NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|556283928|ref|WP_023289814|]
View 

MULTISPECIES: LysR family transcriptional regulator [Klebsiella]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 11426483)

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

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

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-282 2.76e-42

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 145.78  E-value: 2.76e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928   1 MDIKQLKYLIALDQTRHFGQAAAACHITQPTLSMRIRNLEEELNLTLIQRGQRFEGFTPEGERILAWARAVLAAHDGLAA 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928  81 EAAICRGQMVGQLRVGMVPLASLNP-MQLIKPLAEKYPALQFSLLSMTSEQIIDGVSRNQLDLGICYLQHLDERLfKIAR 159
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLlPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGL-VARP 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928 160 LPQTRMGLLhdkrhfdfsdGTPGWDTLATLPLgfltkgmyyresieisfkakgltpksvfeSDSTFQIIQAVQAGICCAI 239
Cdd:COG0583  160 LGEERLVLV----------ASPDHPLARRAPL-----------------------------VNSLEALLAAVAAGLGIAL 200

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....
gi 556283928 240 MPLNNGLEAL-SDNLDILPIAESQVDSQLALIMRQQEPVSTLAE 282
Cdd:COG0583  201 LPRFLAADELaAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVR 244
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-282 2.76e-42

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 145.78  E-value: 2.76e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928   1 MDIKQLKYLIALDQTRHFGQAAAACHITQPTLSMRIRNLEEELNLTLIQRGQRFEGFTPEGERILAWARAVLAAHDGLAA 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928  81 EAAICRGQMVGQLRVGMVPLASLNP-MQLIKPLAEKYPALQFSLLSMTSEQIIDGVSRNQLDLGICYLQHLDERLfKIAR 159
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLlPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGL-VARP 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928 160 LPQTRMGLLhdkrhfdfsdGTPGWDTLATLPLgfltkgmyyresieisfkakgltpksvfeSDSTFQIIQAVQAGICCAI 239
Cdd:COG0583  160 LGEERLVLV----------ASPDHPLARRAPL-----------------------------VNSLEALLAAVAAGLGIAL 200

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....
gi 556283928 240 MPLNNGLEAL-SDNLDILPIAESQVDSQLALIMRQQEPVSTLAE 282
Cdd:COG0583  201 LPRFLAADELaAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVR 244
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 1-241 2.48e-25

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 102.34  E-value: 2.48e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928   1 MDIKQLKYLIALDQTRHFGQAAAACHITQPTLSMRIRNLEEELNLTLIQRGQRFEGFTPEGERILAWARAVLaaHDGLAA 80
Cdd:PRK11242   1 MLLRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRAL--QDLEAG 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928  81 EAAICRGQMV--GQLRVGMVPLASlnpMQLIKPLAEK----YPALQFSLLSMTSEQIIDGVSRNQLDLGICYlqhLDERL 154
Cdd:PRK11242  79 RRAIHDVADLsrGSLRLAMTPTFT---AYLIGPLIDAfharYPGITLTIREMSQERIEALLADDELDVGIAF---APVHS 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928 155 FKIARLP--QTRMGLLHDKRHFDFSDGTP-GWDTLATLPLGFLTKGMYYRESIEISFKAKGLTPKSVFESDSTFQIIQAV 231
Cdd:PRK11242 153 PEIEAQPlfTETLALVVGRHHPLAARRKAlTLDELADEPLVLLSAEFATREQIDRYFRRHGVTPRVAIEANSISAVLEIV 232

                        250
                 ....*....|
gi 556283928 232 QAGICCAIMP 241
Cdd:PRK11242 233 RRGRLATLLP 242
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-235 3.72e-25

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: 101.92  E-value: 3.72e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928   1 MDIKQLKYLIALDQTRHFGQAAAACHITQPTLSMRIRNLEEELNLTLIQRGQRFEGFTPEGERILAWARAVLaaHDGLAA 80
Cdd:NF040786   1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEML--DLWEKL 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928  81 EAAICR--GQMVGQLRVGM--VPLASLNPmQLIKPLAEKYPALQFSLLSMTSEQIIDGVSRNQLDLGI----------CY 146
Cdd:NF040786  79 EEEFDRygKESKGVLRIGAstIPGQYLLP-ELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFtgtklekkrlVY 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928 147 LQHLDERLFKIA--RLPQTRMGllhdKRHFDFSDgtpgwdtLATLPLGFLTKGMYYRESIEISFKAKGLTPKS---VFES 221
Cdd:NF040786 158 TPFYKDRLVLITpnGTEKYRML----KEEISISE-------LQKEPFIMREEGSGTRKEAEKALKSLGISLEDlnvVASL 226

                        250
                 ....*....|....
gi 556283928 222 DSTFQIIQAVQAGI 235
Cdd:NF040786 227 GSTEAIKQSVEAGL 240
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 91-282 6.78e-25

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


Pssm-ID: 460931 [Multi-domain]  Cd Length: 205  Bit Score: 98.90  E-value: 6.78e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928   91 GQLRVGMVPLASLNPM-QLIKPLAEKYPALQFSLLSMTSEQIIDGVSRNQLDLGICYLQHLDERLFKIaRLPQTRMGLLH 169
Cdd:pfam03466   2 GRLRIGAPPTLASYLLpPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEAR-PLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928  170 DKRHFDFSDGTPGWDTLATLPLGFLTKGMYYRESIEISFKAKGLTPKSVFESDSTFQIIQAVQAGICCAIMPLNNGLEAL 249
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAREL 160

                         170       180       190
                  ....*....|....*....|....*....|....
gi 556283928  250 -SDNLDILPIAESQVDSQLALIMRQQEPVSTLAE 282
Cdd:pfam03466 161 aDGRLVALPLPEPPLPRELYLVWRKGRPLSPAVR 194
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 93-288 2.59e-23

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


Pssm-ID: 176102 [Multi-domain]  Cd Length: 197  Bit Score: 94.20  E-value: 2.59e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928  93 LRVGMVPLASLNPM-QLIKPLAEKYPALQFSLLSMTSEQIIDGVSRNQLDLGICYLQHLDERLfKIARLPQTRMGL---- 167
Cdd:cd05466    2 LRIGASPSIAAYLLpPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGL-ESEPLFEEPLVLvvpp 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928 168 ---LHDKRHFDFSDgtpgwdtLATLPLGFLTKGMYYRESIEISFKAKGLTPKSVFESDSTFQIIQAVQAGICCAIMPLNN 244
Cdd:cd05466   81 dhpLAKRKSVTLAD-------LADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESA 153

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 556283928 245 GLEALSDNLDILPIAESQVDSQLALIMRQQEPVSTLAEKCFAEA 288
Cdd:cd05466  154 VEELADGGLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-282 2.76e-42

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 145.78  E-value: 2.76e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928   1 MDIKQLKYLIALDQTRHFGQAAAACHITQPTLSMRIRNLEEELNLTLIQRGQRFEGFTPEGERILAWARAVLAAHDGLAA 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928  81 EAAICRGQMVGQLRVGMVPLASLNP-MQLIKPLAEKYPALQFSLLSMTSEQIIDGVSRNQLDLGICYLQHLDERLfKIAR 159
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLlPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGL-VARP 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928 160 LPQTRMGLLhdkrhfdfsdGTPGWDTLATLPLgfltkgmyyresieisfkakgltpksvfeSDSTFQIIQAVQAGICCAI 239
Cdd:COG0583  160 LGEERLVLV----------ASPDHPLARRAPL-----------------------------VNSLEALLAAVAAGLGIAL 200

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....
gi 556283928 240 MPLNNGLEAL-SDNLDILPIAESQVDSQLALIMRQQEPVSTLAE 282
Cdd:COG0583  201 LPRFLAADELaAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVR 244
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 1-241 2.48e-25

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 102.34  E-value: 2.48e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928   1 MDIKQLKYLIALDQTRHFGQAAAACHITQPTLSMRIRNLEEELNLTLIQRGQRFEGFTPEGERILAWARAVLaaHDGLAA 80
Cdd:PRK11242   1 MLLRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRAL--QDLEAG 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928  81 EAAICRGQMV--GQLRVGMVPLASlnpMQLIKPLAEK----YPALQFSLLSMTSEQIIDGVSRNQLDLGICYlqhLDERL 154
Cdd:PRK11242  79 RRAIHDVADLsrGSLRLAMTPTFT---AYLIGPLIDAfharYPGITLTIREMSQERIEALLADDELDVGIAF---APVHS 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928 155 FKIARLP--QTRMGLLHDKRHFDFSDGTP-GWDTLATLPLGFLTKGMYYRESIEISFKAKGLTPKSVFESDSTFQIIQAV 231
Cdd:PRK11242 153 PEIEAQPlfTETLALVVGRHHPLAARRKAlTLDELADEPLVLLSAEFATREQIDRYFRRHGVTPRVAIEANSISAVLEIV 232

                        250
                 ....*....|
gi 556283928 232 QAGICCAIMP 241
Cdd:PRK11242 233 RRGRLATLLP 242
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-235 3.72e-25

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: 101.92  E-value: 3.72e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928   1 MDIKQLKYLIALDQTRHFGQAAAACHITQPTLSMRIRNLEEELNLTLIQRGQRFEGFTPEGERILAWARAVLaaHDGLAA 80
Cdd:NF040786   1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEML--DLWEKL 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928  81 EAAICR--GQMVGQLRVGM--VPLASLNPmQLIKPLAEKYPALQFSLLSMTSEQIIDGVSRNQLDLGI----------CY 146
Cdd:NF040786  79 EEEFDRygKESKGVLRIGAstIPGQYLLP-ELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFtgtklekkrlVY 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928 147 LQHLDERLFKIA--RLPQTRMGllhdKRHFDFSDgtpgwdtLATLPLGFLTKGMYYRESIEISFKAKGLTPKS---VFES 221
Cdd:NF040786 158 TPFYKDRLVLITpnGTEKYRML----KEEISISE-------LQKEPFIMREEGSGTRKEAEKALKSLGISLEDlnvVASL 226

                        250
                 ....*....|....
gi 556283928 222 DSTFQIIQAVQAGI 235
Cdd:NF040786 227 GSTEAIKQSVEAGL 240
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 91-282 6.78e-25

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


Pssm-ID: 460931 [Multi-domain]  Cd Length: 205  Bit Score: 98.90  E-value: 6.78e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928   91 GQLRVGMVPLASLNPM-QLIKPLAEKYPALQFSLLSMTSEQIIDGVSRNQLDLGICYLQHLDERLFKIaRLPQTRMGLLH 169
Cdd:pfam03466   2 GRLRIGAPPTLASYLLpPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEAR-PLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928  170 DKRHFDFSDGTPGWDTLATLPLGFLTKGMYYRESIEISFKAKGLTPKSVFESDSTFQIIQAVQAGICCAIMPLNNGLEAL 249
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAREL 160

                         170       180       190
                  ....*....|....*....|....*....|....
gi 556283928  250 -SDNLDILPIAESQVDSQLALIMRQQEPVSTLAE 282
Cdd:pfam03466 161 aDGRLVALPLPEPPLPRELYLVWRKGRPLSPAVR 194
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 93-288 2.59e-23

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


Pssm-ID: 176102 [Multi-domain]  Cd Length: 197  Bit Score: 94.20  E-value: 2.59e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928  93 LRVGMVPLASLNPM-QLIKPLAEKYPALQFSLLSMTSEQIIDGVSRNQLDLGICYLQHLDERLfKIARLPQTRMGL---- 167
Cdd:cd05466    2 LRIGASPSIAAYLLpPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGL-ESEPLFEEPLVLvvpp 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928 168 ---LHDKRHFDFSDgtpgwdtLATLPLGFLTKGMYYRESIEISFKAKGLTPKSVFESDSTFQIIQAVQAGICCAIMPLNN 244
Cdd:cd05466   81 dhpLAKRKSVTLAD-------LADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESA 153

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 556283928 245 GLEALSDNLDILPIAESQVDSQLALIMRQQEPVSTLAEKCFAEA 288
Cdd:cd05466  154 VEELADGGLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 1-144 3.84e-22

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 93.56  E-value: 3.84e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928   1 MDIKQLKYLIALDQTRHFGQAAAACHITQPTLSMRIRNLEEELNLTLIQRGQRFEGFTPEGERILAWARAVLAAHDGLAA 80
Cdd:PRK11151   1 MNIRDLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVLKE 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 556283928  81 EAAICRGQMVGQLRVGMVPlaSLNP--MQLIKP-LAEKYPALQFSLLSMTSEQIIDGVSRNQLDLGI 144
Cdd:PRK11151  81 MASQQGETMSGPLHIGLIP--TVGPylLPHIIPmLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCAI 145
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 1-241 1.20e-17

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 80.97  E-value: 1.20e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928   1 MDIKQLKYLIALDQTRHFGQAAAACHITQPTLSMRIRNLEEELNLTLIQRGQRFEGFTPEGERILAWARAVLAahdglAA 80
Cdd:PRK09906   1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILE-----QA 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928  81 EAAICRGQMVG----QLRVGMVPLASLNPMQLIKP-LAEKYPALQFSLLSMTSEQIIDGVSRNQLDLG----------IC 145
Cdd:PRK09906  76 EKAKLRARKIVqedrQLTIGFVPSAEVNLLPKVLPmFRLRHPDTLIELVSLITTQQEEKLRRGELDVGfmrhpvysdeID 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928 146 YLQHLDERLfkIARLPQTrmgllHDKRHFDF--SDGTPGWDTLATLPlgflTKGMYYRESIEISFKAKGLTPKSVFESDS 223
Cdd:PRK09906 156 YLELLDEPL--VVVLPVD-----HPLAHEKEitAAQLDGVNFISTDP----AYSGSLAPIIKAWFAQHNSQPNIVQVATN 224

                        250
                 ....*....|....*...
gi 556283928 224 TFQIIQAVQAGICCAIMP 241
Cdd:PRK09906 225 ILVTMNLVGMGLGCTIIP 242
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-62 5.14e-17

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 73.57  E-value: 5.14e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928    3 IKQLKYLIALDQTRHFGQAAAACHITQPTLSMRIRNLEEELNLTLIQRGQRFEGFTPEGE 62
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK12680 PRK12680
LysR family transcriptional regulator;
1-235 1.26e-14

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 72.73  E-value: 1.26e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928   1 MDIKQLKYLIAL-DQTRHFGQAAAACHITQPTLSMRIRNLEEELNLTL-IQRGQRFEGFTPEGERILAWARAVLAAHDGL 78
Cdd:PRK12680   1 MTLTQLRYLVAIaDAELNITLAAARVHATQPGLSKQLKQLEDELGFLLfVRKGRSLESVTPAGVEVIERARAVLSEANNI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928  79 AAEAAICRGQMVGQLRVGMVPLAS---LNPMqlIKPLAEKYPALQFSLLSMTSEQIIDGVSRNQLDLGICYL------QH 149
Cdd:PRK12680  81 RTYAANQRRESQGQLTLTTTHTQArfvLPPA--VAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVSTaggepsAG 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928 150 LDERLFKIARLPQTRMGllhdkRHFDFSDGTPGWDTLATLPLGFLTKGMYYRESIEISFKAKGLTPKSVFESDSTFQIIQ 229
Cdd:PRK12680 159 IAVPLYRWRRLVVVPRG-----HALDTPRRAPDMAALAEHPLISYESSTRPGSSLQRAFAQLGLEPSIALTALDADLIKT 233


                 ....*.
gi 556283928 230 AVQAGI 235
Cdd:PRK12680 234 YVRAGL 239
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 1-282 4.39e-14

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 71.25  E-value: 4.39e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928   1 MDIKQLKYLIALDQTRHFGQAAAACHITQPTLSMRIRNLEEELNLTLIQRGQRfeGFTP-EGERIL-AWARAVLAAHDgL 78
Cdd:PRK11233   1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKR--GVTPtEAGKILyTHARAILRQCE-Q 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928  79 AAEAAICRGQ-MVGQLRVGMVP--LASLNPMQLIKPLAEKYPALQFSLL----SMTSEQIIDGvsrnQLDLGICYlqhlD 151
Cdd:PRK11233  78 AQLAVHNVGQaLSGQVSIGLAPgtAASSLTMPLLQAVRAEFPGIVLYLHensgATLNEKLMNG----QLDMAVIY----E 149

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928 152 ERlfKIARLpqTRMGLLHDKRHFDFSDGTPGWD----TLATLPLgFLTKGmyY---RESIEISFKAKGLTPKSVFESDST 224
Cdd:PRK11233 150 HS--PVAGL--SSQPLLKEDLFLVGTQDCPGQSvdlaAVAQMNL-FLPRD--YsavRLRVDEAFSLRRLTAKVIGEIESI 222

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 556283928 225 FQIIQAVQAGICCAIMPLNNGLEAL-SDNLDILPIAESQVDSQLALIMRQQEPVSTLAE 282
Cdd:PRK11233 223 ATLTAAIASGMGVTVLPESAARSLCgAVNGWMARITTPSMSLSLSLNLSARLPLSPQAQ 281
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 92-282 2.93e-13

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: 66.85  E-value: 2.93e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928  92 QLRVGMVP-LASLNPMQLIKPLAEKYPALQFSLLSMTSEQIIDGVSRNQLDLGICYLQH----------LDERLFKIARL 160
Cdd:cd08433    1 RVSVGLPPsAASVLAVPLLRAVRRRYPGIRLRIVEGLSGHLLEWLLNGRLDLALLYGPPpipglsteplLEEDLFLVGPA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928 161 PQTRMGllhdkrhfdfsDGTPGWDTLATLPLgFLT---KGMyyRESIEISFKAKGLTPKSVFESDSTFQIIQAVQAGICC 237
Cdd:cd08433   81 DAPLPR-----------GAPVPLAELARLPL-ILPsrgHGL--RRLVDEAAARAGLTLNVVVEIDSVATLKALVAAGLGY 146

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 556283928 238 AIMPLNNGLEAL-SDNLDILPIAESQVDSQLALIMRQQEPVSTLAE 282
Cdd:cd08433  147 TILPASAVAAEVaAGRLVAAPIVDPALTRTLSLATPRDRPLSPAAL 192
PRK09986 PRK09986
LysR family transcriptional regulator;
1-144 9.80e-13

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 67.06  E-value: 9.80e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928   1 MDIKQLKYLIALDQTRHFGQAAAACHITQPTLSMRIRNLEEELNLTLIQRGQRFEGFTPEGERILAWARAVLA-AHDGLA 79
Cdd:PRK09986   7 IDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDnAEQSLA 86

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 556283928  80 AEAAICRGQmVGQLRVGMVPLASLNPMQ-LIKPLAEKYPALQFSLLSMTSEQIIDGVSRNQLDLGI 144
Cdd:PRK09986  87 RVEQIGRGE-AGRIEIGIVGTALWGRLRpAMRHFLKENPNVEWLLRELSPSMQMAALERRELDAGI 151
PBP2_YofA_SoxR_like cd08442
The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, ...
 93-282 3.80e-12

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: 63.78  E-value: 3.80e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928  93 LRVG-MVPLASLNPMQLIKPLAEKYPALQFSLLSMTSEQIIDGVSRNQLDLGICYLQHLDERLFKIArLPQTRMGLLHDK 171
Cdd:cd08442    2 LRLGsMETTAAVRLPPLLAAYHARYPKVDLSLSTGTTGALIQAVLEGRLDGAFVAGPVEHPRLEQEP-VFQEELVLVSPK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928 172 RHFDFSDGTpgwdTLATLPLGFLTKGMYYRESIEISFKAKGLTPKSVFESDSTFQIIQAVQAGICCAIMPLN--NGLEAl 249
Cdd:cd08442   81 GHPPVSRAE----DLAGSTLLAFRAGCSYRRRLEDWLAEEGVSPGKIMEFGSYHAILGCVAAGMGIALLPRSvlDSLQG- 155

                        170       180       190
                 ....*....|....*....|....*....|...
gi 556283928 250 SDNLDILPIAESQVDSQLALIMRQQEPVSTLAE 282
Cdd:cd08442  156 RGSVSIHPLPEPFADVTTWLVWRKDSFTAALQA 188
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 1-240 4.33e-12

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 65.40  E-value: 4.33e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928   1 MDIKQLKYLiaLDQTRH---FGQAAAACHITQPTLSMRIRNLEEELNLTL-IQRGQRFEGFTPEGERILAWARAVLAAHD 76
Cdd:PRK12682   1 MNLQQLRFV--REAVRRnlnLTEAAKALHTSQPGVSKAIIELEEELGIEIfIRHGKRLKGLTEPGKAVLDVIERILREVG 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928  77 GLAAEAAICRGQMVGQLRVgmvplASLNPM------QLIKPLAEKYPALQFSLLSMTSEQIIDGVSRNQLDLGICYLQHL 150
Cdd:PRK12682  79 NIKRIGDDFSNQDSGTLTI-----ATTHTQaryvlpRVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGIATESLA 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928 151 DERlfKIARLPQTRMGL---------LHDKRHFDFsdgtpgwDTLATLPLGFLTKGMYYRESIEISFKAKGLTPKSVFES 221
Cdd:PRK12682 154 DDP--DLATLPCYDWQHavivppdhpLAQEERITL-------EDLAEYPLITYHPGFTGRSRIDRAFAAAGLQPDIVLEA 224

                        250
                 ....*....|....*....
gi 556283928 222 DSTFQIIQAVQAGICCAIM 240
Cdd:PRK12682 225 IDSDVIKTYVRLGLGVGIV 243
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
2-71 6.46e-11

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 61.53  E-value: 6.46e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928   2 DIKQLKYLIALDQTRHFGQAAAACHITQPTLSMRIRNLEEELNLTLIQRGQRFEGfTPEGERILAWARAV 71
Cdd:PRK13348   3 DYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRGRPCRP-TPAGQRLLRHLRQV 71
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-282 8.92e-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: 59.85  E-value: 8.92e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928  92 QLRVGMVPLASLNPM-QLIKPLAEKYPALQFSLLSMTSEQIIDGVSRNQLDLGICYLQHLDERLfKIARLPQTRMGLLHD 170
Cdd:cd08440    1 RVRVAALPSLAATLLpPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEADPDL-EFEPLLRDPFVLVCP 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928 171 KRHFDFSDGTPGWDTLATLPLGFLTKGMYYRESIEISFKAKGLTPKSVFESDSTFQIIQAVQAGICCAIMPLNNGLEALS 250
Cdd:cd08440   80 KDHPLARRRSVTWAELAGYPLIALGRGSGVRALIDRALAAAGLTLRPAYEVSHMSTALGMVAAGLGVAVLPALALPLADH 159

                        170       180       190
                 ....*....|....*....|....*....|..
gi 556283928 251 DNLDILPIAESQVDSQLALIMRQQEPVSTLAE 282
Cdd:cd08440  160 PGLVARPLTEPVVTRTVGLIRRRGRSLSPAAQ 191
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
1-144 1.13e-10

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 61.15  E-value: 1.13e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928   1 MDIKQLKYLI-ALDQTRHFGQAAAACHITQPTLSMRIRNLEEELNLTLIQR-GQRFEGFTPEGERILAWARAVLAAHDGL 78
Cdd:PRK12684   1 MNLHQLRFVReAVRQNFNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRhGKRLRGLTEPGRIILASVERILQEVENL 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 556283928  79 ---AAE-AAICRGQMV-----GQLRVGMvPLAslnpmqlIKPLAEKYPALQFSLLSMTSEQIIDGVSRNQLDLGI 144
Cdd:PRK12684  81 krvGKEfAAQDQGNLTiatthTQARYAL-PAA-------IKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAI 147
rbcR CHL00180
LysR transcriptional regulator; Provisional
 5-144 2.94e-10

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 60.03  E-value: 2.94e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928   5 QLKYLIALDQTRHFGQAAAACHITQPTLSMRIRNLEEELNLTLIQRGQRFEGFTPEGERILAWARAVLAahdgLAAEAai 84
Cdd:CHL00180   9 QLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILA----LCEET-- 82

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 556283928  85 CR-------GQMvGQLRVGmvplAS------LNPmQLIKPLAEKYPALQFSLLSMTSEQIIDGVSRNQLDLGI 144
Cdd:CHL00180  83 CRaledlknLQR-GTLIIG----ASqttgtyLMP-RLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAI 149
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
1-144 4.25e-10

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 59.26  E-value: 4.25e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928   1 MDIKQLKYLIALDQTRHFGQAAAACHITQPTLSMRIRNLEEELNLTLIQRGQRFEGFTPEGERILAWARAVLAAHdgLAA 80
Cdd:PRK03601   1 MDTELLKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYAETLMNTW--QAA 78

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 556283928  81 EAAICRGQMVGQLRVGMVPL---ASLNPMqlIKPLAEKYPALQFSLLSMTSEQIIDGVSRNQLDLGI 144
Cdd:PRK03601  79 KKEVAHTSQHNELSIGASASlweCMLTPW--LGRLYQNQEALQFEARIAQRQSLVKQLHERQLDLLI 143
PBP2_CynR cd08425
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, ...
 91-273 5.19e-10

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: 57.72  E-value: 5.19e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928  91 GQLRVGMVPLASlnpMQLIKPLAE----KYPALQFSLLSMTSEQIIDGVSRNQLDLGICY-------LQH---LDERLFK 156
Cdd:cd08425    1 GSLRLAMTPTFT---AYLIGPLIDrfhaRYPGIALSLREMPQERIEAALADDRLDLGIAFapvrspdIDAqplFDERLAL 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928 157 IA----RLPQTRMGLlhdkrhfdfsdgTPgwDTLATLPLGFLTKGMYYRESIEISFKAKGLTPKSVFESDSTFQIIQAVQ 232
Cdd:cd08425   78 VVgathPLAQRRTAL------------TL--DDLAAEPLALLSPDFATRQHIDRYFQKQGIKPRIAIEANSISAVLEVVR 143

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 556283928 233 AGICCAIMPlnNGLEALSDNLDILPIAESQVDSQLALIMRQ 273
Cdd:cd08425  144 RGRLATILP--DAIAREQPGLCAVALEPPLPGRTAALLRRK 182
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
16-188 3.37e-09

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 56.55  E-value: 3.37e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928  16 RH--FGQAAAACHITQPTLSMRIRNLEEELNLTLIQRGQRFEGFTPEGERILAwarAVLAAHDGLAAEA-AICRGQMVGQ 92
Cdd:PRK10086  27 RHqsFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFW---ALKSSLDTLNQEIlDIKNQELSGT 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928  93 LRVGMVP-LAS--LNPMqlIKPLAEKYPALQFSLLsmTSEQIIDgVSRNQLDLGICY-------LQH---LDERLF---- 155
Cdd:PRK10086 104 LTVYSRPsIAQcwLVPR--LADFTRRYPSISLTIL--TGNENVN-FQRAGIDLAIYFddapsaqLTHhflMDEEILpvcs 178

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 556283928 156 -----------KIARLPQTRmgLLHDKRHFDFSDGTPGWDTLAT 188
Cdd:PRK10086 179 peyaerhaltgNPDNLRHCT--LLHDRQAWSNDSGTDEWHSWAQ 220
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 92-276 6.00e-09

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: 54.82  E-value: 6.00e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928  92 QLRVGMVPLASLNPM-QLIKPLAEKYPALQFSLLSMTSEQIIDGVSRNQLDLGICYLQHLDERLfKIARLPQTRMGL--- 167
Cdd:cd08414    1 RLRIGFVGSALYGLLpRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPPPDPPGL-ASRPLLREPLVValp 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928 168 ----LHDKRHFDFSDgtpgwdtLATLPLGFLTK--GMYYRESIEISFKAKGLTPKSVFESDSTFQIIQAVQAGICCAIMP 241
Cdd:cd08414   80 adhpLAARESVSLAD-------LADEPFVLFPRepGPGLYDQILALCRRAGFTPRIVQEASDLQTLLALVAAGLGVALVP 152

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 556283928 242 lnnglEALS----DNLDILPIAESQVDSQLALIMRQQEP 276
Cdd:cd08414  153 -----ASVArlqrPGVVYRPLADPPPRSELALAWRRDNA 186
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 107-282 7.89e-09

C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which activates the transcription of the cysJI operon encoding sulfite reductase, contains the type 2 periplasmic binding fold; CysL, also known as YwfK, is a regular of sulfur metabolism in Bacillus subtilis. Sulfur is required for the synthesis of proteins and essential cofactors in all living organism. Sulfur can be assimilated either from inorganic sources (sulfate and thiosulfate), or from organic sources (sulfate esters, sulfamates, and sulfonates). CysL activates the transcription of the cysJI operon encoding sulfite reductase, which reduces sulfite to sulfide. Both cysL mutant and cysJI mutant are unable to grow using sulfate or sulfite as the sulfur source. Like other LysR-type regulators, CysL also negatively regulates its own transcription. In Escherichia coli, three LysR-type activators are involved in the regulation of sulfur metabolism: CysB, Cbl and MetR. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176112 [Multi-domain]  Cd Length: 201  Bit Score: 54.42  E-value: 7.89e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928 107 QLIKPLAEKYPALQFSLLSMTSEQIIDGVSRNQLDLGI----CYLQHLDERLFKiarlpQTRMGLLHDKRHFDFSDGTPG 182
Cdd:cd08420   17 RLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLvegpVDHPDLIVEPFA-----EDELVLVVPPDHPLAGRKEVT 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928 183 WDTLATLPLGFLTKGMYYRESIEISFKAKGLTP---KSVFESDSTFQIIQAVQAGICCAIMP-------LNNGLealsdn 252
Cdd:cd08420   92 AEELAAEPWILREPGSGTREVFERALAEAGLDGldlNIVMELGSTEAIKEAVEAGLGISILSrlavrkeLELGR------ 165

                        170       180       190
                 ....*....|....*....|....*....|
gi 556283928 253 LDILPIAESQVDSQLALIMRQQEPVSTLAE 282
Cdd:cd08420  166 LVALPVEGLRLTRPFSLIYHKDKYLSPAAE 195
cysB PRK12681
HTH-type transcriptional regulator CysB;
1-219 1.37e-08

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 54.90  E-value: 1.37e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928   1 MDIKQLKYLI-ALDQTRHFGQAAAACHITQPTLSMRIRNLEEELNLTLIQR-GQRFEGFTPEGERILAWARAVLAAHDGL 78
Cdd:PRK12681   1 MKLQQLRYIVeVVNHNLNVSATAEGLYTSQPGISKQVRMLEDELGIQIFARsGKHLTQVTPAGEEIIRIAREILSKVESI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928  79 AAEAAICRGQMVGQLRVG--------MVPlaslnpmQLIKPLAEKYPALQFSLLSMTSEQIIDGVSRNQLDLGICY-LQH 149
Cdd:PRK12681  81 KSVAGEHTWPDKGSLYIAtthtqaryALP-------PVIKGFIERYPRVSLHMHQGSPTQIAEAAAKGNADFAIATeALH 153

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 556283928 150 LDERLFkiaRLP---------QTRMGLLHDKRHFDFSDgtpgwdtLATLPLGFLTKGMYYRESIEISFKAKGLTPKSVF 219
Cdd:PRK12681 154 LYDDLI---MLPcyhwnrsvvVPPDHPLAKKKKLTIEE-------LAQYPLVTYVFGFTGRSELDTAFNRAGLTPRIVF 222
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 93-288 3.29e-08

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


Pssm-ID: 176107 [Multi-domain]  Cd Length: 196  Bit Score: 52.56  E-value: 3.29e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928  93 LRVGMVPLASLNPM-QLIKPLAEKYPALQFSLLSMTSEQIIDGVSRNQLDLGICYLQhLDERLFKIARLPQTRMGLL--- 168
Cdd:cd08415    2 LRIAALPALALSLLpRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLP-LDHPGLESEPLASGRAVCVlpp 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928 169 -H---DKRHFDFSDgtpgwdtLATLPLGFLTKGMYYRESIEISFKAKGLTPKSVFESDSTFQIIQAVQAGICCAIMplnN 244
Cdd:cd08415   81 gHplaRKDVVTPAD-------LAGEPLISLGRGDPLRQRVDAAFERAGVEPRIVIETQLSHTACALVAAGLGVAIV---D 150

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 556283928 245 GLEALS---DNLDILPIAEsQVDSQLALIMRQQEPVSTLAEkCFAEA 288
Cdd:cd08415  151 PLTAAGyagAGLVVRPFRP-AIPFEFALVRPAGRPLSRLAQ-AFIDL 195
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 92-283 1.01e-07

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: 51.02  E-value: 1.01e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928  92 QLRVGMVPLASLnpMQLIKPLA---EKYPALQFSLLSMTSEQIIDGVSRNQLDLGICyLQHLDERLFKIARLPQTRMGLL 168
Cdd:cd08438    1 HLRLGLPPLGGS--LLFAPLLAafrQRYPNIELELVEYGGKKVEQAVLNGELDVGIT-VLPVDEEEFDSQPLCNEPLVAV 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928 169 HDKRHFDFSDGTPGWDTLATLPLGFLTKGMYYRESIEISFKAKGLTPKSVFESDSTFQIIQAVQAGICCAIMP------L 242
Cdd:cd08438   78 LPRGHPLAGRKTVSLADLADEPFILFNEDFALHDRIIDACQQAGFTPNIAARSSQWDFIAELVAAGLGVALLPrsiaqrL 157

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 556283928 243 NNglealsDNLDILPIAESQVDSQLALIMRQQEPVSTLAEK 283
Cdd:cd08438  158 DN------AGVKVIPLTDPDLRWQLALIWRKGRYLSHAARA 192
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
1-72 1.94e-07

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 51.56  E-value: 1.94e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 556283928   1 MDIKQLKYLIALDQTRHFGQAAAACHITQPTLSMRIRNLEEELNLTLIQRGQRFEGFTPEGERILAWARAVL 72
Cdd:PRK15421   2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVL 73
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
1-192 2.54e-07

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 50.96  E-value: 2.54e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928   1 MDIKQLKYLIALDQTRHFGQAAAACHITQPTLSMRIRNLEEELNLTLIQRGQRFEGFTPEGERILAWARAVLAAHDGLAA 80
Cdd:PRK10094   2 FDPETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPS 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928  81 EaaicrgqmVGQLRVGMVPLASL-------NPM---QLIKPLAEKYPALQFSLlsmtSEQIIDGVsrnqldlgicylqhL 150
Cdd:PRK10094  82 E--------LQQVNDGVERQVNIvinnllyNPQavaQLLAWLNERYPFTQFHI----SRQIYMGV--------------W 135

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 556283928 151 DErlfkiarlpqtrmgLLHDKrhFDFSDGTPGW----DTLATLPLG 192
Cdd:PRK10094 136 DS--------------LLYEG--FSLAIGVTGTealaNTFSLDPLG 165
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
1-71 1.61e-06

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 48.62  E-value: 1.61e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 556283928   1 MDIKQLKYLIALDQTRHFGQAAAACHITQPTLSMRIRNLEEELNLTLIQRGQRFEGfTPEGERILAWARAV 71
Cdd:PRK03635   2 LDYKQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVRTQPCRP-TEAGQRLLRHARQV 71
cbl PRK12679
HTH-type transcriptional regulator Cbl;
1-235 3.56e-06

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 47.50  E-value: 3.56e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928   1 MDIKQLKyLIALDQTRHFG--QAAAACHITQPTLSMRIRNLEEELNLTL-IQRGQRFEGFTPEG-------ERILAWARA 70
Cdd:PRK12679   1 MNFQQLK-IIREAARQDYNltEVANMLFTSQSGVSRHIRELEDELGIEIfIRRGKRLLGMTEPGkallviaERILNEASN 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928  71 VLAAHDGLAAEAAicrgqmvGQLRVGMV-PLASLNPMQLIKPLAEKYPALQFSLLSMTSEQIIDGVSRNQLDLGICYLQH 149
Cdd:PRK12679  80 VRRLADLFTNDTS-------GVLTIATThTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASERL 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928 150 LDERLfkIARLPQTRM--GLLHDKRHfDFSDGTP-GWDTLATLPLGFLTKGMYYRESIEISFKAKGLTPKSVFESDSTFQ 226
Cdd:PRK12679 153 SNDPQ--LVAFPWFRWhhSLLVPHDH-PLTQITPlTLESIAKWPLITYRQGITGRSRIDDAFARKGLLADIVLSAQDSDV 229


                 ....*....
gi 556283928 227 IIQAVQAGI 235
Cdd:PRK12679 230 IKTYVALGL 238
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 1-144 1.32e-05

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 45.80  E-value: 1.32e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928   1 MDIKQLKYLI-ALDQTRHFGQAAAACHITQPTLSMRIRNLEEELNLTL-IQRGQRFEGFTPEGERILAWARAVLAAHDGL 78
Cdd:PRK12683   1 MNFQQLRIIReAVRQNFNLTEVANALYTSQSGVSKQIKDLEDELGVEIfIRRGKRLTGLTEPGKELLQIVERMLLDAENL 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 556283928  79 AAEAAICRGQMVGQLRVG--------MVPlaslnpmQLIKPLAEKYPALQFSLLSMTSEQIIDGVSRNQLDLGI 144
Cdd:PRK12683  81 RRLAEQFADRDSGHLTVAtthtqaryALP-------KVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGI 147
PRK09801 PRK09801
LysR family transcriptional regulator;
4-150 1.56e-05

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 45.80  E-value: 1.56e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928   4 KQLKYLIALDQTRHFGQAAAACHITQPTLSMRIRNLEEELNLTLIQRGQRFEGFTPEGERILAWARAVLAAHDGLAAEAA 83
Cdd:PRK09801   9 KDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVT 88

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 556283928  84 ICRGQMVGQLRVGM---VPLASLNPMqlIKPLAEKYPALQ--FSLLsmtsEQIIDGVSRN-QLDLGI------CYLQHL 150
Cdd:PRK09801  89 QIKTRPEGMIRIGCsfgFGRSHIAPA--ITELMRNYPELQvhFELF----DRQIDLVQDNiDLDIRIndeipdYYIAHL 161
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 98-270 2.16e-05

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: 44.45  E-value: 2.16e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928  98 VPLASLNPM------QLIKPLAEKYPALQFSLLSMTSEQIIDGVSRNQLDLGICYLQHlDERLFKIARLPQTRMGL---- 167
Cdd:cd08434    2 VRLGFLHSLgtslvpDLIRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLALCSPVP-DEPDIEWIPLFTEELVLvvpk 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928 168 ---LHDKRHFDFSDgtpgwdtLATLPLGFLTKGMYYRESIEISFKAKGLTPKSVFESDSTFQIIQAVQAGICCAIMPLNN 244
Cdd:cd08434   81 dhpLAGRDSVDLAE-------LADEPFVLLSPGFGLRPIVDELCAAAGFTPKIAFEGEEDSTIAGLVAAGLGVAILPEMT 153

                        170       180
                 ....*....|....*....|....*.
gi 556283928 245 GLEAlsDNLDILPIAESQVDSQLALI 270
Cdd:cd08434  154 LLNP--PGVKKIPIKDPDAERTIGLA 177
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 92-283 2.64e-05

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


Pssm-ID: 176126 [Multi-domain]  Cd Length: 201  Bit Score: 44.19  E-value: 2.64e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928  92 QLRVGMVPLA--SLNPmQLIKPLAEKYPALQFSLLSMTSEQIIDGVSRNQLDLGICYL-QHLDERLFKIARLPQTRMGLL 168
Cdd:cd08435    1 TVRVGAVPAAapVLLP-PAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAIGRLaDDEQPPDLASEELADEPLVVV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928 169 HDKRHFDFSDGTPGWDTLATLPLGFLTKGMYYRESIEISFKAKGL-TPKSVFESDSTFQIIQAVQAGICCAIMPLNN-GL 246
Cdd:cd08435   80 ARPGHPLARRARLTLADLADYPWVLPPPGTPLRQRLEQLFAAAGLpLPRNVVETASISALLALLARSDMLAVLPRSVaED 159

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 556283928 247 EALSDNLDILPIAESQVDSQLALIMRQQEPVSTLAEK 283
Cdd:cd08435  160 ELRAGVLRELPLPLPTSRRPIGITTRRGGPLSPAARA 196
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 16-170 2.88e-05

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 44.83  E-value: 2.88e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928  16 RH--FGQAAAACHITQPTLSMRIRNLEEELNLTLIQRGQRFEGFTPEGERILAWARAVLAAhdgLA-AEAAICRGQMVGQ 92
Cdd:PRK11139  19 RHlsFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQ---LAeATRKLRARSAKGA 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928  93 LRVGMVP-LAslnpMQLIKP----LAEKYPALQFSLLSMTSEqiiDGVSRNQLDLGI---------CYLQHL-DERLFKI 157
Cdd:PRK11139  96 LTVSLLPsFA----IQWLVPrlssFNEAHPDIDVRLKAVDRL---EDFLRDDVDVAIrygrgnwpgLRVEKLlDEYLLPV 168

                        170       180
                 ....*....|....*....|....*.
gi 556283928 158 A--------RLPQT-----RMGLLHD 170
Cdd:PRK11139 169 CspallnggKPLKTpedlaRHTLLHD 194
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
 92-282 7.46e-05

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


Pssm-ID: 176111  Cd Length: 197  Bit Score: 42.88  E-value: 7.46e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928  92 QLRVGMVPLASLNPMQLIKPLAEKYPALQFSLLSMTSEQIIDGVSRNQLDLGICYL--QHLDERLFKIARLPqtrmgL-- 167
Cdd:cd08419    1 RLRLAVVSTAKYFAPRLLGAFCRRHPGVEVSLRVGNREQVLERLADNEDDLAIMGRppEDLDLVAEPFLDNP-----Lvv 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928 168 -------LHDKRHFDFSDgtpgwdtLATLPLGFLTKGMYYRESIEISFKAKGLTPKSVFESDSTFQIIQAVQAGICCAIM 240
Cdd:cd08419   76 iappdhpLAGQKRIPLER-------LAREPFLLREPGSGTRLAMERFFAEHGVTLRVRMELGSNEAIKQAVMAGLGLSVL 148

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 556283928 241 PLNN-GLEALSDNLDILPIAESQVDSQLALIMRQQEPVSTLAE 282
Cdd:cd08419  149 SLHTlALELATGRLAVLDVEGFPIRRQWYVVHRKGKRLSPAAQ 191
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
1-165 7.82e-05

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 43.50  E-value: 7.82e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928   1 MDIKQLKYLIALDQTRHFGQAAAACHITQPTLSMRIRNLEEELNLTLIQRGQRFEGFTPEGERILAWARAVLAAHDGLAA 80
Cdd:PRK10082  11 IETKWLYDFLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESNLA 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928  81 EaaICRGQMVGQLRVGMVPLASLNPMQLIKPLAEKYPALQFSLLSMTSEQIIDGVSRNQLDlgiCYLQHLDERL----FK 156
Cdd:PRK10082  91 E--LRGGSDYAQRKIKIAAAHSLSLGLLPSIISQMPPLFTWAIEAIDVDEAVDKLREGQSD---CIFSFHDEDLleapFD 165


                 ....*....
gi 556283928 157 IARLPQTRM 165
Cdd:PRK10082 166 HIRLFESQL 174
PBP2_LTTR_aromatics_like_2 cd08448
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-276 1.68e-04

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


Pssm-ID: 176139 [Multi-domain]  Cd Length: 197  Bit Score: 41.87  E-value: 1.68e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928  92 QLRVGMVPLASLNPM-QLIKPLAEKYPALQFSLLSMTSEQIIDGVSRNQLDLGICYLQHLDERL---------FKIA--- 158
Cdd:cd08448    1 RLRIGFVGSMLYRGLpRILRAFRAEYPGIEVALHEMSSAEQIEALLRGELDLGFVHSRRLPAGLsarllhrepFVCClpa 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928 159 --RLPQTRMGLLHDKRHFDF----SDGTPGwdtlatlplgfltkgmYYRESIEISFKAkGLTPKSVFESDSTFQIIQAVQ 232
Cdd:cd08448   81 ghPLAARRRIDLRELAGEPFvlfsREVSPD----------------YYDQIIALCMDA-GFHPKIRHEVRHWLTVVALVA 143

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 556283928 233 AGICCAIMPlnnglEALS----DNLDILPIAESQVDSQLALIMRQQEP 276
Cdd:cd08448  144 AGMGVALVP-----RSLAraglAGVRFLPLKGATQRSELYAAWKASAP 186
PBP2_CysB cd08443
The C-terminal substrate domain of LysR-type transcriptional regulator CysB contains type 2 ...
 109-235 2.11e-04

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


Pssm-ID: 176134  Cd Length: 198  Bit Score: 41.39  E-value: 2.11e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928 109 IKPLAEKYPALQFSLLSMTSEQIIDGVSRNQLDLGICY-LQHLDERLFKIARLPQTRMGLLhdKRHFDFSDGTP-GWDTL 186
Cdd:cd08443   19 IKGFIERYPRVSLQMHQGSPTQIAEMVSKGLVDFAIATeALHDYDDLITLPCYHWNRCVVV--KRDHPLADKQSiSIEEL 96

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 556283928 187 ATLPLGFLTKGMYYRESIEISFKAKGLTPKSVFESDSTFQIIQAVQAGI 235
Cdd:cd08443   97 ATYPIVTYTFGFTGRSELDTAFNRAGLTPNIVLTATDADVIKTYVRLGL 145
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 114-283 2.81e-04

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


Pssm-ID: 176117 [Multi-domain]  Cd Length: 199  Bit Score: 41.14  E-value: 2.81e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928 114 EKYPALQFSLLSMTSEQIIDGVSRNQLDLGICYlqhlderlfKIARLPQTRMGLLHDKR--------HFDFSDGTPGWDT 185
Cdd:cd08426   24 QRYPGVFFTVDVASTADVLEAVLSGEADIGLAF---------SPPPEPGIRVHSRQPAPigavvppgHPLARQPSVTLAQ 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928 186 LATLPLGFLTKGMYYRESIEISFKAKGLTPKSVFESDSTFQIIQAVQAGICCAIMP-LNNGLEALSDNLDILPIAESQVD 264
Cdd:cd08426   95 LAGYPLALPPPSFSLRQILDAAFARAGVQLEPVLISNSIETLKQLVAAGGGISLLTeLAVRREIRRGQLVAVPLADPHMN 174

                        170       180
                 ....*....|....*....|
gi 556283928 265 S-QLALIMRQQEPVSTLAEK 283
Cdd:cd08426  175 HrQLELQTRAGRQLPAAASA 194
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
25-73 6.02e-04

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 40.57  E-value: 6.02e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 556283928  25 CHITQPTLSMRIRNLEEELNLTLIQRGQRFEGFTPEGERILAWARAVLA 73
Cdd:PRK11716   1 MHVSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLL 49
PBP2_LysR cd08456
The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine ...
 92-242 1.04e-03

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


Pssm-ID: 176145 [Multi-domain]  Cd Length: 196  Bit Score: 39.32  E-value: 1.04e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928  92 QLRVGMVPLASLNPM-QLIKPLAEKYPALQFSLLSMTSEQIIDGVSRNQLDLGIC-YLQHL----DERLFKI---ARLPQ 162
Cdd:cd08456    1 ELRIAVLPALSQSFLpRAIKAFLQRHPDVTISIHTRDSPTVEQWLSAQQCDLGLVsTLHEPpgieRERLLRIdgvCVLPP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928 163 TRMglLHDKRHFDFSDgtpgwdtLATLPLGFLTKGMYYRESIEISFKAKGLTPKSVFESDSTFQIIQAVQAGICCAIM-P 241
Cdd:cd08456   81 GHR--LAVKKVLTPSD-------LEGEPFISLARTDGTRQRVDALFEQAGVKRRIVVETSYAATICALVAAGVGVSVVnP 151


                 .
gi 556283928 242 L 242
Cdd:cd08456  152 L 152
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 1-87 3.30e-03

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 38.43  E-value: 3.30e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928   1 MDIKQLKYLIALDQTRHFGQAAAACHITQPTLSMRIRNLEEELNLTLIQRGQRFEGFTPEGERILAWARAVL----AAHD 76
Cdd:PRK14997   2 TDLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLveaqAAQD 81

                         90
                 ....*....|.
gi 556283928  77 GLAAEAAICRG 87
Cdd:PRK14997  82 AIAALQVEPRG 92
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 91-144 3.92e-03

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


Pssm-ID: 176103 [Multi-domain]  Cd Length: 200  Bit Score: 37.50  E-value: 3.92e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 556283928  91 GQLRVGMVP-LAS-LNPmQLIKPLAEKYPALQFSLLSMTSEQIIDGVSRNQLDLGI 144
Cdd:cd08411    1 GPLRLGVIPtIAPyLLP-RLLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAAL 55
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-241 6.16e-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: 176127 [Multi-domain]  Cd Length: 194  Bit Score: 37.20  E-value: 6.16e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928  92 QLRVGMVPlaSLNPMQLIKPLAE---KYPALQFSLLSMTSEQIIDGVSRNQLDLGICylqHLDERlfkiaRLPQTRMGLL 168
Cdd:cd08436    1 RLAIGTIT--SLAAVDLPELLARfhrRHPGVDIRLRQAGSDDLLAAVREGRLDLAFV---GLPER-----RPPGLASREL 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928 169 HDKRH-FDFSDGTP-------GWDTLATLPLGFLTKGMYYRESIEISFKAKGLTPKSVFESDSTFQIIQAVQAGICCAIM 240
Cdd:cd08436   71 AREPLvAVVAPDHPlagrrrvALADLADEPFVDFPPGTGARRQVDRAFAAAGVRRRVAFEVSDVDLLLDLVARGLGVALL 150


                 .
gi 556283928 241 P 241
Cdd:cd08436  151 P 151
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 1-144 7.79e-03

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 37.32  E-value: 7.79e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556283928   1 MDIKQLKYLIALDQTRHFGQAAAACHITQPTLSMRIRNLEEELNLTLIQRGQRFEGFTPEGERILAWARAVLAAHDglAA 80
Cdd:PRK15092  11 LDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFND--EA 88

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 556283928  81 EAAICRGQMVGQLRVGmvplASLNPMQLIKP-----LAEKYPALQFSLLSMTSEQIIDGVSRNQLDLGI 144
Cdd:PRK15092  89 CSSLMYSNLQGVLTIG----ASDDTADTILPfllnrVSSVYPKLALDVRVKRNAFMMEMLESQEVDLAV 153
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

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