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Conserved domains on  [gi|491024256|ref|WP_004885949|]
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MULTISPECIES: tricarballylate utilization LysR family transcriptional regulator TcuR [Klebsiella]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 10444297)

LysR family transcriptional regulator containing an N-terminal helix-turn-helix DNA-binding domain and a C-terminal substrate binding domain; similar to CbbR, AmpR, GalR, YhaJ, and NmcR, which are positive transcriptional regulators of various genes

Gene Ontology:  GO:0003677|GO:0003700|GO:0001216
PubMed:  8257110|19047729
SCOP:  4000316

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Periplasmic_Binding_Protein_Type_2 super family cl21456
Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent ...
 90-287 1.72e-56

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


The actual alignment was detected with superfamily member cd08433:

Pssm-ID: 473866  Cd Length: 198  Bit Score: 181.25  E-value: 1.72e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256  90 HVSVGMAPSTASVLGVPFINAMRESYPDVRLHLVESLSGNLERMINTRQLDLAIVFQQEKILRWSARPVLEERLFLIGTH 169
Cdd:cd08433    1 RVSVGLPPSAASVLAVPLLRAVRRRYPGIRLRIVEGLSGHLLEWLLNGRLDLALLYGPPPIPGLSTEPLLEEDLFLVGPA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256 170 ALLAsLPDDPVSPDQLTTLPLIMPSQGHGLRGRLEAVCQQHNLSVEVVADIDGLALLMQAVRSGLGATLQPGAAISHLDH 249
Cdd:cd08433   81 DAPL-PRGAPVPLAELARLPLILPSRGHGLRRLVDEAAARAGLTLNVVVEIDSVATLKALVAAGLGYTILPASAVAAEVA 159

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 491024256 250 QA-LRVIGIANPVLSRPNFLVSLSDDELTPAGLAARVIL 287
Cdd:cd08433  160 AGrLVAAPIVDPALTRTLSLATPRDRPLSPAALAVRDLL 198
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-61 2.98e-18

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


:

Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 77.04  E-value: 2.98e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 491024256    3 LRQLRYFTRIVETGSMGRAALDLNIGVSALSQQIARLENELAIRLLQRTSRGVTPTSAG 61
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
 
Name Accession Description Interval E-value
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 90-287 1.72e-56

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: 181.25  E-value: 1.72e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256  90 HVSVGMAPSTASVLGVPFINAMRESYPDVRLHLVESLSGNLERMINTRQLDLAIVFQQEKILRWSARPVLEERLFLIGTH 169
Cdd:cd08433    1 RVSVGLPPSAASVLAVPLLRAVRRRYPGIRLRIVEGLSGHLLEWLLNGRLDLALLYGPPPIPGLSTEPLLEEDLFLVGPA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256 170 ALLAsLPDDPVSPDQLTTLPLIMPSQGHGLRGRLEAVCQQHNLSVEVVADIDGLALLMQAVRSGLGATLQPGAAISHLDH 249
Cdd:cd08433   81 DAPL-PRGAPVPLAELARLPLILPSRGHGLRRLVDEAAARAGLTLNVVVEIDSVATLKALVAAGLGYTILPASAVAAEVA 159

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 491024256 250 QA-LRVIGIANPVLSRPNFLVSLSDDELTPAGLAARVIL 287
Cdd:cd08433  160 AGrLVAAPIVDPALTRTLSLATPRDRPLSPAALAVRDLL 198
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 1-299 2.46e-52

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 174.10  E-value: 2.46e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256   1 MELRQLRYFTRIVETGSMGRAALDLNIGVSALSQQIARLENELAIRLLQRTSRGVTPTSAGLAFYSQAQLALRHADDAIL 80
Cdd:PRK11233   1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256  81 AAREA--RLSGHVSVGMAPST-ASVLGVPFINAMRESYPDVRLHLVESLSGNLERMINTRQLDLAIVFQQEKILRWSARP 157
Cdd:PRK11233  81 AVHNVgqALSGQVSIGLAPGTaASSLTMPLLQAVRAEFPGIVLYLHENSGATLNEKLMNGQLDMAVIYEHSPVAGLSSQP 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256 158 VLEERLFLIGTHallaSLPDDPVSPDQLTTLPLIMPSQGHGLRGRLEAVCQQHNLSVEVVADIDGLALLMQAVRSGLGAT 237
Cdd:PRK11233 161 LLKEDLFLVGTQ----DCPGQSVDLAAVAQMNLFLPRDYSAVRLRVDEAFSLRRLTAKVIGEIESIATLTAAIASGMGVT 236

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 491024256 238 LQP-GAAISHLDHQALRVIGIANPVLSRPNFLVSLSDDELTPAGLAARVILSKVMRQLVESDR 299
Cdd:PRK11233 237 VLPeSAARSLCGAVNGWMARITTPSMSLSLSLNLSARLPLSPQAQAVKEILLSLVSSPVMEKR 299
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-279 1.49e-47

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 160.03  E-value: 1.49e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256   1 MELRQLRYFTRIVETGSMGRAALDLNIGVSALSQQIARLENELAIRLLQRTSRGVTPTSAGLAFYSQAQLALRHADDAIL 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256  81 AAREAR--LSGHVSVGMAPSTASVLGVPFINAMRESYPDVRLHLVESLSGNLERMINTRQLDLAIVFQQEKILRWSARPV 158
Cdd:COG0583   81 ELRALRggPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256 159 LEERLFLIGthallaslpddpvspdqlttlplimpSQGHGLRGRLEAVcqqhnlsvevvadiDGLALLMQAVRSGLGATL 238
Cdd:COG0583  161 GEERLVLVA--------------------------SPDHPLARRAPLV--------------NSLEALLAAVAAGLGIAL 200

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|..
gi 491024256 239 QPG-AAISHLDHQALRVIGIANPVLSRPNFLVSLSDDELTPA 279
Cdd:COG0583  201 LPRfLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPA 242
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 88-279 1.17e-29

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: 112.00  E-value: 1.17e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256   88 SGHVSVGMAPSTASVLGVPFINAMRESYPDVRLHLVESLSGNLERMINTRQLDLAIVFQQEKILRWSARPVLEERLFLIG 167
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256  168 T--HALLAslpDDPVSPDQLTTLPLIMPSQGHGLRGRLEAVCQQHNLSVEVVADIDGLALLMQAVRSGLGATLQPGAAIS 245
Cdd:pfam03466  81 PpdHPLAR---GEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVA 157

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 491024256  246 H-LDHQALRVIGIANPVLSRPNFLVSLSDDELTPA 279
Cdd:pfam03466 158 ReLADGRLVALPLPEPPLPRELYLVWRKGRPLSPA 192
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-61 2.98e-18

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 77.04  E-value: 2.98e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 491024256    3 LRQLRYFTRIVETGSMGRAALDLNIGVSALSQQIARLENELAIRLLQRTSRGVTPTSAG 61
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
4-113 1.13e-10

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 61.14  E-value: 1.13e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256   4 RQLRYFTRIVETGSMGRAALDLNIGVSALSQQIARLENELAIRLLQRTsRGVTPTSAGLAFYSQA-QLALRHADdaILAA 82
Cdd:PRK13348   5 KQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRG-RPCRPTPAGQRLLRHLrQVALLEAD--LLST 81

                         90       100       110
                 ....*....|....*....|....*....|.
gi 491024256  83 REARLSGHVSVGMAPSTASvLGVPFINAMRE 113
Cdd:PRK13348  82 LPAERGSPPTLAIAVNADS-LATWFLPALAA 111
 
Name Accession Description Interval E-value
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 90-287 1.72e-56

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: 181.25  E-value: 1.72e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256  90 HVSVGMAPSTASVLGVPFINAMRESYPDVRLHLVESLSGNLERMINTRQLDLAIVFQQEKILRWSARPVLEERLFLIGTH 169
Cdd:cd08433    1 RVSVGLPPSAASVLAVPLLRAVRRRYPGIRLRIVEGLSGHLLEWLLNGRLDLALLYGPPPIPGLSTEPLLEEDLFLVGPA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256 170 ALLAsLPDDPVSPDQLTTLPLIMPSQGHGLRGRLEAVCQQHNLSVEVVADIDGLALLMQAVRSGLGATLQPGAAISHLDH 249
Cdd:cd08433   81 DAPL-PRGAPVPLAELARLPLILPSRGHGLRRLVDEAAARAGLTLNVVVEIDSVATLKALVAAGLGYTILPASAVAAEVA 159

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 491024256 250 QA-LRVIGIANPVLSRPNFLVSLSDDELTPAGLAARVIL 287
Cdd:cd08433  160 AGrLVAAPIVDPALTRTLSLATPRDRPLSPAALAVRDLL 198
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 1-299 2.46e-52

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 174.10  E-value: 2.46e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256   1 MELRQLRYFTRIVETGSMGRAALDLNIGVSALSQQIARLENELAIRLLQRTSRGVTPTSAGLAFYSQAQLALRHADDAIL 80
Cdd:PRK11233   1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256  81 AAREA--RLSGHVSVGMAPST-ASVLGVPFINAMRESYPDVRLHLVESLSGNLERMINTRQLDLAIVFQQEKILRWSARP 157
Cdd:PRK11233  81 AVHNVgqALSGQVSIGLAPGTaASSLTMPLLQAVRAEFPGIVLYLHENSGATLNEKLMNGQLDMAVIYEHSPVAGLSSQP 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256 158 VLEERLFLIGTHallaSLPDDPVSPDQLTTLPLIMPSQGHGLRGRLEAVCQQHNLSVEVVADIDGLALLMQAVRSGLGAT 237
Cdd:PRK11233 161 LLKEDLFLVGTQ----DCPGQSVDLAAVAQMNLFLPRDYSAVRLRVDEAFSLRRLTAKVIGEIESIATLTAAIASGMGVT 236

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 491024256 238 LQP-GAAISHLDHQALRVIGIANPVLSRPNFLVSLSDDELTPAGLAARVILSKVMRQLVESDR 299
Cdd:PRK11233 237 VLPeSAARSLCGAVNGWMARITTPSMSLSLSLNLSARLPLSPQAQAVKEILLSLVSSPVMEKR 299
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-279 1.49e-47

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 160.03  E-value: 1.49e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256   1 MELRQLRYFTRIVETGSMGRAALDLNIGVSALSQQIARLENELAIRLLQRTSRGVTPTSAGLAFYSQAQLALRHADDAIL 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256  81 AAREAR--LSGHVSVGMAPSTASVLGVPFINAMRESYPDVRLHLVESLSGNLERMINTRQLDLAIVFQQEKILRWSARPV 158
Cdd:COG0583   81 ELRALRggPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256 159 LEERLFLIGthallaslpddpvspdqlttlplimpSQGHGLRGRLEAVcqqhnlsvevvadiDGLALLMQAVRSGLGATL 238
Cdd:COG0583  161 GEERLVLVA--------------------------SPDHPLARRAPLV--------------NSLEALLAAVAAGLGIAL 200

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|..
gi 491024256 239 QPG-AAISHLDHQALRVIGIANPVLSRPNFLVSLSDDELTPA 279
Cdd:COG0583  201 LPRfLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPA 242
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 1-264 1.09e-33

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 125.07  E-value: 1.09e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256   1 MELRQLRYFTRIVETGSMGRAALDLNIGVSALSQQIARLENELAIRLLQRTSRGVTPTSAGLAFYSQAQLALRHADDAIL 80
Cdd:PRK11242   1 MLLRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256  81 AAREAR-LS-GHVSVGMAPSTASVLGVPFINAMRESYPDVRLHLVESLSGNLERMINTRQLDLAIVFQQEKILRWSARPV 158
Cdd:PRK11242  81 AIHDVAdLSrGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMSQERIEALLADDELDVGIAFAPVHSPEIEAQPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256 159 LEERLFLI--GTHALLASLpdDPVSPDQLTTLPLIMPSQGHGLRGRLEAVCQQHNLSVEVVADIDGLALLMQAVRSGLGA 236
Cdd:PRK11242 161 FTETLALVvgRHHPLAARR--KALTLDELADEPLVLLSAEFATREQIDRYFRRHGVTPRVAIEANSISAVLEIVRRGRLA 238

                        250       260
                 ....*....|....*....|....*...
gi 491024256 237 TLQPgAAISHlDHQALRVIGIANPVLSR 264
Cdd:PRK11242 239 TLLP-AAIAR-EHDGLCAIPLDPPLPQR 264
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 90-279 1.93e-30

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: 113.46  E-value: 1.93e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256  90 HVSVGMAPSTASVLGVPFINAMRESYPDVRLHLVESLSGNLERMINTRQLDLAIVFQQEKILRWSARPVLEERLFLIG-- 167
Cdd:cd05466    1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVpp 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256 168 THALLASlpdDPVSPDQLTTLPLIMPSQGHGLRGRLEAVCQQHNLSVEVVADIDGLALLMQAVRSGLGATLQPGAAISHL 247
Cdd:cd05466   81 DHPLAKR---KSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEEL 157

                        170       180       190
                 ....*....|....*....|....*....|..
gi 491024256 248 DHQALRVIGIANPVLSRPNFLVSLSDDELTPA 279
Cdd:cd05466  158 ADGGLVVLPLEDPPLSRTIGLVWRKGRYLSPA 189
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 88-279 1.17e-29

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: 112.00  E-value: 1.17e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256   88 SGHVSVGMAPSTASVLGVPFINAMRESYPDVRLHLVESLSGNLERMINTRQLDLAIVFQQEKILRWSARPVLEERLFLIG 167
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256  168 T--HALLAslpDDPVSPDQLTTLPLIMPSQGHGLRGRLEAVCQQHNLSVEVVADIDGLALLMQAVRSGLGATLQPGAAIS 245
Cdd:pfam03466  81 PpdHPLAR---GEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVA 157

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 491024256  246 H-LDHQALRVIGIANPVLSRPNFLVSLSDDELTPA 279
Cdd:pfam03466 158 ReLADGRLVALPLPEPPLPRELYLVWRKGRPLSPA 192
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 1-241 3.45e-23

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 96.76  E-value: 3.45e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256   1 MELRQLRYFTRIVETGSMGRAALDLNIGVSALSQQIARLENELAIRLLQRTSRGVTPTSAGLAFYSQAQLALRHADDAIL 80
Cdd:PRK09906   1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256  81 AAREARLSGHV-SVGMAPStASVLGVPFINAM-RESYPDVRLHLVeSLSgNLERMINTRQLDLAIVFQQEKILRWS--AR 156
Cdd:PRK09906  81 RARKIVQEDRQlTIGFVPS-AEVNLLPKVLPMfRLRHPDTLIELV-SLI-TTQQEEKLRRGELDVGFMRHPVYSDEidYL 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256 157 PVLEERL-FLIGTHALLASLPDDPVSPDQLTTLPLIMPSQGHGLRGRLEAVCQQHNLSVEVVADIDGLALLMQAVRSGLG 235
Cdd:PRK09906 158 ELLDEPLvVVLPVDHPLAHEKEITAAQLDGVNFISTDPAYSGSLAPIIKAWFAQHNSQPNIVQVATNILVTMNLVGMGLG 237


                 ....*.
gi 491024256 236 ATLQPG 241
Cdd:PRK09906 238 CTIIPG 243
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 90-279 1.48e-20

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: 87.20  E-value: 1.48e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256  90 HVSVGMAPSTASVLGVPFINAMRESYPDVRLHLVESLSGNLERMINTRQLDLAIVFQQEKILRWSARPVLEERLFLIG-- 167
Cdd:cd08440    1 RVRVAALPSLAATLLPPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEADPDLEFEPLLRDPFVLVCpk 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256 168 THALLASlpdDPVSPDQLTTLPLIMPSQGHGLRGRLEAVCQQHNLSVEVVADIDGLALLMQAVRSGLGATLQPGAAISHL 247
Cdd:cd08440   81 DHPLARR---RSVTWAELAGYPLIALGRGSGVRALIDRALAAAGLTLRPAYEVSHMSTALGMVAAGLGVAVLPALALPLA 157

                        170       180       190
                 ....*....|....*....|....*....|..
gi 491024256 248 DHQALRVIGIANPVLSRPNFLVSLSDDELTPA 279
Cdd:cd08440  158 DHPGLVARPLTEPVVTRTVGLIRRRGRSLSPA 189
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-61 2.98e-18

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 77.04  E-value: 2.98e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 491024256    3 LRQLRYFTRIVETGSMGRAALDLNIGVSALSQQIARLENELAIRLLQRTSRGVTPTSAG 61
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
17-145 3.46e-16

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 77.35  E-value: 3.46e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256  17 SMGRAALDLNIGVSALSQQIARLENELAIRLLQRTSRGVTPTSAGLAFYSQAQLALRHADDAILAAREARLSGHVSVGMA 96
Cdd:PRK10086  30 SFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLDTLNQEILDIKNQELSGTLTVYSR 109

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 491024256  97 PSTASVLGVPFINAMRESYPDVRLHLvesLSGNLERMINTRQLDLAIVF 145
Cdd:PRK10086 110 PSIAQCWLVPRLADFTRRYPSISLTI---LTGNENVNFQRAGIDLAIYF 155
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 90-263 3.78e-15

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: 72.59  E-value: 3.78e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256  90 HVSVGMAPSTASVLGVPFINAMRESYPDVRLHLVESLSGNLERMINTRQLDLAIVFQqekilrwsarPVLEERL--FLIG 167
Cdd:cd08438    1 HLRLGLPPLGGSLLFAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVL----------PVDEEEFdsQPLC 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256 168 THALLASLPD-------DPVSPDQLTTLPLIMPSQGHGLRGRLEAVCQQHNLSVEVVADIDGLALLMQAVRSGLGATLQP 240
Cdd:cd08438   71 NEPLVAVLPRghplagrKTVSLADLADEPFILFNEDFALHDRIIDACQQAGFTPNIAARSSQWDFIAELVAAGLGVALLP 150

                        170       180
                 ....*....|....*....|...
gi 491024256 241 GAAISHLDHQALRVIGIANPVLS 263
Cdd:cd08438  151 RSIAQRLDNAGVKVIPLTDPDLR 173
PRK09791 PRK09791
LysR family transcriptional regulator;
1-143 6.94e-15

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 73.64  E-value: 6.94e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256   1 MELRQLRYFTRIVETGSMGRAALDLNIGVSALSQQIARLENELAIRLLQRTSRGVTPTSAGLAFYSQAQL---ALRHADD 77
Cdd:PRK09791   5 VKIHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLileELRAAQE 84

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 491024256  78 AILaAREARLSGHVSVGMAPSTASVLGVPFINAMRESYPDVRLHLVEslsGNLERMINT-RQ--LDLAI 143
Cdd:PRK09791  85 DIR-QRQGQLAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRIME---GQLVSMINElRQgeLDFTI 149
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 1-244 1.01e-14

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 73.14  E-value: 1.01e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256   1 MELRQLRYFTRIVETGSMGRAALDLNIGVSALSQQIARLENELAIRLLQRTSRGVTPTSAGLAFYSQAQLALRHA----D 76
Cdd:PRK11151   1 MNIRDLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVkvlkE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256  77 DAILAAREarLSGHVSVGMAPSTASVLgVPFI-NAMRESYPDVRLHLVESLSGNLERMINTRQLDLAIVFQQEKILRWSA 155
Cdd:PRK11151  81 MASQQGET--MSGPLHIGLIPTVGPYL-LPHIiPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCAILALVKESEAFIE 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256 156 RPVLEERLfligthaLLASLPDDP------VSPDQLTTLPLIMPSQGHGLRGRLEAVCQQhnlsveVVADIDG------L 223
Cdd:PRK11151 158 VPLFDEPM-------LLAVYEDHPwanrdrVPMSDLAGEKLLMLEDGHCLRDQAMGFCFE------AGADEDThfratsL 224

                        250       260
                 ....*....|....*....|.
gi 491024256 224 ALLMQAVRSGLGATLQPGAAI 244
Cdd:PRK11151 225 ETLRNMVAAGSGITLLPALAV 245
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 106-279 1.11e-14

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


Pssm-ID: 176112 [Multi-domain]  Cd Length: 201  Bit Score: 71.37  E-value: 1.11e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256 106 PFINAMRESYPDVRLHLVESLSGNLERMINTRQLDLAIV---FQQEKIlrwSARPVLEERLFLIG--THALLAslpDDPV 180
Cdd:cd08420   17 RLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLVegpVDHPDL---IVEPFAEDELVLVVppDHPLAG---RKEV 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256 181 SPDQLTTLPLIMPSQGHGLRGRLEAVCQQHNLSVE---VVADIDGLALLMQAVRSGLGATLQPGAAISH-LDHQALRVIG 256
Cdd:cd08420   91 TAEELAAEPWILREPGSGTREVFERALAEAGLDGLdlnIVMELGSTEAIKEAVEAGLGISILSRLAVRKeLELGRLVALP 170

                        170       180
                 ....*....|....*....|...
gi 491024256 257 IANPVLSRPNFLVSLSDDELTPA 279
Cdd:cd08420  171 VEGLRLTRPFSLIYHKDKYLSPA 193
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 89-264 1.35e-14

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


Pssm-ID: 176103 [Multi-domain]  Cd Length: 200  Bit Score: 71.02  E-value: 1.35e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256  89 GHVSVGMAPSTASVLGVPFINAMRESYPDVRLHLVESLSGNLERMINTRQLDLAIV---FQQEKIlrwSARPVLEERLFL 165
Cdd:cd08411    1 GPLRLGVIPTIAPYLLPRLLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAALLalpVDEPGL---EEEPLFDEPFLL 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256 166 IG--THALLASlpdDPVSPDQLTTLPLIMPSQGHGLRGRLEAVCQQhnLSVEVVADIDG--LALLMQAVRSGLGATLQPG 241
Cdd:cd08411   78 AVpkDHPLAKR---KSVTPEDLAGERLLLLEEGHCLRDQALELCRL--AGAREQTDFEAtsLETLRQMVAAGLGITLLPE 152

                        170       180
                 ....*....|....*....|....*
gi 491024256 242 AAI--SHLDHQALRVIGIANPVLSR 264
Cdd:cd08411  153 LAVpsEELRGDRLVVRPFAEPAPSR 177
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 90-279 2.73e-14

The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA expression of glutamate synthase operon, contains type 2 periplasmic binding fold; GltC, a member of the LysR family of bacterial transcriptional factors, activates the expression of gltA gene of glutamate synthase operon and is essential for cell growth in the absence of glutamate. Glutamate synthase is a heterodimeric protein that encoded by gltA and gltB, whose expression is subject to nutritional regulation. GltC also negatively auto-regulates its own expression. This substrate-binding domain has strong homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176125 [Multi-domain]  Cd Length: 195  Bit Score: 69.87  E-value: 2.73e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256  90 HVSVGMAPSTASVLgVP-FINAMRESYPDVRLHLVESLSGNLERMINTRQLDLAIVFQQEKILRWSARPVLEERLFLI-- 166
Cdd:cd08434    1 TVRLGFLHSLGTSL-VPdLIRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLALCSPVPDEPDIEWIPLFTEELVLVvp 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256 167 GTHAlLASLpdDPVSPDQLTTLPLIMPSQGHGLRGRLEAVCQQHNLSVEVV---ADIDGLALLmqaVRSGLGATLQPGAA 243
Cdd:cd08434   80 KDHP-LAGR--DSVDLAELADEPFVLLSPGFGLRPIVDELCAAAGFTPKIAfegEEDSTIAGL---VAAGLGVAILPEMT 153

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 491024256 244 IshLDHQALRVIGIANPVLSRPNFLVSLSDDELTPA 279
Cdd:cd08434  154 L--LNPPGVKKIPIKDPDAERTIGLAWLKDRYLSPA 187
PRK09986 PRK09986
LysR family transcriptional regulator;
3-240 8.02e-14

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 70.52  E-value: 8.02e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256   3 LRQLRYFTRIVETGSMGRAALDLNIGVSALSQQIARLENELAIRLLQRTSRGVTPTSAGLAFYSQAQLALRHADDAI--- 79
Cdd:PRK09986   9 LKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLarv 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256  80 --LAAREArlsGHVSVGMAPSTASVLGVPFINAMRESYPDVRLHLVESLSGNLERMINTRQLDLAI----VFQQEKILRw 153
Cdd:PRK09986  89 eqIGRGEA---GRIEIGIVGTALWGRLRPAMRHFLKENPNVEWLLRELSPSMQMAALERRELDAGIwrmaDLEPNPGFT- 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256 154 sARPVLEERLfligthaLLASLPDDPVSpdQLTTLPL---------IMPSQGHGLRGRLEAVCQQHNLSVEVVADIDGLA 224
Cdd:PRK09986 165 -SRRLHESAF-------AVAVPEEHPLA--SRSSVPLkalrneyfiTLPFVHSDWGKFLQRVCQQAGFSPQIIRQVNEPQ 234

                        250
                 ....*....|....*.
gi 491024256 225 LLMQAVRSGLGATLQP 240
Cdd:PRK09986 235 TVLAMVSMGIGITLLP 250
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 90-275 1.66e-13

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: 67.92  E-value: 1.66e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256  90 HVSVGMAPSTA-SVLGvPFINAMRESYPDVRLHLVESLSGNLERMINTRQLDLAIVFQQEKILRWSARPVLEERLFLI-- 166
Cdd:cd08414    1 RLRIGFVGSALyGLLP-RLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPPPDPPGLASRPLLREPLVVAlp 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256 167 GTHALLAslpDDPVSPDQLTTLPLIMPSQGH--GLRGRLEAVCQQHNLSVEVVADIDGLALLMQAVRSGLGATLQPgAAI 244
Cdd:cd08414   80 ADHPLAA---RESVSLADLADEPFVLFPREPgpGLYDQILALCRRAGFTPRIVQEASDLQTLLALVAAGLGVALVP-ASV 155

                        170       180       190
                 ....*....|....*....|....*....|.
gi 491024256 245 SHLDHQALRVIGIANPVLSRPNFLVSLSDDE 275
Cdd:cd08414  156 ARLQRPGVVYRPLADPPPRSELALAWRRDNA 186
PBP2_CynR cd08425
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, ...
 89-264 2.71e-13

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: 67.35  E-value: 2.71e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256  89 GHVSVGMAPSTASVLGVPFINAMRESYPDVRLHLVESLSGNLERMINTRQLDLAIVFQQEKILRWSARPVLEERLFLI-G 167
Cdd:cd08425    1 GSLRLAMTPTFTAYLIGPLIDRFHARYPGIALSLREMPQERIEAALADDRLDLGIAFAPVRSPDIDAQPLFDERLALVvG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256 168 THALLASLPDdPVSPDQLTTLPLIMPSQGHGLRGRLEAVCQQHNLSVEVVADIDGLALLMQAVRSGLGATLQPgAAISHl 247
Cdd:cd08425   81 ATHPLAQRRT-ALTLDDLAAEPLALLSPDFATRQHIDRYFQKQGIKPRIAIEANSISAVLEVVRRGRLATILP-DAIAR- 157

                        170
                 ....*....|....*..
gi 491024256 248 DHQALRVIGIANPVLSR 264
Cdd:cd08425  158 EQPGLCAVALEPPLPGR 174
PRK10341 PRK10341
transcriptional regulator TdcA;
4-257 2.45e-12

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 66.42  E-value: 2.45e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256   4 RQLRYFTRIVETGSMGRAALDLNIGVSALSQQIARLENELAIRLLQRTSRGVTPTSAGLAFYSQAQLALRHADDAILAAR 83
Cdd:PRK10341  10 QHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEIN 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256  84 eaRLSGHVSVGMAPSTASVLGVPF----INAMRESYPDVRLHLVESLSGNLERMINTRQLDLAI--VFQQEKILRWSARP 157
Cdd:PRK10341  90 --GMSSEAVVDVSFGFPSLIGFTFmsdmINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIgtLSNEMKLQDLHVEP 167

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256 158 VLEERLFLIGTHALLASlpdDPVSPDQLTTLPLIMPSQGHGLRGRLEAVCQQHNLSVEVVADIDGLALLMQAVRSGLGAT 237
Cdd:PRK10341 168 LFESEFVLVASKSRTCT---GTTTLESLKNEQWVLPQTNMGYYSELLTTLQRNGISIENIVKTDSVVTIYNLVLNADFLT 244

                        250       260
                 ....*....|....*....|
gi 491024256 238 LQPGAAISHLDHQALRVIGI 257
Cdd:PRK10341 245 VIPCDMTSPFGSNQFITIPI 264
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
1-123 4.71e-12

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 65.55  E-value: 4.71e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256   1 ME-LRQLRYFTRIVETGSMGRAALDLNIGVSALSQQIARLENELAIRLLQRTSRGVTPTSAGLAFYSQAQLALRHADDA- 78
Cdd:PRK10632   1 MErLKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVh 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 491024256  79 -ILAAREARLSGHVSVGMAPSTASVLGVPFINAMRESYPDVRLHLV 123
Cdd:PRK10632  81 eQLYAFNNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLV 126
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 90-287 6.88e-12

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


Pssm-ID: 176127 [Multi-domain]  Cd Length: 194  Bit Score: 63.39  E-value: 6.88e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256  90 HVSVGMAPSTASVLGVPFINAMRESYPDVRLHLVESLSGNLERMINTRQLDLAIVfqqekilRWSARPVLEERLFLIGTH 169
Cdd:cd08436    1 RLAIGTITSLAAVDLPELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAFV-------GLPERRPPGLASRELARE 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256 170 ALLASLPDD-------PVSPDQLTTLPLIMPSQGHGLRGRLEAVCQQHNLSVEVVADIDGLALLMQAVRSGLGATLQPGA 242
Cdd:cd08436   74 PLVAVVAPDhplagrrRVALADLADEPFVDFPPGTGARRQVDRAFAAAGVRRRVAFEVSDVDLLLDLVARGLGVALLPAS 153

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 491024256 243 AISHLDHqaLRVIGIAnPVLSRPNFLVSLSDdeltPAGLAARVIL 287
Cdd:cd08436  154 VAARLPG--LAALPLE-PAPRRRLYLAWSAP----PPSPAARAFL 191
rbcR CHL00180
LysR transcriptional regulator; Provisional
 3-264 8.54e-12

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 64.66  E-value: 8.54e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256   3 LRQLRYFTRIVETGSMGRAALDLNIGVSALSQQIARLENELAIRLLQRTSRGVTPTSAGLAF--YSQAQLAL-RHADDAI 79
Cdd:CHL00180   7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLlrYGNRILALcEETCRAL 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256  80 LAAREARlSGHVSVGMAPSTASVLGVPFINAMRESYPDVRLHL-VESLSGNLERMINtRQLDLAIVFQQ-----EKILrw 153
Cdd:CHL00180  87 EDLKNLQ-RGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLqVHSTRRIAWNVAN-GQIDIAIVGGEvptelKKIL-- 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256 154 SARPVLEERLFLIgthaLLASLP---DDPVSPDQLTTLPLIMPSQGHGLRGRLEAVCQQHNLsvevvaDIDGLALLMQ-- 228
Cdd:CHL00180 163 EITPYVEDELALI----IPKSHPfakLKKIQKEDLYRLNFITLDSNSTIRKVIDNILIQNGI------DSKRFKIEMEln 232

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....
gi 491024256 229 -------AVRSGLGATLQPGAAIS-HLDHQALRVIGIANPVLSR 264
Cdd:CHL00180 233 sieaiknAVQSGLGAAFVSVSAIEkELELGLLHWIKIENITIKR 276
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 1-122 5.15e-11

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 62.32  E-value: 5.15e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256   1 MELRQLRYFTRIVETGSMGRAALDLNIGVSALSQQIARLENELAIRLLQRTSRGVTPTSAGLAFYSQAQLALRHADDA-- 78
Cdd:PRK14997   2 TDLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAqd 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 491024256  79 ILAAREARLSGHVSVGMAPSTASVLGVPFINAMRESYPDVRLHL 122
Cdd:PRK14997  82 AIAALQVEPRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQL 125
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 17-191 1.05e-10

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 61.40  E-value: 1.05e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256  17 SMGRAALDLNIGVSALSQQIARLENELAIRLLQRTSRGVTPTSAGLAFYSQAQ---LALRHADDAILaAREARlsGHVSV 93
Cdd:PRK11139  22 SFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIReifDQLAEATRKLR-ARSAK--GALTV 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256  94 GMAPSTASVLGVPFINAMRESYP--DVRLHLVESLSGNLerminTRQLDLAIVFQQEKILRWSARPVLEERLFLIGTHAL 171
Cdd:PRK11139  99 SLLPSFAIQWLVPRLSSFNEAHPdiDVRLKAVDRLEDFL-----RDDVDVAIRYGRGNWPGLRVEKLLDEYLLPVCSPAL 173

                        170       180
                 ....*....|....*....|
gi 491024256 172 LASlPDDPVSPDQLTTLPLI 191
Cdd:PRK11139 174 LNG-GKPLKTPEDLARHTLL 192
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
4-113 1.13e-10

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 61.14  E-value: 1.13e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256   4 RQLRYFTRIVETGSMGRAALDLNIGVSALSQQIARLENELAIRLLQRTsRGVTPTSAGLAFYSQA-QLALRHADdaILAA 82
Cdd:PRK13348   5 KQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRG-RPCRPTPAGQRLLRHLrQVALLEAD--LLST 81

                         90       100       110
                 ....*....|....*....|....*....|.
gi 491024256  83 REARLSGHVSVGMAPSTASvLGVPFINAMRE 113
Cdd:PRK13348  82 LPAERGSPPTLAIAVNADS-LATWFLPALAA 111
PBP2_LTTR_like_2 cd08427
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 90-264 6.56e-09

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


Pssm-ID: 176118 [Multi-domain]  Cd Length: 195  Bit Score: 54.89  E-value: 6.56e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256  90 HVSVGMAPSTASVLGVPFINAMRESYPDVRLHLVESLSGNLERMINTRQLDLAIV----FQQEKILRWSarPVLEERLFL 165
Cdd:cd08427    1 RLRLGAIATVLTGLLPRALARLRRRHPDLEVHIVPGLSAELLARVDAGELDAAIVveppFPLPKDLVWT--PLVREPLVL 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256 166 IGTHALlasLPDDPVSpdQLTTLPLIMPSQgHGLRGRL-EAVCQQHNLSVEVVADIDGLALLMQAVRSGLGATLQPGAAI 244
Cdd:cd08427   79 IAPAEL---AGDDPRE--LLATQPFIRYDR-SAWGGRLvDRFLRRQGIRVREVMELDSLEAIAAMVAQGLGVAIVPDIAV 152

                        170       180
                 ....*....|....*....|
gi 491024256 245 SHLDHQALRVIGIANPVLSR 264
Cdd:cd08427  153 PLPAGPRVRVLPLGDPAFSR 172
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 1-235 1.13e-08

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 55.38  E-value: 1.13e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256   1 MELRQLRYFTRIVETG-SMGRAALDLNIGVSALSQQIARLENELAIRLLQRTSRGVTP-TSAGLAFYSQAQLALRHADDA 78
Cdd:PRK12682   1 MNLQQLRFVREAVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKGlTEPGKAVLDVIERILREVGNI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256  79 ILAARE--ARLSGHVSVGMAPSTASVLGVPFINAMRESYPDVRLHLVESLSGNLERMINTRQLDLAIVfqQEKILRWS-- 154
Cdd:PRK12682  81 KRIGDDfsNQDSGTLTIATTHTQARYVLPRVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGIA--TESLADDPdl 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256 155 -ARPVLEERLFLI--GTHALLASlpdDPVSPDQLTTLPLIMPSQGHGLRGRLEAVCQQHNLSVEVV---ADIDglaLLMQ 228
Cdd:PRK12682 159 aTLPCYDWQHAVIvpPDHPLAQE---ERITLEDLAEYPLITYHPGFTGRSRIDRAFAAAGLQPDIVleaIDSD---VIKT 232


                 ....*..
gi 491024256 229 AVRSGLG 235
Cdd:PRK12682 233 YVRLGLG 239
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
1-254 6.15e-08

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 53.10  E-value: 6.15e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256   1 MELRQLRYFTRIVETGSMGRAALDLNIGVSALSQQIARLENELAIRLLQRTSRGVTPTSAGLAFYSQAQLALRHADDAIL 80
Cdd:PRK15421   2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQ 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256  81 AAREARLSgHVSVGMAPSTASVLGVPFINAMRESYPDVRLHLVESLSGNLERMINTRQLDLAIV--FQQEKILRWSARPV 158
Cdd:PRK15421  82 ACNEPQQT-RLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTsdILPRSGLHYSPMFD 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256 159 LEERLFLIGTHALLASlpdDPVSPDQLTTLP-LIMPSQghglRGRLEAvcQQHNLSVEVVA----DIDGLALLMQAVRSG 233
Cdd:PRK15421 161 YEVRLVLAPDHPLAAK---TRITPEDLASETlLIYPVQ----RSRLDV--WRHFLQPAGVSpslkSVDNTLLLIQMVAAR 231

                        250       260
                 ....*....|....*....|.
gi 491024256 234 LGATLQPGAAISHLDHQALRV 254
Cdd:PRK15421 232 MGIAALPHWVVESFERQGLVV 252
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 90-283 6.27e-08

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


Pssm-ID: 176115 [Multi-domain]  Cd Length: 200  Bit Score: 51.83  E-value: 6.27e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256  90 HVSVGMAPSTASVLGVPFINAMRESYPDVRLHLVESLSGNLERMINTRQLDLAIVF-------QQEKILRWsaRPVLEER 162
Cdd:cd08423    1 TLRVGAFPTAAAALLPPALAALRARHPGLEVRLREAEPPESLDALRAGELDLAVVFdypvtppPDDPGLTR--VPLLDDP 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256 163 LFLI--GTHALLASlpdDPVSPDQLTTLPLIMPSQGHGLRGRLEAVCQQHNLSVEVVADIDGLALLMQAVRSGLGATLQP 240
Cdd:cd08423   79 LDLVlpADHPLAGR---EEVALADLADEPWIAGCPGSPCHRWLVRACRAAGFTPRIAHEADDYATVLALVAAGLGVALVP 155

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 491024256 241 GAAISHLdHQALRVIGIAnPVLSRPNFLVSLSDDELTPAGLAA 283
Cdd:cd08423  156 RLALGAR-PPGVVVRPLR-PPPTRRIYAAVRAGAARRPAVAAA 196
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 90-287 7.16e-08

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: 51.89  E-value: 7.16e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256  90 HVSVGMAPSTASVLGVPFINAMRESYPDVRLHLVESLSGNLERMINTRQLDLAI-----VFQQEKIlrwSARPVLEERLF 164
Cdd:cd08435    1 TVRVGAVPAAAPVLLPPAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAIgrladDEQPPDL---ASEELADEPLV 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256 165 LI-GTHALLASLPddPVSPDQLTTLPLIMPSQGHGLRGRLEAVCQQHNLS-----VEVVADIDGLALLMqavRSGLGATL 238
Cdd:cd08435   78 VVaRPGHPLARRA--RLTLADLADYPWVLPPPGTPLRQRLEQLFAAAGLPlprnvVETASISALLALLA---RSDMLAVL 152

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 491024256 239 QPGAAISHLDHQALRVIGIANPVLSRPNFLVSLSDDELTPAGLAARVIL 287
Cdd:cd08435  153 PRSVAEDELRAGVLRELPLPLPTSRRPIGITTRRGGPLSPAARALLDAL 201
PRK09801 PRK09801
LysR family transcriptional regulator;
4-142 1.81e-07

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 51.57  E-value: 1.81e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256   4 RQLRYFTRIVETGSMGRAALDLNIGVSALSQQIARLENELAIRLLQRTSRGVTPTSAGLAFYSQAQLALRH----ADDai 79
Cdd:PRK09801   9 KDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQyqrlVDD-- 86

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 491024256  80 LAAREARLSGHVSVGMAPSTASVLGVPFINAMRESYPDVRLHLveslsgnlerMINTRQLDLA 142
Cdd:PRK09801  87 VTQIKTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHF----------ELFDRQIDLV 139
PRK12680 PRK12680
LysR family transcriptional regulator;
1-144 3.18e-07

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 51.16  E-value: 3.18e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256   1 MELRQLRYFTRIVETgsmgraalDLNIGVSA---------LSQQIARLENELAIRLLQRTSR---GVTPtsAGLAFYSQA 68
Cdd:PRK12680   1 MTLTQLRYLVAIADA--------ELNITLAAarvhatqpgLSKQLKQLEDELGFLLFVRKGRsleSVTP--AGVEVIERA 70

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 491024256  69 QLALRHADDA-ILAAREARLS-GHVSVGMAPSTASVLGVPFINAMRESYPDVRLHLVESLSGNLERMINTRQLDLAIV 144
Cdd:PRK12680  71 RAVLSEANNIrTYAANQRRESqGQLTLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIV 148
cbl PRK12679
HTH-type transcriptional regulator Cbl;
30-252 3.96e-07

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 50.58  E-value: 3.96e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256  30 SALSQQIARLENELAIRL-LQRTSRGVTPTSAGLAFYSQAQLALRHADD----AILAAREArlSGHVSVGMAPSTASVLG 104
Cdd:PRK12679  31 SGVSRHIRELEDELGIEIfIRRGKRLLGMTEPGKALLVIAERILNEASNvrrlADLFTNDT--SGVLTIATTHTQARYSL 108

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256 105 VPFINAMRESYPDVRLHLVESLSGNLERMINTRQLDLAIVFQqekilRWSARPVLEERLFLIGTHALLasLPDD------ 178
Cdd:PRK12679 109 PEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASE-----RLSNDPQLVAFPWFRWHHSLL--VPHDhpltqi 181

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 491024256 179 -PVSPDQLTTLPLIMPSQGHGLRGRLEAVCQQHNLSVEVVADIDGLALLMQAVRSGLGATLQPGAAISHLDHQAL 252
Cdd:PRK12679 182 tPLTLESIAKWPLITYRQGITGRSRIDDAFARKGLLADIVLSAQDSDVIKTYVALGLGIGLVAEQSSGEQEESNL 256
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 90-279 6.00e-07

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: 49.23  E-value: 6.00e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256  90 HVSVGMAPSTASVLGVPFINAMRESYPDVRLHLVESLSGNLERMINTRQLDLAIVFqqekilrwSARPVLEERLFLIGTH 169
Cdd:cd08426    1 RVRVATGEGLAAELLPSLIARFRQRYPGVFFTVDVASTADVLEAVLSGEADIGLAF--------SPPPEPGIRVHSRQPA 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256 170 ALLASLPDD-------PVSPDQLTTLPLIMPSQGHGLRGRLEAVCQQHNLSVEVVADIDGLALLMQAVRSGLGATLQPGA 242
Cdd:cd08426   73 PIGAVVPPGhplarqpSVTLAQLAGYPLALPPPSFSLRQILDAAFARAGVQLEPVLISNSIETLKQLVAAGGGISLLTEL 152

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 491024256 243 AISH-LDHQALRVIGIANPVL-SRPNFLVSLSDDELTPA 279
Cdd:cd08426  153 AVRReIRRGQLVAVPLADPHMnHRQLELQTRAGRQLPAA 191
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 1-143 7.92e-07

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 49.64  E-value: 7.92e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256   1 MELRQLRYFTRIVETGSMGRAALDLNIGVSALSQQIARLENELAIRLLQRTSRGVTPTSAGLAFYSQAQLALRHADDAIL 80
Cdd:PRK15092  11 LDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEACS 90

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 491024256  81 AAREARLSGHVSVGMAPSTASVLgVPFI-NAMRESYPDVRLHLVESLSGNLERMINTRQLDLAI 143
Cdd:PRK15092  91 SLMYSNLQGVLTIGASDDTADTI-LPFLlNRVSSVYPKLALDVRVKRNAFMMEMLESQEVDLAV 153
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 3-235 9.92e-07

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 49.30  E-value: 9.92e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256   3 LRQLRYFTRIVETGSMGRAALDLNIGVSALSQQIARLENELAIRLLQRTSRGVTPTSAGLAFYSQAQLALRHADDAILAA 82
Cdd:PRK10837   5 LRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQAVEIEQLF 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256  83 REArlSGHVSVGMAPSTASVLGVPFINAMRESYPDVRLHLVeslSGNLERMINTR---QLDLAIVFQQEKILRWSARPVL 159
Cdd:PRK10837  85 RED--NGALRIYASSTIGNYILPAMIARYRRDYPQLPLELS---VGNSQDVINAVldfRVDIGLIEGPCHSPELISEPWL 159

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 491024256 160 EERL--FLIGTHALLASlpddPVSPDQLTTLPLIMPSQGHGLRGRLEAVCQQHNLSVEVVADIDGLALLMQAVRSGLG 235
Cdd:PRK10837 160 EDELvvFAAPDSPLARG----PVTLEQLAAAPWILRERGSGTREIVDYLLLSHLPRFELAMELGNSEAIKHAVRHGLG 233
PBP2_BudR cd08451
The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is ...
 90-286 1.44e-06

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


Pssm-ID: 176142 [Multi-domain]  Cd Length: 199  Bit Score: 47.94  E-value: 1.44e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256  90 HVSVGMAPSTAS---VLGVpfINAMRESYPDVRLHLVESLSGNLERMINTRQLDLAIV---FQQEKILRwsARPVLEERL 163
Cdd:cd08451    1 RLRVGFTSSAAFhplVPGL--IRRFREAYPDVELTLEEANTAELLEALREGRLDAAFVrppVARSDGLV--LELLLEEPM 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256 164 FLI--GTHALLAslpDDPVSPDQLTTLPLIM--PSQGHGLRGRLEAVCQQHNLSVEVVADIDGLALLMQAVRSGLGATLQ 239
Cdd:cd08451   77 LVAlpAGHPLAR---ERSIPLAALADEPFILfpRPVGPGLYDAIIAACRRAGFTPRIGQEAPQMASAINLVAAGLGVSIV 153

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 491024256 240 PgAAISHLDHQALRVIGIANPVLSRPNFLVSLSDDeltPAGLAARVI 286
Cdd:cd08451  154 P-ASMRQLQAPGVVYRPLAGAPLTAPLALAYRRGE---RSPAVRNFI 196
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
30-213 1.82e-06

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 48.28  E-value: 1.82e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256  30 SALSQQIARLENELAIRLLQRTSRGVTPTSAGLAF----------YSQAQLALRHADDAIlaarEARLSGHVSVgmapsT 99
Cdd:PRK11716   6 STLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELrpfaqqtllqWQQLRHTLDQQGPSL----SGELSLFCSV-----T 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256 100 ASVLGVPFI-NAMRESYPDVRLHLVESLSGNLERMINTRQLDLAIvfqqekilrwSARP-VLEERL-FL-IGTHALLASL 175
Cdd:PRK11716  77 AAYSHLPPIlDRFRAEHPLVEIKLTTGDAADAVEKVQSGEADLAI----------AAKPeTLPASVaFSpIDEIPLVLIA 146

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 491024256 176 PDDPVSPDQLTT--------LPLIMPSQGHGlRGRLEAVCQQHNLS 213
Cdd:PRK11716 147 PALPCPVRQQLSqekpdwsrIPFILPEHGPA-RRRIDLWFRRHKIK 191
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
6-69 2.41e-06

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 48.26  E-value: 2.41e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 491024256   6 LRYFTRIVETGSMGRAALDLNIGVSALSQQIARLENELAIRLLQRTSRGVTPTSAGLAFYSQAQ 69
Cdd:PRK10094   7 LRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQAR 70
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
1-70 4.02e-06

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 47.46  E-value: 4.02e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 491024256   1 MELRQLRYFTRIVETGSMGRAALDLNIGVSALSQQIARLENELAIRLLQRTsRGVTPTSAG---LAFYSQAQL 70
Cdd:PRK03635   2 LDYKQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVRT-QPCRPTEAGqrlLRHARQVRL 73
PBP2_YofA_SoxR_like cd08442
The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, ...
 93-279 8.97e-06

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: 45.68  E-value: 8.97e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256  93 VGMAPSTASVLGVPFINAMRESYPDVRLHLVESLSGNLERMINTRQLDLAIVFQQEKILRWSARPVLEERLFLIgTHALL 172
Cdd:cd08442    4 LGSMETTAAVRLPPLLAAYHARYPKVDLSLSTGTTGALIQAVLEGRLDGAFVAGPVEHPRLEQEPVFQEELVLV-SPKGH 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256 173 ASLPDdpvsPDQLTTLPLIMPSQGHGLRGRLEAVCQQHNLSVEVVADIDGLALLMQAVRSGLGATLQPGAAISHL-DHQA 251
Cdd:cd08442   83 PPVSR----AEDLAGSTLLAFRAGCSYRRRLEDWLAEEGVSPGKIMEFGSYHAILGCVAAGMGIALLPRSVLDSLqGRGS 158

                        170       180
                 ....*....|....*....|....*...
gi 491024256 252 LRVIGIANPVLSRPNFLVSlSDDELTPA 279
Cdd:cd08442  159 VSIHPLPEPFADVTTWLVW-RKDSFTAA 185
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 90-242 1.17e-05

The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate domain of LysR-type transcriptional regulators involved in controlling the expression of glutaryl-CoA dehydrogenase (GcdH), S-adenosyl-L-homocysteine hydrolase, cell division protein FtsW, tryptophan synthase, and beta-lactamase. 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: 176123 [Multi-domain]  Cd Length: 194  Bit Score: 45.26  E-value: 1.17e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256  90 HVSVGMAPSTASVLGVPFINAMRESYPDVRLHLVESLSG-NLERmintRQLDLAIVFQQEkilRWS---ARPVLEERLFL 165
Cdd:cd08432    1 VLTVSVTPSFAARWLIPRLARFQARHPDIDLRLSTSDRLvDFAR----EGIDLAIRYGDG---DWPgleAERLMDEELVP 73

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 491024256 166 IGTHALLASLPddPVSPDQLTTLPLIMPSQGHGLRGRLEAVCQQHNLSVEVVADIDGLALLMQAVRSGLGATLQPGA 242
Cdd:cd08432   74 VCSPALLAGLP--LLSPADLARHTLLHDATRPEAWQWWLWAAGVADVDARRGPRFDDSSLALQAAVAGLGVALAPRA 148
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 93-238 1.28e-05

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: 45.25  E-value: 1.28e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256  93 VGMAPSTASVLGVPFINAMRESYPDVRLHLVESLSGNLERMINTRQLDLAIVFQQEKILRWSARPVLEERLFLI--GTHA 170
Cdd:cd08415    4 IAALPALALSLLPRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPLDHPGLESEPLASGRAVCVlpPGHP 83

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 491024256 171 lLASLpdDPVSPDQLTTLPLIMPSQGHGLRGRLEAVCQQHNLSVEVVADIDGLALLMQAVRSGLGATL 238
Cdd:cd08415   84 -LARK--DVVTPADLAGEPLISLGRGDPLRQRVDAAFERAGVEPRIVIETQLSHTACALVAAGLGVAI 148
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
 91-282 2.14e-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: 44.42  E-value: 2.14e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256  91 VSVGMApSTASVLGVPFINAMRESYPDVRLHLVESLSGNLERMINTRQLDLAIVFQQEKILRWSARPVLEERLFLIG--T 168
Cdd:cd08419    2 LRLAVV-STAKYFAPRLLGAFCRRHPGVEVSLRVGNREQVLERLADNEDDLAIMGRPPEDLDLVAEPFLDNPLVVIAppD 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256 169 HALLASlpdDPVSPDQLTTLPLIMPSQGHGLRGRLEAVCQQHNLSVEVVADIDGLALLMQAVRSGLG------ATLQPGA 242
Cdd:cd08419   81 HPLAGQ---KRIPLERLAREPFLLREPGSGTRLAMERFFAEHGVTLRVRMELGSNEAIKQAVMAGLGlsvlslHTLALEL 157

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 491024256 243 AISHLdhQALRVIGiaNPVLsRPNFLVSLSDDELTPAGLA 282
Cdd:cd08419  158 ATGRL--AVLDVEG--FPIR-RQWYVVHRKGKRLSPAAQA 192
PBP2_DntR_like_3 cd08461
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 101-201 2.64e-05

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold; This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. 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: 176150 [Multi-domain]  Cd Length: 198  Bit Score: 44.19  E-value: 2.64e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256 101 SVLGVPFINAMRESYPDVRLHLVESLSGNLERMINTRQLDLAIVFQQEKILRWSARPVLEERLFLIG--THALLASlpdd 178
Cdd:cd08461   12 KAILPPLLAALRQEAPGVRVAIRDLESDNLEAQLERGEVDLALTTPEYAPDGLRSRPLFEERYVCVTrrGHPLLQG---- 87

                         90       100
                 ....*....|....*....|....
gi 491024256 179 PVSPDQLTTLPLIMPS-QGHGLRG 201
Cdd:cd08461   88 PLSLDQFCALDHIVVSpSGGGFAG 111
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 1-143 3.26e-05

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 44.65  E-value: 3.26e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256   1 MELRQLRYFTRIVETG-SMGRAALDLNIGVSALSQQIARLENELAIRLLQRTSRGVTP-TSAGLAFYSQAQLALRHADDA 78
Cdd:PRK12683   1 MNFQQLRIIREAVRQNfNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTGlTEPGKELLQIVERMLLDAENL 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 491024256  79 ILAARE--ARLSGHVSVGMAPSTASVLGVPFINAMRESYPDVRLHLVESLSGNLERMINTRQLDLAI 143
Cdd:PRK12683  81 RRLAEQfaDRDSGHLTVATTHTQARYALPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGI 147
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 90-254 3.80e-05

The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of dinitrotoluene and similar compounds, such as DntR, NahR, and LinR. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. Also included are related LysR-type regulators clustered together in phylogenetic trees, including NodD, ToxR, LeuO, SyrM, TdcA, and PnbR. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176109 [Multi-domain]  Cd Length: 200  Bit Score: 43.74  E-value: 3.80e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256  90 HVSVGMAPSTASVLGVPFINAMRESYPDVRLHLVESLSGNLERMINTRQLDLAIVFQQEKILRWSARPVLEERLFLIG-- 167
Cdd:cd08417    1 TFRIAASDYLEALLLPPLLARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELPPGLRSQPLFEDRFVCVArk 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256 168 THALLAslpdDPVSPDQLTTLPLIMPSQGHGLRGRLEAVCQQHNLSVEVVADIDGLALLMQAVR-SGLGATLQPGAAISH 246
Cdd:cd08417   81 DHPLAG----GPLTLEDYLAAPHVLVSPRGRGHGLVDDALAELGLSRRVALTVPHFLAAPALVAgTDLIATVPRRLAEAL 156


                 ....*...
gi 491024256 247 LDHQALRV 254
Cdd:cd08417  157 AERLGLRV 164
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
1-143 2.17e-04

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 42.27  E-value: 2.17e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256   1 MELRQLRYFTRIVETG-SMGRAALDLNIGVSALSQQIARLENELAIRLLQRTS---RGVTPtsAGLAFYSQAQLALRHAD 76
Cdd:PRK12684   1 MNLHQLRFVREAVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGkrlRGLTE--PGRIILASVERILQEVE 78

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 491024256  77 DAILAARE--ARLSGHVSVGMAPSTASVLGVPFINAMRESYPDVRLHLVESLSGNLERMINTRQLDLAI 143
Cdd:PRK12684  79 NLKRVGKEfaAQDQGNLTIATTHTQARYALPAAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAI 147
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 3-141 3.09e-04

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 41.90  E-value: 3.09e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256   3 LRQLRYFTRIVETGSMGRAALDLNIGVSALSQQIARLENELAIRLLQRTSRGVTPTSAGLAFYSQAQLALRHADDAILAA 82
Cdd:PRK11013   6 LRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLFEEVQRSYYGLDRIVSAA 85

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 491024256  83 ---REARlSGHVSVGMAPSTASVLGVPFINAMRESYPDVRLHLVESLSGNLERMINTRQLDL 141
Cdd:PRK11013  86 eslREFR-QGQLSIACLPVFSQSLLPGLCQPFLARYPDVSLNIVPQESPLLEEWLSAQRHDL 146
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 89-240 3.42e-04

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


Pssm-ID: 176114 [Multi-domain]  Cd Length: 197  Bit Score: 40.89  E-value: 3.42e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256  89 GHVSVGMAPSTASVLGVPFINAMRESYPDVRLHLVESlsgnlERMIN--TRQLDLAIVFQQEKILRWSARPVLEERLFLI 166
Cdd:cd08422    1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLS-----DRLVDlvEEGFDLAIRIGELPDSSLVARRLGPVRRVLV 75

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 491024256 167 GTHALLASLPdDPVSPDQLTTLP-LIMPSQGHGLRGRLEAVCQQHNLSVEVVADIDGLALLMQAVRSGLGATLQP 240
Cdd:cd08422   76 ASPAYLARHG-TPQTPEDLARHRcLGYRLPGRPLRWRFRRGGGEVEVRVRGRLVVNDGEALRAAALAGLGIALLP 149
PBP2_MleR cd08437
The substrate binding domain of LysR-type transcriptional regulator MleR which required for ...
 90-279 3.80e-04

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


Pssm-ID: 176128  Cd Length: 198  Bit Score: 40.78  E-value: 3.80e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256  90 HVSVGMAPSTASVLGVPFINAMRESYPDVRLHLVESLSGNLERMINTRQLDLAivfqqekiLRWSARPVLEERLF--LIG 167
Cdd:cd08437    1 KLRFGLPPIIGNYYFPKLAKDLIKTGLMIQIDTYEGGSAELLEQLLQGDLDIA--------LLGSLTPLENSALHskIIK 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256 168 THAL-LASLPDDP------VSPDQLTTLPLIMPSQGHGLRGRLEAVCQQHNLSVEVVADIDGLALLMQAVRSGLGATLQP 240
Cdd:cd08437   73 TQHFmIIVSKDHPlakakkVNFADLKKENFILLNEHFVHPKAFDSLCQQANFQPNIVYRTNDIHILKSMVRENVGIGFLT 152

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 491024256 241 GAAISHLDHqaLRVIGIANPVlsRPNFLVSLS---DDELTPA 279
Cdd:cd08437  153 DIAVKPDDH--LVAIPLLDNE--QPTFYISLAhrkDQLLTPA 190
cysB PRK12681
HTH-type transcriptional regulator CysB;
1-143 9.26e-04

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 40.27  E-value: 9.26e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256   1 MELRQLRYftrIVETgsmgrAALDLNIGVSA---------LSQQIARLENELAIRLLQRTSR---GVTPtsAGLAFYSQA 68
Cdd:PRK12681   1 MKLQQLRY---IVEV-----VNHNLNVSATAeglytsqpgISKQVRMLEDELGIQIFARSGKhltQVTP--AGEEIIRIA 70

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 491024256  69 QLALRHADDAILAAREARLSGHVSVGMAPS-TASVLGVP-FINAMRESYPDVRLHLVESLSGNLERMINTRQLDLAI 143
Cdd:PRK12681  71 REILSKVESIKSVAGEHTWPDKGSLYIATThTQARYALPpVIKGFIERYPRVSLHMHQGSPTQIAEAAAKGNADFAI 147
PBP2_LTTR_aromatics_like_1 cd08447
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 96-243 1.07e-03

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


Pssm-ID: 176138 [Multi-domain]  Cd Length: 198  Bit Score: 39.55  E-value: 1.07e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256  96 APSTASVLGvPFINAMRESYPDVRLHLVESLSGNLERMINTRQLDLAIVFQQEKILRWSARPVLEERLFLI--GTHALLA 173
Cdd:cd08447    8 AASAYSFLP-RLLAAARAALPDVDLVLREMVTTDQIEALESGRIDLGLLRPPFARPGLETRPLVREPLVAAvpAGHPLAG 86

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 491024256 174 SlpdDPVSPDQLTTLPLIM--PSQG---HGLRGRLEAVCQQHNLSVEVVADIDG-LALlmqaVRSGLGATLQPGAA 243
Cdd:cd08447   87 A---ERLTLEDLDGQPFIMysPTEAryfHDLVVRLFASAGVQPRYVQYLSQIHTmLAL----VRAGLGVALVPASA 155
PBP2_HcaR cd08450
The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in ...
 111-247 1.60e-03

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


Pssm-ID: 176141 [Multi-domain]  Cd Length: 196  Bit Score: 38.90  E-value: 1.60e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256 111 MRESYPDVRLHLVESLSGNLERMINTRQLDLAIVFQQEKILRWSARPVLEERL-FLIGTHALLASLpdDPVSPDQLTTLP 189
Cdd:cd08450   22 LREEHPDLDVELSSLFSPQLAEALMRGKLDVAFMRPEIQSDGIDYQLLLKEPLiVVLPADHRLAGR--EKIPPQDLAGEN 99

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 491024256 190 LIMPSQGHG-LRGRLEAVCQQHNLSVEVVADIDGLALLMQAVRSGLGATLQPGAAISHL 247
Cdd:cd08450  100 FISPAPTAPvLQQVIENYAAQHNIQPNIIQEADNLLSAMSLVASTLGCALLPLYANNLL 158
nhaR PRK11062
transcriptional activator NhaR; Provisional
 6-76 2.29e-03

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 39.22  E-value: 2.29e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 491024256   6 LRYFTRIVETGSMGRAALDLNIGVSALSQQIARLENELAIRLLQRTSRGVTPTSAGlafysqaQLALRHAD 76
Cdd:PRK11062   9 LYYFWMVCKEGSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELG-------ELVFRYAD 72
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 15-77 3.06e-03

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 38.77  E-value: 3.06e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 491024256  15 TGSMGRAALDLNIGVSALSQQIARLENELAIRLLQRTSRGVTPTSAGLAFYSQAQLALRHADD 77
Cdd:PRK11074  16 TGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQE 78
PRK11482 PRK11482
DNA-binding transcriptional regulator;
21-143 6.45e-03

DNA-binding transcriptional regulator;


Pssm-ID: 183159 [Multi-domain]  Cd Length: 317  Bit Score: 37.78  E-value: 6.45e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256  21 AALDLNIGVSALSQQIARLENELAIRLLQRTSRGVTPTsaglAFYSQAQLALRHADDAILAAREARLSGH----VSVGMA 96
Cdd:PRK11482  49 AAKILNLTPSAISQSIQKLRVIFPDPLFIRKGQGVTPT----AYATHLHEYISQGLESILGALDITGSYDkqrtITIATT 124

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 491024256  97 PSTASVLgVPFI-NAMRESYPDVRLHLVEslSGNLERMINTRQLDLAI 143
Cdd:PRK11482 125 PSVGALV-MPVIyQAIKTHYPQLLLRNIP--ISDAENQLSQFQTDLII 169
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
1-143 9.05e-03

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 37.30  E-value: 9.05e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256   1 MELRQLRYFTRIVETGSMGRAALDLNIGVSALSQQIARLENELAIRLLQRTSRGVTPTSAGlafysqaQLALRHADDAI- 79
Cdd:PRK03601   1 MDTELLKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAG-------ERLLPYAETLMn 73

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491024256  80 ---LAARE-ARLSGH--VSVGMAPSTASVLGVPFINAMRESYPDVRLHLVESLSGNLERMINTRQLDLAI 143
Cdd:PRK03601  74 twqAAKKEvAHTSQHneLSIGASASLWECMLTPWLGRLYQNQEALQFEARIAQRQSLVKQLHERQLDLLI 143
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

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