------SEAMALGNFEIeknrvyffrSLREQTEKNsIITEKDRF 164
Cdd:cd08456    2 LRIAVLPALSQ--SFlpRAIKAFLQRHPDVTISIHTrdsptvEQWLSAQQCDL---------GLVSTLHEP-PGIERERL 69
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330 165 -----VAVLPKRHPLAKNAVIALSDLADENFLILGLAESPYYSVEELCREAGFEPKITYQGTRIDLILRMIEEGLGVSLI 239
Cdd:cd08456   70 lridgVCVLPPGHRLAVKKVLTPSDLEGEPFISLARTDGTRQRVDALFEQAGVKRRIVVETSYAATICALVAAGVGVSVV 149
                        170       180
                 ....*....|....*....|
gi 498436330 240 MEKSLGNSLSDQLVTREIEP 259
Cdd:cd08456  150 NPLTALDYAAAGLVVRRFSP 169
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
1-241 8.89e-09

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 55.42  E-value: 8.89e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330   1 MDQQKLQLFLDLTETLNYTETAERNYMTQGNVSKKISALEKELQVPLFDRSNRQIQLTEEGRLLLPDIKRIVRAYQVLTD 80
Cdd:PRK11151   1 MNIRDLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVLKE 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330  81 SLSEYREKKERVLTIHTIPTMPNYRGFDLLTNFLKQHPEIHLNLKESEAmalgnfeieknrvyffRSLREQTEKNSI--- 157
Cdd:PRK11151  81 MASQQGETMSGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQT----------------HQLLAQLDSGKLdca 144
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330 158 ----ITEKDRFVAV----------LPKRHPLAKNAVIALSDLADENFLILGLAESPYYSVEELCREAGFEPKITYQGTRI 223
Cdd:PRK11151 145 ilalVKESEAFIEVplfdepmllaVYEDHPWANRDRVPMSDLAGEKLLMLEDGHCLRDQAMGFCFEAGADEDTHFRATSL 224
                        250
                 ....*....|....*...
gi 498436330 224 DLILRMIEEGLGVSLIME 241
Cdd:PRK11151 225 ETLRNMVAAGSGITLLPA 242
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
4-124 3.92e-08

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 53.61  E-value: 3.92e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330   4 QKLQLFLDLTETLNYTETAERNYMTQGNVSKKISALEKELQVPLFDRSNRQIQLTEEGRLLLPDIKRIVRAYQVLTDSLS 83
Cdd:PRK10632   5 KRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQLY 84
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 498436330  84 EYREKKERVLTIHTIPTMPNYRGFDLLTNFLKQHPEIHLNL 124
Cdd:PRK10632  85 AFNNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNL 125
PRK12680 PRK12680
LysR family transcriptional regulator;
16-241 8.58e-08

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 52.70  E-value: 8.58e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330  16 LNYTETAERNYMTQGNVSKKISALEKELQVPLFDRSNRQIQ-LTEEGRLLLPDIKRI-VRAYQVLTDSLSEYREKKERvL 93
Cdd:PRK12680  17 LNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLEsVTPAGVEVIERARAVlSEANNIRTYAANQRRESQGQ-L 95
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330  94 TIHTIPTMPNYRGFDLLTNFLKQHPEIHLNLKES-EAMAL-----GNFEIeknrVYFFRSLREQTEKNSIITEKDRFVAV 167
Cdd:PRK12680  96 TLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQQAaESAALdllgqGDADI----AIVSTAGGEPSAGIAVPLYRWRRLVV 171
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330 168 LPKRHPLaknavialsDLADENFLILGLAESPYYSVEELCR----------EAGFEPKITYQGTRIDLILRMIEEGLGVS 237
Cdd:PRK12680 172 VPRGHAL---------DTPRRAPDMAALAEHPLISYESSTRpgsslqrafaQLGLEPSIALTALDADLIKTYVRAGLGVG 242

                 ....
gi 498436330 238 LIME 241
Cdd:PRK12680 243 LLAE 246
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
1-66 1.68e-07

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 51.56  E-value: 1.68e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 498436330   1 MDQQKLQLFLDLTETLNYTETAERNYMTQGNVSKKISALEKELQVPLFDRSNRQIQLTEEGRLLLP 66
Cdd:PRK03601   1 MDTELLKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLP 66
PBP2_HcaR cd08450
The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in ...
109-258 4.27e-07

The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in involved in 3-phenylpropionic acid catabolism, contains the type2 periplasmic binding fold; HcaR, a member of the LysR family of transcriptional regulators, controls the expression of the hcA1, A2, B, C, and D operon, encoding for the 3-phenylpropionate dioxygenase complex and 3-phenylpropionate-2',3'-dihydrodiol dehydrogenase, that oxidizes 3-phenylpropionate to 3-(2,3-dihydroxyphenyl) propionate. Dioxygenases play an important role in protecting the cell against the toxic effects of dioxygen. The expression of hcaR is negatively auto-regulated, as for other members of the LysR family, and is strongly repressed in the presence of glucose. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176141 [Multi-domain]  Cd Length: 196  Bit Score: 49.30  E-value: 4.27e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330 109 LLTNFLKQHPEI------HLNLKESEAMALGNFEieknrVYFFRSLREQTEKNSIITEKDRFVAVLPKRHPLAKNAVIAL 182
Cdd:cd08450   18 VLPILREEHPDLdvelssLFSPQLAEALMRGKLD-----VAFMRPEIQSDGIDYQLLLKEPLIVVLPADHRLAGREKIPP 92
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 498436330 183 SDLADENFlILGLAESPYYS--VEELCREAGFEPKITYQGTRIDLILRMIEEGLGVSLIMEkSLGNSLSDQLVTREIE 258
Cdd:cd08450   93 QDLAGENF-ISPAPTAPVLQqvIENYAAQHNIQPNIIQEADNLLSAMSLVASTLGCALLPL-YANNLLPPSVVARPLS 168
PBP2_BenM_CatM_CatR cd08445
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
113-258 5.36e-07

The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in benzoate catabolism; contains the type 2 periplasmic binding fold; This CD includes the C-terminal of LysR-type transcription regulators, BenM, CatM, and CatR, which are involved in the benzoate catabolism. The BenM and CatM are paralogs with overlapping functions. BenM responds synergistically to two effectors, benzoate and cis,cis-muconate, to activate expression of the benABCDE operon which is involved in benzoate catabolism, while CatM responses only to muconate. BenM and CatM share high protein sequence identity and bind to the operator-promoter regions that have similar DNA sequences. In Pseudomonas species, phenolic compounds are converted by different enzymes to central intermediates, such as protocatechuate and catechols. Generally, unsubstituted compounds, such as benzoate, are metabolized by an ortho-cleavage pathway. The catBCA operon encodes three enzymes of the ortho-pathway required for benzoate catabolism: muconate lactonizing enzyme I, muconolactone isomerase, and catechol 1,2-dioxygenase. CatR normally responds to benzoate and cis,cis-muconate, an inducer molecule, to activate transcription of the catBCA operon, whose gene products convert benzoate to catechol. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 176136  Cd Length: 203  Bit Score: 49.15  E-value: 5.36e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330 113 FLKQHPEIHLNLKES------EAMALGNFEIEKNRVYFfrslrEQTEKNSIITEKDRFVAVLPKRHPLAKNA-VIALSDL 185
Cdd:cd08445   23 FRQAAPDVEIELIEMttvqqiEALKEGRIDVGFGRLRI-----EDPAIRRIVLREEPLVVALPAGHPLAQEKaPLTLAQL 97
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 498436330 186 ADENFLILGLAESPYYS--VEELCREAGFEPKITYQGTRIDLILRMIEEGLGVSLIMEkSLGNSLSDQLVTREIE 258
Cdd:cd08445   98 ADEPLILYPASPRPSFAdqVLSLFRDHGLRPRVIQEVRELQTALGLVAAGEGVTLVPA-SVQRLRRDDVVYRPLL 171
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
33-124 6.98e-07

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 49.43  E-value: 6.98e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330  33 SKKISALEKELQVPLFDRSNRQIQLTEEGRLLLPDIKRIVRAYQVLTDSLSEYREKKERVLTIHTIPT-----MPnyrgf 107
Cdd:PRK11716   9 SRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSLFCSVTaayshLP----- 83
                         90
                 ....*....|....*..
gi 498436330 108 DLLTNFLKQHPEIHLNL 124
Cdd:PRK11716  84 PILDRFRAEHPLVEIKL 100
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
9-118 1.19e-06

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 48.90  E-value: 1.19e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330   9 FLDLTETLNYTETAERNYMTQGNVSKKISALEKELQVPLFDRSNRQIQLTEEGRLLLPDIKRIVrayQVLTDSLSE---- 84
Cdd:PRK10082  19 FLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLL---QQLESNLAElrgg 95
                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 498436330  85 --YREKKERVLTIHTIptmpnyrGFDLLTNFLKQHP 118
Cdd:PRK10082  96 sdYAQRKIKIAAAHSL-------SLGLLPSIISQMP 124
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
108-285 1.27e-06

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: 47.87  E-value: 1.27e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330 108 DLLTNFLKQHPEIHLNL-----KESEAMaLGNFE-----IEKnrvyffrslreQTEKNSIITEK---DRFVAVLPKRHPL 174
Cdd:cd08420   17 RLLARFRKRYPEVRVSLtigntEEIAER-VLDGEidlglVEG-----------PVDHPDLIVEPfaeDELVLVVPPDHPL 84
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330 175 AKNAVIALSDLADENFLIL----GLAEspyySVEELCREAGFEP---KITYQGTRIDLILRMIEEGLGVSLIMEKSLGNS 247
Cdd:cd08420   85 AGRKEVTAEELAAEPWILRepgsGTRE----VFERALAEAGLDGldlNIVMELGSTEAIKEAVEAGLGISILSRLAVRKE 160
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 498436330 248 LSDQ-LVTREIEPTNE--SFLNFYLSEDADAPAPKEFFQFL 285
Cdd:cd08420  161 LELGrLVALPVEGLRLtrPFSLIYHKDKYLSPAAEAFLEFL 201
PRK09801 PRK09801
LysR family transcriptional regulator;
4-125 1.55e-06

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 48.88  E-value: 1.55e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330   4 QKLQLFLDLTETLNYTETAERNYMTQGNVSKKISALEKELQVPLFDRSNRQIQLTEEGRLLLPDIKRIVRAYQVLTDSLS 83
Cdd:PRK09801   9 KDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVT 88
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 498436330  84 EYREKKERVLTI---------HTIPTmpnyrgfdlLTNFLKQHPEIHLNLK 125
Cdd:PRK09801  89 QIKTRPEGMIRIgcsfgfgrsHIAPA---------ITELMRNYPELQVHFE 130
PBP2_MdcR cd08416
The C-terminal substrate-binding domian of LysR-type transcriptional regulator MdcR, which ...
160-239 1.90e-06

The C-terminal substrate-binding domian of LysR-type transcriptional regulator MdcR, which involved in the malonate catabolism contains the type 2 periplasmic binding fold; This family includes the C-terminal substrate binding domain of LysR-type transcriptional regulator (LTTR) MdcR that controls the expression of the malonate decarboxylase (mdc) genes. Like other members of the LTTRs, MdcR is a positive regulatory protein for its target promoter and composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins (PBP2). The PBP2 are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate- binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 176108  Cd Length: 199  Bit Score: 47.34  E-value: 1.90e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330 160 EKDRFVAVlPKRHPLAKNAVIALSDLADENFLILGLAESPYYSVEELCREAGFEPKITYQGTRIDLILRMIEEGLGVSLI 239
Cdd:cd08416   73 EDDIFLAV-PATSPLAASSEIDLRDLKDEKFVTLSEGFATYRGFDEAFEIAGFEPNVVMRVNDIFSLMSMVSGGVGYALL 151
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
4-187 1.98e-06

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 48.15  E-value: 1.98e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330   4 QKLQLFLDLTETLNYTETAERNYMTQGNVSKKISALEKELQVPLFDRSNRQIQLTEEGRLLLPdikrivRAYQVLtDSLS 83
Cdd:PRK10837   6 RQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYP------RALALL-EQAV 78
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330  84 E----YREkKERVLTIHTIPTMPNYRGFDLLTNFLKQHPEIHLNLkeseamALGNFEIEKNRVYFFR---SLREQTEKNS 156
Cdd:PRK10837  79 EieqlFRE-DNGALRIYASSTIGNYILPAMIARYRRDYPQLPLEL------SVGNSQDVINAVLDFRvdiGLIEGPCHSP 151
                        170       180       190
                 ....*....|....*....|....*....|....*
gi 498436330 157 -IITE---KDRFVAVLPKRHPLAKNAViALSDLAD 187
Cdd:PRK10837 152 eLISEpwlEDELVVFAAPDSPLARGPV-TLEQLAA 185
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
109-239 6.11e-06

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: 45.96  E-value: 6.11e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330 109 LLTNFLKQHPEIHLNLKeseamaLGNFE-----IEKNRVYFFRSLREQTEKNsiiTEKDRF-----VAVLPKRHPLAKNA 178
Cdd:cd08419   17 LLGAFCRRHPGVEVSLR------VGNREqvlerLADNEDDLAIMGRPPEDLD---LVAEPFldnplVVIAPPDHPLAGQK 87
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 498436330 179 VIALSDLADENFLilgLAES---PYYSVEELCREAGFEPKITYQGTRIDLILRMIEEGLGVSLI 239
Cdd:cd08419   88 RIPLERLAREPFL---LREPgsgTRLAMERFFAEHGVTLRVRMELGSNEAIKQAVMAGLGLSVL 148
PBP2_Chlorocatechol cd08446
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
95-241 7.12e-06

The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the chlorocatechol catabolism, contains the type 2 periplasmic binding fold; This CD includes the substrate binding domain of LysR-type regulators CbnR, ClcR and TfdR, which are involved in the regulation of chlorocatechol breakdown. The chlorocatechol-degradative pathway is often found in bacteria that can use chlorinated aromatic compounds as carbon and energy sources. CbnR is found in the 3-chlorobenzoate degradative bacterium Ralstonia eutropha NH9 and forms a tetramer. CbnR activates the expression of the cbnABCD genes, which are responsible for the degradation of chlorocatechol converted from 3-chlorobenzoate and are transcribed divergently from cbnR. In soil bacterium Pseudomonas putida, the 3-chlorocatechol-degradative pathway is encoded by clcABD operon, which requires the divergently transcribed clcR for activation. TfdR is involved in the activation of tfdA and tfdB gene expression. These genes encode enzymes for the conversion of 2,4-dichlorophenoxyacetic acid and 2,4-dichlorophenol. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176137 [Multi-domain]  Cd Length: 198  Bit Score: 45.73  E-value: 7.12e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330  95 IHTIPTmpnyrgfdLLTNFLKQHPEIHLNL----KESEAMAL--GNFEIEKNRVYffrslrEQTEKNSI--ITEKDRFVA 166
Cdd:cd08446   13 LDTVPR--------LLRAFLTARPDVTVSLhnmtKDEQIEALraGRIHIGFGRFY------PVEPDIAVenVAQERLYLA 78
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330 167 VlPKRHPLAKNAVIALSDLADENfLIL-------GLAEspyySVEELCREAGFEPKITYQGTRIDLILRMIEEGLGVSLI 239
Cdd:cd08446   79 V-PKSHPLAARPAVSLADLRNEP-LILfprggrpSFAD----EVLGLFRRAGVEPRVAQEVEDVVAALALVAAGFGVCIV 152

                 ..
gi 498436330 240 ME 241
Cdd:cd08446  153 PE 154
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
109-238 9.09e-04

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: 39.50  E-value: 9.09e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330 109 LLTNFLKQHPEIHLNLKESEA-------------MALgnfeieknrvyffrsLREQTEKNSIITE---KDRFVAVLPKRH 172
Cdd:cd08433   18 LLRAVRRRYPGIRLRIVEGLSghllewllngrldLAL---------------LYGPPPIPGLSTEpllEEDLFLVGPADA 82
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330 173 PLAKNAVIALSDLADENfLILglaESPYYS----VEELCREAGFEPKITYQGTRIDLILRMIEEGLGVSL 238
Cdd:cd08433   83 PLPRGAPVPLAELARLP-LIL---PSRGHGlrrlVDEAAARAGLTLNVVVEIDSVATLKALVAAGLGYTI 148
PBP2_NocR cd08458
The C-terminal substrate-domain of LysR-type transcriptional regulator, NocR, involved in the ...
165-260 9.18e-04

The C-terminal substrate-domain of LysR-type transcriptional regulator, NocR, involved in the catabolism of nopaline, contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulator NocR, which is involved in the catabolism of nopaline. 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, NocR regulates expression of the divergently transcribed nocB and nocR genes of the nopaline catabolism (noc) region. 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: 176147  Cd Length: 196  Bit Score: 39.69  E-value: 9.18e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330 165 VAVLPKRHPLAKNAVIALSDLADENFLILGLAESPYYSVEELCREAGFEPKITYQGTRIDLILRMIEEGLGVSLIMEKSL 244
Cdd:cd08458   75 VCLLPPGHRLEDKETVHATDLEGESLICLSPVSLLRMQTDAALDSCGVHCNRRIESSLALNLCDLVSRGMGVGIVDPFTA 154
                         90
                 ....*....|....*.
gi 498436330 245 GNSLSDQLVTREIEPT 260
Cdd:cd08458  155 DYYSANPVIQRSFDPV 170
PBP2_IlvR cd08453
The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved ...
165-285 1.52e-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: 38.88  E-value: 1.52e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330 165 VAVLPKRHPLAKNAVIALSDLADENFLIL--GLAESPYYSVEELCREAGFEPKITYQGTRIDLILRMIEEGLGVSLIMEk 242
Cdd:cd08453   78 VLAVPAAWAAEGGAPLALAAVAAEPLVIFprRIAPAFHDAVTGYYRAAGQTPRIAQEAIQMQTIISLVSAGMGVALVPA- 156
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 498436330 243 SLGNSLSDQLVTREIE---PTNESFLNFylSEDADAPAPKEFFQFL 285
Cdd:cd08453  157 SLRNLARPGVVYRELAdpaPVLETGLVW--RRDDASPVLARFLDLV 200
PBP2_DntR_NahR_LinR_like cd08459
The C-terminal substrate binding domain of LysR-type transcriptional regulators that are ...
131-216 1.61e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulators that are involved in the catabolism of dinitrotoluene, naphthalene and gamma-hexachlorohexane; contains the type 2 periplasmic binding fold; This CD includes LysR-like bacterial transcriptional regulators, DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. DntR from Burkholderia species controls genes encoding enzymes for oxidative degradation of the nitro-aromatic compound 2,4-dinitrotoluene. The active form of DntR is homotetrameric, consisting of a dimer of dimers. NahR is a salicylate-dependent transcription activator of the nah and sal operons for naphthalene degradation. Salicylic acid is an intermediate of the oxidative degradation of the aromatic ring in soil bacteria. LinR positively regulates expression of the genes (linD and linE) encoding enzymes for gamma-hexachlorocyclohexane (a haloorganic insecticide) degradation. Expression of linD and linE are induced by their substrates, 2,5-dichlorohydroquinone (2,5-DCHQ) and chlorohydroquinone (CHQ). The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176148 [Multi-domain]  Cd Length: 201  Bit Score: 38.71  E-value: 1.61e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330 131 ALGNFEIEKNRVYFFRSLREqteknsiitekdRFVAVLPKRHPLAKNAvIALSDLADENFLILGLAESPYYSVEELCREA 210
Cdd:cd08459   53 AIGYLPDLGAGFFQQRLFRE------------RYVCLVRKDHPRIGST-LTLEQFLAARHVVVSASGTGHGLVEQALREA 119

                 ....*.
gi 498436330 211 GFEPKI 216
Cdd:cd08459  120 GIRRRI 125
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
29-127 2.08e-03

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 39.20  E-value: 2.08e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330  29 QGNVSKKISALEKELQVPLFDRSNRQIQLTEEGRLLLPDIKRIVRAYQVLTDSLSEYREKKERVLTIHTIPTMPNYRGFD 108
Cdd:PRK14997  30 KSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDAIAALQVEPRGIVKLTCPVTLLHVHIGP 109
                         90
                 ....*....|....*....
gi 498436330 109 LLTNFLKQHPEIHLNLKES 127
Cdd:PRK14997 110 MLAKFMARYPDVSLQLEAT 128
PBP2_CysB_like cd08413
The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains ...
113-241 2.21e-03

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


Pssm-ID: 176105 [Multi-domain]  Cd Length: 198  Bit Score: 38.37  E-value: 2.21e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330 113 FLKQHPEIHLNLKESEAMALgnfeieknrvyfFRSLREQTEKNSIITEKD--------------RFVAVLPKRHPLAKNA 178
Cdd:cd08413   22 FRKRYPKVKLSLHQGTPSQI------------AEMVLKGEADIAIATEALddhpdlvtlpcyrwNHCVIVPPGHPLADLG 89
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 498436330 179 VIALSDLADENFLILGLAESPYYSVEELCREAGFEPKITYQGTRIDLILRMIEEGLGVSLIME 241
Cdd:cd08413   90 PLTLEDLAQYPLITYDFGFTGRSSIDRAFARAGLEPNIVLTALDADVIKTYVRLGLGVGIIAE 152
PBP2_CysB cd08443
The C-terminal substrate domain of LysR-type transcriptional regulator CysB contains type 2 ...
167-239 2.56e-03

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: 38.31  E-value: 2.56e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 498436330 167 VLPKRHPLAKNAVIALSDLADENFLILGLAESPYYSVEELCREAGFEPKITYQGTRIDLILRMIEEGLGVSLI 239
Cdd:cd08443   78 VVKRDHPLADKQSISIEELATYPIVTYTFGFTGRSELDTAFNRAGLTPNIVLTATDADVIKTYVRLGLGVGVI 150
PRK10341 PRK10341
transcriptional regulator TdcA;
4-86 2.60e-03

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 38.69  E-value: 2.60e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330   4 QKLQLFLDLTETLNYTETAERNYMTQGNVSKKISALEKELQVPLFDRSNRQIQLTEEGRLLLPDIKRIVRAYQvltDSLS 83
Cdd:PRK10341  10 QHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMK---NMVN 86

                 ...
gi 498436330  84 EYR 86
Cdd:PRK10341  87 EIN 89
PBP2_MetR cd08441
The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which ...
165-236 3.62e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which regulates the expression of methionine biosynthetic genes, contains type 2 periplasmic binding fold; MetR, a member of the LysR family, is a positive regulator for the metA, metE, metF, and metH genes. The sulfur-containing amino acid methionine is the universal initiator of protein synthesis in all known organisms and its derivative S-adenosylmethionine (SAM) and autoinducer-2 (AI-2) are involved in various cellular processes. SAM plays a central role as methyl donor in methylation reactions, which are essential for the biosynthesis of phospholipids, proteins, DNA and RNA. The interspecies signaling molecule AI-2 is involved in cell-cell communication process (quorum sensing) and gene regulation in bacteria. Although methionine biosynthetic enzymes and metabolic pathways are well conserved in bacteria, the regulation of methionine biosynthesis involves various regulatory mechanisms. In Escherichia coli and Salmonella enterica serovar Typhimurium, MetJ and MetR regulate the expression of methionine biosynthetic genes. The MetJ repressor negatively regulates the E. coli met genes, except for metH. Several of these genes are also under the positive control of MetR with homocysteine as a co-inducer. In Bacillus subtilis, the met genes are controlled by S-box termination-antitermination system. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176132  Cd Length: 198  Bit Score: 37.93  E-value: 3.62e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330 165 VAVLPKRHPLAKNAVIALSDLADENFLIlglaespyYSVEE----LCRE----AGFEPKITYQGTRIDLILRMIEEGLGV 236
Cdd:cd08441   75 VLVVAPDHPLAAKEFITPEDLADETLIT--------YPVERerldVFRHflqpAGIEPKRRRTVELTLMILQLVASGRGV 146
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
166-257 4.05e-03

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


Pssm-ID: 176117 [Multi-domain]  Cd Length: 199  Bit Score: 37.67  E-value: 4.05e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330 166 AVLPKRHPLAKNAVIALSDLADENfliLGLAEsPYYSVEEL----CREAGFEPKITYQGTRIDLILRMIEEGLGVSLIME 241
Cdd:cd08426   76 AVVPPGHPLARQPSVTLAQLAGYP---LALPP-PSFSLRQIldaaFARAGVQLEPVLISNSIETLKQLVAAGGGISLLTE 151
                         90
                 ....*....|....*..
gi 498436330 242 KSLGNSL-SDQLVTREI 257
Cdd:cd08426  152 LAVRREIrRGQLVAVPL 168
PBP2_CynR cd08425
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, ...
93-233 4.61e-03

The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, contains the type 2 periplasmic binding fold; CynR is a LysR-like transcriptional regulator of the cyn operon, which encodes genes that allow cyanate to be used as a sole source of nitrogen. The operon includes three genes in the following order: cynT (cyanate permease), cynS (cyanase), and cynX (a protein of unknown function). CynR negatively regulates its own expression independently of cyanate. CynR binds to DNA and induces bending of DNA in the presence or absence of cyanate, but the amount of bending is decreased by cyanate. The CynR of LysR-type transcriptional regulator family is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins (PBP2). The PBP2 are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176116  Cd Length: 197  Bit Score: 37.31  E-value: 4.61e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330  93 LTIHTIPTMPNYRGFDLLTNFLKQHPEIHLNLKE--SEAM--ALGNFEIEKNrVYFFRSLREQTEKNSIITEkdRFVAVL 168
Cdd:cd08425    3 LRLAMTPTFTAYLIGPLIDRFHARYPGIALSLREmpQERIeaALADDRLDLG-IAFAPVRSPDIDAQPLFDE--RLALVV 79
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 498436330 169 PKRHPLA-KNAVIALSDLADENFLILGLAESPYYSVEELCREAGFEPKITYQGTRIDLILRMIEEG 233
Cdd:cd08425   80 GATHPLAqRRTALTLDDLAAEPLALLSPDFATRQHIDRYFQKQGIKPRIAIEANSISAVLEVVRRG 145
PBP2_YofA_SoxR_like cd08442
The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, ...
109-241 6.99e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, contains the type 2 periplasmic binding fold; YofA is a LysR-like transcriptional regulator of cell growth in Bacillus subtillis. YofA controls cell viability and the formation of constrictions during cell division. YofaA positively regulates expression of the cell division gene ftsW, and thus is essential for cell viability during stationary-phase growth of Bacillus substilis. YofA shows significant homology to SoxR from Arthrobacter sp. TE1826. SoxR is a negative regulator for the sarcosine oxidase gene soxA. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine, which is involved in the metabolism of creatine and choline. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176133  Cd Length: 193  Bit Score: 36.82  E-value: 6.99e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498436330 109 LLTNFLKQHPEIHLNLK--ESEAM--ALGNFEIEKNRVYffrslrEQTEKNSIITEK---DRFVAVLPKRHPlaknAVIA 181
Cdd:cd08442   18 LLAAYHARYPKVDLSLStgTTGALiqAVLEGRLDGAFVA------GPVEHPRLEQEPvfqEELVLVSPKGHP----PVSR 87
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 498436330 182 LSDLADENFLILGLAESPYYSVEELCREAGFEP-KITYQGTrIDLILRMIEEGLGVSLIME 241
Cdd:cd08442   88 AEDLAGSTLLAFRAGCSYRRRLEDWLAEEGVSPgKIMEFGS-YHAILGCVAAGMGIALLPR 147
 
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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