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Conserved domains on  [gi|616690428|gb|KAE88012|]
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hypothetical protein W632_00739 [Staphylococcus aureus VET0402R]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 11426483)

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

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-285 6.78e-40

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 139.62  E-value: 6.78e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428   1 MKIEDYRLLITLDETKTLRKAAEILYISQPAVTQRLKAIENAFGVDIFIRTKKQLITTTEGTMIIEHARDMLKRERLFFD 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428  81 KMQAHIGEVNGTISIGCSSLIGQTLLPEVLSLYNAQFPNVEIQVQVGSTEQIKAN--HRDYHVMITRGNKVM-NLANTHL 157
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDAllEGELDLAIRLGPPPDpGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428 158 FNDDHYFIFPKNrrddvtkLPFieFQADPIyinqikqwyndnleqdyhatitVDQVATCKEMLISGVGVTILPEIMMKNI 237
Cdd:COG0583  161 GEERLVLVASPD-------HPL--ARRAPL----------------------VNSLEALLAAVAAGLGIALLPRFLAADE 209

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*...
gi 616690428 238 SKEQfEFEKVEIDNEPLIRSTFMSYDPSMLQLPQVDSFVNLMTSFVEE 285
Cdd:COG0583  210 LAAG-RLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-285 6.78e-40

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 139.62  E-value: 6.78e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428   1 MKIEDYRLLITLDETKTLRKAAEILYISQPAVTQRLKAIENAFGVDIFIRTKKQLITTTEGTMIIEHARDMLKRERLFFD 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428  81 KMQAHIGEVNGTISIGCSSLIGQTLLPEVLSLYNAQFPNVEIQVQVGSTEQIKAN--HRDYHVMITRGNKVM-NLANTHL 157
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDAllEGELDLAIRLGPPPDpGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428 158 FNDDHYFIFPKNrrddvtkLPFieFQADPIyinqikqwyndnleqdyhatitVDQVATCKEMLISGVGVTILPEIMMKNI 237
Cdd:COG0583  161 GEERLVLVASPD-------HPL--ARRAPL----------------------VNSLEALLAAVAAGLGIALLPRFLAADE 209

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*...
gi 616690428 238 SKEQfEFEKVEIDNEPLIRSTFMSYDPSMLQLPQVDSFVNLMTSFVEE 285
Cdd:COG0583  210 LAAG-RLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 91-279 1.52e-25

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


Pssm-ID: 460931 [Multi-domain]  Cd Length: 205  Bit Score: 100.44  E-value: 1.52e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428   91 GTISIGCSSLIGQTLLPEVLSLYNAQFPNVEIQVQVGSTEQIKA--NHRDYHVMITRGNKVMN-LANTHLFNDDHYFIFP 167
Cdd:pfam03466   2 GRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDllLEGELDLAIRRGPPDDPgLEARPLGEEPLVLVAP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428  168 KN---------RRDDVTKLPFIEFQADPIYINQIKQWyNDNLEQDYHATITVDQVATCKEMLISGVGVTILPEIMMKNIS 238
Cdd:pfam03466  82 PDhplargepvSLEDLADEPLILLPPGSGLRDLLDRA-LRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAREL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 616690428  239 kEQFEFEKVEIDNEPLIRSTFMSYDPSMLQLPQVDSFVNLM 279
Cdd:pfam03466 161 -ADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFL 200
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 14-135 1.97e-24

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


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 99.61  E-value: 1.97e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428  14 ETKTLRKAAEILYISQPAVTQRLKAIENAFGVDIFIRTKKQLITTTEGTMIIEHARDMLKRERLFFDKMQAHIGEVNGTI 93
Cdd:NF040786  14 EYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEEEFDRYGKESKGVL 93

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 616690428  94 SIGCSSLIGQTLLPEVLSLYNAQFPNVEIQVQVGSTEQIKAN 135
Cdd:NF040786  94 RIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIEL 135
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 92-279 2.71e-20

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: 86.11  E-value: 2.71e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428  92 TISIGCSSLIGQTLLPEVLSLYNAQFPNVEIQVQVGSTEQIKA--NHRDYHVMITRG-NKVMNLANTHLFNDDHYFIFPK 168
Cdd:cd05466    1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEalLEGELDLAIVALpVDDPGLESEPLFEEPLVLVVPP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428 169 N----RRDDVT-----KLPFIEFQADPIYINQIKQWYNDNLEQdYHATITVDQVATCKEMLISGVGVTILPEIMMKNIsk 239
Cdd:cd05466   81 DhplaKRKSVTladlaDEPLILFERGSGLRRLLDRAFAEAGFT-PNIALEVDSLEAIKALVAAGLGIALLPESAVEEL-- 157

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 616690428 240 EQFEFEKVEIDNEPLIRSTFMSYDPSMLQLPQVDSFVNLM 279
Cdd:cd05466  158 ADGGLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
rbcR CHL00180
LysR transcriptional regulator; Provisional
 7-180 1.27e-16

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 78.14  E-value: 1.27e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428   7 RLLITLDETKTLRKAAEILYISQPAVTQRLKAIENAFGVDIFIRTKKQLITTTEGTMIIEHARDMLK------RERLFFD 80
Cdd:CHL00180  11 RILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILAlceetcRALEDLK 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428  81 KMQAhigevnGTISIGCSSLIGQTLLPEVLSLYNAQFPNVEIQVQVGSTEQIKAN--HRDYHVMITRGNKVMNLAN---- 154
Cdd:CHL00180  91 NLQR------GTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNvaNGQIDIAIVGGEVPTELKKilei 164

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 616690428 155 THLFNDDHYFIFPKN---------RRDDVTKLPFI 180
Cdd:CHL00180 165 TPYVEDELALIIPKShpfaklkkiQKEDLYRLNFI 199
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-285 6.78e-40

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 139.62  E-value: 6.78e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428   1 MKIEDYRLLITLDETKTLRKAAEILYISQPAVTQRLKAIENAFGVDIFIRTKKQLITTTEGTMIIEHARDMLKRERLFFD 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428  81 KMQAHIGEVNGTISIGCSSLIGQTLLPEVLSLYNAQFPNVEIQVQVGSTEQIKAN--HRDYHVMITRGNKVM-NLANTHL 157
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDAllEGELDLAIRLGPPPDpGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428 158 FNDDHYFIFPKNrrddvtkLPFieFQADPIyinqikqwyndnleqdyhatitVDQVATCKEMLISGVGVTILPEIMMKNI 237
Cdd:COG0583  161 GEERLVLVASPD-------HPL--ARRAPL----------------------VNSLEALLAAVAAGLGIALLPRFLAADE 209

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*...
gi 616690428 238 SKEQfEFEKVEIDNEPLIRSTFMSYDPSMLQLPQVDSFVNLMTSFVEE 285
Cdd:COG0583  210 LAAG-RLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 91-279 1.52e-25

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


Pssm-ID: 460931 [Multi-domain]  Cd Length: 205  Bit Score: 100.44  E-value: 1.52e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428   91 GTISIGCSSLIGQTLLPEVLSLYNAQFPNVEIQVQVGSTEQIKA--NHRDYHVMITRGNKVMN-LANTHLFNDDHYFIFP 167
Cdd:pfam03466   2 GRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDllLEGELDLAIRRGPPDDPgLEARPLGEEPLVLVAP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428  168 KN---------RRDDVTKLPFIEFQADPIYINQIKQWyNDNLEQDYHATITVDQVATCKEMLISGVGVTILPEIMMKNIS 238
Cdd:pfam03466  82 PDhplargepvSLEDLADEPLILLPPGSGLRDLLDRA-LRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAREL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 616690428  239 kEQFEFEKVEIDNEPLIRSTFMSYDPSMLQLPQVDSFVNLM 279
Cdd:pfam03466 161 -ADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFL 200
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 14-135 1.97e-24

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


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 99.61  E-value: 1.97e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428  14 ETKTLRKAAEILYISQPAVTQRLKAIENAFGVDIFIRTKKQLITTTEGTMIIEHARDMLKRERLFFDKMQAHIGEVNGTI 93
Cdd:NF040786  14 EYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEEEFDRYGKESKGVL 93

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 616690428  94 SIGCSSLIGQTLLPEVLSLYNAQFPNVEIQVQVGSTEQIKAN 135
Cdd:NF040786  94 RIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIEL 135
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 92-279 2.71e-20

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: 86.11  E-value: 2.71e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428  92 TISIGCSSLIGQTLLPEVLSLYNAQFPNVEIQVQVGSTEQIKA--NHRDYHVMITRG-NKVMNLANTHLFNDDHYFIFPK 168
Cdd:cd05466    1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEalLEGELDLAIVALpVDDPGLESEPLFEEPLVLVVPP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428 169 N----RRDDVT-----KLPFIEFQADPIYINQIKQWYNDNLEQdYHATITVDQVATCKEMLISGVGVTILPEIMMKNIsk 239
Cdd:cd05466   81 DhplaKRKSVTladlaDEPLILFERGSGLRRLLDRAFAEAGFT-PNIALEVDSLEAIKALVAAGLGIALLPESAVEEL-- 157

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 616690428 240 EQFEFEKVEIDNEPLIRSTFMSYDPSMLQLPQVDSFVNLM 279
Cdd:cd05466  158 ADGGLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
rbcR CHL00180
LysR transcriptional regulator; Provisional
 7-180 1.27e-16

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 78.14  E-value: 1.27e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428   7 RLLITLDETKTLRKAAEILYISQPAVTQRLKAIENAFGVDIFIRTKKQLITTTEGTMIIEHARDMLK------RERLFFD 80
Cdd:CHL00180  11 RILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILAlceetcRALEDLK 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428  81 KMQAhigevnGTISIGCSSLIGQTLLPEVLSLYNAQFPNVEIQVQVGSTEQIKAN--HRDYHVMITRGNKVMNLAN---- 154
Cdd:CHL00180  91 NLQR------GTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNvaNGQIDIAIVGGEVPTELKKilei 164

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 616690428 155 THLFNDDHYFIFPKN---------RRDDVTKLPFI 180
Cdd:CHL00180 165 TPYVEDELALIIPKShpfaklkkiQKEDLYRLNFI 199
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-61 1.63e-15

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 69.34  E-value: 1.63e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 616690428    3 IEDYRLLITLDETKTLRKAAEILYISQPAVTQRLKAIENAFGVDIFIRTKKQLITTTEG 61
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
PRK09791 PRK09791
LysR family transcriptional regulator;
1-127 1.18e-14

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 72.49  E-value: 1.18e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428   1 MKIEDYRLLITLDETKTLRKAAEILYISQPAVTQRLKAIENAFGVDIFIRTKKQLITTTEGTMIIEHARDMLKRERLFFD 80
Cdd:PRK09791   5 VKIHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQE 84

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 616690428  81 KMQAHIGEVNGTISIGCSSLIGQTLLPEVLSLYNAQFPNVEIQVQVG 127
Cdd:PRK09791  85 DIRQRQGQLAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRIMEG 131
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 1-132 1.34e-14

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 72.37  E-value: 1.34e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428   1 MKIEDYRLLITLDETKTLRKAAEILYISQPAVTQRLKAIENAFGVDIFIRTKKQLITTTEGTMIIEHARDMLKRERLFFD 80
Cdd:PRK11151   1 MNIRDLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVLKE 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 616690428  81 KMQAHIGEVNGTISIGCSSLIGQTLLPEVLSLYNAQFPNVEIQVQVGSTEQI 132
Cdd:PRK11151  81 MASQQGETMSGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQL 132
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 20-132 1.10e-13

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 69.72  E-value: 1.10e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428  20 KAAEILYISQPAVTQRLKAIENAFGVDIFIRTKKQLITTTEGTMIIEHARDMLKR----ERLFfdkmqahiGEVNGTISI 95
Cdd:PRK10837  22 QASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQaveiEQLF--------REDNGALRI 93

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 616690428  96 GCSSLIGQTLLPEVLSLYNAQFPNVEIQVQVGSTEQI 132
Cdd:PRK10837  94 YASSTIGNYILPAMIARYRRDYPQLPLELSVGNSQDV 130
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 1-230 5.47e-13

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 67.87  E-value: 5.47e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428   1 MKIEDYRLLITLDETKTLRKAAEILYISQPAVTQRLKAIENAFGVDIFIRTKKQLITTTEGTMIIEHARDMLKR-ERLff 79
Cdd:PRK09906   1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQaEKA-- 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428  80 DKMQAHIGEVNGTISIGCSSLIGQTLLPEVLSLYNAQFPNVEIQ-VQVGSTEQIKANHR-DYHVMITRGN-KVMNLANTH 156
Cdd:PRK09906  79 KLRARKIVQEDRQLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIElVSLITTQQEEKLRRgELDVGFMRHPvYSDEIDYLE 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428 157 LFNDDHYFIFPKN------RRDDVTKLPFIEFQA-DPIYI----NQIKQWYNDNlEQDYHATITVDQVATCKEMLISGVG 225
Cdd:PRK09906 159 LLDEPLVVVLPVDhplaheKEITAAQLDGVNFIStDPAYSgslaPIIKAWFAQH-NSQPNIVQVATNILVTMNLVGMGLG 237


                 ....*
gi 616690428 226 VTILP 230
Cdd:PRK09906 238 CTIIP 242
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 18-167 7.32e-13

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 67.32  E-value: 7.32e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428  18 LRKAAEILYISQPAVTQRLKAIENAFGVDIFIRTKKQLITTTE-GTMIIEHARDMLKRERLFfdkmqAHIGEV-----NG 91
Cdd:PRK12682  19 LTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKGLTEpGKAVLDVIERILREVGNI-----KRIGDDfsnqdSG 93

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 616690428  92 TISIGCSSLIGQTLLPEVLSLYNAQFPNVEIQVQVGSTEQIKAnhrdyhvMITRGNKVMNLANTHLFNDDHYFIFP 167
Cdd:PRK12682  94 TLTIATTHTQARYVLPRVVAAFRKRYPKVNLSLHQGSPDEIAR-------MVISGEADIGIATESLADDPDLATLP 162
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-256 6.36e-11

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


Pssm-ID: 176131 [Multi-domain]  Cd Length: 197  Bit Score: 60.23  E-value: 6.36e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428  92 TISIGCSSLIGQTLLPEVLSLYNAQFPNVEIQVQVGSTEQIKAnhrdyHVM--------ITRGNKVMNLANTHLFNDDHY 163
Cdd:cd08440    1 RVRVAALPSLAATLLPPVLAAFRRRHPGIRVRLRDVSAEQVIE-----AVRsgevdfgiGSEPEADPDLEFEPLLRDPFV 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428 164 FIFPKN----RRDDVT-----KLPFIEFQADpiyiNQIKQWYNDNLEQ---DYHATITVDQVATCKEMLISGVGVTILPE 231
Cdd:cd08440   76 LVCPKDhplaRRRSVTwaelaGYPLIALGRG----SGVRALIDRALAAaglTLRPAYEVSHMSTALGMVAAGLGVAVLPA 151

                        170       180
                 ....*....|....*....|....*
gi 616690428 232 IMMKNISKEQFEFekVEIDNEPLIR 256
Cdd:cd08440  152 LALPLADHPGLVA--RPLTEPVVTR 174
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
18-132 8.85e-10

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 58.45  E-value: 8.85e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428  18 LRKAAEILYISQPAVTQRLKAIENAFGVDIFIRTKKQLITTTE-GTMIIEHA----RDM--LKRerlffdkmqahIG--- 87
Cdd:PRK12684  19 LTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRGLTEpGRIILASVerilQEVenLKR-----------VGkef 87

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 616690428  88 --EVNGTISIGCSSLIGQTLLPEVLSLYNAQFPNVEIQVQVGSTEQI 132
Cdd:PRK12684  88 aaQDQGNLTIATTHTQARYALPAAIKEFKKRYPKVRLSILQGSPTQI 134
cbl PRK12679
HTH-type transcriptional regulator Cbl;
18-167 1.38e-09

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 57.90  E-value: 1.38e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428  18 LRKAAEILYISQPAVTQRLKAIENAFGVDIFIRTKKQLITTTE--------GTMIIEHARDMLKRERLFFDkmqahigEV 89
Cdd:PRK12679  19 LTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRLLGMTEpgkallviAERILNEASNVRRLADLFTN-------DT 91

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 616690428  90 NGTISIGCSSLIGQTLLPEVLSLYNAQFPNVEIQVQVGSTEQIKAnhrdyhvMITRGNKVMNLANTHLFNDDHYFIFP 167
Cdd:PRK12679  92 SGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIAT-------LLQNGEADIGIASERLSNDPQLVAFP 162
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 17-231 1.84e-09

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 57.38  E-value: 1.84e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428  17 TLRKAAEILYISQPAVTQRLKAIENAFGVDIFIRTKKQLITTTEGTMIIEHARDMLKRERLFFDKMQAHIGEVNGTISIG 96
Cdd:PRK11233  17 SLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQLAVHNVGQALSGQVSIG 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428  97 -----CSSLIGQTLLPEVlslyNAQFPNVEIQVQ--VGST--EQIKANHRDYHVMITRGNkVMNLANTHLFNDDHYFIFP 167
Cdd:PRK11233  97 lapgtAASSLTMPLLQAV----RAEFPGIVLYLHenSGATlnEKLMNGQLDMAVIYEHSP-VAGLSSQPLLKEDLFLVGT 171

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428 168 KNRrddvtklpfiefQADPIYINQIKQwYNDNLEQDYHAT-ITVDQ-----------------VATCKEMLISGVGVTIL 229
Cdd:PRK11233 172 QDC------------PGQSVDLAAVAQ-MNLFLPRDYSAVrLRVDEafslrrltakvigeiesIATLTAAIASGMGVTVL 238


                 ..
gi 616690428 230 PE 231
Cdd:PRK11233 239 PE 240
PRK10341 PRK10341
transcriptional regulator TdcA;
21-124 2.12e-09

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 57.18  E-value: 2.12e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428  21 AAEILYISQPAVTQRLKAIENAFGVDIFIRTKKQLITTTEGTMIIEHARDMLKRERLFFDKMQAHIGEVNGTISIGCSSL 100
Cdd:PRK10341  27 AAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEINGMSSEAVVDVSFGFPSL 106

                         90       100
                 ....*....|....*....|....
gi 616690428 101 IGQTLLPEVLSLYNAQFPNVEIQV 124
Cdd:PRK10341 107 IGFTFMSDMINKFKEVFPKAQVSM 130
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 18-132 3.07e-09

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 56.98  E-value: 3.07e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428  18 LRKAAEILYISQPAVTQRLKAIENAFGVDIFIRTKKQLITTTE-GTMIIEHARDML------KRERLFFDKMQahigevN 90
Cdd:PRK12683  19 LTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTGLTEpGKELLQIVERMLldaenlRRLAEQFADRD------S 92

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 616690428  91 GTISIGCSSLIGQTLLPEVLSLYNAQFPNVEIQVQVGSTEQI 132
Cdd:PRK12683  93 GHLTVATTHTQARYALPKVVRQFKEVFPKVHLALRQGSPQEI 134
cysB PRK12681
HTH-type transcriptional regulator CysB;
21-132 3.62e-09

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 56.83  E-value: 3.62e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428  21 AAEILYISQPAVTQRLKAIENAFGVDIFIRTKKQLITTTE-GTMIIEHARDMLKRERLFFDKMQAHIGEVNGTISIGCSS 99
Cdd:PRK12681  22 TAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTQVTPaGEEIIRIAREILSKVESIKSVAGEHTWPDKGSLYIATTH 101

                         90       100       110
                 ....*....|....*....|....*....|...
gi 616690428 100 LIGQTLLPEVLSLYNAQFPNVEIQVQVGSTEQI 132
Cdd:PRK12681 102 TQARYALPPVIKGFIERYPRVSLHMHQGSPTQI 134
PRK09986 PRK09986
LysR family transcriptional regulator;
20-233 1.09e-08

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 55.11  E-value: 1.09e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428  20 KAAEILYISQPAVTQRLKAIENAFGVDIFIRTKKQLITTTEGTMIIEHARdmlkreRLFFDKMQA-----HIGE-VNGTI 93
Cdd:PRK09986  26 RAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESR------RLLDNAEQSlarveQIGRgEAGRI 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428  94 SIGC--SSLIGQtLLPeVLSLYNAQFPNVEIQV-QVGSTEQIKA-NHRDYHVMITRGNKVMNLANTH------------L 157
Cdd:PRK09986 100 EIGIvgTALWGR-LRP-AMRHFLKENPNVEWLLrELSPSMQMAAlERRELDAGIWRMADLEPNPGFTsrrlhesafavaV 177

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 616690428 158 FNDDHYFIFPKNRRDDVTKLPFIEFQadPIYINQIKQWYNDNLEQDYHATIT--VDQVATCKEMLISGVGVTILPEIM 233
Cdd:PRK09986 178 PEEHPLASRSSVPLKALRNEYFITLP--FVHSDWGKFLQRVCQQAGFSPQIIrqVNEPQTVLAMVSMGIGITLLPDSY 253
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 92-132 1.10e-08

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


Pssm-ID: 176112 [Multi-domain]  Cd Length: 201  Bit Score: 54.03  E-value: 1.10e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 616690428  92 TISIGCSSLIGQTLLPEVLSLYNAQFPNVEIQVQVGSTEQI 132
Cdd:cd08420    1 TLRIGASTTIGEYLLPRLLARFRKRYPEVRVSLTIGNTEEI 41
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
5-71 9.34e-08

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 52.08  E-value: 9.34e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428   5 DYRLLITLD---ETKTLRKAAEILYISQPAVTQRLKAIENAFGVDIFIRTKKqLITTTEGTMIIEHARDM 71
Cdd:PRK03635   3 DYKQLEALAavvREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVRTQP-CRPTEAGQRLLRHARQV 71
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 3-124 9.46e-08

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 52.30  E-value: 9.46e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428   3 IEDYRLLITldeTKTLRKAAEILYISQPAVTQRLKAIENAFGVDIFIRTKKQLITTTEGTMIIEHA-RDMLKRERLffDK 81
Cdd:PRK11013   9 IEIFHAVMT---AGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLFEEVqRSYYGLDRI--VS 83

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 616690428  82 MQAHIGEV-NGTISIGCSSLIGQTLLPEVLSLYNAQFPNVEIQV 124
Cdd:PRK11013  84 AAESLREFrQGQLSIACLPVFSQSLLPGLCQPFLARYPDVSLNI 127
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
5-96 9.70e-08

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 52.28  E-value: 9.70e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428   5 DYRLLITLD---ETKTLRKAAEILYISQPAVTQRLKAIENAFGVDIFIRTkKQLITTTEGTMIIEHARDMlkreRLFFDK 81
Cdd:PRK13348   3 DYKQLEALAavvETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRG-RPCRPTPAGQRLLRHLRQV----ALLEAD 77

                         90
                 ....*....|....*...
gi 616690428  82 MQAHIGEVNG---TISIG 96
Cdd:PRK13348  78 LLSTLPAERGsppTLAIA 95
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 7-134 1.05e-07

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 52.27  E-value: 1.05e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428   7 RLLITLDETKTLRKAAEILYISQPAVTQRLKAIENAFGVDIFIRTKKQLITTTEGTMIIEHARDMLkRErlfFDKMQAHI 86
Cdd:PRK11242   7 RYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRAL-QD---LEAGRRAI 82

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 616690428  87 GEVnGTISIGcsSL-IGQT------LLPEVLSLYNAQFPNVEIQVQVGSTEQIKA 134
Cdd:PRK11242  83 HDV-ADLSRG--SLrLAMTptftayLIGPLIDAFHARYPGITLTIREMSQERIEA 134
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
4-124 1.32e-07

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 51.73  E-value: 1.32e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428   4 EDYRLLITLDETKTLRKAAEILYISQPAVTQRLKAIENAFGVDIFIRTKKQLITTTEGTMIIEHARDMLKrerlFFDKMQ 83
Cdd:PRK10094   5 ETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLS----WLESMP 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 616690428  84 AHIGEVNGTISIGCSSLIGQTLL-PE----VLSLYNAQFPNVEIQV 124
Cdd:PRK10094  81 SELQQVNDGVERQVNIVINNLLYnPQavaqLLAWLNERYPFTQFHI 126
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
9-117 1.58e-07

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 51.59  E-value: 1.58e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428   9 LITLDETKTLRKAAEILYISQPAVTQRLKAIENAFGVDIFIRTKKQLITTTEGTMIIEHARDMLKrerlffdKMQAHIGE 88
Cdd:PRK10082  19 FLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQ-------QLESNLAE 91

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 616690428  89 VNG-------TISIGCSSLIGQTLLPEVLSLYNAQF 117
Cdd:PRK10082  92 LRGgsdyaqrKIKIAAAHSLSLGLLPSIISQMPPLF 127
PRK09801 PRK09801
LysR family transcriptional regulator;
4-126 3.24e-06

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 47.72  E-value: 3.24e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428   4 EDYRLLITLDETKTLRKAAEILYISQPAVTQRLKAIENAFGVDIFIRTKKQLITTTEGTMIIEHARDMLKRERLFFDKMQ 83
Cdd:PRK09801   9 KDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVT 88

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 616690428  84 AHIGEVNGTISIGCSSLIGQTLLPEVLSLYNAQFPNVEIQVQV 126
Cdd:PRK09801  89 QIKTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHFEL 131
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
26-138 5.47e-06

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 46.74  E-value: 5.47e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428  26 YISQPAVTQRLKAIENAFGVDIFIRTKKQLITTTEGTMIIEHARDMLKRERLFFDKMQAHIGEVNGTISIGCSSLIGQTL 105
Cdd:PRK11716   2 HVSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSLFCSVTAAYSH 81

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 616690428 106 LPEVLSLYNAQFPNVEIQVQVG----STEQIKANHRD 138
Cdd:PRK11716  82 LPPILDRFRAEHPLVEIKLTTGdaadAVEKVQSGEAD 118
PRK12680 PRK12680
LysR family transcriptional regulator;
3-125 2.76e-05

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 45.00  E-value: 2.76e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428   3 IEDYRLLITLdetktlrkAAEILYISQPAVTQRLKAIENAFGVDIFIRTKKQLITTT-EGTMIIEHARDMLKRERLFFDK 81
Cdd:PRK12680  12 IADAELNITL--------AAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLESVTpAGVEVIERARAVLSEANNIRTY 83

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 616690428  82 MQAHIGEVNGTISIGCSSLIGQTLLPEVLSLYNAQFPNVEIQVQ 125
Cdd:PRK12680  84 AANQRRESQGQLTLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQ 127
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 17-126 4.15e-05

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 44.25  E-value: 4.15e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428  17 TLRKAAEILYISQPAVTQRLKAIENAFGVDIFIRTKKQLITTTEGTMIIEHARDMLKrerlFFDKMQAHI--GEVNGTIS 94
Cdd:PRK15092  27 TFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILR----FNDEACSSLmySNLQGVLT 102

                         90       100       110
                 ....*....|....*....|....*....|..
gi 616690428  95 IGCSSLIGQTLLPEVLSLYNAQFPNVEIQVQV 126
Cdd:PRK15092 103 IGASDDTADTILPFLLNRVSSVYPKLALDVRV 134
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 20-125 4.30e-05

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 44.06  E-value: 4.30e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428  20 KAAEILYISQPAVTQRLKAIENAFGVDIFIRTKKQLITTTEGTMIIEHARDMLKRERLFFDKMQAhiGEVNG--TISIGc 97
Cdd:PRK11139  25 RAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEATRKLRA--RSAKGalTVSLL- 101

                         90       100
                 ....*....|....*....|....*...
gi 616690428  98 SSLIGQTLLPEvLSLYNAQFPNVEIQVQ 125
Cdd:PRK11139 102 PSFAIQWLVPR-LSSFNEAHPDIDVRLK 128
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
21-127 5.87e-05

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 43.84  E-value: 5.87e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428  21 AAEILYISQPAVTQRLKAIENAFGVDIFIRTKKQLITTTEGtmiiehardmlkrERLF------FDKMQAHI-----GEV 89
Cdd:PRK10086  34 AADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEG-------------KRVFwalkssLDTLNQEIldiknQEL 100

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 616690428  90 NGTISIGCSSLIGQTLLPEVLSLYNAQFPNVEIQVQVG 127
Cdd:PRK10086 101 SGTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTILTG 138
PBP2_YofA_SoxR_like cd08442
The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, ...
 106-231 8.40e-05

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


Pssm-ID: 176133  Cd Length: 193  Bit Score: 42.59  E-value: 8.40e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428 106 LPEVLSLYNAQFPNVEIQVQVGSTEQIKANHRDYHV---MITRGNKVMNLANTHLFNDDHYFIFPKNRRD-----DVTKL 177
Cdd:cd08442   15 LPPLLAAYHARYPKVDLSLSTGTTGALIQAVLEGRLdgaFVAGPVEHPRLEQEPVFQEELVLVSPKGHPPvsraeDLAGS 94

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 616690428 178 PFIEFQADPIYINQIKQWYNDNLEQD--------YHATItvdqvaTCkemLISGVGVTILPE 231
Cdd:cd08442   95 TLLAFRAGCSYRRRLEDWLAEEGVSPgkimefgsYHAIL------GC---VAAGMGIALLPR 147
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 1-125 1.87e-04

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 42.28  E-value: 1.87e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428   1 MKIEDYRLLITLDETKTLRKAAEILYISQPAVTQRLKAIENAFGVDIFIRTKKQLITTTEGTMIIEHARDMLKRERLFFD 80
Cdd:PRK14997   2 TDLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQD 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 616690428  81 KMQAHIGEVNGTISIGCSSLIGQTLLPEVLSLYNAQFPNVEIQVQ 125
Cdd:PRK14997  82 AIAALQVEPRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLE 126
PBP2_IlvY cd08430
The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates ...
 92-236 2.95e-04

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: 41.03  E-value: 2.95e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428  92 TISIGCSSLIGQTLLPEVLSLYNAQFPNVEIQVQVG----STEQIKANHRDYHVMITRGNKVMNLANTHLFNDDHYFIFP 167
Cdd:cd08430    1 ELSLYCSVTASYSFLPPILERFRAQHPQVEIKLHTGdpadAIDKVLNGEADIAIAARPDKLPARLAFLPLATSPLVFIAP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428 168 KNRRD----------DVTKLPFIEFQADPIYiNQIKQWYNDNLeqdYHATITVdQVATcKEMLIS----GVGVTILPEIM 233
Cdd:cd08430   81 NIACAvtqqlsqgeiDWSRLPFILPERGLAR-ERLDQWFRRRG---IKPNIYA-QVAG-HEAIVSmvalGCGVGIVPELV 154


                 ...
gi 616690428 234 MKN 236
Cdd:cd08430  155 LDN 157
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
5-144 3.55e-04

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 41.16  E-value: 3.55e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428   5 DYRLLITLDE---TKTLRKAAEILYISQPAVTQRLKAIENAFGVDIFIRTKKQLITTTEGTMIIEHARDMLkrerlffDK 81
Cdd:PRK03601   2 DTELLKTFLEvsrTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYAETLM-------NT 74

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 616690428  82 MQAHIGEVNGT-----ISIGCSSLIGQTLLPEVLS-LYNAQfPNVEIQVQVgSTEQ--IKANH-RDYHVMIT 144
Cdd:PRK03601  75 WQAAKKEVAHTsqhneLSIGASASLWECMLTPWLGrLYQNQ-EALQFEARI-AQRQslVKQLHeRQLDLLIT 144
PBP2_TdcA cd08418
The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is ...
 93-124 5.25e-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: 5.25e-04
                         10        20        30
                 ....*....|....*....|....*....|..
gi 616690428  93 ISIGCSSLIGQTLLPEVLSLYNAQFPNVEIQV 124
Cdd:cd08418    2 VSIGVSSLIAHTLMPAVINRFKEQFPDVQISI 33
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 92-134 1.21e-03

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: 39.03  E-value: 1.21e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 616690428  92 TISIGCSSLIGQTLLPEVLSLYNAQFPNVEIQVQ-VGSTEQIKA 134
Cdd:cd08414    1 RLRIGFVGSALYGLLPRLLRRFRARYPDVELELReMTTAEQLEA 44
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 92-132 1.22e-03

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: 39.06  E-value: 1.22e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 616690428  92 TISIGCSSLIGQTLLPEVLSLYNAQFPNVEIQVQVGSTEQI 132
Cdd:cd08412    1 TLRIGCFSTLAPYYLPGLLRRFREAYPGVEVRVVEGNQEEL 41
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
14-127 2.55e-03

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 38.97  E-value: 2.55e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428  14 ETKTLRKAAEILYISQPAVTQRLKAIENAFGVDIFIRTKKQLITTTEGTMIIEHARDMLKRERLFFDKMQAHIGEVNGTI 93
Cdd:PRK10632  15 EFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQLYAFNNTPIGTL 94

                         90       100       110
                 ....*....|....*....|....*....|....
gi 616690428  94 SIGCSSLIGQTLLPEVLSLYNAQFPNVEIQVQVG 127
Cdd:PRK10632  95 RIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTG 128
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 92-132 4.73e-03

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: 37.16  E-value: 4.73e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 616690428  92 TISIGCSSLIGQTLLPEVLSLYNAQFPNVEIQVQVGSTEQI 132
Cdd:cd08415    1 TLRIAALPALALSLLPRAIARFRARHPDVRISLHTLSSSTV 41
ModE COG2005
DNA-binding transcriptional regulator ModE (molybdenum-dependent) [Transcription];
5-88 4.96e-03

DNA-binding transcriptional regulator ModE (molybdenum-dependent) [Transcription];


Pssm-ID: 441608 [Multi-domain]  Cd Length: 118  Bit Score: 36.34  E-value: 4.96e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616690428   5 DYRLLITLDETKTLRKAAEILYISQPAVTQRLKAIENAFGVDIFIRTK--K-----QLitTTEGTMIIEHARDMLKRERL 77
Cdd:COG2005   23 RIELLEAIDETGSISAAAKAMGMSYKRAWDLIDAMNNLLGEPLVERQTggKggggaRL--TPEGRRLLALYRRLEAEAQR 100

                         90
                 ....*....|.
gi 616690428  78 FFDKMQAHIGE 88
Cdd:COG2005  101 ALAALFEELFA 111
 
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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