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Conserved domains on  [gi|2502538194|ref|WP_281868639|]
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MULTISPECIES: LysR family transcriptional regulator [Brevibacillus]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 11426483)

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

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-292 1.37e-55

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 180.83  E-value: 1.37e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194   1 MNLHALRIFVEVASRQSVTAAAEALAISQPAVSAQIRKLENELGLSLLAPDGRGISLTDEGRFLFEKARRIYDWEREIES 80
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194  81 QLAEIRQGEKGKLRIASTYLPSNYLVPKWLAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAIVIKEAWEDDLpiDRV 160
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGL--VAR 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 161 HMTDVLYWFILPAAHPLAGKeisiEQLVQEPFLLReqgsstrewlfslcrehgvrrprvglqyhgliesiQSVRAGYGTM 240
Cdd:COG0583   159 PLGEERLVLVASPDHPLARR----APLVNSLEALL-----------------------------------AAVAAGLGIA 199

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2502538194 241 LAPALAVEEMVERNEIGRVTVPGVEIKRPVYICTRAGeSSHRPVVERFLERV 292
Cdd:COG0583   200 LLPRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRR-RHLSPAVRAFLDFL 250
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-292 1.37e-55

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 180.83  E-value: 1.37e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194   1 MNLHALRIFVEVASRQSVTAAAEALAISQPAVSAQIRKLENELGLSLLAPDGRGISLTDEGRFLFEKARRIYDWEREIES 80
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194  81 QLAEIRQGEKGKLRIASTYLPSNYLVPKWLAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAIVIKEAWEDDLpiDRV 160
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGL--VAR 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 161 HMTDVLYWFILPAAHPLAGKeisiEQLVQEPFLLReqgsstrewlfslcrehgvrrprvglqyhgliesiQSVRAGYGTM 240
Cdd:COG0583   159 PLGEERLVLVASPDHPLARR----APLVNSLEALL-----------------------------------AAVAAGLGIA 199

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2502538194 241 LAPALAVEEMVERNEIGRVTVPGVEIKRPVYICTRAGeSSHRPVVERFLERV 292
Cdd:COG0583   200 LLPRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRR-RHLSPAVRAFLDFL 250
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-295 6.59e-51

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


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 169.72  E-value: 6.59e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194   1 MNLHALRIFVEVASRQSVTAAAEALAISQPAVSAQIRKLENELGLSLLAPDGRGISLTDEGRFLFEKARRIYDWEREIES 80
Cdd:NF040786    1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194  81 QLAEIRQGEKGKLRIASTYLPSNYLVPKWLAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAIV----IKEA------ 150
Cdd:NF040786   81 EFDRYGKESKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTgtklEKKRlvytpf 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 151 WEDDLpidrvhmtdvlyWFILPAAHPLAGK---EISIEQLVQEPFLLREQGSSTREWLFSLCREHGVRRP------RVGL 221
Cdd:NF040786  161 YKDRL------------VLITPNGTEKYRMlkeEISISELQKEPFIMREEGSGTRKEAEKALKSLGISLEdlnvvaSLGS 228

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2502538194 222 QyhgliESI-QSVRAGYGTMLAPALAVEEMVERNEIGRVTVPGVEIKRPVYICTRAGeSSHRPVVERFLERVLGK 295
Cdd:NF040786  229 T-----EAIkQSVEAGLGISVISELAAEKEVERGRVLIFPIPGLPKNRDFYLVYNKN-RQLSPTAEAFLQFVKER 297
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 92-290 4.74e-37

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: 131.07  E-value: 4.74e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194  92 KLRIASTYLPSNYLVPKWLAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAIVikEAWEDDLPIDRVH-MTDVLYwFI 170
Cdd:cd08420     1 TLRIGASTTIGEYLLPRLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLV--EGPVDHPDLIVEPfAEDELV-LV 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 171 LPAAHPLAGK-EISIEQLVQEPFLLREQGSSTREWLFSLCREHGV--RRPRVGLQYHGlIESI-QSVRAGYGTMLAPALA 246
Cdd:cd08420    78 VPPDHPLAGRkEVTAEELAAEPWILREPGSGTREVFERALAEAGLdgLDLNIVMELGS-TEAIkEAVEAGLGISILSRLA 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 2502538194 247 VEEMVERNEIGRVTVPGVEIKRPVYICTRAgESSHRPVVERFLE 290
Cdd:cd08420   157 VRKELELGRLVALPVEGLRLTRPFSLIYHK-DKYLSPAAEAFLE 199
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 91-293 8.26e-35

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: 125.09  E-value: 8.26e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194  91 GKLRIASTYLPSNYLVPKWLAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAIVIkeAWEDDLPIDRVHMTDVLYWFI 170
Cdd:pfam03466   2 GRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRR--GPPDDPGLEARPLGEEPLVLV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 171 LPAAHPLAGKE-ISIEQLVQEPFLLREQGSSTREWLFSLCREHGVrRPRVGLQYHGLIESIQSVRAGYGTMLAPALAVEE 249
Cdd:pfam03466  80 APPDHPLARGEpVSLEDLADEPLILLPPGSGLRDLLDRALRAAGL-RPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAR 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 2502538194 250 MVERNEIGRVTVPGVEIKRPVYICTRAGeSSHRPVVERFLERVL 293
Cdd:pfam03466 159 ELADGRLVALPLPEPPLPRELYLVWRKG-RPLSPAVRAFIEFLR 201
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 3-290 1.20e-34

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 127.11  E-value: 1.20e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194   3 LHALRIFVEVASRQSVTAAAEALAISQPAVSAQIRKLENELGLSLLAPDGRGISLTDEGRFLFEKARRIYDWEREIEsQL 82
Cdd:PRK10837    5 LRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQAVEIE-QL 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194  83 AeirQGEKGKLRIASTYLPSNYLVPKWLAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAIV---------IKEAW-E 152
Cdd:PRK10837   84 F---REDNGALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNSQDVINAVLDFRVDIGLIegpchspelISEPWlE 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 153 DDLPIdrvhmtdvlywFILPaAHPLAGKEISIEQLVQEPFLLREQGSSTREWLFSLCREHgVRRPRVGLQYhGLIESIQ- 231
Cdd:PRK10837  161 DELVV-----------FAAP-DSPLARGPVTLEQLAAAPWILRERGSGTREIVDYLLLSH-LPRFELAMEL-GNSEAIKh 226

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 232 SVRAGYGTMLAPALAVEEMVERNEIGRVTVPGVEIKRPVY-ICTRAGESSHrpVVERFLE 290
Cdd:PRK10837  227 AVRHGLGISCLSRRVIADQLQAGTLVEVAVPLPRLMRTLYrIHHRQKHLSN--ALQRFLS 284
HTH_DTXR smart00529
Helix-turn-helix diphteria tox regulatory element; iron dependent repressor
 22-85 2.85e-04

Helix-turn-helix diphteria tox regulatory element; iron dependent repressor


Pssm-ID: 197774 [Multi-domain]  Cd Length: 95  Bit Score: 39.12  E-value: 2.85e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2502538194   22 AEALAISQPAVSAQIRKLEnELGLSLLAPDgRGISLTDEGRflfEKARRIYDWEREIESQLAEI 85
Cdd:smart00529   5 AERLNVSPPTVTEMLKKLE-KMGLVEYEPY-RGITLTEKGR---RLARRLLRKHRLLERFLVDV 63
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-292 1.37e-55

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 180.83  E-value: 1.37e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194   1 MNLHALRIFVEVASRQSVTAAAEALAISQPAVSAQIRKLENELGLSLLAPDGRGISLTDEGRFLFEKARRIYDWEREIES 80
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194  81 QLAEIRQGEKGKLRIASTYLPSNYLVPKWLAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAIVIKEAWEDDLpiDRV 160
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGL--VAR 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 161 HMTDVLYWFILPAAHPLAGKeisiEQLVQEPFLLReqgsstrewlfslcrehgvrrprvglqyhgliesiQSVRAGYGTM 240
Cdd:COG0583   159 PLGEERLVLVASPDHPLARR----APLVNSLEALL-----------------------------------AAVAAGLGIA 199

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2502538194 241 LAPALAVEEMVERNEIGRVTVPGVEIKRPVYICTRAGeSSHRPVVERFLERV 292
Cdd:COG0583   200 LLPRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRR-RHLSPAVRAFLDFL 250
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-295 6.59e-51

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


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 169.72  E-value: 6.59e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194   1 MNLHALRIFVEVASRQSVTAAAEALAISQPAVSAQIRKLENELGLSLLAPDGRGISLTDEGRFLFEKARRIYDWEREIES 80
Cdd:NF040786    1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194  81 QLAEIRQGEKGKLRIASTYLPSNYLVPKWLAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAIV----IKEA------ 150
Cdd:NF040786   81 EFDRYGKESKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTgtklEKKRlvytpf 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 151 WEDDLpidrvhmtdvlyWFILPAAHPLAGK---EISIEQLVQEPFLLREQGSSTREWLFSLCREHGVRRP------RVGL 221
Cdd:NF040786  161 YKDRL------------VLITPNGTEKYRMlkeEISISELQKEPFIMREEGSGTRKEAEKALKSLGISLEdlnvvaSLGS 228

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2502538194 222 QyhgliESI-QSVRAGYGTMLAPALAVEEMVERNEIGRVTVPGVEIKRPVYICTRAGeSSHRPVVERFLERVLGK 295
Cdd:NF040786  229 T-----EAIkQSVEAGLGISVISELAAEKEVERGRVLIFPIPGLPKNRDFYLVYNKN-RQLSPTAEAFLQFVKER 297
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 92-290 4.74e-37

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: 131.07  E-value: 4.74e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194  92 KLRIASTYLPSNYLVPKWLAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAIVikEAWEDDLPIDRVH-MTDVLYwFI 170
Cdd:cd08420     1 TLRIGASTTIGEYLLPRLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLV--EGPVDHPDLIVEPfAEDELV-LV 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 171 LPAAHPLAGK-EISIEQLVQEPFLLREQGSSTREWLFSLCREHGV--RRPRVGLQYHGlIESI-QSVRAGYGTMLAPALA 246
Cdd:cd08420    78 VPPDHPLAGRkEVTAEELAAEPWILREPGSGTREVFERALAEAGLdgLDLNIVMELGS-TEAIkEAVEAGLGISILSRLA 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 2502538194 247 VEEMVERNEIGRVTVPGVEIKRPVYICTRAgESSHRPVVERFLE 290
Cdd:cd08420   157 VRKELELGRLVALPVEGLRLTRPFSLIYHK-DKYLSPAAEAFLE 199
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 91-293 8.26e-35

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: 125.09  E-value: 8.26e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194  91 GKLRIASTYLPSNYLVPKWLAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAIVIkeAWEDDLPIDRVHMTDVLYWFI 170
Cdd:pfam03466   2 GRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRR--GPPDDPGLEARPLGEEPLVLV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 171 LPAAHPLAGKE-ISIEQLVQEPFLLREQGSSTREWLFSLCREHGVrRPRVGLQYHGLIESIQSVRAGYGTMLAPALAVEE 249
Cdd:pfam03466  80 APPDHPLARGEpVSLEDLADEPLILLPPGSGLRDLLDRALRAAGL-RPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAR 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 2502538194 250 MVERNEIGRVTVPGVEIKRPVYICTRAGeSSHRPVVERFLERVL 293
Cdd:pfam03466 159 ELADGRLVALPLPEPPLPRELYLVWRKG-RPLSPAVRAFIEFLR 201
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 92-290 9.62e-35

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: 125.02  E-value: 9.62e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194  92 KLRIASTYLPSNYLVPKWLAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAIVIKEAWEDDLpiDRVHMTDVLYWFIL 171
Cdd:cd05466     1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGL--ESEPLFEEPLVLVV 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 172 PAAHPLAGKE-ISIEQLVQEPFLLREQGSSTREWLFSLCREHGVrRPRVGLQyHGLIESIQS-VRAGYGTMLAPALAVEE 249
Cdd:cd05466    79 PPDHPLAKRKsVTLADLADEPLILFERGSGLRRLLDRAFAEAGF-TPNIALE-VDSLEAIKAlVAAGLGIALLPESAVEE 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 2502538194 250 mVERNEIGRVTVPGVEIKRPVYICTRAGEsSHRPVVERFLE 290
Cdd:cd05466   157 -LADGGLVVLPLEDPPLSRTIGLVWRKGR-YLSPAARAFLE 195
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 3-290 1.20e-34

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 127.11  E-value: 1.20e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194   3 LHALRIFVEVASRQSVTAAAEALAISQPAVSAQIRKLENELGLSLLAPDGRGISLTDEGRFLFEKARRIYDWEREIEsQL 82
Cdd:PRK10837    5 LRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQAVEIE-QL 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194  83 AeirQGEKGKLRIASTYLPSNYLVPKWLAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAIV---------IKEAW-E 152
Cdd:PRK10837   84 F---REDNGALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNSQDVINAVLDFRVDIGLIegpchspelISEPWlE 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 153 DDLPIdrvhmtdvlywFILPaAHPLAGKEISIEQLVQEPFLLREQGSSTREWLFSLCREHgVRRPRVGLQYhGLIESIQ- 231
Cdd:PRK10837  161 DELVV-----------FAAP-DSPLARGPVTLEQLAAAPWILRERGSGTREIVDYLLLSH-LPRFELAMEL-GNSEAIKh 226

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 232 SVRAGYGTMLAPALAVEEMVERNEIGRVTVPGVEIKRPVY-ICTRAGESSHrpVVERFLE 290
Cdd:PRK10837  227 AVRHGLGISCLSRRVIADQLQAGTLVEVAVPLPRLMRTLYrIHHRQKHLSN--ALQRFLS 284
rbcR CHL00180
LysR transcriptional regulator; Provisional
 3-274 1.37e-30

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 116.66  E-value: 1.37e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194   3 LHALRIFVEVASRQSVTAAAEALAISQPAVSAQIRKLENELGLSLLAPDGRGISLTDEGRFLFEKARRIYDWEREIESQL 82
Cdd:CHL00180    7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRAL 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194  83 AEIRQGEKGKLRIASTYLPSNYLVPKWLAEFKQHYEHVDVEIRTrNSLQSIEL-LLSCQVDLAIVIKEAwEDDLpIDRVH 161
Cdd:CHL00180   87 EDLKNLQRGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQV-HSTRRIAWnVANGQIDIAIVGGEV-PTEL-KKILE 163

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 162 MTDVLY---WFILPAAHPLAGKE-ISIEQLVQEPFLLREQGSSTREWLFSLCREHGV--RRPRVGLQYHGlIESIQ-SVR 234
Cdd:CHL00180  164 ITPYVEdelALIIPKSHPFAKLKkIQKEDLYRLNFITLDSNSTIRKVIDNILIQNGIdsKRFKIEMELNS-IEAIKnAVQ 242

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|
gi 2502538194 235 AGYGTMLAPALAVEEMVERNEIGRVTVPGVEIKRPVYICT 274
Cdd:CHL00180  243 SGLGAAFVSVSAIEKELELGLLHWIKIENITIKRMLSIIT 282
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
1-191 2.76e-29

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 113.53  E-value: 2.76e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194   1 MNLHALRIFVEVAsRQ--SVTAAAEALAISQPAVSAQIRKLENELGLSLLAPDG-RGISLTDEGRFLFEKARRIYdweRE 77
Cdd:PRK12684    1 MNLHQLRFVREAV-RQnfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGkRLRGLTEPGRIILASVERIL---QE 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194  78 IESQL---AEIRQGEKGKLRIASTYLPSNYLVPKWLAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAIViKEAWEDD 154
Cdd:PRK12684   77 VENLKrvgKEFAAQDQGNLTIATTHTQARYALPAAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAIA-TEAIADY 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 2502538194 155 lpiDRVHMTDVLYW---FILPAAHP-LAGKEISIEQLVQEP 191
Cdd:PRK12684  156 ---KELVSLPCYQWnhcVVVPPDHPlLERKPLTLEDLAQYP 193
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 1-248 6.42e-29

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 111.97  E-value: 6.42e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194   1 MNLHALRIFVEVASRQSVTAAAEALAISQPAVSAQIRKLENELGLSLLAPDGRGISLTDEGRFLFEKARRIYdweREIES 80
Cdd:PRK11242    1 MLLRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRAL---QDLEA 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194  81 ---QLAEIRQGEKGKLRIASTYLPSNYLVPKWLAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAIVIKEAWEDDlpI 157
Cdd:PRK11242   78 grrAIHDVADLSRGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMSQERIEALLADDELDVGIAFAPVHSPE--I 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 158 DRVHMTDVLYWFILPAAHPLAGKE--ISIEQLVQEPFLLREQGSSTREWLFSLCREHGVrRPRVGLQYHGLIESIQSVRA 235
Cdd:PRK11242  156 EAQPLFTETLALVVGRHHPLAARRkaLTLDELADEPLVLLSAEFATREQIDRYFRRHGV-TPRVAIEANSISAVLEIVRR 234

                         250
                  ....*....|....
gi 2502538194 236 G-YGTMLAPALAVE 248
Cdd:PRK11242  235 GrLATLLPAAIARE 248
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 1-202 1.57e-25

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 103.15  E-value: 1.57e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194   1 MNLHALRIFVEVASRQ-SVTAAAEALAISQPAVSAQIRKLENELGLSLLAPDG-RGISLTDEGRFLFEKARRIYDWEREI 78
Cdd:PRK12682    1 MNLQQLRFVREAVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGkRLKGLTEPGKAVLDVIERILREVGNI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194  79 ESQLAEIRQGEKGKLRIASTYLPSNYLVPKWLAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAIViKEAWEDD---- 154
Cdd:PRK12682   81 KRIGDDFSNQDSGTLTIATTHTQARYVLPRVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGIA-TESLADDpdla 159

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 2502538194 155 -LPIDRVHMTdvlywFILPAAHPLAGKE-ISIEQLVQEPFLLREQGSSTR 202
Cdd:PRK12682  160 tLPCYDWQHA-----VIVPPDHPLAQEErITLEDLAEYPLITYHPGFTGR 204
cysB PRK12681
HTH-type transcriptional regulator CysB;
1-191 2.54e-25

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 103.05  E-value: 2.54e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194   1 MNLHALRIFVEVASRQ-SVTAAAEALAISQPAVSAQIRKLENELGLSLLAPDGRGIS-LTDEGRFLFEKARRIYDWEREI 78
Cdd:PRK12681    1 MKLQQLRYIVEVVNHNlNVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTqVTPAGEEIIRIAREILSKVESI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194  79 ESQLAEIRQGEKGKLRIASTYLPSNYLVPKWLAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAIvIKEAWE--DDLP 156
Cdd:PRK12681   81 KSVAGEHTWPDKGSLYIATTHTQARYALPPVIKGFIERYPRVSLHMHQGSPTQIAEAAAKGNADFAI-ATEALHlyDDLI 159

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 2502538194 157 idrvhMTDVLYW---FILPAAHPLAGKE-ISIEQLVQEP 191
Cdd:PRK12681  160 -----MLPCYHWnrsVVVPPDHPLAKKKkLTIEELAQYP 193
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 1-202 1.06e-24

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 100.89  E-value: 1.06e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194   1 MNLHALRIFVEVASRQ-SVTAAAEALAISQPAVSAQIRKLENELGLSLLAPDG-RGISLTDEGRFLFEKARRIYDWEREI 78
Cdd:PRK12683    1 MNFQQLRIIREAVRQNfNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGkRLTGLTEPGKELLQIVERMLLDAENL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194  79 ESQLAEIRQGEKGKLRIASTYLPSNYLVPKWLAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAIViKEAWEDD---- 154
Cdd:PRK12683   81 RRLAEQFADRDSGHLTVATTHTQARYALPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGIA-TEALDREpdlv 159

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 2502538194 155 -LPIDRVHMTdvlywFILPAAHPLAG-KEISIEQLVQEPFLLREQGSSTR 202
Cdd:PRK12683  160 sFPYYSWHHV-----VVVPKGHPLTGrENLTLEAIAEYPIITYDQGFTGR 204
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
 92-290 1.90e-22

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: 92.18  E-value: 1.90e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194  92 KLRIA--STylpSNYLVPKWLAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAIVIKEawEDDLPIDRVHMTDVLYWF 169
Cdd:cd08419     1 RLRLAvvST---AKYFAPRLLGAFCRRHPGVEVSLRVGNREQVLERLADNEDDLAIMGRP--PEDLDLVAEPFLDNPLVV 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 170 ILPAAHPLAG-KEISIEQLVQEPFLLREQGSSTREWLFSLCREHGVrRPRVGLQYHGLiESI-QSVRAGYGTMLAPALAV 247
Cdd:cd08419    76 IAPPDHPLAGqKRIPLERLAREPFLLREPGSGTRLAMERFFAEHGV-TLRVRMELGSN-EAIkQAVMAGLGLSVLSLHTL 153

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 2502538194 248 EEMVERNEIGRVTVPGVEIKRPVYICTRAGE--SshrPVVERFLE 290
Cdd:cd08419   154 ALELATGRLAVLDVEGFPIRRQWYVVHRKGKrlS---PAAQAFLD 195
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 3-145 4.04e-21

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 91.06  E-value: 4.04e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194   3 LHALRIFvEVASRQ-SVTAAAEALAISQPAVSAQIRKLENELGLSLLAPDGRGISLTDEGRFLFEKARRIYDwereiesQ 81
Cdd:PRK11139    8 LNALRAF-EAAARHlSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFD-------Q 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2502538194  82 LAE-----IRQGEKGKLRIAStyLPS---NYLVPKwLAEFKQHYEHVDVEIRTRNSLqsiELLLSCQVDLAI 145
Cdd:PRK11139   80 LAEatrklRARSAKGALTVSL--LPSfaiQWLVPR-LSSFNEAHPDIDVRLKAVDRL---EDFLRDDVDVAI 145
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 93-292 1.91e-20

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: 86.79  E-value: 1.91e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194  93 LRIASTYLPSNYLVPKWLAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAIVIKEAWEDDL---PIDRVHMtdVLywf 169
Cdd:cd08414     2 LRIGFVGSALYGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPPPDPPGLasrPLLREPL--VV--- 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 170 ILPAAHPLAGKE-ISIEQLVQEPFLL--REQGSSTREWLFSLCREHGVrRPRVGLQYHGLIESIQSVRAGYGTMLAPALA 246
Cdd:cd08414    77 ALPADHPLAAREsVSLADLADEPFVLfpREPGPGLYDQILALCRRAGF-TPRIVQEASDLQTLLALVAAGLGVALVPASV 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 2502538194 247 VeeMVERNEIGRVTVPGVEIKRPVYICTRAGESShrPVVERFLERV 292
Cdd:cd08414   156 A--RLQRPGVVYRPLADPPPRSELALAWRRDNAS--PALRAFLELA 197
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-62 2.68e-20

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 82.43  E-value: 2.68e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194   3 LHALRIFVEVASRQSVTAAAEALAISQPAVSAQIRKLENELGLSLLAPDGRGISLTDEGR 62
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 1-244 2.69e-20

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 88.67  E-value: 2.69e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194   1 MNLHALRIFVEVASRQSVTAAAEALAISQPAVSAQIRKLENELGLSLLAPDGRGISLTDEGRFLFEKARRIYDwerEIES 80
Cdd:PRK09906    1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILE---QAEK 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194  81 QLAEIRQGEKGKLRIASTYLPSN--YLVPKWLAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAIVIKEAWEDDlpID 158
Cdd:PRK09906   78 AKLRARKIVQEDRQLTIGFVPSAevNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPVYSDE--ID 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 159 RVHMTDVLYWFILPAAHPLAG-KEISIEQLVQEPFLLR--EQGSSTREWLFSLCREHGVrRPRVGLQYHGLIESIQSVRA 235
Cdd:PRK09906  156 YLELLDEPLVVVLPVDHPLAHeKEITAAQLDGVNFISTdpAYSGSLAPIIKAWFAQHNS-QPNIVQVATNILVTMNLVGM 234


                  ....*....
gi 2502538194 236 GYGTMLAPA 244
Cdd:PRK09906  235 GLGCTIIPG 243
PRK09986 PRK09986
LysR family transcriptional regulator;
1-244 3.33e-20

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 88.63  E-value: 3.33e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194   1 MNLHALRIFVEVASRQSVTAAAEALAISQPAVSAQIRKLENELGLSLLAPDGRGISLTDEGRFLFEKARRIYDwerEIES 80
Cdd:PRK09986    7 IDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLD---NAEQ 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194  81 QLAEIRQ---GEKGKLRIA--STYLPSNyLVPKwLAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAI--VIKEAWED 153
Cdd:PRK09986   84 SLARVEQigrGEAGRIEIGivGTALWGR-LRPA-MRHFLKENPNVEWLLRELSPSMQMAALERRELDAGIwrMADLEPNP 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 154 DLPIDRVHMTDVLywFILPAAHPLAGKE-ISIEQLVQEPFL-LREQGSSTREWLFSLCREHG--------VRRPRVGLQY 223
Cdd:PRK09986  162 GFTSRRLHESAFA--VAVPEEHPLASRSsVPLKALRNEYFItLPFVHSDWGKFLQRVCQQAGfspqiirqVNEPQTVLAM 239

                         250       260
                  ....*....|....*....|.
gi 2502538194 224 hgliesiqsVRAGYGTMLAPA 244
Cdd:PRK09986  240 ---------VSMGIGITLLPD 251
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 92-290 3.94e-20

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: 86.05  E-value: 3.94e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194  92 KLRIASTYLPSNYLVPKWLAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAIVIKEAWEDDlpIDRVHMTDVLYWFIL 171
Cdd:cd08434     1 TVRLGFLHSLGTSLVPDLIRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLALCSPVPDEPD--IEWIPLFTEELVLVV 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 172 PAAHPLAGK-EISIEQLVQEPFLLREQGSSTREWLFSLCREHGVrRPRVGLQY------HGLiesiqsVRAGYGTMLAPA 244
Cdd:cd08434    79 PKDHPLAGRdSVDLAELADEPFVLLSPGFGLRPIVDELCAAAGF-TPKIAFEGeedstiAGL------VAAGLGVAILPE 151

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 2502538194 245 LAVEEMVERNEIgRVTVPGVEikRPVYICTRAgessHR---PVVERFLE 290
Cdd:cd08434   152 MTLLNPPGVKKI-PIKDPDAE--RTIGLAWLK----DRylsPAARRFKD 193
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 105-291 7.30e-20

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: 85.34  E-value: 7.30e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 105 LVPKWLAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAIVIKEAW---EDDLPIDRVH-MTDVLYwFILPAAHPLAGK 180
Cdd:cd08423    14 LLPPALAALRARHPGLEVRLREAEPPESLDALRAGELDLAVVFDYPVtppPDDPGLTRVPlLDDPLD-LVLPADHPLAGR 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 181 E-ISIEQLVQEPFLLREQGSSTREWLFSLCREHGVrRPRVGLQYHGLIESIQSVRAGYGTMLAPALAVEemVERNEIGRV 259
Cdd:cd08423    93 EeVALADLADEPWIAGCPGSPCHRWLVRACRAAGF-TPRIAHEADDYATVLALVAAGLGVALVPRLALG--ARPPGVVVR 169

                         170       180       190
                  ....*....|....*....|....*....|..
gi 2502538194 260 TVPGVeIKRPVYICTRAGeSSHRPVVERFLER 291
Cdd:cd08423   170 PLRPP-PTRRIYAAVRAG-AARRPAVAAALEA 199
PRK12680 PRK12680
LysR family transcriptional regulator;
1-247 1.44e-17

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 81.59  E-value: 1.44e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194   1 MNLHALRIFVEVASRQ-SVTAAAEALAISQPAVSAQIRKLENELGLSLLAPDGRGI-SLTDEGRFLFEKARRIYDWEREI 78
Cdd:PRK12680    1 MTLTQLRYLVAIADAElNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLeSVTPAGVEVIERARAVLSEANNI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194  79 ESQLAEIRQGEKGKLRIASTYLPSNYLVPKWLAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAIVIKEAWEddlPID 158
Cdd:PRK12680   81 RTYAANQRRESQGQLTLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVSTAGGE---PSA 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 159 RVHMTdvLY-W---FILPAAHPL--AGKEISIEQLVQEPFLLREqgSSTREwLFSLCREHGVR--RPRVGLQY--HGLIE 228
Cdd:PRK12680  158 GIAVP--LYrWrrlVVVPRGHALdtPRRAPDMAALAEHPLISYE--SSTRP-GSSLQRAFAQLglEPSIALTAldADLIK 232

                         250
                  ....*....|....*....
gi 2502538194 229 SIqsVRAGYGTMLAPALAV 247
Cdd:PRK12680  233 TY--VRAGLGVGLLAEMAV 249
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 1-277 1.96e-17

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 80.84  E-value: 1.96e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194   1 MNLHALRIFVEVASRQSVTAAAEALAISQPAVSAQIRKLENELGLSLLAPDGRGISLTDEGRFLFEKARRIYdweREIE- 79
Cdd:PRK11151    1 MNIRDLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVL---REVKv 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194  80 -SQLAEiRQGEK--GKLRIA--STYLPsnYLVPKWLAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAIV--IKEAwe 152
Cdd:PRK11151   78 lKEMAS-QQGETmsGPLHIGliPTVGP--YLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCAILalVKES-- 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 153 ddLPIDRVHMTDVLYWFILPAAHPLAGKE-ISIEQLVQEPFLLREQGSSTREWLFSLCREHGVRRprvglQYHGLIESIQ 231
Cdd:PRK11151  153 --EAFIEVPLFDEPMLLAVYEDHPWANRDrVPMSDLAGEKLLMLEDGHCLRDQAMGFCFEAGADE-----DTHFRATSLE 225

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2502538194 232 SVR----AGYGTMLAPALAVEEmvERNEIGRVTVPGV--EIKRPVYICTRAG 277
Cdd:PRK11151  226 TLRnmvaAGSGITLLPALAVPN--ERKRDGVCYLPCIkpEPRRTIGLVYRPG 275
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 93-290 9.54e-16

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: 74.14  E-value: 9.54e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194  93 LRIASTYLPSNYLVPKWLAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAIVIKEAWEDDLPIDRVHMTD-VLywfIL 171
Cdd:cd08415     2 LRIAALPALALSLLPRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPLDHPGLESEPLASGRaVC---VL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 172 PAAHPLAGKE-ISIEQLVQEPFLLREQGSSTREWLFSLCREHGV-RRPRVGLQYHGLIESIqsVRAGYGTMLAPALAVEE 249
Cdd:cd08415    79 PPGHPLARKDvVTPADLAGEPLISLGRGDPLRQRVDAAFERAGVePRIVIETQLSHTACAL--VAAGLGVAIVDPLTAAG 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 2502538194 250 MVERNEIGRVTVPGVEIkrPVYICTRAGESSHRpVVERFLE 290
Cdd:cd08415   157 YAGAGLVVRPFRPAIPF--EFALVRPAGRPLSR-LAQAFID 194
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
3-176 1.27e-15

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 75.81  E-value: 1.27e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194   3 LHALRIFVEVASRQSVTAAAEALAISQPAVSAQIRKLENELGLSLLAPDGRGISLTDEGRFLFEKARRIYDwerEIESQL 82
Cdd:PRK10086   16 LSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLD---TLNQEI 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194  83 AEIRQGE-KGKLRIASTylPS---NYLVPKwLAEFKQHYEHVDVEIRTRNSLQSielLLSCQVDLAIvikeaWEDDLPID 158
Cdd:PRK10086   93 LDIKNQElSGTLTVYSR--PSiaqCWLVPR-LADFTRRYPSISLTILTGNENVN---FQRAGIDLAI-----YFDDAPSA 161

                         170
                  ....*....|....*...
gi 2502538194 159 RVHMTDVLYWFILPAAHP 176
Cdd:PRK10086  162 QLTHHFLMDEEILPVCSP 179
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-290 2.09e-15

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: 73.33  E-value: 2.09e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194  92 KLRIAStyLPS--NYLVPKWLAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAIVIKEAWEDDLPIDRVhMTDVLYwF 169
Cdd:cd08440     1 RVRVAA--LPSlaATLLPPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEADPDLEFEPL-LRDPFV-L 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 170 ILPAAHPLAGKE-ISIEQLVQEPFLLREQGSSTREWLFSLCREHGVrRPRVGLQYHGLIESIQSVRAGYGTMLAPALAVe 248
Cdd:cd08440    77 VCPKDHPLARRRsVTWAELAGYPLIALGRGSGVRALIDRALAAAGL-TLRPAYEVSHMSTALGMVAAGLGVAVLPALAL- 154

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 2502538194 249 EMVERNEIGRVTVPGVEIKRPVYICTRAGESShRPVVERFLE 290
Cdd:cd08440   155 PLADHPGLVARPLTEPVVTRTVGLIRRRGRSL-SPAAQAFLD 195
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 1-145 1.64e-14

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 72.37  E-value: 1.64e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194   1 MNLHALRIFVEVASRQSVTAAAEALAISQPAVSAQIRKLENELGLSLLAPDGRGISLTDEGRFLFEKARRIYDWEREIES 80
Cdd:PRK15092   11 LDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEACS 90

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2502538194  81 QLaeIRQGEKGKLRIASTYLPSNYLVPKWLAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAI 145
Cdd:PRK15092   91 SL--MYSNLQGVLTIGASDDTADTILPFLLNRVSSVYPKLALDVRVKRNAFMMEMLESQEVDLAV 153
cbl PRK12679
HTH-type transcriptional regulator Cbl;
1-202 1.94e-14

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 72.53  E-value: 1.94e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194   1 MNLHALRIFVEVASRQ-SVTAAAEALAISQPAVSAQIRKLENELGLSLLAPDG-RGISLTDEGRFLFEKARRIYDWEREI 78
Cdd:PRK12679    1 MNFQQLKIIREAARQDyNLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGkRLLGMTEPGKALLVIAERILNEASNV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194  79 EsQLAEIRQGE-KGKLRIASTYLPSNYLVPKWLAEFKQHYEHVDVEIrTRNSLQSIE-LLLSCQVDLAIVIKEAWEDDL- 155
Cdd:PRK12679   81 R-RLADLFTNDtSGVLTIATTHTQARYSLPEVIKAFRELFPEVRLEL-IQGTPQEIAtLLQNGEADIGIASERLSNDPQl 158

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2502538194 156 ---PIDRVHMTdvlywFILPAAHPLAGK-EISIEQLVQEPFLLREQGSSTR 202
Cdd:PRK12679  159 vafPWFRWHHS-----LLVPHDHPLTQItPLTLESIAKWPLITYRQGITGR 204
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
5-191 2.69e-14

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 71.76  E-value: 2.69e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194   5 ALRIFVEVASRQSVTAAAEALAISQPAVSAQIRKLENELGLSLLAPDGRGISLTDEGRFLFEKARRIYDWEREIESQLAE 84
Cdd:PRK10094    6 TLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPSELQQ 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194  85 IRQGEKGKLRIA-STYLPSNYLVPKWLAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAIVIK--EAWEDDLPIDRvh 161
Cdd:PRK10094   86 VNDGVERQVNIViNNLLYNPQAVAQLLAWLNERYPFTQFHISRQIYMGVWDSLLYEGFSLAIGVTgtEALANTFSLDP-- 163

                         170       180       190
                  ....*....|....*....|....*....|..
gi 2502538194 162 MTDVLYWFILPAAHPLAGKE--ISIEQLVQEP 191
Cdd:PRK10094  164 LGSVQWRFVMAADHPLANVEepLTEAQLRRFP 195
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 2-290 4.31e-14

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 71.18  E-value: 4.31e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194   2 NLHALRIFVEVASRQSVTAAAEALAISQPAVSAQIRKLENELGLSLLAPDGRGISLTDEGRFLFEKARRIYDWEREIESQ 81
Cdd:PRK11013    5 SLRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLFEEVQRSYYGLDRIVSA 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194  82 LAEIRQGEKGKLRIASTYLPSNYLVPKWLAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAIVikeawEDDLP---ID 158
Cdd:PRK11013   85 AESLREFRQGQLSIACLPVFSQSLLPGLCQPFLARYPDVSLNIVPQESPLLEEWLSAQRHDLGLT-----ETLHTpagTE 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 159 RVHMTDVLYWFILPAAHPLAGKE-ISIEQLVQEPFLLREQGSSTREWLFSLCREHGVRRpRVGLQYHGLIESIQSVRAGY 237
Cdd:PRK11013  160 RTELLTLDEVCVLPAGHPLAAKKvLTPDDFAGENFISLSRTDSYRQLLDQLFAEHGVKR-RMVVETHSAASVCAMVRAGV 238

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 238 GTMLAPALAVEEMVERNEIGR---VTVP-GVEIKRPVyictragessHRP---VVERFLE 290
Cdd:PRK11013  239 GVSIVNPLTALDYAGSGLVVRrfsISVPfTVSLIRPL----------HRPasaLVDAFSE 288
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 93-235 6.25e-14

The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator PAO1-like, a member of the type 2 periplasmic binding fold protein superfamily; This family includes the C-terminal substrate domain of a putative LysR-type transcriptional regulator from the plant pathogen Pseudomonas aeruginosa PAO1and its closely related homologs. The LysR-type transcriptional regulators (LTTRs) are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of N2 fixing bacteria, and synthesis of virulence factors, to a name a few. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 176104 [Multi-domain]  Cd Length: 198  Bit Score: 69.11  E-value: 6.25e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194  93 LRIASTYLPSNYLVPKWLAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAIVIKEAWEDDlpIDRVHMTDVLYWFILP 172
Cdd:cd08412     2 LRIGCFSTLAPYYLPGLLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALTYDLDLPED--IAFEPLARLPPYVWLP 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2502538194 173 AAHPLAGKE-ISIEQLVQEPFLLREQGSStREWLFSLCREHGVrRPRVGLQYHglieSIQSVRA 235
Cdd:cd08412    80 ADHPLAGKDeVSLADLAAEPLILLDLPHS-REYFLSLFAAAGL-TPRIAYRTS----SFEAVRS 137
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
27-262 1.03e-13

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 69.85  E-value: 1.03e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194  27 ISQPAVSAQIRKLENELGLSLLAPDGRGISLTDEGRFLFEKARRIY-DWEReIESQLAEIRQGEKGKLRIASTYLPSNYL 105
Cdd:PRK11716    3 VSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLlQWQQ-LRHTLDQQGPSLSGELSLFCSVTAAYSH 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 106 VPKWLAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAIVIK-EAWEDDL---PIDRVHMTdvlywFILP-----AAHP 176
Cdd:PRK11716   82 LPPILDRFRAEHPLVEIKLTTGDAADAVEKVQSGEADLAIAAKpETLPASVafsPIDEIPLV-----LIAPalpcpVRQQ 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 177 LAGKEISIEQLvqePFLLREQGSSTR---EWLfslcREHGVrRPRVGLQYHGLiESIQS-VRAGYGTMLAPALAVEEMVE 252
Cdd:PRK11716  157 LSQEKPDWSRI---PFILPEHGPARRridLWF----RRHKI-KPNIYATVSGH-EAIVSmVALGCGVGLLPEVVLENSPV 227

                         250
                  ....*....|
gi 2502538194 253 RNEIGRVTVP 262
Cdd:PRK11716  228 RNRVQILERV 237
PRK09791 PRK09791
LysR family transcriptional regulator;
3-124 2.63e-13

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 69.02  E-value: 2.63e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194   3 LHALRIFVEVASRQSVTAAAEALAISQPAVSAQIRKLENELGLSLLAPDGRGISLTDEGRFLFEKARRIYDWEREIESQL 82
Cdd:PRK09791    7 IHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQEDI 86

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 2502538194  83 AEiRQGE-KGKLRIASTYLPSNYLVPKWLAEFKQHYEHVDVEI 124
Cdd:PRK09791   87 RQ-RQGQlAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRI 128
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-292 3.01e-13

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: 67.33  E-value: 3.01e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194  92 KLRIASTYLPSNYLVPKWLAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAIVIKEAWEDDlpIDRVHMTDVLYWFIL 171
Cdd:cd08426     1 RVRVATGEGLAAELLPSLIARFRQRYPGVFFTVDVASTADVLEAVLSGEADIGLAFSPPPEPG--IRVHSRQPAPIGAVV 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 172 PAAHPLAG-KEISIEQLVQEPFLLREQGSSTREWLFSLCRehgvrrpRVGLQYHGLIES------IQSVRAGYGTMLAPA 244
Cdd:cd08426    79 PPGHPLARqPSVTLAQLAGYPLALPPPSFSLRQILDAAFA-------RAGVQLEPVLISnsietlKQLVAAGGGISLLTE 151

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2502538194 245 LAVEEMVERNEIgrVTVPGVE---IKRPVYICTRAGESShRPVVERFLERV 292
Cdd:cd08426   152 LAVRREIRRGQL--VAVPLADphmNHRQLELQTRAGRQL-PAAASAFLQLL 199
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 1-283 7.22e-13

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 67.79  E-value: 7.22e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194   1 MNLHALRIFVEVASRQSVTAAAEALAISQPAVSAQIRKLENELGLSLLAPDGRGISLTDEGRFLFEKARRIYdweREIE- 79
Cdd:PRK11233    1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAIL---RQCEq 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194  80 SQLAEIRQGE--KGKLRI--ASTYLPSNYLVPKWLAEFKQH-----YEHvdveirtRNSLQSI-ELLLSCQVDLAIVIke 149
Cdd:PRK11233   78 AQLAVHNVGQalSGQVSIglAPGTAASSLTMPLLQAVRAEFpgivlYLH-------ENSGATLnEKLMNGQLDMAVIY-- 148

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 150 aweDDLPIDRVH----MTDVLYwfiLPAAHPLAGKEISIEQLVQEPFLLREQGSSTREWL---FSLCRehgvRRPRVglq 222
Cdd:PRK11233  149 ---EHSPVAGLSsqplLKEDLF---LVGTQDCPGQSVDLAAVAQMNLFLPRDYSAVRLRVdeaFSLRR----LTAKV--- 215

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2502538194 223 yHGLIESIQSVRA----GYGTMLAPALAVEEMVERNE--IGRVTVPGVEIkrPVYICTrageSSHRP 283
Cdd:PRK11233  216 -IGEIESIATLTAaiasGMGVTVLPESAARSLCGAVNgwMARITTPSMSL--SLSLNL----SARLP 275
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 92-250 8.16e-13

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: 66.04  E-value: 8.16e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194  92 KLRIASTYLPSNYLVPKWLAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAIVIKEAWEDDL---PIDRvhmtDVLyW 168
Cdd:cd08438     1 HLRLGLPPLGGSLLFAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVLPVDEEEFdsqPLCN----EPL-V 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 169 FILPAAHPLAGKE-ISIEQLVQEPFLLREQGSSTREWLFSLCREHGVrRPRVGL---QYHGLIEsiqSVRAGYGTMLAPA 244
Cdd:cd08438    76 AVLPRGHPLAGRKtVSLADLADEPFILFNEDFALHDRIIDACQQAGF-TPNIAArssQWDFIAE---LVAAGLGVALLPR 151


                  ....*.
gi 2502538194 245 LAVEEM 250
Cdd:cd08438   152 SIAQRL 157
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 92-290 1.26e-11

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: 62.68  E-value: 1.26e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194  92 KLRIASTYLPSNYLVPKWLAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAI--VIKEAWEDDLPIDRVhMTDVLYwF 169
Cdd:cd08435     1 TVRVGAVPAAAPVLLPPAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAIgrLADDEQPPDLASEEL-ADEPLV-V 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 170 ILPAAHPLA-GKEISIEQLVQEPFLLREQGSSTREWLFSLCREHGVRRPRVglqyhgLIE--SIQSVRAgygtMLA---- 242
Cdd:cd08435    79 VARPGHPLArRARLTLADLADYPWVLPPPGTPLRQRLEQLFAAAGLPLPRN------VVEtaSISALLA----LLArsdm 148

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2502538194 243 ----PALAVEEMVERNEIGRVTVPGVEIKRPVYICTRAGEsSHRPVVERFLE 290
Cdd:cd08435   149 lavlPRSVAEDELRAGVLRELPLPLPTSRRPIGITTRRGG-PLSPAARALLD 199
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
17-290 2.23e-11

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 63.50  E-value: 2.23e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194  17 SVTAAAEALAISQPAVSAQIRKLENELGLSLLAPDGRGISLTDEGRFLFEKARRIYDwerEIESQLAEIRQGEKGKLRIA 96
Cdd:PRK15421   18 SLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLP---QISQALQACNEPQQTRLRIA 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194  97 -STYLPSNYLVPKwLAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAIVikeawEDDLPIDRVH---MTDVLYWFILP 172
Cdd:PRK15421   95 iECHSCIQWLTPA-LENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMT-----SDILPRSGLHyspMFDYEVRLVLA 168

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 173 AAHPLAGK-EISIEQLVQEPFLLreqgsstrewlfslcreHGVRRPRVGLQYHGLIES---------------IQSVRAG 236
Cdd:PRK15421  169 PDHPLAAKtRITPEDLASETLLI-----------------YPVQRSRLDVWRHFLQPAgvspslksvdntlllIQMVAAR 231

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2502538194 237 YGTMLAPALAVEEmVERNEIGRVTVPGVEIKRPVYICTRAGEsSHRPVVERFLE 290
Cdd:PRK15421  232 MGIAALPHWVVES-FERQGLVVTKTLGEGLWSRLYAAVRDGE-QRQPVTEAFIR 283
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 106-292 7.87e-11

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


Pssm-ID: 176127 [Multi-domain]  Cd Length: 194  Bit Score: 60.31  E-value: 7.87e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 106 VPKWLAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAIVikeAWEDDLP-------IDRVHMTdvlywFILPAAHPLA 178
Cdd:cd08436    15 LPELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAFV---GLPERRPpglasreLAREPLV-----AVVAPDHPLA 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 179 G-KEISIEQLVQEPFLLREQGSSTREWLFSLCREHGVRRpRVGLQYhGLIESIQS-VRAGYGTMLAPALAVEEMverNEI 256
Cdd:cd08436    87 GrRRVALADLADEPFVDFPPGTGARRQVDRAFAAAGVRR-RVAFEV-SDVDLLLDlVARGLGVALLPASVAARL---PGL 161

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 2502538194 257 GRVTVPGvEIKRPVYICTRAGESShrPVVERFLERV 292
Cdd:cd08436   162 AALPLEP-APRRRLYLAWSAPPPS--PAARAFLELL 194
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 91-292 1.06e-10

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: 59.85  E-value: 1.06e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194  91 GKLRIASTYLPSNYLVPKWLAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAIVIKEAWEDDLpidrvhMTDVLY--- 167
Cdd:cd08411     1 GPLRLGVIPTIAPYLLPRLLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAALLALPVDEPGL------EEEPLFdep 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 168 -WFILPAAHPLAGKE-ISIEQLVQEPFLLREQGSSTREWLFSLCREHGVRRPRvglQYHGL-IESI-QSVRAGYGTMLAP 243
Cdd:cd08411    75 fLLAVPKDHPLAKRKsVTPEDLAGERLLLLEEGHCLRDQALELCRLAGAREQT---DFEATsLETLrQMVAAGLGITLLP 151

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2502538194 244 ALAVeeMVERNEIGRVTV---PGVEIKRPVYICTRAGeSSHRPVVERFLERV 292
Cdd:cd08411   152 ELAV--PSEELRGDRLVVrpfAEPAPSRTIGLVWRRS-SPRAAAFEALAELI 200
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
3-98 2.59e-10

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 60.16  E-value: 2.59e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194   3 LHALRIFVEVASRQSVTAAAEALAISQPAVSAQIRKLENELGLSLLAPDGRGISLTDEGRFLFEKARRIYDWEREIESQL 82
Cdd:PRK10632    4 LKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQL 83

                          90
                  ....*....|....*.
gi 2502538194  83 AEIRQGEKGKLRIAST 98
Cdd:PRK10632   84 YAFNNTPIGTLRIGCS 99
PBP2_LTTR_like_1 cd08421
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 102-279 4.24e-10

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


Pssm-ID: 176113  Cd Length: 198  Bit Score: 58.30  E-value: 4.24e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 102 SNYLvPKWLAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAIVIKEAWEDDLPIdRVHMTDVLYwFILPAAHPLAG-K 180
Cdd:cd08421    12 VEFL-PEDLASFLAAHPDVRIDLEERLSADIVRAVAEGRADLGIVAGNVDAAGLET-RPYRTDRLV-VVVPRDHPLAGrA 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 181 EISIEQLVQEPFLLREQGSStrewLFSLCREHGV---RRPRVGLQYHGlIESI-QSVRAGYGTMLAPALAVEEMveRNEI 256
Cdd:cd08421    89 SVAFADTLDHDFVGLPAGSA----LHTFLREAAArlgRRLRLRVQVSS-FDAVcRMVAAGLGIGIVPESAARRY--ARAL 161

                         170       180
                  ....*....|....*....|....*
gi 2502538194 257 GRVTVPGVEI--KRPVYICTRAGES 279
Cdd:cd08421   162 GLRVVPLDDAwaRRRLLLCVRSFDA 186
PBP2_LysR cd08456
The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine ...
 93-290 5.02e-10

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


Pssm-ID: 176145 [Multi-domain]  Cd Length: 196  Bit Score: 57.81  E-value: 5.02e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194  93 LRIASTYLPSNYLVPKWLAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAIVIKEAWEDDLPIDRVHMTDVLywFILP 172
Cdd:cd08456     2 LRIAVLPALSQSFLPRAIKAFLQRHPDVTISIHTRDSPTVEQWLSAQQCDLGLVSTLHEPPGIERERLLRIDGV--CVLP 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 173 AAHPLAGKE-ISIEQLVQEPFLLREQGSSTREWLFSLCREHGVRRpRVGLQYHGLIESIQSVRAGYGTMLAPALAVEEMV 251
Cdd:cd08456    80 PGHRLAVKKvLTPSDLEGEPFISLARTDGTRQRVDALFEQAGVKR-RIVVETSYAATICALVAAGVGVSVVNPLTALDYA 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 2502538194 252 ERNEIGRVTVPgvEIKRPVYICTrageSSHRP---VVERFLE 290
Cdd:cd08456   159 AAGLVVRRFSP--AVPFEVSLIR----PKHRPssaLVAAFSA 194
PBP2_CynR cd08425
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, ...
 91-248 5.37e-10

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


Pssm-ID: 176116  Cd Length: 197  Bit Score: 57.72  E-value: 5.37e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194  91 GKLRIASTYLPSNYLVPKWLAEFKQHYEHVDVEIRtRNSLQSIE-LLLSCQVDLAIVIKEAWEDDlpIDRVHMTDVLYWF 169
Cdd:cd08425     1 GSLRLAMTPTFTAYLIGPLIDRFHARYPGIALSLR-EMPQERIEaALADDRLDLGIAFAPVRSPD--IDAQPLFDERLAL 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 170 ILPAAHPLAGKE--ISIEQLVQEPFLLREQGSSTREWLFSLCREHGVrRPRVGLQYHGLIESIQSVRAG-YGTMLAPALA 246
Cdd:cd08425    78 VVGATHPLAQRRtaLTLDDLAAEPLALLSPDFATRQHIDRYFQKQGI-KPRIAIEANSISAVLEVVRRGrLATILPDAIA 156


                  ..
gi 2502538194 247 VE 248
Cdd:cd08425   157 RE 158
PBP2_BudR cd08451
The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is ...
 105-292 6.69e-10

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: 57.57  E-value: 6.69e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 105 LVPKWLAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAIVikeawedDLPIDR---VHMTDVL---YWFILPAAHPLA 178
Cdd:cd08451    15 LVPGLIRRFREAYPDVELTLEEANTAELLEALREGRLDAAFV-------RPPVARsdgLVLELLLeepMLVALPAGHPLA 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 179 GKE-ISIEQLVQEPFLL--REQGSSTREWLFSLCREHGVrRPRVGLQYHGLIESIQSVRAGYGTMLAPAlaveemvernE 255
Cdd:cd08451    88 RERsIPLAALADEPFILfpRPVGPGLYDAIIAACRRAGF-TPRIGQEAPQMASAINLVAAGLGVSIVPA----------S 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 2502538194 256 IGRVTVPGVEIKR--------PVYICTRAGESShrPVVERFLERV 292
Cdd:cd08451   157 MRQLQAPGVVYRPlagapltaPLALAYRRGERS--PAVRNFIALV 199
PBP2_CysB_like cd08413
The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains ...
 92-191 9.58e-10

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


Pssm-ID: 176105 [Multi-domain]  Cd Length: 198  Bit Score: 57.25  E-value: 9.58e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194  92 KLRIASTYLPSNYLVPKWLAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAIViKEAWEDDlpiDRVHMTDVLYW--- 168
Cdd:cd08413     1 QLTIATTHTQARYVLPPVIAAFRKRYPKVKLSLHQGTPSQIAEMVLKGEADIAIA-TEALDDH---PDLVTLPCYRWnhc 76

                          90       100
                  ....*....|....*....|....
gi 2502538194 169 FILPAAHPLAGK-EISIEQLVQEP 191
Cdd:cd08413    77 VIVPPGHPLADLgPLTLEDLAQYP 100
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 12-201 2.77e-09

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 56.87  E-value: 2.77e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194  12 VASRQSVTAAAEALAISQPAVSAQIRKLENELGLSLLAPDGRGISLTDEGRFLFEKARRIYDWEREIESQLAEIRQGEKG 91
Cdd:PRK11074   13 VARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRRQCQQVANGWRG 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194  92 KLRIASTYLPSNYLVPKWLAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAIVIKEAweddLPI-DRVHMTD--VLYW 168
Cdd:PRK11074   93 QLSIAVDNIVRPDRTRQLIVDFYRHFDDVELIIRQEVFNGVWDALADGRVDIAIGATRA----IPVgGRFAFRDmgMLSW 168

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 2502538194 169 -FILPAAHPLAGKE--ISIEQLVQEPFLLREQGSST 201
Cdd:PRK11074  169 aCVVSSDHPLASMDgpLSDDELRPYPSLCLEDTSRT 204
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
1-145 3.09e-09

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 56.56  E-value: 3.09e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194   1 MNLHALRIFVEVASRQSVTAAAEALAISQPAVSAQIRKLENELGLSLLAPDGRGISLTDEGRFLFEKARRIYD-Wereie 79
Cdd:PRK03601    1 MDTELLKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYAETLMNtW----- 75

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2502538194  80 sQLAE---IRQGEKGKLRI-ASTYLPSNYLVPkWLAEFKQHYEHVDVEIR--TRNSLqsIELLLSCQVDLAI 145
Cdd:PRK03601   76 -QAAKkevAHTSQHNELSIgASASLWECMLTP-WLGRLYQNQEALQFEARiaQRQSL--VKQLHERQLDLLI 143
PRK09801 PRK09801
LysR family transcriptional regulator;
6-153 3.20e-09

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 56.97  E-value: 3.20e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194   6 LRIFVEVASRQSVTAAAEALAISQPAVSAQIRKLENELGLSLLAPDGRGISLTDEGRFLFEKARRIYDWEREIESQLAEI 85
Cdd:PRK09801   11 LQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVTQI 90

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2502538194  86 RQGEKGKLRIASTY-LPSNYLVP------KWLAEFKQHYEHVDVEIRtrnslqsielLLSCQVDLAIVIKEAWED 153
Cdd:PRK09801   91 KTRPEGMIRIGCSFgFGRSHIAPaitelmRNYPELQVHFELFDRQID----------LVQDNIDLDIRINDEIPD 155
PBP2_CysB cd08443
The C-terminal substrate domain of LysR-type transcriptional regulator CysB contains type 2 ...
 92-288 1.23e-08

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


Pssm-ID: 176134  Cd Length: 198  Bit Score: 54.11  E-value: 1.23e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194  92 KLRIASTYLPSNYLVPKWLAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAIViKEAWEDDlpiDRVHMTDVLYW--- 168
Cdd:cd08443     1 SLYVATTHTQARYVLPPVIKGFIERYPRVSLQMHQGSPTQIAEMVSKGLVDFAIA-TEALHDY---DDLITLPCYHWnrc 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 169 FILPAAHPLAGKE-ISIEQLVQEPFLLREQGSSTREWLFSLCREHGVrRPRVGLQYHGlIESIQS-VRAGYGTMLAPALA 246
Cdd:cd08443    77 VVVKRDHPLADKQsISIEELATYPIVTYTFGFTGRSELDTAFNRAGL-TPNIVLTATD-ADVIKTyVRLGLGVGVIASMA 154

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 2502538194 247 VE-----EMVERN--EIGRVTVPGVEIKRPVYIctragESSHRPVVERF 288
Cdd:cd08443   155 YDpvddpDLVIRDarDLFPWSVTKIAFRRGTFL-----RSYMYDFIQRF 198
PRK10341 PRK10341
transcriptional regulator TdcA;
6-86 2.88e-08

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 54.10  E-value: 2.88e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194   6 LRIFVEVASRQSVTAAAEALAISQPAVSAQIRKLENELGLSLLAPDGRGISLTDEGRFLFEKARRIydwEREIESQLAEI 85
Cdd:PRK10341   12 LVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESI---TREMKNMVNEI 88


                  .
gi 2502538194  86 R 86
Cdd:PRK10341   89 N 89
PBP2_LTTR_aromatics_like_1 cd08447
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 105-266 4.79e-08

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: 52.26  E-value: 4.79e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 105 LVPKWLAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAIVIKEAWEDDLPIDRVHMTDVLywFILPAAHPLAGKE-IS 183
Cdd:cd08447    14 FLPRLLAAARAALPDVDLVLREMVTTDQIEALESGRIDLGLLRPPFARPGLETRPLVREPLV--AAVPAGHPLAGAErLT 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 184 IEQLVQEPFLlreQGSSTR-----EWLFSLCREHGVrRPRVgLQYHGLIESIQS-VRAGYGTMLAPALAVE---EMVERN 254
Cdd:cd08447    92 LEDLDGQPFI---MYSPTEaryfhDLVVRLFASAGV-QPRY-VQYLSQIHTMLAlVRAGLGVALVPASASRlrfEGVVFR 166

                         170
                  ....*....|..
gi 2502538194 255 EIGRVTVPGVEI 266
Cdd:cd08447   167 PLDLPRDVPVEL 178
PBP2_IlvY cd08430
The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates ...
 107-262 5.03e-08

The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates the expression of ilvC gene that encoding acetohydroxy acid isomeroreductase for the biosynthesis of branched amino acids; contains the type 2 periplasmic bindin; In Escherichia coli, IlvY is required for the regulation of ilvC gene expression that encodes acetohydroxy acid isomeroreductase (AHIR), a key enzyme in the biosynthesis of branched-chain amino acids (isoleucine, valine, and leucine). The ilvGMEDA operon genes encode remaining enzyme activities required for the biosynthesis of these amino acids. Activation of ilvC transcription by IlvY requires the additional binding of a co-inducer molecule (either alpha-acetolactate or alpha-acetohydoxybutyrate, the substrates for AHIR) to a preformed complex of IlvY protein-DNA. Like many other LysR-family members, IlvY negatively auto-regulates the transcription of its own divergently transcribed ilvY gene in an inducer-independent manner. 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: 176121  Cd Length: 199  Bit Score: 52.20  E-value: 5.03e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 107 PKWLAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAIVIKeawEDDLP--IDRVHMTDVLYWFILPAAHPLAGKEISI 184
Cdd:cd08430    16 PPILERFRAQHPQVEIKLHTGDPADAIDKVLNGEADIAIAAR---PDKLParLAFLPLATSPLVFIAPNIACAVTQQLSQ 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 185 EQLVQE--PFLLREQGSStREWLFSLCREHGVrRPRVGLQYHGLiESIQS-VRAGYGTMLAPALAVEEMVERNEIGRVTV 261
Cdd:cd08430    93 GEIDWSrlPFILPERGLA-RERLDQWFRRRGI-KPNIYAQVAGH-EAIVSmVALGCGVGIVPELVLDNSPLKDKVRILEV 169


                  .
gi 2502538194 262 P 262
Cdd:cd08430   170 Q 170
PBP2_BenM_CatM_CatR cd08445
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 105-280 1.52e-07

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


Pssm-ID: 176136  Cd Length: 203  Bit Score: 50.69  E-value: 1.52e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 105 LVPKWLAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLA---IVIkeaweDDLPIDRVHMTDVLYWFILPAAHPLA--G 179
Cdd:cd08445    15 LLPELIRRFRQAAPDVEIELIEMTTVQQIEALKEGRIDVGfgrLRI-----EDPAIRRIVLREEPLVVALPAGHPLAqeK 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 180 KEISIEQLVQEPFLL--REQGSSTREWLFSLCREHGVrRPRVGLQYHGLIESIQSVRAGYGTMLAPALAveEMVERNEIG 257
Cdd:cd08445    90 APLTLAQLADEPLILypASPRPSFADQVLSLFRDHGL-RPRVIQEVRELQTALGLVAAGEGVTLVPASV--QRLRRDDVV 166

                         170       180
                  ....*....|....*....|...
gi 2502538194 258 RVTVPGVEIKRPVYICTRAGESS 280
Cdd:cd08445   167 YRPLLDPDATSPIIMSVRAGDES 189
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
9-162 2.94e-07

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 50.82  E-value: 2.94e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194   9 FVEVASRQSVTAAAEALAISQPAVSAQIRKLENELGLSLLAPDGRGISLTDEGRFLFEKARRIYdweREIESQLAEIRQG 88
Cdd:PRK10082   19 FLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLL---QQLESNLAELRGG 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194  89 E---KGKLRIASTYLPSNYLVPKWLAE----FKQHYEHVDVEirtrnslQSIELLLSCQVDLAIVIKEAWEDDLPIDRVH 161
Cdd:PRK10082   96 SdyaQRKIKIAAAHSLSLGLLPSIISQmpplFTWAIEAIDVD-------EAVDKLREGQSDCIFSFHDEDLLEAPFDHIR 168


                  .
gi 2502538194 162 M 162
Cdd:PRK10082  169 L 169
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 94-216 9.25e-07

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


Pssm-ID: 176109 [Multi-domain]  Cd Length: 200  Bit Score: 48.36  E-value: 9.25e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194  94 RIASTYLPSNYLVPKWLAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAIvikeAWEDDLPiDRVHMTDVL---YWFI 170
Cdd:cd08417     3 RIAASDYLEALLLPPLLARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAI----GVFPELP-PGLRSQPLFedrFVCV 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 2502538194 171 LPAAHPLAGKEISIEQLVQEPFLLREQGSSTREWLFSLCREHGVRR 216
Cdd:cd08417    78 ARKDHPLAGGPLTLEDYLAAPHVLVSPRGRGHGLVDDALAELGLSR 123
PBP2_XapR cd08449
The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved ...
 110-290 1.10e-06

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


Pssm-ID: 176140 [Multi-domain]  Cd Length: 197  Bit Score: 48.42  E-value: 1.10e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 110 LAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAIViKEAWEDDLPidrvHMTDVLYW-----FILPAAHPLAGKE-IS 183
Cdd:cd08449    19 LRRFKRQYPNVTVRFHELSPEAQKAALLSKRIDLGFV-RFADTLNDP----PLASELLWrepmvVALPEEHPLAGRKsLT 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 184 IEQLVQEPF-LLREQGSSTREWLFSLCREHGVrRPRVGLQyhgLIESiQS----VRAGYGTMLAPAlaveemvernEIGR 258
Cdd:cd08449    94 LADLRDEPFvFLRLANSRFADFLINCCLQAGF-TPQITQE---VVEP-QTlmalVAAGFGVALVPE----------SYAR 158

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 2502538194 259 VTVPGV-------EIKRPVYICTRAGESShrPVVERFLE 290
Cdd:cd08449   159 LPWPGVrfiplkqAISADLYAVYHPDSAT--PVIQAFLA 195
PBP2_LTTR_aromatics_like_2 cd08448
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 106-292 1.13e-06

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


Pssm-ID: 176139 [Multi-domain]  Cd Length: 197  Bit Score: 48.42  E-value: 1.13e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 106 VPKWLAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAIVIKEAWEDDL---PIDRVHMTDVLywfilPAAHPLAGKE- 181
Cdd:cd08448    15 LPRILRAFRAEYPGIEVALHEMSSAEQIEALLRGELDLGFVHSRRLPAGLsarLLHREPFVCCL-----PAGHPLAARRr 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 182 ISIEQLVQEPFLL--REQGSSTREWLFSLCREHGVrRPRVGLQYHGLIESIQSVRAGYGTMLAP-ALAVeemVERNEIGR 258
Cdd:cd08448    90 IDLRELAGEPFVLfsREVSPDYYDQIIALCMDAGF-HPKIRHEVRHWLTVVALVAAGMGVALVPrSLAR---AGLAGVRF 165

                         170       180       190
                  ....*....|....*....|....*....|....
gi 2502538194 259 VTVPGVEIKRPVYICTRAGESShrPVVERFLERV 292
Cdd:cd08448   166 LPLKGATQRSELYAAWKASAPN--PALQAFLAAL 197
nhaR PRK11062
transcriptional activator NhaR; Provisional
 1-77 1.33e-06

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 48.85  E-value: 1.33e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2502538194   1 MNLHALRIFVEVASRQSVTAAAEALAISQPAVSAQIRKLENELGLSLLAPDGRGISLTDEGRFLFEKARRIYDWERE 77
Cdd:PRK11062    4 INYNHLYYFWMVCKEGSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGELVFRYADKMFTLSQE 80
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
6-84 1.66e-06

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 48.81  E-value: 1.66e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2502538194   6 LRIFVEVASRQSVTAAAEALAISQPAVSAQIRKLENELGLSLLApDGRGISLTDEGRFLFEKARRIYDWEREIESQLAE 84
Cdd:PRK13348    7 LEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLV-RGRPCRPTPAGQRLLRHLRQVALLEADLLSTLPA 84
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
5-96 2.63e-06

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 47.85  E-value: 2.63e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194   5 ALRIFVEVASRQSVTAAAEALAISQPAVSAQIRKLENELGLSLLApDGRGISLTDEGRFLFEKARRIYDWEREIESQLAE 84
Cdd:PRK03635    6 QLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLV-RTQPCRPTEAGQRLLRHARQVRLLEAELLGELPA 84

                          90
                  ....*....|..
gi 2502538194  85 iRQGEKGKLRIA 96
Cdd:PRK03635   85 -LDGTPLTLSIA 95
PBP2_AlsR cd08452
The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which ...
 105-289 3.92e-06

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


Pssm-ID: 176143 [Multi-domain]  Cd Length: 197  Bit Score: 46.73  E-value: 3.92e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 105 LVPKWLAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAIVIKEAWEDDLPIDRVHMTDVLywFILPAAHPLAGK-EIS 183
Cdd:cd08452    14 FLPPIVREYRKKFPSVKVELRELSSPDQVEELLKGRIDIGFLHPPIQHTALHIETVQSSPCV--LALPKQHPLASKeEIT 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 184 IEQLVQEPF--LLREQGSSTREWLFSLCREHGVrRPRVGLQYHGLIESIQSVRAGYGTMLAPALAveEMVERNEIGRVTV 261
Cdd:cd08452    92 IEDLRDEPIitVAREAWPTLYDEIIQLCEQAGF-RPKIVQEATEYQTVIGLVSAGIGVTFVPSSA--KKLFNLEVAYRKI 168

                         170       180
                  ....*....|....*....|....*...
gi 2502538194 262 PGVEIKRPVYICTRagESSHRPVVERFL 289
Cdd:cd08452   169 DQINLNAEWSIAYR--KDNHNPLLKHFI 194
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 93-284 5.01e-06

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: 46.42  E-value: 5.01e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194  93 LRIASTylPS---NYLVPKwLAEFKQHYEHVDVEIRTRNSLQSielLLSCQVDLAIVI-KEAWEDdlpIDRVHMTDVLyw 168
Cdd:cd08432     2 LTVSVT--PSfaaRWLIPR-LARFQARHPDIDLRLSTSDRLVD---FAREGIDLAIRYgDGDWPG---LEAERLMDEE-- 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 169 fILPAAHP--LAG-KEISIEQLVQEPfLLREqgSSTREWLFSLCREHGVR--RPRVGLQYHGLIESIQSVRAGYGTMLAP 243
Cdd:cd08432    71 -LVPVCSPalLAGlPLLSPADLARHT-LLHD--ATRPEAWQWWLWAAGVAdvDARRGPRFDDSSLALQAAVAGLGVALAP 146

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 2502538194 244 ALAVEEMVERneiGRVTVP-GVEIKRP--VYICTRAGESSHRPV 284
Cdd:cd08432   147 RALVADDLAA---GRLVRPfDLPLPSGgaYYLVYPPGRAESPAV 187
PBP2_YofA_SoxR_like cd08442
The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, ...
 107-290 1.03e-05

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: 45.29  E-value: 1.03e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 107 PKWLAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAIVIK----------EAWEDDLpidrvhmtdVLywfILPAAHP 176
Cdd:cd08442    16 PPLLAAYHARYPKVDLSLSTGTTGALIQAVLEGRLDGAFVAGpvehprleqePVFQEEL---------VL---VSPKGHP 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 177 lagKEISIEQLVQEPFLLREQGSSTREWLFSLCREHGVRRPRV---GlQYHGLiesIQSVRAGYGTMLAPALAVEEMVER 253
Cdd:cd08442    84 ---PVSRAEDLAGSTLLAFRAGCSYRRRLEDWLAEEGVSPGKImefG-SYHAI---LGCVAAGMGIALLPRSVLDSLQGR 156

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 2502538194 254 NEIGRVTVPGVEIKRPVYICTRAGESShrPVVERFLE 290
Cdd:cd08442   157 GSVSIHPLPEPFADVTTWLVWRKDSFT--AALQAFLD 191
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 110-286 1.08e-05

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: 45.28  E-value: 1.08e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 110 LAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAIVIkeaweDDLPIDRVHMTDVL---YWFILPAAHPLA-GKEISIE 185
Cdd:cd08433    19 LRAVRRRYPGIRLRIVEGLSGHLLEWLLNGRLDLALLY-----GPPPIPGLSTEPLLeedLFLVGPADAPLPrGAPVPLA 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 186 QLVQEPFLLREQGSSTREWLfslcrEHGVRRPRVGLQYHGLIESIQS----VRAGYGTMLAPALAVEEMVERNE--IGRV 259
Cdd:cd08433    94 ELARLPLILPSRGHGLRRLV-----DEAAARAGLTLNVVVEIDSVATlkalVAAGLGYTILPASAVAAEVAAGRlvAAPI 168

                         170       180
                  ....*....|....*....|....*..
gi 2502538194 260 TVPGVEikRPVYICTrageSSHRPVVE 286
Cdd:cd08433   169 VDPALT--RTLSLAT----PRDRPLSP 189
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 1-290 2.68e-05

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 44.98  E-value: 2.68e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194   1 MNLHALRIFVEVASRQSVTAAAEALAISQPAVSAQIRKLENELGLSLLAPDGRGISLTDEGRFLFEKARRIYDWEREIES 80
Cdd:PRK14997    2 TDLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQD 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194  81 QLAEIRQGEKGKLRIASTYLPSNYLVPKWLAEFKQHYEHVDVEIRTRNSLQSIellLSCQVDLAIVIK-EAWEDDLPIDR 159
Cdd:PRK14997   82 AIAALQVEPRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLEATNRRVDV---VGEGVDVAIRVRpRPFEDSDLVMR 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 160 VHMTDVLYWFILPAAHPLAGKEISIEQLVQEPFLLREQGSSTREWlfSLCREHGVR-----RPRvgLQYHGLIESIQSVR 234
Cdd:PRK14997  159 VLADRGHRLFASPDLIARMGIPSAPAELSHWPGLSLASGKHIHRW--ELYGPQGARaevhfTPR--MITTDMLALREAAM 234

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2502538194 235 AGYGTMLAPALAVEEMVERNEIGRVT---VPGVEIKRPVYICTRAGESSHRPVVERFLE 290
Cdd:PRK14997  235 AGVGLVQLPVLMVKEQLAAGELVAVLeewEPRREVIHAVFPSRRGLLPSVRALVDFLTE 293
MntR COG1321
Mn-dependent transcriptional regulator MntR, DtxR family [Transcription];
17-85 5.76e-05

Mn-dependent transcriptional regulator MntR, DtxR family [Transcription];


Pssm-ID: 440932 [Multi-domain]  Cd Length: 135  Bit Score: 42.11  E-value: 5.76e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2502538194  17 SVTAAAEALAISQPAVSAQIRKLEnELGLSLLAPDGrGISLTDEGRflfEKARRIYDWEREIESQLAEI 85
Cdd:COG1321    26 RTSDIAERLGVSPPSVTEMLKKLE-EKGLVEYEPYG-GITLTEEGR---ELALRIVRRHRLLERFLVEV 89
PBP2_DntR_like_3 cd08461
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-221 6.96e-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: 43.04  E-value: 6.96e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194  93 LRIASTYLPSNYLVPKWLAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAIVIKEAWEDDLPidRVHMTDVLYWFILP 172
Cdd:cd08461     2 LVIAATDYAQKAILPPLLAALRQEAPGVRVAIRDLESDNLEAQLERGEVDLALTTPEYAPDGLR--SRPLFEERYVCVTR 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2502538194 173 AAHPLAGKEISIEQLVQEPFLLREQG-----SSTREWLFSLcrehGVRRpRVGL 221
Cdd:cd08461    80 RGHPLLQGPLSLDQFCALDHIVVSPSgggfaGSTDEALAAL----GLTR-NVVL 128
PBP2_HcaR cd08450
The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in ...
 105-193 1.24e-04

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: 42.36  E-value: 1.24e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 105 LVPKWLAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAIVIKEAWEDDlpIDRVHMTDVLYWFILPAAHPLAG-KEIS 183
Cdd:cd08450    14 WLPEVLPILREEHPDLDVELSSLFSPQLAEALMRGKLDVAFMRPEIQSDG--IDYQLLLKEPLIVVLPADHRLAGrEKIP 91

                          90
                  ....*....|
gi 2502538194 184 IEQLVQEPFL 193
Cdd:cd08450    92 PQDLAGENFI 101
leuO PRK09508
leucine transcriptional activator; Reviewed
 3-272 1.72e-04

leucine transcriptional activator; Reviewed


Pssm-ID: 181918 [Multi-domain]  Cd Length: 314  Bit Score: 42.70  E-value: 1.72e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194   3 LHALRIFVEVASRQSVTAAAEALAISQPAVSAQIRKLENELGLSLLAPDGRGISLTDEGRFLFEKARRIYDWER-EIESQ 81
Cdd:PRK09508   24 LNLLTVFDAVMQEQNITRAAHNLGMSQPAVSNAVARLKVMFNDELFVRYGRGIQPTARARQLFGPVRQALQLVQnELPGS 103

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194  82 LAEIRQGEKG-KLRIAStylPS-NYLVPKWLAEFKQHYEHVDVEIRTrnSL-QSIELLLSCQ-VDLAIVIKEAWEDDL-- 155
Cdd:PRK09508  104 GFEPESSERVfNLCICS---PLdIRLTSQIYNRIEQIAPNIHVVFKS--SLnQNIEHQLRYQeTEFVISYEEFDRPEFts 178

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 156 -PIdrvhMTDVLywfILPAA--HPLAGKEISIEQLVQEPFL---LREQGSSTREWLfslcrEHGVRRPRVGLQYHGLIES 229
Cdd:PRK09508  179 vPL----FKDEL---VLVASknHPRIKGPITEEQLYNEQHAvvsLDRFASFSQPWY-----DTVDKQASIAYQGTALSSV 246

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|...
gi 2502538194 230 IQSVRAGYGTMLAPALAVEEMVERNEIGRVTVPGVEIKRPVYI 272
Cdd:PRK09508  247 LNVVSQTHLVAIAPRWLAEEFAESLELQILPLPLKNNSRTCYL 289
HTH_DTXR smart00529
Helix-turn-helix diphteria tox regulatory element; iron dependent repressor
 22-85 2.85e-04

Helix-turn-helix diphteria tox regulatory element; iron dependent repressor


Pssm-ID: 197774 [Multi-domain]  Cd Length: 95  Bit Score: 39.12  E-value: 2.85e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2502538194   22 AEALAISQPAVSAQIRKLEnELGLSLLAPDgRGISLTDEGRflfEKARRIYDWEREIESQLAEI 85
Cdd:smart00529   5 AERLNVSPPTVTEMLKKLE-KMGLVEYEPY-RGITLTEKGR---RLARRLLRKHRLLERFLVDV 63
PBP2_Cbl cd08444
The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is ...
 93-202 3.77e-04

The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is required for expression of sulfate starvation-inducible (ssi) genes, contains the type 2 periplasmic binding fold; Cbl is a member of the LysR transcriptional regulators that comprise the largest family of prokaryotic transcription factor. Cbl shows high sequence similarity to CysB, the LysR-type transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the function of Cbl is required for expression of sulfate starvation-inducible (ssi) genes, coupled with the biosynthesis of cysteine from the organic sulfur sources (sulfonates). The ssi genes include the ssuEADCB and tauABCD operons encoding uptake systems for organosulfur compounds, aliphatic sulfonates, and taurine. The genes in these operons encode an ABC-type transport system required for uptake of aliphatic sulfonates and a desulfonation enzyme. Both Cbl and CysB require expression of the tau and ssu genes. Like many other members of the LTTR family, the Cbl is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176135  Cd Length: 198  Bit Score: 40.95  E-value: 3.77e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194  93 LRIASTYLPSNYLVPKWLAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAIViKEAWEDDlpiDRVHMTDVLYWF--- 169
Cdd:cd08444     2 LTIATTHTQARYALPWVVQAFKEQFPNVHLVLHQGSPEEIASMLANGQADIGIA-TEALENH---PELVSFPYYDWHhhi 77

                          90       100       110
                  ....*....|....*....|....*....|....
gi 2502538194 170 ILPAAHPLAG-KEISIEQLVQEPFLLREQGSSTR 202
Cdd:cd08444    78 IVPVGHPLESiTPLTIETIAKWPIITYHGGFTGR 111
PBP2_OccR cd08457
The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the ...
 93-248 4.03e-04

The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the catabolism of octopine, contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulator OccR, which is involved in the catabolism of octopine. Opines are low molecular weight compounds found in plant crown gall tumors produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. In Agrobacterium tumefaciens, OccR protein activates the occQ operon of the Ti plasmid in response to octopine. This operon encodes proteins required for the uptake and catabolism of octopine, an arginine derivative. The occ operon also encodes the TraR protein, which is a quorum-sensing transcriptional regulator of the Ti plasmid tra regulon. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176146 [Multi-domain]  Cd Length: 196  Bit Score: 40.55  E-value: 4.03e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194  93 LRIASTYLPSNYLVPKWLAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAIVIKEAWEDdlPIDRVHMTDVLYWFILP 172
Cdd:cd08457     2 LRIAAMPALANGFLPRFLAAFLRLRPNLHLSLMGLSSSQVLEAVASGRADLGIADGPLEER--QGFLIETRSLPAVVAVP 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2502538194 173 AAHPLAGK-EISIEQLVQEPFLLREQGSSTREWLFSLCREHGVRRPRVgLQYHGLIESIQSVRAGYG-TMLAPALAVE 248
Cdd:cd08457    80 MGHPLAQLdVVSPQDLAGERIITLENGYLFRMRVEVALGKIGVKRRPI-IEVNLSHTALSLVREGLGiAIIDPATAIG 156
HTH_MARR smart00347
helix_turn_helix multiple antibiotic resistance protein;
3-84 4.34e-04

helix_turn_helix multiple antibiotic resistance protein;


Pssm-ID: 197670 [Multi-domain]  Cd Length: 101  Bit Score: 38.73  E-value: 4.34e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194    3 LHALRIFVEvASRQSVTAAAEALAISQPAVSAQIRKLEnELGLSLLAP---DGRG--ISLTDEGRFLFEKARRIYD-WER 76
Cdd:smart00347  13 FLVLRILYE-EGPLSVSELAKRLGVSPSTVTRVLDRLE-KKGLVRREPspeDRRSvlVSLTEEGRELIEQLLEARSeTLA 90


                   ....*...
gi 2502538194   77 EIESQLAE 84
Cdd:smart00347  91 ELLAGLTA 98
PBP2_MetR cd08441
The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which ...
 110-292 6.23e-04

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


Pssm-ID: 176132  Cd Length: 198  Bit Score: 40.24  E-value: 6.23e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 110 LAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAIVikeawEDDLPIDRVHMTDVLYW---FILPAAHPLAGKE-ISIE 185
Cdd:cd08441    19 LDQFRERWPDVELDLSSGFHFDPLPALLRGELDLVIT-----SDPLPLPGIAYEPLFDYevvLVVAPDHPLAAKEfITPE 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 186 QLVQEPfllreqgsstrewLFSlcreHGVRRPRVGLQYHGLIES----------------IQSVRAGYGTMLAPALAVEE 249
Cdd:cd08441    94 DLADET-------------LIT----YPVERERLDVFRHFLQPAgiepkrrrtveltlmiLQLVASGRGVAALPNWAVRE 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 2502538194 250 MVERNEIGRVTVPGVEIKRPVYICTRAgESSHRPVVERFLERV 292
Cdd:cd08441   157 YLDQGLVVARPLGEEGLWRTLYAAVRT-EDADQPYLQDFLELA 198
MarR COG1846
DNA-binding transcriptional regulator, MarR family [Transcription];
17-84 7.62e-04

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


Pssm-ID: 441451 [Multi-domain]  Cd Length: 142  Bit Score: 39.18  E-value: 7.62e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2502538194  17 SVTAAAEALAISQPAVSAQIRKLEnELGLSLLAP---DGRG--ISLTDEGRFLFEKARRIY-DWEREIESQLAE 84
Cdd:COG1846    54 TQSELAERLGLTKSTVSRLLDRLE-EKGLVEREPdpeDRRAvlVRLTEKGRALLEEARPALeALLAELLAGLSE 126
PBP2_IlvR cd08453
The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved ...
 105-292 1.95e-03

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


Pssm-ID: 176144 [Multi-domain]  Cd Length: 200  Bit Score: 38.50  E-value: 1.95e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 105 LVPKWLAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAIVIKeaweddlPIDRVHMTDVLYWFIL--------PAAHP 176
Cdd:cd08453    14 VLPELVRRFREAYPDVELQLREATSDVQLEALLAGEIDAGIVIP-------PPGASAPPALAYRPLLseplvlavPAAWA 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 177 LAGKE-ISIEQLVQEPFLL--REQGSSTREWLFSLCREHGVrRPRVGlQyhgliESIQS------VRAGYGTMLAPAlAV 247
Cdd:cd08453    87 AEGGApLALAAVAAEPLVIfpRRIAPAFHDAVTGYYRAAGQ-TPRIA-Q-----EAIQMqtiislVSAGMGVALVPA-SL 158

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 2502538194 248 EEMverneiGRVTVPGVEIKRPVYICT-----RAGESShrPVVERFLERV 292
Cdd:cd08453   159 RNL------ARPGVVYRELADPAPVLEtglvwRRDDAS--PVLARFLDLV 200
PstS COG0226
ABC-type phosphate transport system, periplasmic component [Inorganic ion transport and ...
 90-297 7.78e-03

ABC-type phosphate transport system, periplasmic component [Inorganic ion transport and metabolism];


Pssm-ID: 439996 [Multi-domain]  Cd Length: 275  Bit Score: 37.17  E-value: 7.78e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194  90 KGKLRIA--STYLPsnyLVPKWLAEFKQHYEHVDVEIRTRNSLQSIELLLSCQVDLAIVIKEAWEDDlpIDRVHMTDVLY 167
Cdd:COG0226     3 SGTITIAgsSTVYP---LAEAWAEAFQKANPGVTINVQSGGSGGGIKQFIAGTVDIGNSSRPLKDEE--LEAAKENGVEL 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 168 WF-------ILPAAHPLAG-KEISIEQLVQ------------------EPFLL--REQGSSTREwLFS---LCREHGVRR 216
Cdd:COG0226    78 VEipvaidgIAVVVNPDNPvKNLTGEQLADifsgkitnwndiggklpdEPITVvgRSDGSGTTD-YFTeylLGVGAEVRE 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502538194 217 PRVGLQ-YHGLIESIQSVR-----AGYGTMLA---PALAVEemverNEIGRVTVPGVE--------IKRPVYICTRAGES 279
Cdd:COG0226   157 GVEGAEgNEGVVQAVAQTPgaigyVGLSYAEQnklKALAID-----NKAGKFVEPTAEniaagsypLSRPLYIYVKKEPD 231

                         250
                  ....*....|....*...
gi 2502538194 280 SHRPVVERFLERVLGKGA 297
Cdd:COG0226   232 AKAPAVKAFLDFVLSDGG 249
 
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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