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Conserved domains on  [gi|446287942|ref|WP_000365797|]
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MULTISPECIES: HTH-type transcriptional activator IlvY [Salmonella]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 11485465)

LysR family transcriptional regulator IlvY activates the expression of ilvC gene that encodes acetohydroxy acid isomeroreductase, a key enzyme in the biosynthesis of branched-chain amino acids

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
25-295 1.64e-172

HTH-type transcriptional activator IlvY;


:

Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 477.77  E-value: 1.64e-172
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942  25 MHVSPSTLSRQIQRLEEDLGQPLFVRDNRTVTLTEAGEELRVFAQQTLLQYQQLRHTLDQQGPSLSGELHIFCSVTAAYS 104
Cdd:PRK11716   1 MHVSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSLFCSVTAAYS 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 105 HLPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAIAGKPETLPGAVAFSMLENLAVVLIAPALPCPVRNQVSVD 184
Cdd:PRK11716  81 HLPPILDRFRAEHPLVEIKLTTGDAADAVEKVQSGEADLAIAAKPETLPASVAFSPIDEIPLVLIAPALPCPVRQQLSQE 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 185 KPDWSTVPFIMADQGPVRRRIELWFRRHKISnPQIYATVGGHEAMVSMVALGCGVALLPEVVLENSpePVRNRVMILERS 264
Cdd:PRK11716 161 KPDWSRIPFILPEHGPARRRIDLWFRRHKIK-PNIYATVSGHEAIVSMVALGCGVGLLPEVVLENS--PVRNRVQILERV 237

                        250       260       270
                 ....*....|....*....|....*....|.
gi 446287942 265 DEKTPFELGVCAQKKRLHEPLIDAFWKILPN 295
Cdd:PRK11716 238 PPITPFELGVCVQKKRLEEPLIDAFWQLLEN 268
 
Name Accession Description Interval E-value
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
25-295 1.64e-172

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 477.77  E-value: 1.64e-172
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942  25 MHVSPSTLSRQIQRLEEDLGQPLFVRDNRTVTLTEAGEELRVFAQQTLLQYQQLRHTLDQQGPSLSGELHIFCSVTAAYS 104
Cdd:PRK11716   1 MHVSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSLFCSVTAAYS 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 105 HLPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAIAGKPETLPGAVAFSMLENLAVVLIAPALPCPVRNQVSVD 184
Cdd:PRK11716  81 HLPPILDRFRAEHPLVEIKLTTGDAADAVEKVQSGEADLAIAAKPETLPASVAFSPIDEIPLVLIAPALPCPVRQQLSQE 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 185 KPDWSTVPFIMADQGPVRRRIELWFRRHKISnPQIYATVGGHEAMVSMVALGCGVALLPEVVLENSpePVRNRVMILERS 264
Cdd:PRK11716 161 KPDWSRIPFILPEHGPARRRIDLWFRRHKIK-PNIYATVSGHEAIVSMVALGCGVGLLPEVVLENS--PVRNRVQILERV 237

                        250       260       270
                 ....*....|....*....|....*....|.
gi 446287942 265 DEKTPFELGVCAQKKRLHEPLIDAFWKILPN 295
Cdd:PRK11716 238 PPITPFELGVCVQKKRLEEPLIDAFWQLLEN 268
PBP2_IlvY cd08430
The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates ...
 92-292 1.63e-117

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: 335.70  E-value: 1.63e-117
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942  92 ELHIFCSVTAAYSHLPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAIAGKPETLPGAVAFSMLENLAVVLIAP 171
Cdd:cd08430    1 ELSLYCSVTASYSFLPPILERFRAQHPQVEIKLHTGDPADAIDKVLNGEADIAIAARPDKLPARLAFLPLATSPLVFIAP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 172 ALPCPVRNQVSVDKPDWSTVPFIMADQGPVRRRIELWFRRHKISnPQIYATVGGHEAMVSMVALGCGVALLPEVVLENSp 251
Cdd:cd08430   81 NIACAVTQQLSQGEIDWSRLPFILPERGLARERLDQWFRRRGIK-PNIYAQVAGHEAIVSMVALGCGVGIVPELVLDNS- 158

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 446287942 252 ePVRNRVMILERSDEKTPFELGVCAQKKRLHEPLIDAFWKI 292
Cdd:cd08430  159 -PLKDKVRILEVQPELEPFEVGLCCLKKRLNEPLIKAFWQV 198
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-293 8.30e-56

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 180.83  E-value: 8.30e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942   1 MDLRDLKTFLHLAESRHFGRSARAMHVSPSTLSRQIQRLEEDLGQPLFVRDNRTVTLTEAGEELRVFAQQTLLQYQQLRH 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942  81 TLDQQGPSLSGELHIFCSVTAAYSHLPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAIAGKPETLPGAVAFSM 160
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 161 LENLAVVLIAPALPcpvrnqvsvdkpdwstvpfiMADQGPVrrrielwfrrhkisnpqiyatVGGHEAMVSMVALGCGVA 240
Cdd:COG0583  161 GEERLVLVASPDHP--------------------LARRAPL---------------------VNSLEALLAAVAAGLGIA 199

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|...
gi 446287942 241 LLPEVVLEnsPEPVRNRVMILERSDEKTPFELGVCAQKKRLHEPLIDAFWKIL 293
Cdd:COG0583  200 LLPRFLAA--DELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFL 250
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 90-293 4.29e-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: 125.86  E-value: 4.29e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942   90 SGELHIFCSVTAAYSHLPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAIAGKPETLPGAVAFSMLENLAVVLI 169
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942  170 APALPCPVRNQVSVDkpDWSTVPFIMADQG-PVRRRIELWFRRHKISnPQIYATVGGHEAMVSMVALGCGVALLPEVVLE 248
Cdd:pfam03466  81 PPDHPLARGEPVSLE--DLADEPLILLPPGsGLRDLLDRALRAAGLR-PRVVLEVNSLEALLQLVAAGLGIALLPRSAVA 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 446287942  249 NSPEpvRNRVMILERSDEKTPFELGVCAQKKRLHEPLIDAFWKIL 293
Cdd:pfam03466 158 RELA--DGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFL 200
HTH_MARR smart00347
helix_turn_helix multiple antibiotic resistance protein;
22-64 1.89e-04

helix_turn_helix multiple antibiotic resistance protein;


Pssm-ID: 197670 [Multi-domain]  Cd Length: 101  Bit Score: 39.88  E-value: 1.89e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 446287942    22 ARAMHVSPSTLSRQIQRLEEDlGqplFVR------DNRTV--TLTEAGEEL 64
Cdd:smart00347  31 AKRLGVSPSTVTRVLDRLEKK-G---LVRrepspeDRRSVlvSLTEEGREL 77
 
Name Accession Description Interval E-value
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
25-295 1.64e-172

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 477.77  E-value: 1.64e-172
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942  25 MHVSPSTLSRQIQRLEEDLGQPLFVRDNRTVTLTEAGEELRVFAQQTLLQYQQLRHTLDQQGPSLSGELHIFCSVTAAYS 104
Cdd:PRK11716   1 MHVSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSLFCSVTAAYS 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 105 HLPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAIAGKPETLPGAVAFSMLENLAVVLIAPALPCPVRNQVSVD 184
Cdd:PRK11716  81 HLPPILDRFRAEHPLVEIKLTTGDAADAVEKVQSGEADLAIAAKPETLPASVAFSPIDEIPLVLIAPALPCPVRQQLSQE 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 185 KPDWSTVPFIMADQGPVRRRIELWFRRHKISnPQIYATVGGHEAMVSMVALGCGVALLPEVVLENSpePVRNRVMILERS 264
Cdd:PRK11716 161 KPDWSRIPFILPEHGPARRRIDLWFRRHKIK-PNIYATVSGHEAIVSMVALGCGVGLLPEVVLENS--PVRNRVQILERV 237

                        250       260       270
                 ....*....|....*....|....*....|.
gi 446287942 265 DEKTPFELGVCAQKKRLHEPLIDAFWKILPN 295
Cdd:PRK11716 238 PPITPFELGVCVQKKRLEEPLIDAFWQLLEN 268
PBP2_IlvY cd08430
The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates ...
 92-292 1.63e-117

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: 335.70  E-value: 1.63e-117
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942  92 ELHIFCSVTAAYSHLPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAIAGKPETLPGAVAFSMLENLAVVLIAP 171
Cdd:cd08430    1 ELSLYCSVTASYSFLPPILERFRAQHPQVEIKLHTGDPADAIDKVLNGEADIAIAARPDKLPARLAFLPLATSPLVFIAP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 172 ALPCPVRNQVSVDKPDWSTVPFIMADQGPVRRRIELWFRRHKISnPQIYATVGGHEAMVSMVALGCGVALLPEVVLENSp 251
Cdd:cd08430   81 NIACAVTQQLSQGEIDWSRLPFILPERGLARERLDQWFRRRGIK-PNIYAQVAGHEAIVSMVALGCGVGIVPELVLDNS- 158

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 446287942 252 ePVRNRVMILERSDEKTPFELGVCAQKKRLHEPLIDAFWKI 292
Cdd:cd08430  159 -PLKDKVRILEVQPELEPFEVGLCCLKKRLNEPLIKAFWQV 198
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-293 8.30e-56

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 180.83  E-value: 8.30e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942   1 MDLRDLKTFLHLAESRHFGRSARAMHVSPSTLSRQIQRLEEDLGQPLFVRDNRTVTLTEAGEELRVFAQQTLLQYQQLRH 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942  81 TLDQQGPSLSGELHIFCSVTAAYSHLPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAIAGKPETLPGAVAFSM 160
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 161 LENLAVVLIAPALPcpvrnqvsvdkpdwstvpfiMADQGPVrrrielwfrrhkisnpqiyatVGGHEAMVSMVALGCGVA 240
Cdd:COG0583  161 GEERLVLVASPDHP--------------------LARRAPL---------------------VNSLEALLAAVAAGLGIA 199

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|...
gi 446287942 241 LLPEVVLEnsPEPVRNRVMILERSDEKTPFELGVCAQKKRLHEPLIDAFWKIL 293
Cdd:COG0583  200 LLPRFLAA--DELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFL 250
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 90-293 4.29e-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: 125.86  E-value: 4.29e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942   90 SGELHIFCSVTAAYSHLPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAIAGKPETLPGAVAFSMLENLAVVLI 169
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942  170 APALPCPVRNQVSVDkpDWSTVPFIMADQG-PVRRRIELWFRRHKISnPQIYATVGGHEAMVSMVALGCGVALLPEVVLE 248
Cdd:pfam03466  81 PPDHPLARGEPVSLE--DLADEPLILLPPGsGLRDLLDRALRAAGLR-PRVVLEVNSLEALLQLVAAGLGIALLPRSAVA 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 446287942  249 NSPEpvRNRVMILERSDEKTPFELGVCAQKKRLHEPLIDAFWKIL 293
Cdd:pfam03466 158 RELA--DGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFL 200
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 92-293 3.80e-31

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: 115.00  E-value: 3.80e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942  92 ELHIFCSVTAAYSHLPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAIAGKPETLPGaVAFSMLENLAVVLIAP 171
Cdd:cd05466    1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPG-LESEPLFEEPLVLVVP 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 172 ALPcPVRNQVSVDKPDWSTVPFIMADQGPV-RRRIELWFRRHKISnPQIYATVGGHEAMVSMVALGCGVALLPEVVLEns 250
Cdd:cd05466   80 PDH-PLAKRKSVTLADLADEPLILFERGSGlRRLLDRAFAEAGFT-PNIALEVDSLEAIKALVAAGLGIALLPESAVE-- 155

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 446287942 251 pEPVRNRVMILERSDEKTPFELGVCAQKKRLHEPLIDAFWKIL 293
Cdd:cd05466  156 -ELADGGLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-62 1.22e-24

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 93.60  E-value: 1.22e-24
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942    3 LRDLKTFLHLAESRHFGRSARAMHVSPSTLSRQIQRLEEDLGQPLFVRDNRTVTLTEAGE 62
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 1-265 5.79e-24

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 98.49  E-value: 5.79e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942   1 MDLRDLKTFLHLAESRHFGRSARAMHVSPSTLSRQIQRLEEDLGQPLFVRDNRTVTLTEAGEELRVFAQQTLLQYQQLRH 80
Cdd:PRK11242   1 MLLRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942  81 TLDQQGPSLSGELHIFCSVTAAYSHLPPILDRFRAEHPSVEIKLT--TGDAADAMdkVVTGEADLAIAGKPETLPGAVAF 158
Cdd:PRK11242  81 AIHDVADLSRGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIRemSQERIEAL--LADDELDVGIAFAPVHSPEIEAQ 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 159 SML-ENLAVVlIAPALPCPVRnQVSVDKPDWSTVPFIM-ADQGPVRRRIELWFRRHKISnPQIYATVGGHEAMVSMVALG 236
Cdd:PRK11242 159 PLFtETLALV-VGRHHPLAAR-RKALTLDELADEPLVLlSAEFATREQIDRYFRRHGVT-PRVAIEANSISAVLEIVRRG 235

                        250       260       270
                 ....*....|....*....|....*....|....*...
gi 446287942 237 CGVALLPEVV---------LENSPEPVRNRVMILERSD 265
Cdd:PRK11242 236 RLATLLPAAIarehdglcaIPLDPPLPQRTAALLRRKG 273
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 1-260 5.58e-21

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 90.47  E-value: 5.58e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942   1 MDLRDLKTFLHLAESRHFGRSARAMHVSPSTLSRQIQRLEEDLGQPLFVRDNRTVTLTEAGEELRVFAQQTLLQYQQLRH 80
Cdd:PRK11151   1 MNIRDLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVLKE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942  81 TLDQQGPSLSGELHIFCSVTAAYSHLPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAI-AGKPETLPgavaFS 159
Cdd:PRK11151  81 MASQQGETMSGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCAIlALVKESEA----FI 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 160 MLE--NLAVVLiapALPC--PVRNQVSVDKPDWSTVPFIMADQGPVRRRIEL--WFRRHKISNPQIYATvgGHEAMVSMV 233
Cdd:PRK11151 157 EVPlfDEPMLL---AVYEdhPWANRDRVPMSDLAGEKLLMLEDGHCLRDQAMgfCFEAGADEDTHFRAT--SLETLRNMV 231

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|
gi 446287942 234 ALGCGVALLPEVVLEN-------------SPEPVRNRVMI 260
Cdd:PRK11151 232 AAGSGITLLPALAVPNerkrdgvcylpciKPEPRRTIGLV 271
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 1-243 1.22e-20

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 89.44  E-value: 1.22e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942   1 MDLRDLKTFLHLAESRHFGRSARAMHVSPSTLSRQIQRLEEDLGQPLFVRDNRTVTLTEAGEelrVFaqqtllqYQQLRH 80
Cdd:PRK09906   1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGE---VF-------LQDARA 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942  81 TLDQ---------QGPSLSGELHIFCSVTAAYSHLPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAIAgKPET 151
Cdd:PRK09906  71 ILEQaekaklrarKIVQEDRQLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFM-RHPV 149

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 152 LPGAVAFSMLENLAVVLIAPAlPCPVRNQVSVDKPDWSTVPFIMAD---QGPVRRRIELWFRRHKIsNPQIYATVGGHEA 228
Cdd:PRK09906 150 YSDEIDYLELLDEPLVVVLPV-DHPLAHEKEITAAQLDGVNFISTDpaySGSLAPIIKAWFAQHNS-QPNIVQVATNILV 227

                        250
                 ....*....|....*
gi 446287942 229 MVSMVALGCGVALLP 243
Cdd:PRK09906 228 TMNLVGMGLGCTIIP 242
PRK09986 PRK09986
LysR family transcriptional regulator;
1-244 1.20e-19

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 86.70  E-value: 1.20e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942   1 MDLRDLKTFLHLAESRHFGRSARAMHVSPSTLSRQIQRLEEDLGQPLFVRDNRTVTLTEAGEELRvfaqqtllqyQQLRH 80
Cdd:PRK09986   7 IDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILM----------EESRR 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942  81 TLDQQGPSLS----------GELHIFCSVTAAYSHLPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAI--AGK 148
Cdd:PRK09986  77 LLDNAEQSLArveqigrgeaGRIEIGIVGTALWGRLRPAMRHFLKENPNVEWLLRELSPSMQMAALERRELDAGIwrMAD 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 149 PETLPGAVAFSML-ENLAVVL-------IAPALPC-PVRNQVSVdkpdwsTVPFIMADQGPV--RRRIELWFrrhkisNP 217
Cdd:PRK09986 157 LEPNPGFTSRRLHeSAFAVAVpeehplaSRSSVPLkALRNEYFI------TLPFVHSDWGKFlqRVCQQAGF------SP 224

                        250       260
                 ....*....|....*....|....*..
gi 446287942 218 QIYATVGGHEAMVSMVALGCGVALLPE 244
Cdd:PRK09986 225 QIIRQVNEPQTVLAMVSMGIGITLLPD 251
PBP2_YofA_SoxR_like cd08442
The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, ...
 100-269 2.40e-18

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: 81.11  E-value: 2.40e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 100 TAAYSHLPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLA-IAGKPE--TLPGAVAFSmlENLavVLIAPALPCP 176
Cdd:cd08442    9 TTAAVRLPPLLAAYHARYPKVDLSLSTGTTGALIQAVLEGRLDGAfVAGPVEhpRLEQEPVFQ--EEL--VLVSPKGHPP 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 177 VRnqvsvDKPDWSTVPFIMADQG-PVRRRIELWFRRHKISNPQIYaTVGGHEAMVSMVALGCGVALLPEVVLENS----- 250
Cdd:cd08442   85 VS-----RAEDLAGSTLLAFRAGcSYRRRLEDWLAEEGVSPGKIM-EFGSYHAILGCVAAGMGIALLPRSVLDSLqgrgs 158

                        170       180
                 ....*....|....*....|....*.
gi 446287942 251 ------PEPVR-NRVMILERSDEKTP 269
Cdd:cd08442  159 vsihplPEPFAdVTTWLVWRKDSFTA 184
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 1-253 3.75e-18

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 82.73  E-value: 3.75e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942   1 MDLRDLKTFLHLAesRH---FGRSARAMHVSPSTLSRQIQRLEEDLGQPLFVRD-NRTVTLTEAGEELRVFAQQTLLQYQ 76
Cdd:PRK12682   1 MNLQQLRFVREAV--RRnlnLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHgKRLKGLTEPGKAVLDVIERILREVG 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942  77 QLRHTLDQQGPSLSGELHIFCSVTAAYSHLPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAIAgkPETL---P 153
Cdd:PRK12682  79 NIKRIGDDFSNQDSGTLTIATTHTQARYVLPRVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGIA--TESLaddP 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 154 GAVAFSMLENLAVVLIAPALPCPVRNQVSVDkpDWSTVPFIMADQGPV-RRRIELWFRRHKIsNPQIYATVGGHEAMVSM 232
Cdd:PRK12682 157 DLATLPCYDWQHAVIVPPDHPLAQEERITLE--DLAEYPLITYHPGFTgRSRIDRAFAAAGL-QPDIVLEAIDSDVIKTY 233

                        250       260
                 ....*....|....*....|.
gi 446287942 233 VALGCGVALLPEVVLENSPEP 253
Cdd:PRK12682 234 VRLGLGVGIVAEMAYRPDRDG 254
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 106-293 6.24e-18

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: 79.84  E-value: 6.24e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 106 LPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAIAGKPETLPGAVAFSMLENLAVVLIAPALPCPVRNQVSVDk 185
Cdd:cd08420   15 LPRLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLVEGPVDHPDLIVEPFAEDELVLVVPPDHPLAGRKEVTAE- 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 186 pDWSTVPFIMADQGP-VRRRIELWFRRHKI--SNPQIYATVGGHEAMVSMVALGCGVALLPEVVLEnspEPVRN---RVM 259
Cdd:cd08420   94 -ELAAEPWILREPGSgTREVFERALAEAGLdgLDLNIVMELGSTEAIKEAVEAGLGISILSRLAVR---KELELgrlVAL 169

                        170       180       190
                 ....*....|....*....|....*....|....
gi 446287942 260 ILERSDEKTPFELgVCaQKKRLHEPLIDAFWKIL 293
Cdd:cd08420  170 PVEGLRLTRPFSL-IY-HKDKYLSPAAEAFLEFL 201
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 22-242 1.48e-17

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 80.86  E-value: 1.48e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942  22 ARAMHVSPSTLSRQIQRLEEDLGQPLFVRDNRTVT-LTEAGEELRVFAQQTLLQYQQLRHTLDQQGPSLSGELHIFCSVT 100
Cdd:PRK12683  23 ANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTgLTEPGKELLQIVERMLLDAENLRRLAEQFADRDSGHLTVATTHT 102

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 101 AAYSHLPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAIAGKP-ETLPGAVAFSMLENLAVVLIAPALPCPVRN 179
Cdd:PRK12683 103 QARYALPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGIATEAlDREPDLVSFPYYSWHHVVVVPKGHPLTGRE 182

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446287942 180 QVSVDkpDWSTVPFIMADQGPV-RRRIELWFRRHKISnPQIYATVGGHEAMVSMVALGCGVALL 242
Cdd:PRK12683 183 NLTLE--AIAEYPIITYDQGFTgRSRIDQAFAEAGLV-PDIVLTALDADVIKTYVELGMGVGIV 243
cbl PRK12679
HTH-type transcriptional regulator Cbl;
1-252 2.15e-16

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 77.93  E-value: 2.15e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942   1 MDLRDLKtFLHLAESRHFGRS--ARAMHVSPSTLSRQIQRLEEDLGQPLFVR-DNRTVTLTEAGEELRVFAQQTLLQYQQ 77
Cdd:PRK12679   1 MNFQQLK-IIREAARQDYNLTevANMLFTSQSGVSRHIRELEDELGIEIFIRrGKRLLGMTEPGKALLVIAERILNEASN 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942  78 LRHTLDQQGPSLSGELHIFCSVTAAYSHLPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAIAGkpETL---PG 154
Cdd:PRK12679  80 VRRLADLFTNDTSGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIAS--ERLsndPQ 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 155 AVAFSMLENLAVVLIAPALPCPVRNQVSVDkpDWSTVPFIMADQGPV-RRRIELWFRRHKISnPQIYATVGGHEAMVSMV 233
Cdd:PRK12679 158 LVAFPWFRWHHSLLVPHDHPLTQITPLTLE--SIAKWPLITYRQGITgRSRIDDAFARKGLL-ADIVLSAQDSDVIKTYV 234

                        250
                 ....*....|....*....
gi 446287942 234 ALGCGVALLPEVVLENSPE 252
Cdd:PRK12679 235 ALGLGIGLVAEQSSGEQEE 253
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 100-293 7.47e-16

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: 74.08  E-value: 7.47e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 100 TAAYSHLPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAIAGKPETLPGAVAFSMLENLAVVLIAPALPCPVRN 179
Cdd:cd08414    9 SALYGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPPPDPPGLASRPLLREPLVVALPADHPLAARE 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 180 QVSVDkpDWSTVPFIM--ADQGPV-RRRIELWFRRHKISnPQIYATVGGHEAMVSMVALGCGVALLPEVVLENSPEPVRn 256
Cdd:cd08414   89 SVSLA--DLADEPFVLfpREPGPGlYDQILALCRRAGFT-PRIVQEASDLQTLLALVAAGLGVALVPASVARLQRPGVV- 164

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 446287942 257 rvmILERSDEKTPFELGvCAQKKRLHEPLIDAFWKIL 293
Cdd:cd08414  165 ---YRPLADPPPRSELA-LAWRRDNASPALRAFLELA 197
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 1-244 1.26e-15

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 75.49  E-value: 1.26e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942   1 MDLRDLKTFLHLAESRHFGRSARAMHVSPSTLSRQIQRLEEDLGQPLFVRDNRTVTLTEAGEELRVFAQQTLLQYQQLRH 80
Cdd:PRK11233   1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942  81 TLDQQGPSLSGELHI-FCSVTAAYSHLPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAIAGKPETLPGAVAFS 159
Cdd:PRK11233  81 AVHNVGQALSGQVSIgLAPGTAASSLTMPLLQAVRAEFPGIVLYLHENSGATLNEKLMNGQLDMAVIYEHSPVAGLSSQP 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 160 ML-ENLAVVliaPALPCPVRnqvSVDKPDWSTVP-FIMADQGPVRRRIELWFRRHKISnPQIYATVGGHEAMVSMVALGC 237
Cdd:PRK11233 161 LLkEDLFLV---GTQDCPGQ---SVDLAAVAQMNlFLPRDYSAVRLRVDEAFSLRRLT-AKVIGEIESIATLTAAIASGM 233


                 ....*..
gi 446287942 238 GVALLPE 244
Cdd:PRK11233 234 GVTVLPE 240
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 105-258 2.75e-15

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


Pssm-ID: 176127 [Multi-domain]  Cd Length: 194  Bit Score: 72.63  E-value: 2.75e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 105 HLPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAIAGKPETLPGAVAFSMLENLAVVLI-APALPCPVRNQVSV 183
Cdd:cd08436   14 DLPELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAFVGLPERRPPGLASRELAREPLVAVvAPDHPLAGRRRVAL 93

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446287942 184 DkpDWSTVPFIMADQG-PVRRRIELWFRRHKISnPQIYATVGGHEAMVSMVALGCGVALLPEVVLENSPEPVRNRV 258
Cdd:cd08436   94 A--DLADEPFVDFPPGtGARRQVDRAFAAAGVR-RRVAFEVSDVDLLLDLVARGLGVALLPASVAARLPGLAALPL 166
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 92-289 3.52e-15

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: 72.58  E-value: 3.52e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942  92 ELHIFCSVTAAYSHLPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAIaGKPETLPGAVAFSMLENLAVVLIAP 171
Cdd:cd08412    1 TLRIGCFSTLAPYYLPGLLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLAL-TYDLDLPEDIAFEPLARLPPYVWLP 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 172 AlPCPVRNQVSVDKPDWSTVPFIMADQGPVRRRIELWFRRHKISnPQIYATVGGHEAMVSMVALGCGVALLPEVVLEN-S 250
Cdd:cd08412   80 A-DHPLAGKDEVSLADLAAEPLILLDLPHSREYFLSLFAAAGLT-PRIAYRTSSFEAVRSLVANGLGYSLLNDRPYRPwS 157

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 446287942 251 PEPvrNRVMILERSDEKTPFELGVcAQKKRLH-EPLIDAF 289
Cdd:cd08412  158 YDG--KRLVRRPLADPVPPLRLGL-AWRRGARlTRAARAF 194
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
3-127 4.65e-15

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 73.88  E-value: 4.65e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942   3 LRDLKTFLHLAesRH--FGRSARAMHVSPSTLSRQIQRLEEDLGQPLFVRDNRTVTLTEAGEelRVFAQQTLLQYQQLRH 80
Cdd:PRK10086  16 LSKLHTFEVAA--RHqsFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGK--RVFWALKSSLDTLNQE 91

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 446287942  81 TLDQQGPSLSGELHIFCSVTAAYSHLPPILDRFRAEHPSVEIKLTTG 127
Cdd:PRK10086  92 ILDIKNQELSGTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTILTG 138
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 100-255 7.67e-15

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


Pssm-ID: 176115 [Multi-domain]  Cd Length: 200  Bit Score: 71.48  E-value: 7.67e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 100 TAAYSHLPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAIAG-----KPETLPGAVAFSMLENLAVVLIAPALP 174
Cdd:cd08423    9 TAAAALLPPALAALRARHPGLEVRLREAEPPESLDALRAGELDLAVVFdypvtPPPDDPGLTRVPLLDDPLDLVLPADHP 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 175 CPVRNQVSVDkpDWSTVPFIMADQG-PVRRRIELWFRRHKISnPQIYATVGGHEAMVSMVALGCGVALLPEVVLENSPEP 253
Cdd:cd08423   89 LAGREEVALA--DLADEPWIAGCPGsPCHRWLVRACRAAGFT-PRIAHEADDYATVLALVAAGLGVALVPRLALGARPPG 165


                 ..
gi 446287942 254 VR 255
Cdd:cd08423  166 VV 167
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
1-249 1.19e-14

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 72.74  E-value: 1.19e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942   1 MDLRDLKTFLHLAESRHFGRSARAMHVSPSTLSRQIQRLEEDLGQPLFVRDNRTVTLTEAGEELRVFAQQTLLQYQQLRH 80
Cdd:PRK15421   2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQ 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942  81 TLDQQGPSlsgELHIFCSVTAAYSHLPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAIAGkpETLP-GAVAFS 159
Cdd:PRK15421  82 ACNEPQQT---RLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTS--DILPrSGLHYS 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 160 MLENLAVVLI-APALPCPVRNQVSVDkpDWSTVPFIMAdqgPVRR-RIELWfrRHKIS----NPQIyATVGGHEAMVSMV 233
Cdd:PRK15421 157 PMFDYEVRLVlAPDHPLAAKTRITPE--DLASETLLIY---PVQRsRLDVW--RHFLQpagvSPSL-KSVDNTLLLIQMV 228

                        250
                 ....*....|....*.
gi 446287942 234 ALGCGVALLPEVVLEN 249
Cdd:PRK15421 229 AARMGIAALPHWVVES 244
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
2-64 2.11e-14

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 71.93  E-value: 2.11e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446287942   2 DLRDLKTFLHLAESRHFGRSARAMHVSPSTLSRQIQRLEEDLGQPLFVRDnRTVTLTEAGEEL 64
Cdd:PRK13348   3 DYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRG-RPCRPTPAGQRL 64
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
1-187 2.38e-14

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 71.93  E-value: 2.38e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942   1 MDLRDLKtFLHLAESRHFGRS--ARAMHVSPSTLSRQIQRLEEDLGQPLFVRD-NRTVTLTEAGEELRVFAQQTLLQYQQ 77
Cdd:PRK12684   1 MNLHQLR-FVREAVRQNFNLTeaAKALYTSQPGVSKAIIELEDELGVEIFTRHgKRLRGLTEPGRIILASVERILQEVEN 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942  78 LRHTLDQQGPSLSGELHIFCSVTAAYSHLPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAIAGKpetlpgavA 157
Cdd:PRK12684  80 LKRVGKEFAAQDQGNLTIATTHTQARYALPAAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAIATE--------A 151

                        170       180       190
                 ....*....|....*....|....*....|
gi 446287942 158 FSMLENLAvvliapALPCPVRNQVSVDKPD 187
Cdd:PRK12684 152 IADYKELV------SLPCYQWNHCVVVPPD 175
rbcR CHL00180
LysR transcriptional regulator; Provisional
 3-242 7.59e-14

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 70.43  E-value: 7.59e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942   3 LRDLKTFLHLAESRHFGRSARAMHVSPSTLSRQIQRLEEDLGQPLFVRDNRTVTLTEAGEELRVFAQQTLLQYQQLRHTL 82
Cdd:CHL00180   7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRAL 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942  83 DQQGPSLSGELHIFCSVTAAYSHLPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAIAGkpetlpGAVAFSMLE 162
Cdd:CHL00180  87 EDLKNLQRGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVG------GEVPTELKK 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 163 NLAV--------VLIAPALPcPVRNQVSVDKPDWSTVPFIMAD-QGPVRRRIELWFRRHKISNPQ--IYATVGGHEAMVS 231
Cdd:CHL00180 161 ILEItpyvedelALIIPKSH-PFAKLKKIQKEDLYRLNFITLDsNSTIRKVIDNILIQNGIDSKRfkIEMELNSIEAIKN 239

                        250
                 ....*....|.
gi 446287942 232 MVALGCGVALL 242
Cdd:CHL00180 240 AVQSGLGAAFV 250
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-253 1.21e-13

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


Pssm-ID: 176131 [Multi-domain]  Cd Length: 197  Bit Score: 67.94  E-value: 1.21e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942  93 LHIFCSVTAAYSHLPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAIAGKPETLPGaVAFSML--ENLAVVLiA 170
Cdd:cd08440    2 VRVAALPSLAATLLPPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEADPD-LEFEPLlrDPFVLVC-P 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 171 PALPCPVRNQVSVDkpDWSTVPFIMADQG-PVRRRIELWFRRHKIsNPQIYATVGGHEAMVSMVALGCGVALLPEVVLEN 249
Cdd:cd08440   80 KDHPLARRRSVTWA--ELAGYPLIALGRGsGVRALIDRALAAAGL-TLRPAYEVSHMSTALGMVAAGLGVAVLPALALPL 156


                 ....
gi 446287942 250 SPEP 253
Cdd:cd08440  157 ADHP 160
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 92-275 1.23e-13

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: 67.97  E-value: 1.23e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942  92 ELHIFCSVTAAYSHLPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAIAGKPETLPGAVAFSMLENLAVVLIAP 171
Cdd:cd08415    1 TLRIAALPALALSLLPRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPLDHPGLESEPLASGRAVCVLPP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 172 ALPCPVRNQVSVDkpDWSTVPFI-MADQGPVRRRIELWFRRHKIsNPQIYATVGGHEAMVSMVALGCGVALL-PEVVLEN 249
Cdd:cd08415   81 GHPLARKDVVTPA--DLAGEPLIsLGRGDPLRQRVDAAFERAGV-EPRIVIETQLSHTACALVAAGLGVAIVdPLTAAGY 157

                        170       180
                 ....*....|....*....|....*.
gi 446287942 250 SPEPVRNRVMilersDEKTPFELGVC 275
Cdd:cd08415  158 AGAGLVVRPF-----RPAIPFEFALV 178
PBP2_LTTR_like_2 cd08427
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 99-289 1.66e-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: 176118 [Multi-domain]  Cd Length: 195  Bit Score: 67.60  E-value: 1.66e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942  99 VTAAYSHLPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAIAGKPE-TLPGAVAFSMLENLAVVLIAPAlPCPV 177
Cdd:cd08427    8 ATVLTGLLPRALARLRRRHPDLEVHIVPGLSAELLARVDAGELDAAIVVEPPfPLPKDLVWTPLVREPLVLIAPA-ELAG 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 178 RNQVSVdkpdWSTVPFIMAD-QGPVRRRIELWFRRHKISnPQIYATVGGHEAMVSMVALGCGVALLPEVVLENsPEPVRN 256
Cdd:cd08427   87 DDPREL----LATQPFIRYDrSAWGGRLVDRFLRRQGIR-VREVMELDSLEAIAAMVAQGLGVAIVPDIAVPL-PAGPRV 160

                        170       180       190
                 ....*....|....*....|....*....|....
gi 446287942 257 RVMILersDEKTPF-ELGVCAQKKRLHEPLIDAF 289
Cdd:cd08427  161 RVLPL---GDPAFSrRVGLLWRRSSPRSRLIQAL 191
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
 100-243 1.80e-13

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: 67.53  E-value: 1.80e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 100 TAAYsHLPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAIAGKPETLPGAVAFSMLENLAVVlIAPAlPCPVRN 179
Cdd:cd08419    9 TAKY-FAPRLLGAFCRRHPGVEVSLRVGNREQVLERLADNEDDLAIMGRPPEDLDLVAEPFLDNPLVV-IAPP-DHPLAG 85

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446287942 180 QVSVDKPDWSTVPFIMADQGP-VRRRIELWFRRHKISnPQIYATVGGHEAMVSMVALGCGVALLP 243
Cdd:cd08419   86 QKRIPLERLAREPFLLREPGSgTRLAMERFFAEHGVT-LRVRMELGSNEAIKQAVMAGLGLSVLS 149
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 1-149 6.20e-13

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 67.71  E-value: 6.20e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942   1 MDLRDLKTFLHLAESRHFGRSARAMHVSPSTLSRQIQRLEEDLGQPLFVRDNRTVTLTEAGEELRVFAQQTLLQYQQLRH 80
Cdd:PRK14997   2 TDLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQD 81

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446287942  81 TLDQQGPSLSGELHIFCSVTAAYSHLPPILDRFRAEHPSVEIKLttgDAADAMDKVVTGEADLAIAGKP 149
Cdd:PRK14997  82 AIAALQVEPRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQL---EATNRRVDVVGEGVDVAIRVRP 147
PRK12680 PRK12680
LysR family transcriptional regulator;
1-255 1.05e-12

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 67.34  E-value: 1.05e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942   1 MDLRDLKTFLHLAESR-HFGRSARAMHVSPSTLSRQIQRLEEDLGQPLFVRDNRTV-TLTEAGEELRVFAQQTLLQYQQL 78
Cdd:PRK12680   1 MTLTQLRYLVAIADAElNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLeSVTPAGVEVIERARAVLSEANNI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942  79 RHTLDQQGPSLSGELHIFCSVTAAYSHLPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAIAGKPETLPG---A 155
Cdd:PRK12680  81 RTYAANQRRESQGQLTLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVSTAGGEPSagiA 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 156 VAFSMLENLAVVLIAPALPCPVRnqvSVDKPDWSTVPFIMADQGPvrrRIELWFRRHKISN---PQIYATVGGHEAMVSM 232
Cdd:PRK12680 161 VPLYRWRRLVVVPRGHALDTPRR---APDMAALAEHPLISYESST---RPGSSLQRAFAQLglePSIALTALDADLIKTY 234

                        250       260
                 ....*....|....*....|...
gi 446287942 233 VALGCGVALLPEVVLENSPEPVR 255
Cdd:PRK12680 235 VRAGLGVGLLAEMAVNANDEDLR 257
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 13-145 1.36e-12

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 66.79  E-value: 1.36e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942  13 AESRH--FGRSARAMHVSPSTLSRQIQRLEEDLGQPLFVRDNRTVTLTEAGeelRVFAQQTLLQYQQLRHTLDQ-QGPSL 89
Cdd:PRK11139  16 AAARHlsFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEG---QRYFLDIREIFDQLAEATRKlRARSA 92

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 446287942  90 SGELHIFCSVTAAYSHLPPILDRFRAEHPSVEIKLTtgdAADAMDKVVTGEADLAI 145
Cdd:PRK11139  93 KGALTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLK---AVDRLEDFLRDDVDVAI 145
PRK09791 PRK09791
LysR family transcriptional regulator;
3-145 1.91e-12

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 66.32  E-value: 1.91e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942   3 LRDLKTFLHLAESRHFGRSARAMHVSPSTLSRQIQRLEEDLGQPLFVRDNRTVTLTEAGEELRVFAQQTLLQYQQLRHTL 82
Cdd:PRK09791   7 IHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQEDI 86

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446287942  83 DQQGPSLSGELHIFCSVTAAYSHLPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAI 145
Cdd:PRK09791  87 RQRQGQLAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDFTI 149
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 1-156 3.15e-12

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 65.82  E-value: 3.15e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942   1 MDLRDLKTFLHLAESRHFGRSARAMHVSPSTLSRQIQRLEEDLGQPLFVRDNRTVTLTEAGEELRVFAqqtllqyqqlRH 80
Cdd:PRK15092  11 LDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYA----------RK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942  81 TL---DQQGPSL-----SGELHIFCSVTAAYSHLPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAIA-GKPET 151
Cdd:PRK15092  81 ILrfnDEACSSLmysnlQGVLTIGASDDTADTILPFLLNRVSSVYPKLALDVRVKRNAFMMEMLESQEVDLAVTtHRPSS 160


                 ....*
gi 446287942 152 LPGAV 156
Cdd:PRK15092 161 FPALN 165
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
1-68 6.16e-12

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 64.65  E-value: 6.16e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446287942   1 MDLRDLKTFLHLAESRHFGRSARAMHVSPSTLSRQIQRLEEDLGQPLFVRDNRTVTLTEAGEELRVFA 68
Cdd:PRK03601   1 MDTELLKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYA 68
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
1-64 6.20e-12

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 64.83  E-value: 6.20e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446287942   1 MDLRDLKTFLHLAESRHFGRSARAMHVSPSTLSRQIQRLEEDLGQPLFVRDNRTVTLTEAGEEL 64
Cdd:PRK10094   2 FDPETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHL 65
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 106-255 2.16e-09

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: 56.01  E-value: 2.16e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 106 LPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAIAGKPETLPGaVAFSMLENLAVVLIAPAlPCPVRNQVSVDK 185
Cdd:cd08434   15 VPDLIRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLALCSPVPDEPD-IEWIPLFTEELVLVVPK-DHPLAGRDSVDL 92

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446287942 186 PDWSTVPFIMADQGPVRRRI--ELwFRRHKISnPQIyaTVGGHE--AMVSMVALGCGVALLPEVVLENsPEPVR 255
Cdd:cd08434   93 AELADEPFVLLSPGFGLRPIvdEL-CAAAGFT-PKI--AFEGEEdsTIAGLVAAGLGVAILPEMTLLN-PPGVK 161
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 106-274 5.82e-09

The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold; This CD includes the substrate binding domain of CidR which positively up-regulates the expression of cidABC operon in the presence of acetic acid produced by the metabolism of excess glucose. The CidR affects the control of murein hydrolase activity by enhancing cidABC expression in the presence of acetic acid. Thus, up-regulation of cidABC expression results in increased murein hydrolase activity. This substrate binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176129 [Multi-domain]  Cd Length: 197  Bit Score: 54.87  E-value: 5.82e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 106 LPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAIAGKPETLPGAVAFSmLENLAVVLIAPALPcPVRNQVSVDK 185
Cdd:cd08438   15 FAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVLPVDEEEFDSQP-LCNEPLVAVLPRGH-PLAGRKTVSL 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 186 PDWSTVPFIMADQG-PVRRRIELWFRRHKISnPQIYATVGGHEAMVSMVALGCGVALLPEVVLEnspEPVRNRVMILERS 264
Cdd:cd08438   93 ADLADEPFILFNEDfALHDRIIDACQQAGFT-PNIAARSSQWDFIAELVAAGLGVALLPRSIAQ---RLDNAGVKVIPLT 168

                        170
                 ....*....|
gi 446287942 265 DEKTPFELGV 274
Cdd:cd08438  169 DPDLRWQLAL 178
PBP2_LysR cd08456
The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine ...
 92-289 1.62e-08

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: 53.58  E-value: 1.62e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942  92 ELHIFCSVTAAYSHLPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAIAGKPETLPGAVAFSMLENLAVVLIAP 171
Cdd:cd08456    1 ELRIAVLPALSQSFLPRAIKAFLQRHPDVTISIHTRDSPTVEQWLSAQQCDLGLVSTLHEPPGIERERLLRIDGVCVLPP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 172 ALPCPVRNQVSVDkpDWSTVPFI-MADQGPVRRRIELWFRRHKIsNPQIyaTVGGHEAMV--SMVALGCGVALL-PEVVL 247
Cdd:cd08456   81 GHRLAVKKVLTPS--DLEGEPFIsLARTDGTRQRVDALFEQAGV-KRRI--VVETSYAATicALVAAGVGVSVVnPLTAL 155

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 446287942 248 ENSPEPVRNRvmileRSDEKTPFELGVCAQKKRLHEPLIDAF 289
Cdd:cd08456  156 DYAAAGLVVR-----RFSPAVPFEVSLIRPKHRPSSALVAAF 192
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
6-293 3.23e-08

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 53.90  E-value: 3.23e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942   6 LKTFLHLAESRHFGRSARAMHVSPSTLSRQIQRLEEDLGQPLFvrdNRTVTLTEAGEELRVFaqqtllqYQQLRHTLDQQ 85
Cdd:PRK10082  16 LYDFLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELF---NRQVTPLQLSEQGKIF-------HSQIRHLLQQL 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942  86 GPSLS----GELHIFCSVTAAYSH------LPPILDRFRaehPSVEIKLTTGDAADAMDKVVTGEADLAIAGKPETLPGA 155
Cdd:PRK10082  86 ESNLAelrgGSDYAQRKIKIAAAHslslglLPSIISQMP---PLFTWAIEAIDVDEAVDKLREGQSDCIFSFHDEDLLEA 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 156 vAFSMLENLAVVLIaPALPCPVRNQV--SVDKPDWSTVPFimADQGPVRRRIELWFRRH-KISNPQIYatVGGHEAMVSM 232
Cdd:PRK10082 163 -PFDHIRLFESQLF-PVCASDEHGEAlfNLAQPHFPLLNY--SRNSYMGRLINRTLTRHsELSFSTFF--VSSMSELLKQ 236

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446287942 233 VAL-GCGVALLPEVVLENspEPVRNRVMILERSDEKTPFELGVCAQKKRLHePLIDAFWKIL 293
Cdd:PRK10082 237 VALdGCGIAWLPEYAIQQ--EIRSGQLVVLNRDELVIPIQAYAYRMNTRMN-PVAERFWREL 295
PBP2_IlvR cd08453
The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved ...
 100-246 4.35e-08

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: 52.36  E-value: 4.35e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 100 TAAYSHLPPILDRFRAEHPSVEIKLT--TGDAadAMDKVVTGEAD--LAIAGKPETLPGAVAFSMLENLAVVLIAPALPC 175
Cdd:cd08453    9 TADYSVLPELVRRFREAYPDVELQLReaTSDV--QLEALLAGEIDagIVIPPPGASAPPALAYRPLLSEPLVLAVPAAWA 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 176 PVRnQVSVDKPDWSTVPFIMadqgpvrrrielwFRRHkiSNPQIYATV------GGHEA-----------MVSMVALGCG 238
Cdd:cd08453   87 AEG-GAPLALAAVAAEPLVI-------------FPRR--IAPAFHDAVtgyyraAGQTPriaqeaiqmqtIISLVSAGMG 150


                 ....*...
gi 446287942 239 VALLPEVV 246
Cdd:cd08453  151 VALVPASL 158
cysB PRK12681
HTH-type transcriptional regulator CysB;
22-146 7.17e-08

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 52.98  E-value: 7.17e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942  22 ARAMHVSPSTLSRQIQRLEEDLGQPLFVRDNRTVT-LTEAGEEL-----RVFAQQTLLQYQQLRHTLDQQGpslsgELHI 95
Cdd:PRK12681  23 AEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTqVTPAGEEIiriarEILSKVESIKSVAGEHTWPDKG-----SLYI 97

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 446287942  96 FCSVTAAYSHLPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAIA 146
Cdd:PRK12681  98 ATTHTQARYALPPVIKGFIERYPRVSLHMHQGSPTQIAEAAAKGNADFAIA 148
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 107-244 7.23e-08

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: 51.83  E-value: 7.23e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 107 PPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAIAGKPETLPGAVAFSML-ENLavVLIAPAlPCPVRNQVSVDK 185
Cdd:cd08433   16 VPLLRAVRRRYPGIRLRIVEGLSGHLLEWLLNGRLDLALLYGPPPIPGLSTEPLLeEDL--FLVGPA-DAPLPRGAPVPL 92

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 186 PDWSTVPFIMADQG-PVRRRIELWFRRHKIsNPQIYATVGGHEAMVSMVALGCGVALLPE 244
Cdd:cd08433   93 AELARLPLILPSRGhGLRRLVDEAAARAGL-TLNVVVEIDSVATLKALVAAGLGYTILPA 151
PBP2_HcaR cd08450
The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in ...
 106-244 8.85e-08

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: 51.22  E-value: 8.85e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 106 LPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAIAgKPETLPGAVAFSMLENLAVVLIAPAlPCPVRNQVSVDK 185
Cdd:cd08450   15 LPEVLPILREEHPDLDVELSSLFSPQLAEALMRGKLDVAFM-RPEIQSDGIDYQLLLKEPLIVVLPA-DHRLAGREKIPP 92

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446287942 186 PDWSTVPFIMADQ--GPVRRRIELWFRRHKISnPQIYATVGGHEAMVSMVALGCGVALLPE 244
Cdd:cd08450   93 QDLAGENFISPAPtaPVLQQVIENYAAQHNIQ-PNIIQEADNLLSAMSLVASTLGCALLPL 152
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 3-248 1.23e-07

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 52.00  E-value: 1.23e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942   3 LRDLKTFLHLAESRHFGRSARAMHVSPSTLSRQIQRLEEDLGQPLFVRDNRTVTLTEAGEEL--RVFAQqtllqyqqlrh 80
Cdd:PRK10837   5 LRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLypRALAL----------- 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942  81 tLDQQGP------SLSGELHIFCSVTAAYSHLPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAIAGKPETLPG 154
Cdd:PRK10837  74 -LEQAVEieqlfrEDNGALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNSQDVINAVLDFRVDIGLIEGPCHSPE 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 155 AVAFSMLENLAVVLIAPALPCpVRNQVSVDkpDWSTVPFIMADQGPVRRRIELWFRRHKISNPQIYATVGGHEAMVSMVA 234
Cdd:PRK10837 153 LISEPWLEDELVVFAAPDSPL-ARGPVTLE--QLAAAPWILRERGSGTREIVDYLLLSHLPRFELAMELGNSEAIKHAVR 229

                        250
                 ....*....|....
gi 446287942 235 LGCGVALLPEVVLE 248
Cdd:PRK10837 230 HGLGISCLSRRVIA 243
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
1-64 1.40e-07

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 51.70  E-value: 1.40e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446287942   1 MDLRDLKTFLHLAESRHFGRSARAMHVSPSTLSRQIQRLEEDLGQPLFVRDnRTVTLTEAGEEL 64
Cdd:PRK03635   2 LDYKQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVRT-QPCRPTEAGQRL 64
PBP2_LTTR_aromatics_like_1 cd08447
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 100-257 1.51e-07

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: 50.72  E-value: 1.51e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 100 TAAYSHLPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAIAGKPETLPGAVAFSMLENLAVVLIAPALPCPVRN 179
Cdd:cd08447    9 ASAYSFLPRLLAAARAALPDVDLVLREMVTTDQIEALESGRIDLGLLRPPFARPGLETRPLVREPLVAAVPAGHPLAGAE 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 180 QVSVDkpDWSTVPFIMadQGPVRRR--IEL---WFRRHKISnPQIYATVGGHEAMVSMVALGCGVALLPEVVLENSPEPV 254
Cdd:cd08447   89 RLTLE--DLDGQPFIM--YSPTEARyfHDLvvrLFASAGVQ-PRYVQYLSQIHTMLALVRAGLGVALVPASASRLRFEGV 163


                 ...
gi 446287942 255 RNR 257
Cdd:cd08447  164 VFR 166
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 95-245 2.73e-07

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


Pssm-ID: 176117 [Multi-domain]  Cd Length: 199  Bit Score: 50.00  E-value: 2.73e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942  95 IFCSVTAAYSHLPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAIAGKPETLPG--AVAFSMLENLAVVliAPA 172
Cdd:cd08426    4 VATGEGLAAELLPSLIARFRQRYPGVFFTVDVASTADVLEAVLSGEADIGLAFSPPPEPGirVHSRQPAPIGAVV--PPG 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446287942 173 LPCPVRNQVSVDkpDWSTVPFIMADQG-PVRRRIELWFRRHKISNPQIYATvGGHEAMVSMVALGCGVALLPEV 245
Cdd:cd08426   82 HPLARQPSVTLA--QLAGYPLALPPPSfSLRQILDAAFARAGVQLEPVLIS-NSIETLKQLVAAGGGISLLTEL 152
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 93-248 4.60e-07

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: 49.19  E-value: 4.60e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942  93 LHIFCSVTAAYSHLPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAI-AGKPETLPGAVAFSMLENLAVVLIA- 170
Cdd:cd08435    2 VRVGAVPAAAPVLLPPAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAIgRLADDEQPPDLASEELADEPLVVVAr 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446287942 171 PALPCPVRNQVSVDkpDWSTVPFIMADQG-PVRRRIELWFRRHKISNPQIYATVGGHEAMVSMVALGCGVALLPEVVLE 248
Cdd:cd08435   82 PGHPLARRARLTLA--DLADYPWVLPPPGtPLRQRLEQLFAAAGLPLPRNVVETASISALLALLARSDMLAVLPRSVAE 158
PRK09801 PRK09801
LysR family transcriptional regulator;
4-172 4.78e-07

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 50.42  E-value: 4.78e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942   4 RDLKTFLHLAESRHFGRSARAMHVSPSTLSRQIQRLEEDLGQPLFVRDNRTVTLTEAGEELRVFAQQTLLQYQQLRHTLD 83
Cdd:PRK09801   9 KDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVT 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942  84 QQGPSLSGELHIFCSVTAAYSHLPPILDRFRAEHPSVEIKLttgDAADAMDKVVTGEADLAIAGKPETLPGAVAFSMLEN 163
Cdd:PRK09801  89 QIKTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHF---ELFDRQIDLVQDNIDLDIRINDEIPDYYIAHLLTKN 165


                 ....*....
gi 446287942 164 LAVVLIAPA 172
Cdd:PRK09801 166 KRILCAAPE 174
PBP2_GcdR_like cd08481
The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, ...
 106-289 6.84e-07

The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, contains the type 2 periplasmic binding fold; GcdR is involved in the glutaconate/glutarate-specific activation of the Pg promoter driving expression of a glutaryl-CoA dehydrogenase-encoding gene (gcdH). The GcdH protein is essential for the anaerobic catabolism of many aromatic compounds and some alicyclic and dicarboxylic acids. The structural topology of this substrate-binding domain is most similar 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: 176170 [Multi-domain]  Cd Length: 194  Bit Score: 48.83  E-value: 6.84e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 106 LPPILDRFRAEHPSVEIKLTTGDAA-DAMDkvvtGEADLAIAGKPETLPGAVA-FSMLENLAVVlIAPALPcpvrNQVSV 183
Cdd:cd08481   15 LIPRLPDFLARHPDITVNLVTRDEPfDFSQ----GSFDAAIHFGDPVWPGAESeYLMDEEVVPV-CSPALL----AGRAL 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 184 DKP-DWSTVPFImadqgPVRRRIELW---FRRHKISNPQIYATVG-GHEAMVSMVAL-GCGVALLPEVVLENspEPVRNR 257
Cdd:cd08481   86 AAPaDLAHLPLL-----QQTTRPEAWrdwFEEVGLEVPTAYRGMRfEQFSMLAQAAVaGLGVALLPRFLIEE--ELARGR 158

                        170       180       190
                 ....*....|....*....|....*....|..
gi 446287942 258 VMILERSDEKTPFELGVCAQKKRLHEPLIDAF 289
Cdd:cd08481  159 LVVPFNLPLTSDKAYYLVYPEDKAESPPVQAF 190
PBP2_LTTR_like_1 cd08421
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-248 8.54e-07

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


Pssm-ID: 176113  Cd Length: 198  Bit Score: 48.67  E-value: 8.54e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942  93 LHIFCSVTAAYSHLPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAIAGkpetlpGAVAFSMLENLA------V 166
Cdd:cd08421    2 VRLLANTSAIVEFLPEDLASFLAAHPDVRIDLEERLSADIVRAVAEGRADLGIVA------GNVDAAGLETRPyrtdrlV 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 167 VLIAPALPCPVRNQVSVDkpDWSTVPFI-MADQGPVRRRIELWFRRHKISnPQIYATVGGHEAMVSMVALGCGVALLPEV 245
Cdd:cd08421   76 VVVPRDHPLAGRASVAFA--DTLDHDFVgLPAGSALHTFLREAAARLGRR-LRLRVQVSSFDAVCRMVAAGLGIGIVPES 152


                 ...
gi 446287942 246 VLE 248
Cdd:cd08421  153 AAR 155
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
3-137 9.01e-07

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 49.37  E-value: 9.01e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942   3 LRDLKTFLHLAESRHFGRSARAMHVSPSTLSRQIQRLEEDLGQPLFVRDNRTVTLTEAGeelRVFAQQTLLQYQQLRHTL 82
Cdd:PRK10632   4 LKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAG---RIYYQGCRRMLHEVQDVH 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446287942  83 DQQ---GPSLSGELHIFCSVTAAYSHLPPILDRFRAEHPSVEIKLTTGDA-----ADAMDKVV 137
Cdd:PRK10632  81 EQLyafNNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTGIPapdliADGLDVVI 143
PRK10341 PRK10341
transcriptional regulator TdcA;
6-145 9.38e-07

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 49.48  E-value: 9.38e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942   6 LKTFLHLAESRHFGRSARAMHVSPSTLSRQIQRLEEDLGQPLFVRDNRTVTLTEAGEELRVFAQQTLLQYQQLRHTLDQQ 85
Cdd:PRK10341  12 LVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEINGM 91

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942  86 GPSLSGELHIFCSVTAAYSHLPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAI 145
Cdd:PRK10341  92 SSEAVVDVSFGFPSLIGFTFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAI 151
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 18-62 1.21e-06

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 49.17  E-value: 1.21e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 446287942  18 FGRSARAMHVSPSTLSRQIQRLEEDLGQPLFVRDNRTVTLTEAGE 62
Cdd:PRK11074  19 FSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGE 63
MntR COG1321
Mn-dependent transcriptional regulator MntR, DtxR family [Transcription];
6-64 4.69e-06

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


Pssm-ID: 440932 [Multi-domain]  Cd Length: 135  Bit Score: 45.19  E-value: 4.69e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446287942   6 LKTFLHLAESRHFGRS---ARAMHVSPSTLSRQIQRLEED-LgqpLFVRDNRTVTLTEAGEEL 64
Cdd:COG1321   12 LKAIYELSEEGGPVRTsdiAERLGVSPPSVTEMLKKLEEKgL---VEYEPYGGITLTEEGREL 71
PBP2_MdcR cd08416
The C-terminal substrate-binding domian of LysR-type transcriptional regulator MdcR, which ...
 106-243 2.56e-05

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


Pssm-ID: 176108  Cd Length: 199  Bit Score: 44.26  E-value: 2.56e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 106 LPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAIAGKPETL--PGAVAFSMLEN---LAVVLIAPALPCPvrnq 180
Cdd:cd08416   15 VPRIIMGLKLRRPELDIELTLGSNKDLLKKLKDGELDAILVATPEGLndPDFEVVPLFEDdifLAVPATSPLAASS---- 90

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446287942 181 vSVDKPDWSTVPFIMADQG-PVRRRIELWFRRHKISnPQIYATVGGHEAMVSMVALGCGVALLP 243
Cdd:cd08416   91 -EIDLRDLKDEKFVTLSEGfATYRGFDEAFEIAGFE-PNVVMRVNDIFSLMSMVSGGVGYALLP 152
PBP2_MetR cd08441
The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which ...
 106-243 3.09e-05

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: 44.09  E-value: 3.09e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 106 LPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAIAGKPETLPGaVAFSMLENLAVVLIapalpcpvrnqVSVDK 185
Cdd:cd08441   15 LMPVLDQFRERWPDVELDLSSGFHFDPLPALLRGELDLVITSDPLPLPG-IAYEPLFDYEVVLV-----------VAPDH 82

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446287942 186 PdWSTVPFIMADQ--------GPV-RRRIELWfrRHKIS----NPQIYATVGGHEAMVSMVALGCGVALLP 243
Cdd:cd08441   83 P-LAAKEFITPEDladetlitYPVeRERLDVF--RHFLQpagiEPKRRRTVELTLMILQLVASGRGVAALP 150
PBP2_HupR cd08431
The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which ...
 103-174 3.47e-05

The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which regulates expression of the heme uptake receptor HupA; contains the type 2 periplasmic binding fold; HupR, a member of the LysR family, activates hupA transcription under low-iron conditions in the presence of hemin. The expression of many iron-uptake genes, such as hupA, is regulated at the transcriptional level by iron and an iron-binding repressor protein called Fur (ferric uptake regulation). Under iron-abundant conditions with heme, the active Fur repressor protein represses transcription of the iron-uptake gene hupA, and prevents transcriptional activation via HupR. Under low-iron conditions with heme, the Fur repressor is inactive and transcription of the hupA is allowed. 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: 176122 [Multi-domain]  Cd Length: 195  Bit Score: 43.80  E-value: 3.47e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446287942 103 YSHLPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAIAGKPETLPGAVAFSMLENLAVVL-IAPALP 174
Cdd:cd08431   12 LQPLYPLIAEFYQLNKATRIRLSEEVLGGTWDALASGRADLVIGATGELPPGGVKTRPLGEVEFVFaVAPNHP 84
PBP2_CysB_like cd08413
The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains ...
 92-245 4.20e-05

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: 43.38  E-value: 4.20e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942  92 ELHIFCSVTAAYSHLPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAIAgkPETL---PGAVAFSMLE-NLAVV 167
Cdd:cd08413    1 QLTIATTHTQARYVLPPVIAAFRKRYPKVKLSLHQGTPSQIAEMVLKGEADIAIA--TEALddhPDLVTLPCYRwNHCVI 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 168 liapaLPC--PVRNQVSVDKPDWSTVPFIMADQGPV-RRRIELWFRRHKISnPQIYATVGGHEAMVSMVALGCGVALLPE 244
Cdd:cd08413   79 -----VPPghPLADLGPLTLEDLAQYPLITYDFGFTgRSSIDRAFARAGLE-PNIVLTALDADVIKTYVRLGLGVGIIAE 152


                 .
gi 446287942 245 V 245
Cdd:cd08413  153 M 153
PBP2_MleR cd08437
The substrate binding domain of LysR-type transcriptional regulator MleR which required for ...
 106-293 5.88e-05

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


Pssm-ID: 176128  Cd Length: 198  Bit Score: 43.09  E-value: 5.88e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 106 LPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAIAGKPETLPGA--VAFSMLENLAVVLIAPALPCPVRNQVSV 183
Cdd:cd08437   15 FPKLAKDLIKTGLMIQIDTYEGGSAELLEQLLQGDLDIALLGSLTPLENSalHSKIIKTQHFMIIVSKDHPLAKAKKVNF 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 184 DkpDWSTVPFIMADQGPVRRRIELWFRRHKISNPQIYATVGGHEAMVSMVALGCGVALLPEVVLENSPepvrnRVMILER 263
Cdd:cd08437   95 A--DLKKENFILLNEHFVHPKAFDSLCQQANFQPNIVYRTNDIHILKSMVRENVGIGFLTDIAVKPDD-----HLVAIPL 167

                        170       180       190
                 ....*....|....*....|....*....|.
gi 446287942 264 SDEKTP-FELGVCAQKKRLHEPLIDAFWKIL 293
Cdd:cd08437  168 LDNEQPtFYISLAHRKDQLLTPAQKKLLDLL 198
PBP2_CysB cd08443
The C-terminal substrate domain of LysR-type transcriptional regulator CysB contains type 2 ...
 93-289 1.04e-04

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


Pssm-ID: 176134  Cd Length: 198  Bit Score: 42.55  E-value: 1.04e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942  93 LHIFCSVTAAYSHLPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAIAgkPETLPGAVAFSMLE----NLAVVl 168
Cdd:cd08443    2 LYVATTHTQARYVLPPVIKGFIERYPRVSLQMHQGSPTQIAEMVSKGLVDFAIA--TEALHDYDDLITLPcyhwNRCVV- 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 169 IAPALPCPVRNQVSVDKpdWSTVPFIMADQGPV-RRRIELWFRRHKISnPQIYATVGGHEAMVSMVALGCGVALLPEVVL 247
Cdd:cd08443   79 VKRDHPLADKQSISIEE--LATYPIVTYTFGFTgRSELDTAFNRAGLT-PNIVLTATDADVIKTYVRLGLGVGVIASMAY 155

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 446287942 248 ENSPEP---VRNRVMILERSDEKTPFELGVCAqkKRLHEPLIDAF 289
Cdd:cd08443  156 DPVDDPdlvIRDARDLFPWSVTKIAFRRGTFL--RSYMYDFIQRF 198
HTH_MARR smart00347
helix_turn_helix multiple antibiotic resistance protein;
22-64 1.89e-04

helix_turn_helix multiple antibiotic resistance protein;


Pssm-ID: 197670 [Multi-domain]  Cd Length: 101  Bit Score: 39.88  E-value: 1.89e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 446287942    22 ARAMHVSPSTLSRQIQRLEEDlGqplFVR------DNRTV--TLTEAGEEL 64
Cdd:smart00347  31 AKRLGVSPSTVTRVLDRLEKK-G---LVRrepspeDRRSVlvSLTEEGREL 77
PRK15243 PRK15243
virulence genes transcriptional activator SpvR;
4-64 2.01e-04

virulence genes transcriptional activator SpvR;


Pssm-ID: 185155 [Multi-domain]  Cd Length: 297  Bit Score: 42.35  E-value: 2.01e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446287942   4 RDLKTFLHLAESRHFGRSARAMHVSPSTLSRQIQRLEEDLGQPLFVRDNRTVTLTEAGEEL 64
Cdd:PRK15243   7 KKLKIFITLMETGSFSIATSVLYITRTPLSRVISDLERELKQRLFIRKNGTLIPTEFAQTI 67
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 91-145 3.29e-04

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


Pssm-ID: 176114 [Multi-domain]  Cd Length: 197  Bit Score: 40.89  E-value: 3.29e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 446287942  91 GELHIFCSVTAAYSHLPPILDRFRAEHPSVEIKLTTGDA-ADamdkVVTGEADLAI 145
Cdd:cd08422    1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRlVD----LVEEGFDLAI 52
PBP2_TdcA cd08418
The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is ...
 102-145 4.61e-04

The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is involved in the degradation of L-serine and L-threonine, contains the type 2 periplasmic binding fold; TdcA, a member of the LysR family, activates the expression of the anaerobically-regulated tdcABCDEFG operon which is involved in the degradation of L-serine and L-threonine to acetate and propionate, respectively. The tdc operon is comprised of one regulatory gene tdcA and six structural genes, tdcB to tdcG. The expression of the tdc operon is affected by several transcription factors including the cAMP receptor protein (CRP), integration host factor (IHF), histone-like protein (HU), and the operon specific regulators TdcA and TcdR. TcdR is divergently transcribed from the operon and encodes a small protein that is required for efficient expression of the Escherichia coli tdc operon. 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: 176110 [Multi-domain]  Cd Length: 201  Bit Score: 40.41  E-value: 4.61e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 446287942 102 AYSHLPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAI 145
Cdd:cd08418   11 AHTLMPAVINRFKEQFPDVQISIYEGQLSSLLPELRDGRLDFAI 54
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 93-245 5.64e-04

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: 40.26  E-value: 5.64e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942  93 LHIFCSVTAAYSHLPPILDRFRAEHPSVEIKLTTGDAADAMDkvvTGEADLAIAGKPETLPGAVAFSMLENLAVVLIAPA 172
Cdd:cd08432    2 LTVSVTPSFAARWLIPRLARFQARHPDIDLRLSTSDRLVDFA---REGIDLAIRYGDGDWPGLEAERLMDEELVPVCSPA 78

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446287942 173 LpcpvRNQVSVDKP-DWSTVPFIMADQGPVRRRieLWFRRHKISNPQIYATVG-GHEAMVSMVAL-GCGVALLPEV 245
Cdd:cd08432   79 L----LAGLPLLSPaDLARHTLLHDATRPEAWQ--WWLWAAGVADVDARRGPRfDDSSLALQAAVaGLGVALAPRA 148
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 20-241 5.98e-04

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 40.75  E-value: 5.98e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942  20 RSARAMHVSPSTLSRQIQRLEEDLGQPLFVRDNRTVTLTEAGeeLRVFAQQTLLQYQQLRhtLDQQGPSL----SGELHI 95
Cdd:PRK11013  23 EAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQG--LRLFEEVQRSYYGLDR--IVSAAESLrefrQGQLSI 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942  96 FCSVTAAYSHLPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAIAGKPETLPGAVAFSMLENLAVVLIAPALPC 175
Cdd:PRK11013  99 ACLPVFSQSLLPGLCQPFLARYPDVSLNIVPQESPLLEEWLSAQRHDLGLTETLHTPAGTERTELLTLDEVCVLPAGHPL 178

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446287942 176 PVRNQVSVDkpDWSTVPFI-MADQGPVRRRIELWFRRHKISNPQIYATvggHEA--MVSMVALGCGVAL 241
Cdd:PRK11013 179 AAKKVLTPD--DFAGENFIsLSRTDSYRQLLDQLFAEHGVKRRMVVET---HSAasVCAMVRAGVGVSI 242
PBP2_Chlorocatechol cd08446
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 91-246 6.38e-04

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


Pssm-ID: 176137 [Multi-domain]  Cd Length: 198  Bit Score: 39.96  E-value: 6.38e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942  91 GELHIFCSVTAAYSHLPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAIAGKPETLPGAVAFSMLENLAVVLIA 170
Cdd:cd08446    1 GELDVGYFGSAILDTVPRLLRAFLTARPDVTVSLHNMTKDEQIEALRAGRIHIGFGRFYPVEPDIAVENVAQERLYLAVP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 171 PALPCPVRNQVSVDkpDWSTVPFIMADQGPVR----RRIELwFRRHKISnPQIYATVGGHEAMVSMVALGCGVALLPEVV 246
Cdd:cd08446   81 KSHPLAARPAVSLA--DLRNEPLILFPRGGRPsfadEVLGL-FRRAGVE-PRVAQEVEDVVAALALVAAGFGVCIVPESV 156
PBP2_Cbl cd08444
The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is ...
 92-248 6.76e-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: 39.80  E-value: 6.76e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942  92 ELHIFCSVTAAYSHLPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAIAGKP-ETLPGAVAFSMLENLAVVLIA 170
Cdd:cd08444    1 ELTIATTHTQARYALPWVVQAFKEQFPNVHLVLHQGSPEEIASMLANGQADIGIATEAlENHPELVSFPYYDWHHHIIVP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 171 PALPCPVRNQVSVDK-PDWstvPFIMADQGPV-RRRIELWFRRHKISnPQIYATVGGHEAMVSMVALGCGVALLPEVVLE 248
Cdd:cd08444   81 VGHPLESITPLTIETiAKW---PIITYHGGFTgRSRIDRAFSRAELT-PNIVLSALDADVIKTYVGLGMGIGIVAEMAFE 156
PBP2_LTTR_aromatics_like_2 cd08448
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-244 8.68e-04

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


Pssm-ID: 176139 [Multi-domain]  Cd Length: 197  Bit Score: 39.56  E-value: 8.68e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942  92 ELHIFCSVTAAYSHLPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAIAGKPETLPGAVAFSMLENLAVVliap 171
Cdd:cd08448    1 RLRIGFVGSMLYRGLPRILRAFRAEYPGIEVALHEMSSAEQIEALLRGELDLGFVHSRRLPAGLSARLLHREPFVC---- 76

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446287942 172 ALPC--PVRNQVSVDKPDWSTVPFIM--ADQGP-VRRRIELWFRRHKISnPQIYATVGGHEAMVSMVALGCGVALLPE 244
Cdd:cd08448   77 CLPAghPLAARRRIDLRELAGEPFVLfsREVSPdYYDQIIALCMDAGFH-PKIRHEVRHWLTVVALVAAGMGVALVPR 153
PBP2_OccR cd08457
The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the ...
 102-293 9.48e-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: 39.39  E-value: 9.48e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 102 AYSHLPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAIAGKPETLPGAVAFSMLENLAVVLIAPALPCPVRNQV 181
Cdd:cd08457   11 ANGFLPRFLAAFLRLRPNLHLSLMGLSSSQVLEAVASGRADLGIADGPLEERQGFLIETRSLPAVVAVPMGHPLAQLDVV 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 182 SVDkpDWSTVPFIMADQG-PVRRRIELWFRRHKISNPQIYATVGGHEAMvSMVALGCGVALLPEVVLENSPEpvrnRVMI 260
Cdd:cd08457   91 SPQ--DLAGERIITLENGyLFRMRVEVALGKIGVKRRPIIEVNLSHTAL-SLVREGLGIAIIDPATAIGLPL----DGIV 163

                        170       180       190
                 ....*....|....*....|....*....|...
gi 446287942 261 LERSDEKTPFELGVCAQKKRLHEPLIDAFWKIL 293
Cdd:cd08457  164 IRPFDTFIDAGFLVVRAANGPPSTMVDRFIDEF 196
MarR COG1846
DNA-binding transcriptional regulator, MarR family [Transcription];
22-65 1.23e-03

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


Pssm-ID: 441451 [Multi-domain]  Cd Length: 142  Bit Score: 38.41  E-value: 1.23e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 446287942  22 ARAMHVSPSTLSRQIQRLEEDlGqplFVR------DNR--TVTLTEAGEELR 65
Cdd:COG1846   59 AERLGLTKSTVSRLLDRLEEK-G---LVErepdpeDRRavLVRLTEKGRALL 106
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 106-234 1.27e-03

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: 39.12  E-value: 1.27e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 106 LPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAIAGKPETLPGAVAFSMLENLAVVLIAPALPcPVRNQVSVDk 185
Cdd:cd08417   15 LPPLLARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELPPGLRSQPLFEDRFVCVARKDHP-LAGGPLTLE- 92

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 446287942 186 pDWSTVPFIMADQGPVRRR-IELWFRRHKISnPQIYATVGGHEAMVSMVA 234
Cdd:cd08417   93 -DYLAAPHVLVSPRGRGHGlVDDALAELGLS-RRVALTVPHFLAAPALVA 140
PBP2_BvgS_D2 cd13707
The second of the two tandem periplasmic domains of sensor-kinase BvgS; the type 2 ...
 108-186 1.67e-03

The second of the two tandem periplasmic domains of sensor-kinase BvgS; the type 2 peripasmic-binding fold protein; This group contains the second domain of the periplasmic solute-binding domains of BvgS and related proteins. BvgS is composed of two periplasmic domains homologous to bacterial periplasmic-binding proteins (PBPs), a transmembrane region followed successively by a cytoplasmic PAS (Per/ARNT/SIM), a Histidine-kinase (HK), a receiver and a Histidine phosphotransfer (Hpt) domains. The sensor protein BvgS can autophosphorylate and phosphorylate the response regulator BvgA. The BvgAS phosphorelay controls the expression of virulence factors in response to certain environmental stimuli in Bordetella pertussis. Its close homologs, Escherichia coli EvgS and Klebsiella pneumoniae KvgS, appear to be involved in the transcriptional regulation of drug efflux pumps and in countering free radical stresses and sensing iron limiting conditions, respectively. The periplasmic sensor domain of BvgS belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 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 receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270425 [Multi-domain]  Cd Length: 221  Bit Score: 39.12  E-value: 1.67e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 108 PILDRFRAEHPSVEIKLTtGDAADAMDKVVTGEADLAIAgkpeTLPGA---VAFSMLENLAVVLIAPALPCPVRNQVSVD 184
Cdd:cd13707  119 ALEDLLRRRYPQIELVEV-DNTAEALALVASGKADATVA----SLISArylINHYFRDRLKIAGILGEPPAPIAFAVRRD 193


                 ..
gi 446287942 185 KP 186
Cdd:cd13707  194 QP 195
nhaR PRK11062
transcriptional activator NhaR; Provisional
 20-62 1.83e-03

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 39.22  E-value: 1.83e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 446287942  20 RSARAMHVSPSTLSRQIQRLEEDLGQPLFVRDNRTVTLTEAGE 62
Cdd:PRK11062  23 GAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGE 65
PBP2_LrhA_like cd08439
The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of ...
 92-156 3.09e-03

The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of closely related homologs, contains the type 2 periplasmic binding fold; This CD represents the LrhA subfamily of LysR-like bacterial transcriptional regulators, including LrhA, HexA, PecT, and DgdR. LrhA is involved in control of the transcription of flagellar, motility, and chemotaxis genes by regulating the synthesis and concentration of FlhD(2)C(2), the master regulator for the expression of flagellar and chemotaxis genes. The LrhA protein has strong homology to HexA and PecT from plant pathogenic bacteria, in which HexA and PecT act as repressors of motility and of virulence factors, such as exoenzymes required for lytic reactions. DgdR also shares similar characteristics to those of LrhA, HexA and PecT. 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: 176130  Cd Length: 185  Bit Score: 37.70  E-value: 3.09e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446287942  92 ELHIFCSVTAAYSHLPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLA-IAGKPETLPGAV 156
Cdd:cd08439    1 TLRIGCPDDYADTILPFLLNRFASVYPRLAIEVVCKRTPRLMEMLERGEVDLAlITHPPPGASATI 66
PBP2_BudR cd08451
The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is ...
 92-269 3.10e-03

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: 37.93  E-value: 3.10e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942  92 ELHI-FCSVTAAYSHLPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAIAGKPETLPGAVAFSML--ENLAVVL 168
Cdd:cd08451    1 RLRVgFTSSAAFHPLVPGLIRRFREAYPDVELTLEEANTAELLEALREGRLDAAFVRPPVARSDGLVLELLleEPMLVAL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 169 iAPALPCPVRNqvSVDKPDWSTVPFIMadqgpVRRR--------IELWFRRHKIS------NPQIYATvggheamVSMVA 234
Cdd:cd08451   81 -PAGHPLARER--SIPLAALADEPFIL-----FPRPvgpglydaIIAACRRAGFTprigqeAPQMASA-------INLVA 145

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 446287942 235 LGCGVALLPE----------VVLENSPEPVRNRVMILERSDEKTP 269
Cdd:cd08451  146 AGLGVSIVPAsmrqlqapgvVYRPLAGAPLTAPLALAYRRGERSP 190
PRK10216 PRK10216
HTH-type transcriptional regulator YidZ;
1-153 5.01e-03

HTH-type transcriptional regulator YidZ;


Pssm-ID: 182312 [Multi-domain]  Cd Length: 319  Bit Score: 37.88  E-value: 5.01e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942   1 MDLRDLKTFLHLAESRHFGRSARAMHVSPSTLSRQIQRLEEDLGQPLFVRDNRTVTLTEAGEEL-RVFAQQTLLQYQQLR 79
Cdd:PRK10216   8 LDLNLLLCLQLLMQERSVTKAAKRMNVTPSAVSKSLAKLRAWFDDPLFVNTPLGLSPTPLMVSMeQNLAEWMQMGNQLLD 87

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446287942  80 HTLDQQGPSLSGELhifcsvtAAYSHLPPIL-----DRFRAEHPSVEIKLTTGDaADAMDKVVTGEADLAIAGKpETLP 153
Cdd:PRK10216  88 KPHHQTPRGLKFEL-------AAESPLMMIMlnalsKRIYQRYPQATIKLRNWD-YDSLDAITRGEVDIGFTGR-ESHP 157
PBP2_CrgA_like_1 cd08470
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 91-145 5.58e-03

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding domain; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 1. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176159  Cd Length: 197  Bit Score: 37.29  E-value: 5.58e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 446287942  91 GELHIFCSVTAAYSHLPPILDRFRAEHPSVEIKLttgDAADAMDKVVTGEADLAI 145
Cdd:cd08470    1 GLLRITCPVAYGERFIAPLVNDFMQRYPKLEVDI---ELTNRVVDLVSEGFDLAI 52
PBP2_CrgA_like_4 cd08473
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 90-128 8.78e-03

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 4. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176162 [Multi-domain]  Cd Length: 202  Bit Score: 36.76  E-value: 8.78e-03
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 446287942  90 SGELHIFCSVTAAYSHLPPILDRFRAEHPSVEIKLTTGD 128
Cdd:cd08473    2 RGTVRVSCPPALAQELLAPLLPRFMAAYPQVRLQLEATN 40
PBP2_AlsR cd08452
The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which ...
 100-292 8.82e-03

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: 36.71  E-value: 8.82e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 100 TAAYSHLPPILDRFRAEHPSVEIKLTTGDAADAMDKVVTGEADLAIAGKPetLPG-AVAFSMLENLAVVLiapALP--CP 176
Cdd:cd08452    9 AAIYEFLPPIVREYRKKFPSVKVELRELSSPDQVEELLKGRIDIGFLHPP--IQHtALHIETVQSSPCVL---ALPkqHP 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446287942 177 VRNQVSVDKPDWSTVPFIMADQG--PVRRRIELWFRRHKISNPQIYATVGGHEAMVSMVALGCGVALLPeVVLENSpepV 254
Cdd:cd08452   84 LASKEEITIEDLRDEPIITVAREawPTLYDEIIQLCEQAGFRPKIVQEATEYQTVIGLVSAGIGVTFVP-SSAKKL---F 159

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 446287942 255 RNRVMILERSDEKTPFELGVcAQKKRLHEPLIDAFWKI 292
Cdd:cd08452  160 NLEVAYRKIDQINLNAEWSI-AYRKDNHNPLLKHFIHI 196
 
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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