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Conserved domains on  [gi|972349739|ref|WP_059004790|]
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LysR family transcriptional regulator [Bittarella massiliensis (ex Durand et al. 2017)]

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];
5-290 6.47e-65

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 204.33  E-value: 6.47e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739   5 LEHYRVFREVARQGGFSAAAGKLFVSQSAVSQTVKHLESQLGVPLFDRRGKRLSLTSEGELLYGYVDAALKTLEQGQQSL 84
Cdd:COG0583    3 LRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAEL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  85 REQQNLEQGQLRVGVSDTISRFVILGQLERFHREYPHIRLVIQNGTSIEAVEMLAEHSVDLAFVNSPVRDQRVEEHRFFR 164
Cdd:COG0583   83 RALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPLGE 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 165 VHDVFLAGPRYPLPQRplaaaevaalplillerksnaRRLVDDWfaaqglpispeielgshDLLLDFARIGLGVCCAIEE 244
Cdd:COG0583  163 ERLVLVASPDHPLARR---------------------APLVNSL-----------------EALLAAVAAGLGIALLPRF 204

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*.
gi 972349739 245 FAEDYLRRGLVVKLPVDFSLPPRHISWCKLRDVSLSPSAKRFVDFI 290
Cdd:COG0583  205 LAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFL 250
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
5-290 6.47e-65

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 204.33  E-value: 6.47e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739   5 LEHYRVFREVARQGGFSAAAGKLFVSQSAVSQTVKHLESQLGVPLFDRRGKRLSLTSEGELLYGYVDAALKTLEQGQQSL 84
Cdd:COG0583    3 LRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAEL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  85 REQQNLEQGQLRVGVSDTISRFVILGQLERFHREYPHIRLVIQNGTSIEAVEMLAEHSVDLAFVNSPVRDQRVEEHRFFR 164
Cdd:COG0583   83 RALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPLGE 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 165 VHDVFLAGPRYPLPQRplaaaevaalplillerksnaRRLVDDWfaaqglpispeielgshDLLLDFARIGLGVCCAIEE 244
Cdd:COG0583  163 ERLVLVASPDHPLARR---------------------APLVNSL-----------------EALLAAVAAGLGIALLPRF 204

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*.
gi 972349739 245 FAEDYLRRGLVVKLPVDFSLPPRHISWCKLRDVSLSPSAKRFVDFI 290
Cdd:COG0583  205 LAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFL 250
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 5-222 3.50e-42

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 147.03  E-value: 3.50e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739   5 LEHYRVFREVARQGGFSAAAGKLFVSQSAVSQTVKHLESQLGVPLFDRRGKRLSLTSEGELLYGYVDAALKTLEQGQQSL 84
Cdd:PRK11242   3 LRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRRAI 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  85 REQQNLEQGQLRVGVSDTISRFVILGQLERFHREYPHIRLVIQNgTSIEAVE-MLAEHSVDLAFVNSPVRDQRVEEHRFF 163
Cdd:PRK11242  83 HDVADLSRGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIRE-MSQERIEaLLADDELDVGIAFAPVHSPEIEAQPLF 161

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 972349739 164 RVHDVFLAGPRYPLPQR--PLAAAEVAALPLILLERKSNARRLVDDWFAAQGlpISPEIEL 222
Cdd:PRK11242 162 TETLALVVGRHHPLAARrkALTLDELADEPLVLLSAEFATREQIDRYFRRHG--VTPRVAI 220
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 95-290 3.04e-41

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: 141.58  E-value: 3.04e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  95 LRVGVSDTISRFVILGQLERFHREYPHIRLVIQNGTSIEAVEMLAEHSVDLAFVNSPVRDQRVEEHRFFRVHDVFLAGPR 174
Cdd:cd05466    2 LRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPPD 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 175 YPLPQRP-LAAAEVAALPLILLERKSNARRLVDDWFAAQGLPISPEIELGSHDLLLDFARIGLGVCCAIEEFAEDYLRRG 253
Cdd:cd05466   82 HPLAKRKsVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEELADGG 161

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 972349739 254 LVVkLPVDFSLPPRHISWCKLRDVSLSPSAKRFVDFI 290
Cdd:cd05466  162 LVV-LPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 92-290 2.92e-39

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: 136.65  E-value: 2.92e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739   92 QGQLRVGVSDTISRFVILGQLERFHREYPHIRLVIQNGTSIEAVEMLAEHSVDLAFVNSPVRDQRVEEHRFFRVHDVFLA 171
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  172 GPRYPLPQR-PLAAAEVAALPLILLERKSNARRLVDDWFAAQGLPISPEIELGSHDLLLDFARIGLGVCCAIEEFAEDYL 250
Cdd:pfam03466  81 PPDHPLARGePVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAREL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 972349739  251 RRGLVVKLPVDFSLPPRHISWCKLRDVSLSPSAKRFVDFI 290
Cdd:pfam03466 161 ADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFL 200
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 14-217 7.04e-11

multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, including founding member GSU2202 from Geobacter sulfurreducens PCA, are LysR family transcriptional regulators found regularly in the vicinity of multiheme cytochromes such as GSU2203, a decaheme c-type cytochrome.


Pssm-ID: 468965 [Multi-domain]  Cd Length: 301  Bit Score: 61.68  E-value: 7.04e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  14 VARQGGFSAAAGKLFVSQSAVSQTVKHLESQLGVPLFDRRGKRLSLTSEGELLygyVDAALKTLEQGQQSLREQQNLEQG 93
Cdd:NF041036  12 VAEEGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMV---LEKARRILDIEDSLMDELKSFKGR 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  94 Q-LRVGVSDTISRFVILGQLERFHREYPHIR-LVIQNGTSIEAVEMLAEHSVDLAFVNSPVRDQRVEEHRFFRVHD--VF 169
Cdd:NF041036  89 QrLSICCTPTFGMAHLPGVLNRFMLRNADVVdLKFLFHSPAQALEGIQNKEFDLAIIEHCADLDLGRFHTYPLPQDelVF 168

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 972349739 170 LAGPRYPLPQRPLAAAEVAALPLILLERKSNARRLVDDWFAAQGLPIS 217
Cdd:NF041036 169 VSAPSLGLPTPNVTLERLLELCLITRRDGCSSRDLLRRNLAEQGRDLD 216
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 13-66 7.79e-11

transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity. [Cellular processes, Toxin production and resistance, DNA metabolism, DNA replication, recombination, and repair, Regulatory functions, DNA interactions]


Pssm-ID: 274509 [Multi-domain]  Cd Length: 292  Bit Score: 61.47  E-value: 7.79e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 972349739   13 EVARQGGFSAAAGKLFVSQSAVSQTVKHLESQLGVPLFdRRGKRLSLTSEGELL 66
Cdd:TIGR03298  11 AVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLL-VRTQPCRATEAGQRL 63
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
5-290 6.47e-65

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 204.33  E-value: 6.47e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739   5 LEHYRVFREVARQGGFSAAAGKLFVSQSAVSQTVKHLESQLGVPLFDRRGKRLSLTSEGELLYGYVDAALKTLEQGQQSL 84
Cdd:COG0583    3 LRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAEL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  85 REQQNLEQGQLRVGVSDTISRFVILGQLERFHREYPHIRLVIQNGTSIEAVEMLAEHSVDLAFVNSPVRDQRVEEHRFFR 164
Cdd:COG0583   83 RALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPLGE 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 165 VHDVFLAGPRYPLPQRplaaaevaalplillerksnaRRLVDDWfaaqglpispeielgshDLLLDFARIGLGVCCAIEE 244
Cdd:COG0583  163 ERLVLVASPDHPLARR---------------------APLVNSL-----------------EALLAAVAAGLGIALLPRF 204

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*.
gi 972349739 245 FAEDYLRRGLVVKLPVDFSLPPRHISWCKLRDVSLSPSAKRFVDFI 290
Cdd:COG0583  205 LAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFL 250
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 5-222 3.50e-42

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 147.03  E-value: 3.50e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739   5 LEHYRVFREVARQGGFSAAAGKLFVSQSAVSQTVKHLESQLGVPLFDRRGKRLSLTSEGELLYGYVDAALKTLEQGQQSL 84
Cdd:PRK11242   3 LRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRRAI 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  85 REQQNLEQGQLRVGVSDTISRFVILGQLERFHREYPHIRLVIQNgTSIEAVE-MLAEHSVDLAFVNSPVRDQRVEEHRFF 163
Cdd:PRK11242  83 HDVADLSRGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIRE-MSQERIEaLLADDELDVGIAFAPVHSPEIEAQPLF 161

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 972349739 164 RVHDVFLAGPRYPLPQR--PLAAAEVAALPLILLERKSNARRLVDDWFAAQGlpISPEIEL 222
Cdd:PRK11242 162 TETLALVVGRHHPLAARrkALTLDELADEPLVLLSAEFATREQIDRYFRRHG--VTPRVAI 220
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 95-290 3.04e-41

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: 141.58  E-value: 3.04e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  95 LRVGVSDTISRFVILGQLERFHREYPHIRLVIQNGTSIEAVEMLAEHSVDLAFVNSPVRDQRVEEHRFFRVHDVFLAGPR 174
Cdd:cd05466    2 LRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPPD 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 175 YPLPQRP-LAAAEVAALPLILLERKSNARRLVDDWFAAQGLPISPEIELGSHDLLLDFARIGLGVCCAIEEFAEDYLRRG 253
Cdd:cd05466   82 HPLAKRKsVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEELADGG 161

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 972349739 254 LVVkLPVDFSLPPRHISWCKLRDVSLSPSAKRFVDFI 290
Cdd:cd05466  162 LVV-LPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 1-289 9.98e-40

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 140.21  E-value: 9.98e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739   1 MEVKLEHYRVFREVARQGGFSAAAGKLFVSQSAVSQTVKHLESQLGVPLFDRRGKRLSLTSEGELLYgyvDAALKTLEQG 80
Cdd:PRK10837   1 MHITLRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLY---PRALALLEQA 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  81 ---QQSLREqqnlEQGQLRVGVSDTISRFVILGQLERFHREYPHIRLVIQNGTSIEAVEMLAEHSVDLAFVNSPVRDQRV 157
Cdd:PRK10837  78 veiEQLFRE----DNGALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNSQDVINAVLDFRVDIGLIEGPCHSPEL 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 158 EEHRFFRVHDVFLAGPRYPLPQRPLAAAEVAALPLILLERKSNARRLVDDWFAAQgLP-ISPEIELGSHDLLLDFARIGL 236
Cdd:PRK10837 154 ISEPWLEDELVVFAAPDSPLARGPVTLEQLAAAPWILRERGSGTREIVDYLLLSH-LPrFELAMELGNSEAIKHAVRHGL 232

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 972349739 237 GVCCAIEEFAEDYLRRGLVVKLPVDfsLPP--RHISWCKLRDVSLSPSAKRFVDF 289
Cdd:PRK10837 233 GISCLSRRVIADQLQAGTLVEVAVP--LPRlmRTLYRIHHRQKHLSNALQRFLSY 285
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 92-290 2.92e-39

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: 136.65  E-value: 2.92e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739   92 QGQLRVGVSDTISRFVILGQLERFHREYPHIRLVIQNGTSIEAVEMLAEHSVDLAFVNSPVRDQRVEEHRFFRVHDVFLA 171
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  172 GPRYPLPQR-PLAAAEVAALPLILLERKSNARRLVDDWFAAQGLPISPEIELGSHDLLLDFARIGLGVCCAIEEFAEDYL 250
Cdd:pfam03466  81 PPDHPLARGePVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAREL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 972349739  251 RRGLVVKLPVDFSLPPRHISWCKLRDVSLSPSAKRFVDFI 290
Cdd:pfam03466 161 ADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFL 200
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 4-276 7.61e-32

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 120.10  E-value: 7.61e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739   4 KLEHYRVFREVARQG-GFSAAAGKLFVSQSAVSQTVKHLESQLGVPLFDRRGKRL-SLTSEGELLygyvdaalktLEQGQ 81
Cdd:PRK12682   2 NLQQLRFVREAVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLkGLTEPGKAV----------LDVIE 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  82 QSLREQQNLEQ----------GQLRVGVSDTISRFVILGQLERFHREYPHIRLVIQNGTSIEAVEMLAEHSVDLAFVN-S 150
Cdd:PRK12682  72 RILREVGNIKRigddfsnqdsGTLTIATTHTQARYVLPRVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGIATeS 151

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 151 PVRDQRVEEHRFFRVHDVFLAGPRYPLPQRP-LAAAEVAALPLILLERKSNARRLVDDWFAAQGLpiSPEIELGS--HDL 227
Cdd:PRK12682 152 LADDPDLATLPCYDWQHAVIVPPDHPLAQEErITLEDLAEYPLITYHPGFTGRSRIDRAFAAAGL--QPDIVLEAidSDV 229

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*....
gi 972349739 228 LLDFARIGLGVCCaIEEFAEDYLRRGLVVKLPVDfSLPPRHISWCKLRD 276
Cdd:PRK12682 230 IKTYVRLGLGVGI-VAEMAYRPDRDGDLVALPAG-HLFGPNTAWVALKR 276
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
4-238 1.42e-28

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 111.22  E-value: 1.42e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739   4 KLEHYRVFREVARQG-GFSAAAGKLFVSQSAVSQTVKHLESQLGVPLFDRRGKRL-SLTSEGELLYGYVDAALKTLEQGQ 81
Cdd:PRK12684   2 NLHQLRFVREAVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLrGLTEPGRIILASVERILQEVENLK 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  82 QSLREQQNLEQGQLRVGVSDTISRFVILGQLERFHREYPHIRLVIQNGTSIEAVEMLAEHSVDLAfvnspVRDQRVEEHR 161
Cdd:PRK12684  82 RVGKEFAAQDQGNLTIATTHTQARYALPAAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLA-----IATEAIADYK 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 162 ------FFRVHDVFLAGPRYPLPQ-RPLAAAEVAALPLILLERKSNARRLVDDWFAAQGLpiSPEIELGS--HDLLLDFA 232
Cdd:PRK12684 157 elvslpCYQWNHCVVVPPDHPLLErKPLTLEDLAQYPLITYDFAFAGRSKINKAFALRGL--KPDIVLEAidADVIKTYV 234


                 ....*.
gi 972349739 233 RIGLGV 238
Cdd:PRK12684 235 ELGLGV 240
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 4-238 2.55e-28

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 110.52  E-value: 2.55e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739   4 KLEHYRVFREVARQG-GFSAAAGKLFVSQSAVSQTVKHLESQLGVPLFDRRGKRLS-LTSEGELLYGYVDAALKTLEQGQ 81
Cdd:PRK12683   2 NFQQLRIIREAVRQNfNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTgLTEPGKELLQIVERMLLDAENLR 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  82 QSLREQQNLEQGQLRVGVSDTISRFVILGQLERFHREYPHIRLVIQNGTSIEAVEMLAEHSVDLAFVNSPV-RDQRVEEH 160
Cdd:PRK12683  82 RLAEQFADRDSGHLTVATTHTQARYALPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGIATEALdREPDLVSF 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 161 RFFRVHDVFLAGPRYPLPQR-PLAAAEVAALPLILLERKSNARRLVDDWFAAQGLpiSPEIELGS--HDLLLDFARIGLG 237
Cdd:PRK12683 162 PYYSWHHVVVVPKGHPLTGReNLTLEAIAEYPIITYDQGFTGRSRIDQAFAEAGL--VPDIVLTAldADVIKTYVELGMG 239


                 .
gi 972349739 238 V 238
Cdd:PRK12683 240 V 240
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 94-290 5.37e-28

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: 106.81  E-value: 5.37e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  94 QLRVGVSDTISRFVILGQLERFHREYPHIRLVIQNGTSIEAVEMLAEHSVDLAFVNSPVRDQRVEEHRFFRVHDVFLAGP 173
Cdd:cd08420    1 TLRIGASTTIGEYLLPRLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLVEGPVDHPDLIVEPFAEDELVLVVPP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 174 RYPLPQR-PLAAAEVAALPLILLERKSNARRLVDDWFAAQGLPIS---PEIELGSHDLLLDFARIGLGVCCAIEEFAEDY 249
Cdd:cd08420   81 DHPLAGRkEVTAEELAAEPWILREPGSGTREVFERALAEAGLDGLdlnIVMELGSTEAIKEAVEAGLGISILSRLAVRKE 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 972349739 250 LRRGLVVKLPVDFSLPPRHISWCKLRDVSLSPSAKRFVDFI 290
Cdd:cd08420  161 LELGRLVALPVEGLRLTRPFSLIYHKDKYLSPAAEAFLEFL 201
rbcR CHL00180
LysR transcriptional regulator; Provisional
 5-279 1.17e-26

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 105.87  E-value: 1.17e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739   5 LEHYRVFREVARQGGFSAAAGKLFVSQSAVSQTVKHLESQLGVPLFDRRGKRLSLTSEGELLYGYVDAALKTLEQGQQSL 84
Cdd:CHL00180   7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRAL 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  85 REQQNLEQGQLRVGVSDTISRFVILGQLERFHREYPHIRLVIQ-NGTSIEAVEmLAEHSVDLAFVNSPVRD--QRVEEHR 161
Cdd:CHL00180  87 EDLKNLQRGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQvHSTRRIAWN-VANGQIDIAIVGGEVPTelKKILEIT 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 162 FFRVHDVFLAGPR-YPLPQRPLAAAE-VAALPLILLERKSNARRLVDDWFAAQGLPISP---EIELGSHDLLLDFARIGL 236
Cdd:CHL00180 166 PYVEDELALIIPKsHPFAKLKKIQKEdLYRLNFITLDSNSTIRKVIDNILIQNGIDSKRfkiEMELNSIEAIKNAVQSGL 245

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*..
gi 972349739 237 GVC----CAIEEfaEDYLRRglvvklpvdfslpprhISWCKLRDVSL 279
Cdd:CHL00180 246 GAAfvsvSAIEK--ELELGL----------------LHWIKIENITI 274
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 14-291 4.43e-22

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 93.47  E-value: 4.43e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  14 VARQGGFSAAAGKLFVSQSAVSQTVKHLESQLGVPLFDRRGKRLSLTSEGELlygYVDAALKTLEQGQQSLREQQ---NL 90
Cdd:PRK11074  13 VARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEW---FVKEARSVIKKMQETRRQCQqvaNG 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  91 EQGQLRVGVsDTISRFVILGQL-ERFHREYPHIRLVIQ----NGtSIEAvemLAEHSVDLAF---VNSPVRDQrveehrf 162
Cdd:PRK11074  90 WRGQLSIAV-DNIVRPDRTRQLiVDFYRHFDDVELIIRqevfNG-VWDA---LADGRVDIAIgatRAIPVGGR------- 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 163 FRVHD------VFLAGPRYPLPQ--RPLAAAEVAALPLILLERKS------------NARRL-VDDWFAAqglpispeie 221
Cdd:PRK11074 158 FAFRDmgmlswACVVSSDHPLASmdGPLSDDELRPYPSLCLEDTSrtlpkritwlldNQRRLvVPDWESA---------- 227

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 972349739 222 lgshdllLDFARIGLGVCCAIEEFAEDYLRRGLVV--KLPVDFSLPPRHISWcklRDVSLSPSAKRFVDFIG 291
Cdd:PRK11074 228 -------INCLSAGLCVGMVPTHFAKPLINSGKLVelTLENPFPDSPCCLTW---QQNDMSPALAWLLDYLG 289
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
5-64 7.02e-22

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 86.28  E-value: 7.02e-22
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739    5 LEHYRVFREVARQGGFSAAAGKLFVSQSAVSQTVKHLESQLGVPLFDRRGKRLSLTSEGE 64
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
cbl PRK12679
HTH-type transcriptional regulator Cbl;
9-238 1.19e-21

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 92.57  E-value: 1.19e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739   9 RVFREVARQG-GFSAAAGKLFVSQSAVSQTVKHLESQLGVPLFDRRGKR-LSLTSEGELLYGYVDAALKTLEQGQQSLRE 86
Cdd:PRK12679   7 KIIREAARQDyNLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRlLGMTEPGKALLVIAERILNEASNVRRLADL 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  87 QQNLEQGQLRVGVSDTISRFVILGQLERFHREYPHIRLVIQNGTSIEAVEMLAEHSVDLAFVNSP-VRDQRVEEHRFFRV 165
Cdd:PRK12679  87 FTNDTSGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASERlSNDPQLVAFPWFRW 166

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 972349739 166 HDVFLAGPRYPLPQ-RPLAAAEVAALPLILLERKSNARRLVDDWFAAQGLpiSPEIELGSH--DLLLDFARIGLGV 238
Cdd:PRK12679 167 HHSLLVPHDHPLTQiTPLTLESIAKWPLITYRQGITGRSRIDDAFARKGL--LADIVLSAQdsDVIKTYVALGLGI 240
PRK09791 PRK09791
LysR family transcriptional regulator;
3-140 4.73e-21

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 90.59  E-value: 4.73e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739   3 VKLEHYRVFREVARQGGFSAAAGKLFVSQSAVSQTVKHLESQLGVPLFDRRGKRLSLTSEGELLYGYVDAALKTLEQGQQ 82
Cdd:PRK09791   5 VKIHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQE 84

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 972349739  83 SLREQQNLEQGQLRVGVSDTISRFVILGQLERFHREYPHIRLVIQNGtsiEAVEMLAE 140
Cdd:PRK09791  85 DIRQRQGQLAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRIMEG---QLVSMINE 139
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 9-290 7.56e-21

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 89.90  E-value: 7.56e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739   9 RVFREVARQGGFSAAAGKLFVSQSAVSQTVKHLESQLGVPLFDRRGKRLSLTSEGELLYGYVDAALKTLEQGQQSLREQQ 88
Cdd:PRK11139  12 RAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEATRKLRARS 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  89 NleQGQLRVGVSDTISRFVILGQLERFHREYPHIRLVIQngTSIEAVEMLAEHsVDLAFVNSPVRDQRVEEHRFFRvhDV 168
Cdd:PRK11139  92 A--KGALTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLK--AVDRLEDFLRDD-VDVAIRYGRGNWPGLRVEKLLD--EY 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 169 F--LAGPRYPLPQRPLA-AAEVAALPLIllerKSNARRLVDDWFAAQGLPISPEIE--LGSH-DLLLDFARIGLGVCCAI 242
Cdd:PRK11139 165 LlpVCSPALLNGGKPLKtPEDLARHTLL----HDDSREDWRAWFRAAGLDDLNVQQgpIFSHsSMALQAAIHGQGVALGN 240

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*....
gi 972349739 243 EEFAEDYLRRGLVVkLPVDFSLP-PRHISWCKLRDVSLSPSAKRFVDFI 290
Cdd:PRK11139 241 RVLAQPEIEAGRLV-CPFDTVLPsPNAFYLVCPDSQAELPKVAAFRQWL 288
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
28-220 4.48e-20

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 87.18  E-value: 4.48e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  28 FVSQSAVSQTVKHLESQLGVPLFDRRGKRLSLTSEGELLYGYvdaALKTLEQGQQ---SLREQQNLEQGQLRVGVSDTIS 104
Cdd:PRK11716   2 HVSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPF---AQQTLLQWQQlrhTLDQQGPSLSGELSLFCSVTAA 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 105 RFVILGQLERFHREYPHIRLVIQNGTSIEAVEMLAEHSVDLAFVNSPvrDQ---RVEEHRFFRVHDVFLAgPRYPLP-QR 180
Cdd:PRK11716  79 YSHLPPILDRFRAEHPLVEIKLTTGDAADAVEKVQSGEADLAIAAKP--ETlpaSVAFSPIDEIPLVLIA-PALPCPvRQ 155

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 972349739 181 PLAAAEV--AALPLILLERkSNARRLVDDWFAAQGlpISPEI 220
Cdd:PRK11716 156 QLSQEKPdwSRIPFILPEH-GPARRRIDLWFRRHK--IKPNI 194
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 1-294 6.66e-20

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 87.52  E-value: 6.66e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739   1 MEvkLEHYRVFREVARQGGFSAAAGKLFVSQSAVSQTVKHLESQLGVPLFDRRGKRLSLTSEGELlygYVDAALKTLEQG 80
Cdd:PRK09906   1 ME--LRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEV---FLQDARAILEQA 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  81 QQS--LREQQNLEQGQLRVGvsdtisrFVILGQLERFHREYPHIRLViQNGTSIEAV--------EMLAEHSVDLAFVNS 150
Cdd:PRK09906  76 EKAklRARKIVQEDRQLTIG-------FVPSAEVNLLPKVLPMFRLR-HPDTLIELVslittqqeEKLRRGELDVGFMRH 147

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 151 PVRDQRVEEHRFFRVHDVFLAGPRYPLPQR---PLAAAEVAALPLILLERKSNARRLVDDWFAAQGlpISPEIELGSHDL 227
Cdd:PRK09906 148 PVYSDEIDYLELLDEPLVVVLPVDHPLAHEkeiTAAQLDGVNFISTDPAYSGSLAPIIKAWFAQHN--SQPNIVQVATNI 225

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 972349739 228 LLDFARIGLGVCCAIEEFAEDYLRRGLVVKLPVDFSLPPRH--ISWcklRDVSLSPSAKRFVDFIGGRY 294
Cdd:PRK09906 226 LVTMNLVGMGLGCTIIPGYMNNFNTGQVVFRPLAGNVPSIAllMAW---KKGEMKPALRDFIAIVQERL 291
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 95-288 5.50e-19

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: 82.61  E-value: 5.50e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  95 LRVGVSDTISRFVILGQLERFHREYPHIRLVIQNGTSIEAVEMLAEHSVDLAFVNSPVRDQRVEEHRFFRVHDVFLAGPR 174
Cdd:cd08415    2 LRIAALPALALSLLPRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPLDHPGLESEPLASGRAVCVLPPG 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 175 YPLPQRP-LAAAEVAALPLILLERKSNARRLVDDWFAAQGLPISPEIELGSHDLLLDFARIGLGVccAI-EEF-AEDYLR 251
Cdd:cd08415   82 HPLARKDvVTPADLAGEPLISLGRGDPLRQRVDAAFERAGVEPRIVIETQLSHTACALVAAGLGV--AIvDPLtAAGYAG 159

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 972349739 252 RGLVVK-----LPVDFSLpprhiswCKLRDVSLSPSAKRFVD 288
Cdd:cd08415  160 AGLVVRpfrpaIPFEFAL-------VRPAGRPLSRLAQAFID 194
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
 94-290 7.77e-19

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: 82.55  E-value: 7.77e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  94 QLRVGVSDTISRFV--ILGqleRFHREYPHIRLVIQNGTSIEAVEMLAEHSVDLAFVNSPVRDQRVEEHRFFRVHDVFLA 171
Cdd:cd08419    1 RLRLAVVSTAKYFAprLLG---AFCRRHPGVEVSLRVGNREQVLERLADNEDDLAIMGRPPEDLDLVAEPFLDNPLVVIA 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 172 GPRYPLP-QRPLAAAEVAALPLILLERKSNARRLVDDWFAAQGLPISPEIELGSHDLLLDFARIGLGV------CCAIEe 244
Cdd:cd08419   78 PPDHPLAgQKRIPLERLAREPFLLREPGSGTRLAMERFFAEHGVTLRVRMELGSNEAIKQAVMAGLGLsvlslhTLALE- 156

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 972349739 245 faedyLRRGLVVKLPVDfSLPPRhISWC--KLRDVSLSPSAKRFVDFI 290
Cdd:cd08419  157 -----LATGRLAVLDVE-GFPIR-RQWYvvHRKGKRLSPAAQAFLDFL 197
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 94-283 2.56e-18

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: 81.10  E-value: 2.56e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  94 QLRVGVSDTISRFVILGQLERFHREYPHIRLVIQNGTSIEAVEMLAEHSVDLAFVNSPVRDQRVEEhRFFRVHDVFLAGP 173
Cdd:cd08433    1 RVSVGLPPSAASVLAVPLLRAVRRRYPGIRLRIVEGLSGHLLEWLLNGRLDLALLYGPPPIPGLST-EPLLEEDLFLVGP 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 174 RYPLPQ--RPLAAAEVAALPLILLERKSNARRLVDDWFAAQGLPISPEIELGSHDLLLDFARIGLGvcCAI--EEFAEDY 249
Cdd:cd08433   80 ADAPLPrgAPVPLAELARLPLILPSRGHGLRRLVDEAAARAGLTLNVVVEIDSVATLKALVAAGLG--YTIlpASAVAAE 157

                        170       180       190
                 ....*....|....*....|....*....|....
gi 972349739 250 LRRGLVVKLPVDFSLPPRHISWCKLRDVSLSPSA 283
Cdd:cd08433  158 VAAGRLVAAPIVDPALTRTLSLATPRDRPLSPAA 191
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 112-290 3.65e-18

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: 80.65  E-value: 3.65e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 112 LERFHREYPHIRLVIQNGTSIEAVEMLAEHSVDLAFVNSPVRDQRVEEHRFFRvHDVFLAGPR-YPLPQRP-LAAAEVAA 189
Cdd:cd08440   19 LAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEADPDLEFEPLLR-DPFVLVCPKdHPLARRRsVTWAELAG 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 190 LPLILLERKSNARRLVDDWFAAQGLPISPEIELGSHDLLLDFARIGLGVcCAIEEFAEDYLRRGLVVKLPVDFSLPPRHI 269
Cdd:cd08440   98 YPLIALGRGSGVRALIDRALAAAGLTLRPAYEVSHMSTALGMVAAGLGV-AVLPALALPLADHPGLVARPLTEPVVTRTV 176

                        170       180
                 ....*....|....*....|.
gi 972349739 270 SWCKLRDVSLSPSAKRFVDFI 290
Cdd:cd08440  177 GLIRRRGRSLSPAAQAFLDLL 197
PRK12680 PRK12680
LysR family transcriptional regulator;
23-238 2.94e-17

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 80.44  E-value: 2.94e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  23 AAGKLFVSQSAVSQTVKHLESQLGVPLFDRRGKRL-SLTSEGELLYGYVDAALKTLEQGQQSLREQQNLEQGQLRVGVSD 101
Cdd:PRK12680  22 AAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLeSVTPAGVEVIERARAVLSEANNIRTYAANQRRESQGQLTLTTTH 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 102 TISRFVILGQLERFHREYPHIRLVIQNGTSIEAVEMLAEHSVDLAFV----NSPVRDQRVEEHRFFRVHDVflagPR-YP 176
Cdd:PRK12680 102 TQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVstagGEPSAGIAVPLYRWRRLVVV----PRgHA 177

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 972349739 177 L--PQRPLAAAEVAALPLILLERKSNARRLVDDWFAAQGLpiSPEIELGS--HDLLLDFARIGLGV 238
Cdd:PRK12680 178 LdtPRRAPDMAALAEHPLISYESSTRPGSSLQRAFAQLGL--EPSIALTAldADLIKTYVRAGLGV 241
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 9-215 1.05e-16

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 78.53  E-value: 1.05e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739   9 RVFREVARQGGFSAAAGKLFVSQSAVSQTVKHLESQLGVPLFDRRGKRLSLTSEGELLYGYVDAALKTLEQGQQSLReQQ 88
Cdd:PRK15092  17 RTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEACSSLM-YS 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  89 NLeQGQLRVGVSD----TISRFVilgqLERFHREYPHIRLVIQNGTSIEAVEMLAEHSVDLAfvnspVRDQRVEEHRFF- 163
Cdd:PRK15092  96 NL-QGVLTIGASDdtadTILPFL----LNRVSSVYPKLALDVRVKRNAFMMEMLESQEVDLA-----VTTHRPSSFPALn 165

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 972349739 164 -RVHDV-FLAGPRYPL-PQRPlaaaevaaLPLILLERKSNARRLVDDWFAAQGLP 215
Cdd:PRK15092 166 lRTSPTlWYCAAEYVLqKGEP--------IPLVLLDEPSPFRDMALATLNAAGIP 212
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
10-146 1.66e-16

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 78.12  E-value: 1.66e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  10 VFREVARQGGFSAAAGKLFVSQSAVSQTVKHLESQLGVPLFDRRGKRLSLTSEGELLYgyvdAALK-TLEQGQQSLREQQ 88
Cdd:PRK10086  21 TFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVF----WALKsSLDTLNQEILDIK 96

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 972349739  89 NLE-QGQLRVGVSDTISRFVILGQLERFHREYPHIRLVIQNGTsiEAVEmLAEHSVDLA 146
Cdd:PRK10086  97 NQElSGTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTILTGN--ENVN-FQRAGIDLA 152
PBP2_CysB_like cd08413
The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains ...
 94-288 1.87e-16

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: 76.12  E-value: 1.87e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  94 QLRVGVSDTISRFVILGQLERFHREYPHIRLVIQNGTSIEAVEMLAEHSVDLAfVNSPVRDQRVEEHRF--FRVHDVFLA 171
Cdd:cd08413    1 QLTIATTHTQARYVLPPVIAAFRKRYPKVKLSLHQGTPSQIAEMVLKGEADIA-IATEALDDHPDLVTLpcYRWNHCVIV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 172 GPRYPLPQR-PLAAAEVAALPLILLERKSNARRLVDDWFAAQGLpiSPEIELGS--HDLLLDFARIGLGVcCAIEEFAED 248
Cdd:cd08413   80 PPGHPLADLgPLTLEDLAQYPLITYDFGFTGRSSIDRAFARAGL--EPNIVLTAldADVIKTYVRLGLGV-GIIAEMAYD 156

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 972349739 249 YLRRGLVVKLPVDFSLPPrHISWCKL-RDVSLSPSAKRFVD 288
Cdd:cd08413  157 PQRDADLVALDAGHLFGP-NTTRIALrRGTYLRSYAYDFIE 196
PBP2_CynR cd08425
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, ...
 93-290 2.52e-16

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


Pssm-ID: 176116  Cd Length: 197  Bit Score: 75.44  E-value: 2.52e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  93 GQLRVGVSDTISRFVILGQLERFHREYPHIRLVIQNgTSIEAVE-MLAEHSVDLAFVNSPVRDQRVEEHRFFRVHDVFLA 171
Cdd:cd08425    1 GSLRLAMTPTFTAYLIGPLIDRFHARYPGIALSLRE-MPQERIEaALADDRLDLGIAFAPVRSPDIDAQPLFDERLALVV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 172 GPRYPLPQR--PLAAAEVAALPLILLERKSNARRLVDDWFAAQGLPISPEIELGSHDLLLDFARIG--LGVCCAIEEFAE 247
Cdd:cd08425   80 GATHPLAQRrtALTLDDLAAEPLALLSPDFATRQHIDRYFQKQGIKPRIAIEANSISAVLEVVRRGrlATILPDAIAREQ 159

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 972349739 248 DYLRRglvvkLPVDFSLPPRHISWCKLRDVSLSPSAKRFVDFI 290
Cdd:cd08425  160 PGLCA-----VALEPPLPGRTAALLRRKGAYRSAAARAFAALA 197
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 112-290 2.93e-16

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: 75.33  E-value: 2.93e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 112 LERFHREYPHIRLVIQNGTSIEAVEMLAEHSVDLAFVNSPVRD-QRVEEHRFFRVHDVFLAGPRYPLPQRP-LAAAEVAA 189
Cdd:cd08436   19 LARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAFVGLPERRpPGLASRELAREPLVAVVAPDHPLAGRRrVALADLAD 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 190 LPLILLERKSNARRLVDDWFAAQGLPISPEIELGSHDLLLDFARIGLGVCCAIEEFAEdylRRGLVVKLPVDFSlpPRHI 269
Cdd:cd08436   99 EPFVDFPPGTGARRQVDRAFAAAGVRRRVAFEVSDVDLLLDLVARGLGVALLPASVAA---RLPGLAALPLEPA--PRRR 173

                        170       180
                 ....*....|....*....|.
gi 972349739 270 SWCKLRDVSLSPSAKRFVDFI 290
Cdd:cd08436  174 LYLAWSAPPPSPAARAFLELL 194
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 94-270 3.99e-16

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: 74.94  E-value: 3.99e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  94 QLRVGVSDTISrFVILGQL-ERFHREYPHIRLVIQNGTSIEAVEMLAEHSVDLAFVNSPVRDQRVEEHRFFRVHDVFLAG 172
Cdd:cd08417    1 TFRIAASDYLE-ALLLPPLlARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELPPGLRSQPLFEDRFVCVAR 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 173 PRYPLPQRPLAAAEVAALPLILLERKSNARRLVDDWFAAQGLPISPEIELGSHDLLLDFARIGLGVCCAIEEFAEDYLRR 252
Cdd:cd08417   80 KDHPLAGGPLTLEDYLAAPHVLVSPRGRGHGLVDDALAELGLSRRVALTVPHFLAAPALVAGTDLIATVPRRLAEALAER 159

                        170
                 ....*....|....*...
gi 972349739 253 GLVVKLPVDFSLPPRHIS 270
Cdd:cd08417  160 LGLRVLPLPFELPPFTVS 177
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 1-265 5.37e-16

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 76.57  E-value: 5.37e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739   1 MEVKLEHYRVFREVARQGGFSAAAGKLFVSQSAVSQTVKHLESQLGVPLFDRRGKRLSLTSEGELLYGYVDAALKTLE-- 78
Cdd:PRK11013   2 AAVSLRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLFEEVQRSYYGLDri 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  79 -QGQQSLREqqnLEQGQLRVGVSDTISRFVILGQLERFHREYPHIRLVIQNGTSIEAVEMLAEHSVDLAFVNSPVRDQRV 157
Cdd:PRK11013  82 vSAAESLRE---FRQGQLSIACLPVFSQSLLPGLCQPFLARYPDVSLNIVPQESPLLEEWLSAQRHDLGLTETLHTPAGT 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 158 EEHRFFRVHDVFLAGPRYPLPQRP-LAAAEVAALPLILLERKSNARRLVDDWFAAQGLPISPEIELGSHDLLLDFARIGL 236
Cdd:PRK11013 159 ERTELLTLDEVCVLPAGHPLAAKKvLTPDDFAGENFISLSRTDSYRQLLDQLFAEHGVKRRMVVETHSAASVCAMVRAGV 238

                        250       260
                 ....*....|....*....|....*....
gi 972349739 237 GVCCAIEEFAEDYLRRGLVVKlPVDFSLP 265
Cdd:PRK11013 239 GVSIVNPLTALDYAGSGLVVR-RFSISVP 266
cysB PRK12681
HTH-type transcriptional regulator CysB;
4-146 8.09e-16

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 76.48  E-value: 8.09e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739   4 KLEHYRVFREVARQG-GFSAAAGKLFVSQSAVSQTVKHLESQLGVPLFDRRGKRLS-LTSEGELLYGYVDAALKTLEQGQ 81
Cdd:PRK12681   2 KLQQLRYIVEVVNHNlNVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTqVTPAGEEIIRIAREILSKVESIK 81

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 972349739  82 QSLREQQNLEQGQLRVGVSDTISRFVILGQLERFHREYPHIRLVIQNGTSIEAVEMLAEHSVDLA 146
Cdd:PRK12681  82 SVAGEHTWPDKGSLYIATTHTQARYALPPVIKGFIERYPRVSLHMHQGSPTQIAEAAAKGNADFA 146
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
3-256 1.57e-15

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 75.44  E-value: 1.57e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739   3 VKLEHYRVFREVARQGGFSAAAGKLFVSQSAVSQTVKHLESQLGVPLFDRRGKRLSLTSEGELLYGYVDAALKTLEQGQQ 82
Cdd:PRK15421   2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQ 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  83 SLREQQnleQGQLRVGVSDTISRFVILGQLERFHREYPHIRLVIQNGTSIEAVEMLAEHSVDLAFVNSPVRDQRVEEHRF 162
Cdd:PRK15421  82 ACNEPQ---QTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLHYSPM 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 163 FRVHDVFLAGPRYPLPQRPLAAAEVAALPLILLERKSNARrlVDDW-FAAQGLPISPEIELGSHDLLL-DFARIGLGVCC 240
Cdd:PRK15421 159 FDYEVRLVLAPDHPLAAKTRITPEDLASETLLIYPVQRSR--LDVWrHFLQPAGVSPSLKSVDNTLLLiQMVAARMGIAA 236

                        250
                 ....*....|....*.
gi 972349739 241 AIEEFAEDYLRRGLVV 256
Cdd:PRK15421 237 LPHWVVESFERQGLVV 252
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
1-140 4.66e-15

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 74.03  E-value: 4.66e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739   1 MEvKLEHYRVFREVARQGGFSAAAGKLFVSQSAVSQTVKHLESQLGVPLFDRRGKRLSLTSEGELLYGYVDAALKTLEQG 80
Cdd:PRK10632   1 ME-RLKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDV 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 972349739  81 QQSLREQQNLEQGQLRVGVSDTISRFVILGQLERFHREYP--HIRLViqngTSIEAVEMLAE 140
Cdd:PRK10632  80 HEQLYAFNNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPglSVNLV----TGIPAPDLIAD 137
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-290 1.14e-14

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: 71.19  E-value: 1.14e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  94 QLRVGVSDTISRFVILGQLERFHREYPHIRLVIQNGTSIEAVEMLAEHSVDLAFVNSPVRDQRVEEHRFFRVHDVFLAGP 173
Cdd:cd08426    1 RVRVATGEGLAAELLPSLIARFRQRYPGVFFTVDVASTADVLEAVLSGEADIGLAFSPPPEPGIRVHSRQPAPIGAVVPP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 174 RYPLP-QRPLAAAEVAALPLILLERKSNARRLVDDWFAAQGLPISPEIELGSHDLLLDFARIGLGVCCAIEEFAEDYLRR 252
Cdd:cd08426   81 GHPLArQPSVTLAQLAGYPLALPPPSFSLRQILDAAFARAGVQLEPVLISNSIETLKQLVAAGGGISLLTELAVRREIRR 160

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 972349739 253 GLVVKLPV-DFSLPPRHISWCKLRDVSLSPSAKRFVDFI 290
Cdd:cd08426  161 GQLVAVPLaDPHMNHRQLELQTRAGRQLPAAASAFLQLL 199
PRK09986 PRK09986
LysR family transcriptional regulator;
3-195 3.25e-14

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 71.29  E-value: 3.25e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739   3 VKLEHYRVFREVARQGGFSAAAGKLFVSQSAVSQTVKHLESQLGVPLFDRRGKRLSLTSEGELLYGYVDAALKTLEQGQQ 82
Cdd:PRK09986   7 IDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLA 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  83 SLREQQNLEQGQLRVGVSDTISRFVILGQLERFHREYPHIRLVIQNGTSIEAVEMLAEHSVDLAF-------VNSPVRDQ 155
Cdd:PRK09986  87 RVEQIGRGEAGRIEIGIVGTALWGRLRPAMRHFLKENPNVEWLLRELSPSMQMAALERRELDAGIwrmadlePNPGFTSR 166

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 972349739 156 RVEEHRFfrvhdvFLAGPR-YPLPQRP-LAAAEVAALPLILL 195
Cdd:PRK09986 167 RLHESAF------AVAVPEeHPLASRSsVPLKALRNEYFITL 202
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 114-290 5.89e-14

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


Pssm-ID: 176125 [Multi-domain]  Cd Length: 195  Bit Score: 69.10  E-value: 5.89e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 114 RFHREYPHIRLVIQNGTSIEAVEMLAEHSVDLAFVNSPVRDQRVEEHRFFRvHDVFLAGPR-YPLPQR-PLAAAEVAALP 191
Cdd:cd08434   21 AFRKEYPNVTFELHQGSTDELLDDLKNGELDLALCSPVPDEPDIEWIPLFT-EELVLVVPKdHPLAGRdSVDLAELADEP 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 192 LILLERKSNARRLVDDWFAAQGlpISPEIELGSHDL--LLDFARIGLGVccAIEEFAEDYLRRGlVVKLPVDFSLPPRHI 269
Cdd:cd08434  100 FVLLSPGFGLRPIVDELCAAAG--FTPKIAFEGEEDstIAGLVAAGLGV--AILPEMTLLNPPG-VKKIPIKDPDAERTI 174

                        170       180
                 ....*....|....*....|.
gi 972349739 270 SWCKLRDVSLSPSAKRFVDFI 290
Cdd:cd08434  175 GLAWLKDRYLSPAARRFKDFV 195
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 94-288 1.79e-13

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: 67.68  E-value: 1.79e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  94 QLRVGVSDTISRFVILGQLERFHREYPHIRLVIQNGTSIEAVEMLAEHSVDLAF--VNSPVRDQRVEEHRFFRVHDVFLA 171
Cdd:cd08435    1 TVRVGAVPAAAPVLLPPAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAIgrLADDEQPPDLASEELADEPLVVVA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 172 GPRYPLPQRP-LAAAEVAALPLILLERKSNARRLVDDWFAAQGLPI-SPEIELGSHDLLLDF-ARIGLgVCCAIEEFAED 248
Cdd:cd08435   81 RPGHPLARRArLTLADLADYPWVLPPPGTPLRQRLEQLFAAAGLPLpRNVVETASISALLALlARSDM-LAVLPRSVAED 159

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 972349739 249 YLRRGLVVKLPVDFSLPPRHISWCKLRDVSLSPSAKRFVD 288
Cdd:cd08435  160 ELRAGVLRELPLPLPTSRRPIGITTRRGGPLSPAARALLD 199
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 94-290 1.84e-13

The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; This CD includes the C-terminal substrate binding domain of LTTRs involved in degradation of aromatic compounds, such as CbnR, BenM, CatM, ClcR and TfdR, as well as that of other transcriptional regulators clustered together in phylogenetic trees, including XapR, HcaR, MprR, IlvR, BudR, AlsR, LysR, and OccR. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 176106 [Multi-domain]  Cd Length: 197  Bit Score: 67.53  E-value: 1.84e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  94 QLRVGVSDTISRFVILGQLERFHREYPHIRLVIQNGTSIEAVEMLAEHSVDLAFVNSPVRDQRVEEHRFFRVHdVFLAGP 173
Cdd:cd08414    1 RLRIGFVGSALYGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPPPDPPGLASRPLLREP-LVVALP 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 174 R-YPLPQRP-LAAAEVAALPLILLERKSNA--RRLVDDWFAAQGLPISPEIELGSHDLLLDFARIGLGVCCAIEEFAEdy 249
Cdd:cd08414   80 AdHPLAAREsVSLADLADEPFVLFPREPGPglYDQILALCRRAGFTPRIVQEASDLQTLLALVAAGLGVALVPASVAR-- 157

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 972349739 250 LRRGLVVKLPVDFSLPPRHIS--WcklRDVSLSPSAKRFVDFI 290
Cdd:cd08414  158 LQRPGVVYRPLADPPPRSELAlaW---RRDNASPALRAFLELA 197
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 93-290 4.37e-13

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: 66.70  E-value: 4.37e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  93 GQLRVGVSDTISRFVILGQLERFHREYPHIRLVIQngTSIEAVEMLAEHsVDLAFVNSPVRDQRVEEHRFFRVHDVFLAG 172
Cdd:cd08422    1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELV--LSDRLVDLVEEG-FDLAIRIGELPDSSLVARRLGPVRRVLVAS 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 173 P----RYPLPQRPlaaAEVAALPLILLerksNARRLVDDW-FAAQG----LPISPEIELGSHDLLLDFARIGLGVCCAIE 243
Cdd:cd08422   78 PaylaRHGTPQTP---EDLARHRCLGY----RLPGRPLRWrFRRGGgeveVRVRGRLVVNDGEALRAAALAGLGIALLPD 150

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 972349739 244 EFAEDYLRRG-LVVKLPvDFSLPPRHISWCKLRDVSLSPSAKRFVDFI 290
Cdd:cd08422  151 FLVAEDLASGrLVRVLP-DWRPPPLPIYAVYPSRRHLPAKVRAFIDFL 197
PRK10341 PRK10341
transcriptional regulator TdcA;
4-126 7.38e-13

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 67.58  E-value: 7.38e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739   4 KLEHYRVFREVARQGGFSAAAGKLFVSQSAVSQTVKHLESQLGVPLFDRRGKRLSLTSEGELLYGYVDAALKTLEQGQQS 83
Cdd:PRK10341   8 KTQHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNE 87

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 972349739  84 LREQQNLEQGQLRVGVSDTISRFVILGQLERFHREYPHIRLVI 126
Cdd:PRK10341  88 INGMSSEAVVDVSFGFPSLIGFTFMSDMINKFKEVFPKAQVSM 130
PBP2_YofA_SoxR_like cd08442
The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, ...
 112-290 3.77e-12

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


Pssm-ID: 176133  Cd Length: 193  Bit Score: 63.78  E-value: 3.77e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 112 LERFHREYPHIRLVIQNGTSIEAVEMLAEHSVDLAFVNSPVRDQRVEEHRFFRVHDVfLAGPRYPLPQRplAAAEVAALP 191
Cdd:cd08442   19 LAAYHARYPKVDLSLSTGTTGALIQAVLEGRLDGAFVAGPVEHPRLEQEPVFQEELV-LVSPKGHPPVS--RAEDLAGST 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 192 LILLERKSNARRLVDDWFAAQGLPISPEIELGSHDLLLDFARIGLGVccAI-EEFAEDYLRRGLVVK---LPVDFSLPPR 267
Cdd:cd08442   96 LLAFRAGCSYRRRLEDWLAEEGVSPGKIMEFGSYHAILGCVAAGMGI--ALlPRSVLDSLQGRGSVSihpLPEPFADVTT 173

                        170       180
                 ....*....|....*....|...
gi 972349739 268 HISWcklRDVSLSPSAKRFVDFI 290
Cdd:cd08442  174 WLVW---RKDSFTAALQAFLDLL 193
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
6-273 4.72e-12

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 65.21  E-value: 4.72e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739   6 EHYRVFREVARQGGFSAAAGKLFVSQSAVSQTVKHLESQLGVPLFDRRGKRLSLTSEGELLygyvdaalktLEQGQQSLR 85
Cdd:PRK10094   5 ETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHL----------LSQARDWLS 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  86 EQQNL--EQGQLRVGVSDTI---------SRFVILGQLERFHREYPHIRLVIQNGTSIEAVEMLAEHSVDLAF---VNSP 151
Cdd:PRK10094  75 WLESMpsELQQVNDGVERQVnivinnllyNPQAVAQLLAWLNERYPFTQFHISRQIYMGVWDSLLYEGFSLAIgvtGTEA 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 152 VRDQrVEEHRFFRVHDVFLAGPRYPLP--QRPLAAAEVAALPLILLErkSNARRLVDDwfAAQGLPISPEIELGSHDLLL 229
Cdd:PRK10094 155 LANT-FSLDPLGSVQWRFVMAADHPLAnvEEPLTEAQLRRFPAVNIE--DSARTLTKR--VAWRLPGQKEIIVPDMETKI 229

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*.
gi 972349739 230 DFARIGLGVCCAIEEFAEDYLRRG-LVVKLPVDFSLP-PRHISWCK 273
Cdd:PRK10094 230 AAHLAGVGIGFLPKSLCQSMIDNQqLVSRVIPTMRPPsPLSLAWRK 275
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 18-221 8.79e-12

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 64.32  E-value: 8.79e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  18 GGFSAAAGKLFVSQSAVSQTVKHLESQLGVPLFDRRGKRLSLTSEGELLYGYVDAALKTLEQGQQSLREQQNLEQGQLRV 97
Cdd:PRK11233  16 GSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQLAVHNVGQALSGQVSI 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  98 GVS-DTISRFVILGQLERFHREYPHIRLVIQNGTSIEAVEMLAEHSVDLAFV--NSPVRDQR----VEEhrffrvhDVFL 170
Cdd:PRK11233  96 GLApGTAASSLTMPLLQAVRAEFPGIVLYLHENSGATLNEKLMNGQLDMAVIyeHSPVAGLSsqplLKE-------DLFL 168

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 972349739 171 AGPRyPLPQRPLAAAEVAALPLILLERKSNARRLVDDWFAAQGLP--ISPEIE 221
Cdd:PRK11233 169 VGTQ-DCPGQSVDLAAVAQMNLFLPRDYSAVRLRVDEAFSLRRLTakVIGEIE 220
PBP2_Cbl cd08444
The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is ...
 94-288 1.50e-11

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: 62.14  E-value: 1.50e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  94 QLRVGVSDTISRFVILGQLERFHREYPHIRLVIQNGTSIEAVEMLAEHSVDLAFVNSPV-RDQRVEEHRFFRVHDVFLAG 172
Cdd:cd08444    1 ELTIATTHTQARYALPWVVQAFKEQFPNVHLVLHQGSPEEIASMLANGQADIGIATEALeNHPELVSFPYYDWHHHIIVP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 173 PRYPLPQR-PLAAAEVAALPLILLERKSNARRLVDDWFAAQGLpiSPEIELGS--HDLLLDFARIGLGVCCAIEEFAEDY 249
Cdd:cd08444   81 VGHPLESItPLTIETIAKWPIITYHGGFTGRSRIDRAFSRAEL--TPNIVLSAldADVIKTYVGLGMGIGIVAEMAFEGQ 158

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 972349739 250 LRRGLvVKLPVDfSLPPRHISWCKLR-DVSLSPSAKRFVD 288
Cdd:cd08444  159 RDTNL-IKLDTS-HLFGKNTTWIALRrGGDLRNFAYRFIE 196
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
14-66 1.64e-11

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 63.64  E-value: 1.64e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 972349739  14 VARQGGFSAAAGKLFVSQSAVSQTVKHLESQLGVPLFdRRGKRLSLTSEGELL 66
Cdd:PRK03635  13 VVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLL-VRTQPCRPTEAGQRL 64
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
11-78 2.75e-11

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 62.68  E-value: 2.75e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 972349739  11 FREVARQGGFSAAAGKLFVSQSAVSQTVKHLESQLGVPLFdRRGKRLSLTSEGELLYGYVDaALKTLE 78
Cdd:PRK13348  10 LAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLL-VRGRPCRPTPAGQRLLRHLR-QVALLE 75
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 112-290 3.34e-11

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: 61.06  E-value: 3.34e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 112 LERFHREYPHIRLVIQngTSIEAVEMLAEHsVDLAFVNSPVRDQRVEEHRFFRVHDVFLAGPRYPLPQRPLAAAEVAALP 191
Cdd:cd08432   19 LARFQARHPDIDLRLS--TSDRLVDFAREG-IDLAIRYGDGDWPGLEAERLMDEELVPVCSPALLAGLPLLSPADLARHT 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 192 LIlleRKSNARRLVDDWFAAQGLPiSPEIELGSH----DLLLDFARIGLGVCCAIEEFAEDYLRRG-LVVklPVDFSLPP 266
Cdd:cd08432   96 LL---HDATRPEAWQWWLWAAGVA-DVDARRGPRfddsSLALQAAVAGLGVALAPRALVADDLAAGrLVR--PFDLPLPS 169

                        170       180
                 ....*....|....*....|....*
gi 972349739 267 RHISW-CKLRDVSLSPSAKRFVDFI 290
Cdd:cd08432  170 GGAYYlVYPPGRAESPAVAAFRDWL 194
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 14-217 7.04e-11

multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, including founding member GSU2202 from Geobacter sulfurreducens PCA, are LysR family transcriptional regulators found regularly in the vicinity of multiheme cytochromes such as GSU2203, a decaheme c-type cytochrome.


Pssm-ID: 468965 [Multi-domain]  Cd Length: 301  Bit Score: 61.68  E-value: 7.04e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  14 VARQGGFSAAAGKLFVSQSAVSQTVKHLESQLGVPLFDRRGKRLSLTSEGELLygyVDAALKTLEQGQQSLREQQNLEQG 93
Cdd:NF041036  12 VAEEGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMV---LEKARRILDIEDSLMDELKSFKGR 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  94 Q-LRVGVSDTISRFVILGQLERFHREYPHIR-LVIQNGTSIEAVEMLAEHSVDLAFVNSPVRDQRVEEHRFFRVHD--VF 169
Cdd:NF041036  89 QrLSICCTPTFGMAHLPGVLNRFMLRNADVVdLKFLFHSPAQALEGIQNKEFDLAIIEHCADLDLGRFHTYPLPQDelVF 168

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 972349739 170 LAGPRYPLPQRPLAAAEVAALPLILLERKSNARRLVDDWFAAQGLPIS 217
Cdd:NF041036 169 VSAPSLGLPTPNVTLERLLELCLITRRDGCSSRDLLRRNLAEQGRDLD 216
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 13-66 7.79e-11

transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity. [Cellular processes, Toxin production and resistance, DNA metabolism, DNA replication, recombination, and repair, Regulatory functions, DNA interactions]


Pssm-ID: 274509 [Multi-domain]  Cd Length: 292  Bit Score: 61.47  E-value: 7.79e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 972349739   13 EVARQGGFSAAAGKLFVSQSAVSQTVKHLESQLGVPLFdRRGKRLSLTSEGELL 66
Cdd:TIGR03298  11 AVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLL-VRTQPCRATEAGQRL 63
PBP2_LTTR_like_1 cd08421
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 111-290 3.26e-10

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


Pssm-ID: 176113  Cd Length: 198  Bit Score: 58.30  E-value: 3.26e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 111 QLERFHREYPHIRLVIQNGTSIEAVEMLAEHSVDLAFVNSPVRDQRVEEHRFFRVHDVFLAGPRYPLPQRP-LAAAEVAA 189
Cdd:cd08421   18 DLASFLAAHPDVRIDLEERLSADIVRAVAEGRADLGIVAGNVDAAGLETRPYRTDRLVVVVPRDHPLAGRAsVAFADTLD 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 190 LPLILLERKSNARRLVDDWFAAQGLPISPEIELGSHDLLLDFARIGLGVccAI--EEFAEDYLRRGLVVKLPVDFSLPPR 267
Cdd:cd08421   98 HDFVGLPAGSALHTFLREAAARLGRRLRLRVQVSSFDAVCRMVAAGLGI--GIvpESAARRYARALGLRVVPLDDAWARR 175

                        170       180
                 ....*....|....*....|...
gi 972349739 268 HISWCKLRDVSLSPSAKRFVDFI 290
Cdd:cd08421  176 RLLLCVRSFDALPPAARALVDHL 198
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 94-290 4.31e-10

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: 57.95  E-value: 4.31e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  94 QLRVGVSDTISRFVILGQLERFHREYPHIRLVIQNGTSIEAVEMLAEHSVDLAFVNSPVRDQRVEEHRFFRvHDVFLAGP 173
Cdd:cd08438    1 HLRLGLPPLGGSLLFAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVLPVDEEEFDSQPLCN-EPLVAVLP 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 174 R-YPLPQRP-LAAAEVAALPLILLERKSNARRLVDDWFAAQGlpISPEI--ELGSHDLLLDFARIGLGVCCAIEEFAEDY 249
Cdd:cd08438   80 RgHPLAGRKtVSLADLADEPFILFNEDFALHDRIIDACQQAG--FTPNIaaRSSQWDFIAELVAAGLGVALLPRSIAQRL 157

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 972349739 250 LRRGLVVkLPVDFSLPPRHISWCKLRDVSLSPSAKRFVDFI 290
Cdd:cd08438  158 DNAGVKV-IPLTDPDLRWQLALIWRKGRYLSHAARAWLALL 197
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
20-286 5.47e-10

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 59.30  E-value: 5.47e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  20 FSAAAGKLFVSQSAVSQTVKHLESQLGVPLFDRRGKRLSLTSEGELLYGYVDAALKTLEQGQQSLREQQNLEQGQLRVGV 99
Cdd:PRK10082  28 FSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESNLAELRGGSDYAQRKIKIAA 107

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 100 SDTISrfviLGQLERFHREYPHI-RLVIQNGTSIEAVEMLAEHSVDLAF-------VNSPVRDQRVEEHRFFRVHDVFLA 171
Cdd:PRK10082 108 AHSLS----LGLLPSIISQMPPLfTWAIEAIDVDEAVDKLREGQSDCIFsfhdedlLEAPFDHIRLFESQLFPVCASDEH 183

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 172 G-PRYPLPQrplaaaevAALPLILLERKSNARRLVDDWFAAQG-LPISPEIELGSHDLLLDFARIGLGVCCAIEEFAEDY 249
Cdd:PRK10082 184 GeALFNLAQ--------PHFPLLNYSRNSYMGRLINRTLTRHSeLSFSTFFVSSMSELLKQVALDGCGIAWLPEYAIQQE 255

                        250       260       270
                 ....*....|....*....|....*....|....*..
gi 972349739 250 LRRGLVVKLPVDFSLPPRHiSWCKLRDVSLSPSAKRF 286
Cdd:PRK10082 256 IRSGQLVVLNRDELVIPIQ-AYAYRMNTRMNPVAERF 291
PRK09801 PRK09801
LysR family transcriptional regulator;
9-179 2.42e-09

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 57.35  E-value: 2.42e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739   9 RVFREVARQGGFSAAAGKLFVSQSAVSQTVKHLESQLGVPLFDRRGKRLSLTSEGELLYgyvDAALKTLEQGQQSLREQQ 88
Cdd:PRK09801  12 QVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCY---EHALEILTQYQRLVDDVT 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  89 NLE---QGQLRVGVSDTISRFVILGQLERFHREYPHIRLVIQ-NGTSIEavemLAEHSVDLAF-VNSPVRDQRVeEHRFF 163
Cdd:PRK09801  89 QIKtrpEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHFElFDRQID----LVQDNIDLDIrINDEIPDYYI-AHLLT 163

                        170       180
                 ....*....|....*....|
gi 972349739 164 RVHDVFLAGP----RYPLPQ 179
Cdd:PRK09801 164 KNKRILCAAPeylqKYPQPQ 183
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
11-145 4.84e-09

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 56.18  E-value: 4.84e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  11 FREVARQGGFSAAAGKLFVSQSAVSQTVKHLESQLGVPLFDRRGKRLSLTSEGELLYGYVDAALKTLEQGQQSL-REQQN 89
Cdd:PRK03601   9 FLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYAETLMNTWQAAKKEVaHTSQH 88

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 972349739  90 LEqgqLRVGVSDTISRFVILGQLERFHREYPHIRLVIQNGTSIEAVEMLAEHSVDL 145
Cdd:PRK03601  89 NE---LSIGASASLWECMLTPWLGRLYQNQEALQFEARIAQRQSLVKQLHERQLDL 141
PBP2_LysR cd08456
The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine ...
 94-291 8.34e-09

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: 54.35  E-value: 8.34e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  94 QLRVGVSDTISRFVILGQLERFHREYPHIRLVIQNGTSIEAVEMLAEHSVDLAFVNSPVRDQRVEEHRFFRVHDVFLAGP 173
Cdd:cd08456    1 ELRIAVLPALSQSFLPRAIKAFLQRHPDVTISIHTRDSPTVEQWLSAQQCDLGLVSTLHEPPGIERERLLRIDGVCVLPP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 174 RYPLPQRP-LAAAEVAALPLILLERKSNARRLVDDWFAAQGlpISPEIELGSHDLLLDFARIGLGVCCAIEE--FAEDYL 250
Cdd:cd08456   81 GHRLAVKKvLTPSDLEGEPFISLARTDGTRQRVDALFEQAG--VKRRIVVETSYAATICALVAAGVGVSVVNplTALDYA 158

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 972349739 251 RRGLVVKlpvDFSlPPRHISWCKLRDvSLSPSAKRFVDFIG 291
Cdd:cd08456  159 AAGLVVR---RFS-PAVPFEVSLIRP-KHRPSSALVAAFSA 194
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 5-191 1.59e-08

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 54.61  E-value: 1.59e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739   5 LEHYRVFREVARQGGFSAAAGKLFVSQSAVSQTVKHLESQLGVPLFDRRGKRLSLTSEGELLYGYVDAALKTLEQGQQSL 84
Cdd:PRK14997   4 LNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDAI 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  85 REQQNLEQGQLRVGVSDTISRFVILGQLERFHREYPHIRLVIQngTSIEAVEMLAEhSVDLAFvnsPVRDQRVEEHRFF- 163
Cdd:PRK14997  84 AALQVEPRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLE--ATNRRVDVVGE-GVDVAI---RVRPRPFEDSDLVm 157

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 972349739 164 -----RVHDVFlAGPryPLPQR---PLAAAEVAALP 191
Cdd:PRK14997 158 rvladRGHRLF-ASP--DLIARmgiPSAPAELSHWP 190
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 93-196 1.89e-08

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


Pssm-ID: 176103 [Multi-domain]  Cd Length: 200  Bit Score: 53.30  E-value: 1.89e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  93 GQLRVGVSDTISRFVILGQLERFHREYPHIRLVIQNGTSIEAVEMLAEHSVDLAFVNSPVRDQRVEEHRFFRvHDVFLAG 172
Cdd:cd08411    1 GPLRLGVIPTIAPYLLPRLLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAALLALPVDEPGLEEEPLFD-EPFLLAV 79

                         90       100
                 ....*....|....*....|....*.
gi 972349739 173 PR-YPLPQR-PLAAAEVAALPLILLE 196
Cdd:cd08411   80 PKdHPLAKRkSVTPEDLAGERLLLLE 105
PBP2_CysB cd08443
The C-terminal substrate domain of LysR-type transcriptional regulator CysB contains type 2 ...
 94-238 2.51e-08

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


Pssm-ID: 176134  Cd Length: 198  Bit Score: 52.95  E-value: 2.51e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  94 QLRVGVSDTISRFVILGQLERFHREYPHIRLVIQNGTSIEAVEMLAEHSVDLAFVNSPVRD----QRVEEHRFFRvhdVF 169
Cdd:cd08443    1 SLYVATTHTQARYVLPPVIKGFIERYPRVSLQMHQGSPTQIAEMVSKGLVDFAIATEALHDyddlITLPCYHWNR---CV 77

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 972349739 170 LAGPRYPLPQR-PLAAAEVAALPLILLERKSNARRLVDDWFAAQGLpiSPEIELGSH--DLLLDFARIGLGV 238
Cdd:cd08443   78 VVKRDHPLADKqSISIEELATYPIVTYTFGFTGRSELDTAFNRAGL--TPNIVLTATdaDVIKTYVRLGLGV 147
PBP2_DntR_like_2 cd08464
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 96-214 4.31e-08

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


Pssm-ID: 176153 [Multi-domain]  Cd Length: 200  Bit Score: 52.24  E-value: 4.31e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  96 RVGVSDTIsRFVILGQL-ERFHREYPHIRLVIQNGTSIEAVEMLAEHSVDLAFVNSPVRDQRVEEHRFFRVHDVFLAGPR 174
Cdd:cd08464    3 RIGLSDDV-ESWLAPPLlAALRAEAPGVRLVFRQVDPFNVGDMLDRGEIDLAIGVFGELPAWLKREVLYTEGYACLFDPQ 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 972349739 175 YPLPQRPLAAAEVAALPLILLERKSNARRLVDDWFAAQGL 214
Cdd:cd08464   82 QLSLSAPLTLEDYVARPHVLVSYRGGLRGFVDDALAELGR 121
nhaR PRK11062
transcriptional activator NhaR; Provisional
 7-258 6.67e-08

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 52.70  E-value: 6.67e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739   7 HYRVFREVARQGGFSAAAGKLFVSQSAVSQTVKHLESQLGVPLFDRRGKRLSLTSEGELLYGYVDaalKTLEQGQQSL-- 84
Cdd:PRK11062   8 HLYYFWMVCKEGSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGELVFRYAD---KMFTLSQEMLdi 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  85 ---REQQNLeqgQLRVGVSDTISRFVILGQLERFHREYPHIRLVIQNGTSIEAVEMLAEHSVDLAFVNSPVRDQRVEE-- 159
Cdd:PRK11062  85 vnyRKESNL---LFDVGVADALSKRLVSRVLLTAVPEDESIHLRCFESTHEMLLEQLSQHKLDMILSDCPVDSTQQEGlf 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 160 --------HRFFrvhdvflagPRYPLPQRPLAAA-EVAALpLILLERKSNARRLVdDWFAAQGLpiSPEIeLGSHD---L 227
Cdd:PRK11062 162 skklgecgVSFF---------CTNPLPEKPFPAClEERRL-LIPGRRTMLGRKLL-NWFNSQGL--NVEI-LGEFDdaaL 227

                        250       260       270
                 ....*....|....*....|....*....|.
gi 972349739 228 LLDFARIGLGVCCAIEEFAEDYLRRGLVVKL 258
Cdd:PRK11062 228 MKAFGAYHDAIFVAPSLYAQDFYADHSVVEI 258
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 95-288 1.21e-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: 176115 [Multi-domain]  Cd Length: 200  Bit Score: 51.06  E-value: 1.21e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  95 LRVGVSDTISRFVILGQLERFHREYPHIRLVIQNGTSIEAVEMLAEHSVDLAFV-----NSPVRDQRVEEHRFFRvhDVF 169
Cdd:cd08423    2 LRVGAFPTAAAALLPPALAALRARHPGLEVRLREAEPPESLDALRAGELDLAVVfdypvTPPPDDPGLTRVPLLD--DPL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 170 -LAGPR-YPLPQRP-LAAAEVAALPLILLERKSNARRLVDDWFAAQGlpISPEIELGSHDLL--LDFARIGLGVcCAIEE 244
Cdd:cd08423   80 dLVLPAdHPLAGREeVALADLADEPWIAGCPGSPCHRWLVRACRAAG--FTPRIAHEADDYAtvLALVAAGLGV-ALVPR 156

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 972349739 245 FAEDYLRRGLVVkLPVDfSLPPRHISWCKLRDVSLSPSAKRFVD 288
Cdd:cd08423  157 LALGARPPGVVV-RPLR-PPPTRRIYAAVRAGAARRPAVAAALE 198
PBP2_DntR_NahR_LinR_like cd08459
The C-terminal substrate binding domain of LysR-type transcriptional regulators that are ...
 96-215 1.22e-07

The C-terminal substrate binding domain of LysR-type transcriptional regulators that are involved in the catabolism of dinitrotoluene, naphthalene and gamma-hexachlorohexane; contains the type 2 periplasmic binding fold; This CD includes LysR-like bacterial transcriptional regulators, DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. DntR from Burkholderia species controls genes encoding enzymes for oxidative degradation of the nitro-aromatic compound 2,4-dinitrotoluene. The active form of DntR is homotetrameric, consisting of a dimer of dimers. NahR is a salicylate-dependent transcription activator of the nah and sal operons for naphthalene degradation. Salicylic acid is an intermediate of the oxidative degradation of the aromatic ring in soil bacteria. LinR positively regulates expression of the genes (linD and linE) encoding enzymes for gamma-hexachlorocyclohexane (a haloorganic insecticide) degradation. Expression of linD and linE are induced by their substrates, 2,5-dichlorohydroquinone (2,5-DCHQ) and chlorohydroquinone (CHQ). 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: 176148 [Multi-domain]  Cd Length: 201  Bit Score: 51.04  E-value: 1.22e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  96 RVGVSDtISRFVILGQL-ERFHREYPHIRLVIQNGTSIEAVEMLAEHSVDLAFVNSPVRDQRVEEHRFFRVHDVFLAGPR 174
Cdd:cd08459    3 RIAMSD-IGEMYFLPRLlAALREVAPGVRIETVRLPVDELEEALESGEIDLAIGYLPDLGAGFFQQRLFRERYVCLVRKD 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 972349739 175 YPLPQRPLAAAEVAALPLILLERKSNARRLVDDWFAAQGLP 215
Cdd:cd08459   82 HPRIGSTLTLEQFLAARHVVVSASGTGHGLVEQALREAGIR 122
PBP2_OccR cd08457
The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the ...
 95-238 1.23e-07

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: 50.95  E-value: 1.23e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  95 LRVGVSDTISRFVILGQLERFHREYPHIRLVIQNGTSIEAVEMLAEHSVDLAFVNSPVRDQRVEEHRFFRVHDVFLAGPR 174
Cdd:cd08457    2 LRIAAMPALANGFLPRFLAAFLRLRPNLHLSLMGLSSSQVLEAVASGRADLGIADGPLEERQGFLIETRSLPAVVAVPMG 81

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 972349739 175 YPLPQRP-LAAAEVAALPLILLERKSNARRLVDDWFAAQGLPISPEIELGSHDLLLDFARIGLGV 238
Cdd:cd08457   82 HPLAQLDvVSPQDLAGERIITLENGYLFRMRVEVALGKIGVKRRPIIEVNLSHTALSLVREGLGI 146
PBP2_LTTR_like_2 cd08427
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 95-288 3.58e-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: 176118 [Multi-domain]  Cd Length: 195  Bit Score: 49.49  E-value: 3.58e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  95 LRVGVSDTISRFVILGQLERFHREYPHIRLVIQNGTSIEAVEMLAEHSVDLAFVNSPVR--DQRVEEHRFFRVHDVFLAG 172
Cdd:cd08427    2 LRLGAIATVLTGLLPRALARLRRRHPDLEVHIVPGLSAELLARVDAGELDAAIVVEPPFplPKDLVWTPLVREPLVLIAP 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 173 PRypLPQRPLAAAeVAALPLILLERKSNARRLVDDWFAAQGLPISPEIELGSHDLLLDFARIGLGVccAIEEFAEDYLRR 252
Cdd:cd08427   82 AE--LAGDDPREL-LATQPFIRYDRSAWGGRLVDRFLRRQGIRVREVMELDSLEAIAAMVAQGLGV--AIVPDIAVPLPA 156

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 972349739 253 GL-VVKLPVDFSLPPRHISWCKLRDVSLSPSAKRFVD 288
Cdd:cd08427  157 GPrVRVLPLGDPAFSRRVGLLWRRSSPRSRLIQALLE 193
PBP2_NhaR cd08429
The C-terminal substrate binding domain of LysR-type transcriptional activator of the nhaA ...
 94-258 4.56e-07

The C-terminal substrate binding domain of LysR-type transcriptional activator of the nhaA gene, encoding Na+/H+ antiporter, contains the type 2 periplasmic binding fold; NhaR is a positive regulator of the LysR family and is known to be an activator of the nhaA gene encoding a Na(+)/H(+) antiporter. In Escherichia coli, NhaA is the vital antiporter that protects against high sodium stress, and it is essential for growth in high sodium levels, while NhaB becomes essential only if NhaA is not available. The nhaA gene of nhaAR operon is induced by monovalent cations. The nhaR of the operon activates nhaAR, as well as the osmC transcription which is induced at elevated osmolarity. OsmC is transcribed from the two overlapping promoters (osmCp1 and osmP2) and that NhaR is shown to activate only the expression of osmCp1. NhaR also activates the transcription of the pgaABCD operon which is required for production of the biofilm adhesion, poly-beta-1,6-N-acetyl-d-glucosamine (PGA) .Thus, it is suggested that NhaR has an extended role in promoting bacterial survival. 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: 176120 [Multi-domain]  Cd Length: 204  Bit Score: 49.24  E-value: 4.56e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  94 QLRVGVSDTISRFVILGQLERFHREYPHIRLVIQNGTSIEAVEMLAEHSVDLAFVNSPVR---DQRVEEHRFFRVHDVFL 170
Cdd:cd08429    1 LFRVGVADAVPKSIAYRLLEPAMDLHEPIRLVCREGKLEQLLADLALHRLDMVLADRPMPsslDVKGYSHRLGECGVSFF 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 171 AGPRYPLPQRPLAAAEVAALPLILLERKSNARRLVDDWFAAQGlpISPEIeLGSHD---LLLDFARIGLGVCCAIEEFAE 247
Cdd:cd08429   81 AAPPLAKRLEKPFPASLDEAPLLLPGEDSALRRKLLQWFERQG--LRPQI-VGEFDdsaLMKAFGQAGAGIFAAPTVIAD 157

                        170
                 ....*....|.
gi 972349739 248 DYLRRGLVVKL 258
Cdd:cd08429  158 EVARQYGVVEI 168
PBP2_IlvY cd08430
The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates ...
 112-286 5.56e-07

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: 49.12  E-value: 5.56e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 112 LERFHREYPHIRLVIQNGTSIEAVEMLAEHSVDLAFVNSPvrDQ---RVEEHRFFRVHDVFLAGPRYPLPQRPLAAAEV- 187
Cdd:cd08430   19 LERFRAQHPQVEIKLHTGDPADAIDKVLNGEADIAIAARP--DKlpaRLAFLPLATSPLVFIAPNIACAVTQQLSQGEId 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 188 -AALPLILLERKSnARRLVDDWFAAQGlpISPEI--ELGSHDLLLDFARIGLGVCCAIEEFAEDYLRRGLVVKLPVDFSL 264
Cdd:cd08430   97 wSRLPFILPERGL-ARERLDQWFRRRG--IKPNIyaQVAGHEAIVSMVALGCGVGIVPELVLDNSPLKDKVRILEVQPEL 173

                        170       180
                 ....*....|....*....|..
gi 972349739 265 PPRHISWCKLRDVSLSPSAKRF 286
Cdd:cd08430  174 EPFEVGLCCLKKRLNEPLIKAF 195
PBP2_CrgA_like_3 cd08472
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-293 3.47e-06

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 3. 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: 176161  Cd Length: 202  Bit Score: 46.74  E-value: 3.47e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  93 GQLRVGVSDTISRFVILGQLERFHREYPHIRLVIqnGTSIEAVEMLAEhSVDLAFVNSPVRDQRVEEHRFFRVHDVFLAG 172
Cdd:cd08472    1 GRLRVDVPGSLARLLLIPALPDFLARYPDIELDL--GVSDRPVDLIRE-GVDCVIRVGELADSSLVARRLGELRMVTCAS 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 173 P----RYPLPQRPlaaAEVAALPLILLERKSNARRLvdDW-FAAQGLPIspEIELGSH------DLLLDFARIGLGVCCA 241
Cdd:cd08472   78 PaylaRHGTPRHP---EDLERHRAVGYFSARTGRVL--PWeFQRDGEER--EVKLPSRvsvndsEAYLAAALAGLGIIQV 150

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 972349739 242 IEEFAEDYLRRG-LVVKLPvDFSLPPRHISWCKLRDVSLSPSAKRFVDFIGGR 293
Cdd:cd08472  151 PRFMVRPHLASGrLVEVLP-DWRPPPLPVSLLYPHRRHLSPRVRVFVDWVAEL 202
PBP_like_2 pfam12849
PBP superfamily domain; This domain belongs to the periplasmic binding protein superfamily.
 86-189 7.55e-06

PBP superfamily domain; This domain belongs to the periplasmic binding protein superfamily.


Pssm-ID: 432831 [Multi-domain]  Cd Length: 267  Bit Score: 46.38  E-value: 7.55e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739   86 EQQNLEQGQLRVGVSDTISRFVILgQLERFHREYPHIRLVIQNGTSIEAVEMLAEHSVDLAFVNSPVRDQRVEEHRFFRV 165
Cdd:pfam12849   3 AASAPTVGTILIAGSSTQAPGLLD-LAEAFEKKYPGAKVKVTSVGSGEGIKALLNGDVDVALVSRPLTEEEFEAFGANGA 81

                          90       100       110
                  ....*....|....*....|....*....|....
gi 972349739  166 H----------DVFLAGPRyPLPQRPLAAAEVAA 189
Cdd:pfam12849  82 GglvevpvaydGIAIVVNK-DNPANILTVEALKK 114
PBP2_DntR_like_3 cd08461
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 95-215 9.97e-06

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


Pssm-ID: 176150 [Multi-domain]  Cd Length: 198  Bit Score: 45.35  E-value: 9.97e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  95 LRVGVSDTISRFVILGQLERFHREYPHIRLVIQNGTSIEAVEMLAEHSVDLAFVNSPVRDQRVEEHRFFRVHDVFLAGPR 174
Cdd:cd08461    2 LVIAATDYAQKAILPPLLAALRQEAPGVRVAIRDLESDNLEAQLERGEVDLALTTPEYAPDGLRSRPLFEERYVCVTRRG 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 972349739 175 YPLPQRPLAAAEVAALPLILLE-RKSNARRLVDDWFAAQGLP 215
Cdd:cd08461   82 HPLLQGPLSLDQFCALDHIVVSpSGGGFAGSTDEALAALGLT 123
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 3-148 1.95e-05

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 45.41  E-value: 1.95e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739   3 VKLEHYRVFREvarqggfsaAAGKLFVSQSAVSQTVKHLESQLGVPLFDRRGKRLSLTSEGELLygyvdaalktLEQGQQ 82
Cdd:PRK11151  10 VALAEHRHFRR---------AADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLL----------VDQART 70

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 972349739  83 SLREQQNLEQ----------GQLRVGVSDTISRFVILGQLERFHREYPHIRLVIQNGTSIEAVEMLAEHSVD---LAFV 148
Cdd:PRK11151  71 VLREVKVLKEmasqqgetmsGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDcaiLALV 149
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 94-289 4.30e-05

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: 43.69  E-value: 4.30e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  94 QLRVGVSDTISRFVILGQLERFHREYPHIRLVIQNGTSIEAVEMLAEHSVDLAFVNSPVRDQRVEEHRFFRVHDVFLAGP 173
Cdd:cd08412    1 TLRIGCFSTLAPYYLPGLLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALTYDLDLPEDIAFEPLARLPPYVWLPA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 174 RYPLPQRP-LAAAEVAALPLILLERKSnARRLVDDWFAAQGLpiSPEIELGSHDllLDFARI----GLGVCCAIEEFAED 248
Cdd:cd08412   81 DHPLAGKDeVSLADLAAEPLILLDLPH-SREYFLSLFAAAGL--TPRIAYRTSS--FEAVRSlvanGLGYSLLNDRPYRP 155

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 972349739 249 YLRRGL-VVKLPVDFSLPPRHISWCKLRDVSLSPSAKRFVDF 289
Cdd:cd08412  156 WSYDGKrLVRRPLADPVPPLRLGLAWRRGARLTRAARAFVDF 197
PBP2_PnbR cd08469
The C-terminal substrate binding domain of LysR-type transcriptional regulator PnbR, which is ...
 94-215 5.62e-05

The C-terminal substrate binding domain of LysR-type transcriptional regulator PnbR, which is involved in regulating the pnb genes encoding enzymes for 4-nitrobenzoate catabolism, contains the type 2 periplasmic binding fold; PnbR is the regulator of one or both of the two pnb genes that encoding enzymes for 4-nitrobenzoate catabolism. In Pseudomonas putida strain, pnbA encodes a 4-nitrobenzoate reductase, which is responsible for catalyzing the direct reduction of 4-nitrobenzoate to 4-hydroxylaminobenzoate, and pnbB encodes a 4-hydroxylaminobenzoate lyase, which catalyzes the conversion of 4-hydroxylaminobenzoate to 3, 4-dihydroxybenzoic acid and ammonium. 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: 176158  Cd Length: 221  Bit Score: 43.55  E-value: 5.62e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  94 QLRVGVSDTISRfVILGQL-ERFHREYPHIRLVIQNGTSIEAVEMLAEHSVDLA---FVNSPvrdQRVEEHRFFRVHDVF 169
Cdd:cd08469    1 SFVIAANDYVTA-VLLPALvRRLETEAPGIDLRIRPVTRLDLAEQLDLGRIDLVigiFEQIP---PRFRRRTLFDEDEVW 76

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 972349739 170 LAGPRYPLPQRPLAAAEVAALPLILLERKSNARRLVDDWFAAQGLP 215
Cdd:cd08469   77 VMRKDHPAARGALTIETLARYPHIVVSLGGEEEGAVSGFISERGLA 122
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-266 1.04e-04

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 5. 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: 176163 [Multi-domain]  Cd Length: 202  Bit Score: 42.45  E-value: 1.04e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  93 GQLRVGVSDTISRFVILGQLERFHREYPHIRLviqngtsieavemlaEHSVDLAFVNspvrdqrVEEHRF---FRVHD-- 167
Cdd:cd08474    3 GTLRINAPRVAARLLLAPLLARFLARYPDIRL---------------ELVVDDGLVD-------IVAEGFdagIRLGEsv 60

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 168 ------VFLAGP-------------RYPLPQRPlaaAEVAALPLILLERKSNARrlVDDW-FAAQGLPISPEIE----LG 223
Cdd:cd08474   61 ekdmvaVPLGPPlrmavvaspaylaRHGTPEHP---RDLLNHRCIRYRFPTSGA--LYRWeFERGGRELEVDVEgpliLN 135

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 972349739 224 SHDLLLDFARIGLGVCCAIEEFAEDYLRRG-LVVKLPvDFSLPP 266
Cdd:cd08474  136 DSDLMLDAALDGLGIAYLFEDLVAEHLASGrLVRVLE-DWSPPF 178
PBP2_DntR_like_1 cd08460
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 112-266 1.75e-04

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


Pssm-ID: 176149 [Multi-domain]  Cd Length: 200  Bit Score: 41.81  E-value: 1.75e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 112 LERFHREYPHIRLVIQnGTSIEAVEMLAEHSVDLAFVNSPVRDQRVEEHRFFRVHDVFLAGPRYPLPQRPLAAAEVAALP 191
Cdd:cd08460   19 LAAVAAEAPGVRLRFV-PESDKDVDALREGRIDLEIGVLGPTGPEIRVQTLFRDRFVGVVRAGHPLARGPITPERYAAAP 97

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 972349739 192 LILLERKSNARRLVDDWFAAQGLPISPEIELGSHDLLLDFARIGLGVCCAIEEFAEDYLRRGLVVKLPVDFSLPP 266
Cdd:cd08460   98 HVSVSRRGRLHGPIDDALAALGLTRRVVAVVPTFAAALFLARGSDLIALVPERVTAAARAGLGLRTFPLPLELPA 172
PBP2_MleR cd08437
The substrate binding domain of LysR-type transcriptional regulator MleR which required for ...
 94-290 2.78e-04

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


Pssm-ID: 176128  Cd Length: 198  Bit Score: 41.16  E-value: 2.78e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  94 QLRVGVSDTISRFVILGQLERFHREYPHIRLVIQNGTSIEAVEMLAEHSVDLAFVNS--PVRDQRVEEHRFFRVHDVFLA 171
Cdd:cd08437    1 KLRFGLPPIIGNYYFPKLAKDLIKTGLMIQIDTYEGGSAELLEQLLQGDLDIALLGSltPLENSALHSKIIKTQHFMIIV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 172 GPRYPLP-QRPLAAAEVAALPLILLErKSNARRLVDDWFAAQGlPISPEIELGSHD--LLLDFARIGLGVCCAIeEFA-- 246
Cdd:cd08437   81 SKDHPLAkAKKVNFADLKKENFILLN-EHFVHPKAFDSLCQQA-NFQPNIVYRTNDihILKSMVRENVGIGFLT-DIAvk 157

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 972349739 247 -EDYLrrglvVKLPVDFSLPPR-HISWCKLRDVSLSPSAKRFVDFI 290
Cdd:cd08437  158 pDDHL-----VAIPLLDNEQPTfYISLAHRKDQLLTPAQKKLLDLL 198
PBP2_Chlorocatechol cd08446
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 93-290 2.83e-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: 41.11  E-value: 2.83e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  93 GQLRVGVSDTISRFVILGQLERFHREYPHIRLVIQNGTSIEAVEMLAEHSVDLAFvnspvrdqrveeHRFFRVHD----- 167
Cdd:cd08446    1 GELDVGYFGSAILDTVPRLLRAFLTARPDVTVSLHNMTKDEQIEALRAGRIHIGF------------GRFYPVEPdiave 68

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 168 ------VFLAGPR-YPLPQRP-LAAAEVAALPLILLERKSNaRRLVD---DWFAAQGlpISPEIELGSHDL--LLDFARI 234
Cdd:cd08446   69 nvaqerLYLAVPKsHPLAARPaVSLADLRNEPLILFPRGGR-PSFADevlGLFRRAG--VEPRVAQEVEDVvaALALVAA 145

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 972349739 235 GLGVCCAIEEFAEdyLRRGLVVKLPVDFSLPPRHISwCKLRDVSLSPSAKRFVDFI 290
Cdd:cd08446  146 GFGVCIVPESVAA--LRWPGVVFRPLADAEAKVPLS-CIYRKDDRSPILRAFLDVV 198
PBP2_CrgA_like_9 cd08479
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-290 3.89e-04

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 9. 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: 176168 [Multi-domain]  Cd Length: 198  Bit Score: 40.66  E-value: 3.89e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  93 GQLRVGVSDTISRFVILGQLERFHREYPHIRLVIqngTSIEAVEMLAEHSVDLAFVNSPVRDQRVEEHRFFRVHDVFLAG 172
Cdd:cd08479    1 GLLRVNASFGFGRRHIAPALSDFAKRYPELEVQL---ELTDRPVDLVEEGFDLDIRVGDLPDSSLIARKLAPNRRILCAS 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 173 PRY----PLPQRPlaaAEVAALPLILLERKSNArrlVDDW--FAAQG---LPISPEIELGSHDLLLDFARIGLGVCCAIE 243
Cdd:cd08479   78 PAYlerhGAPASP---EDLARHDCLVIRENDED---FGLWrlRNGDGeatVRVRGALSSNDGEVVLQWALDGHGIILRSE 151

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 972349739 244 EFAEDYLRRGLVVKLPVDFSLPPRHISWCKLRDVSLSPSAKRFVDFI 290
Cdd:cd08479  152 WDVAPYLRSGRLVRVLPDWQLPDADIWAVYPSRLSRSARVRVFVDFL 198
PBP2_BudR cd08451
The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is ...
 94-211 5.55e-04

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: 40.24  E-value: 5.55e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  94 QLRVG-VSDTISRFVILGQLERFHREYPHIRLVIQNGTSIEAVEMLAEHSVDLAFVNSPV-RDQRVEEHRFFRvHDVFLA 171
Cdd:cd08451    1 RLRVGfTSSAAFHPLVPGLIRRFREAYPDVELTLEEANTAELLEALREGRLDAAFVRPPVaRSDGLVLELLLE-EPMLVA 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 972349739 172 GPR-YPLPQ-RPLAAAEVAALPLILLERkSNARRLVDDWFAA 211
Cdd:cd08451   80 LPAgHPLAReRSIPLAALADEPFILFPR-PVGPGLYDAIIAA 120
PBP2_LrhA_like cd08439
The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of ...
 95-238 6.73e-04

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: 40.01  E-value: 6.73e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  95 LRVGVSDTISRFVILGQLERFHREYPHIRLVIQNGTSIEAVEMLAEHSVDLAFVNSPVRDQrveEHRFFRVHD-VFLAGP 173
Cdd:cd08439    2 LRIGCPDDYADTILPFLLNRFASVYPRLAIEVVCKRTPRLMEMLERGEVDLALITHPPPGA---SATILRRSPtVWYCAA 78

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 972349739 174 RYPL-PQRPlaaaevaaLPLILLERKSNARRLVDDWFAAQGLPISPEIELGSHDLLLDFARIGLGV 238
Cdd:cd08439   79 GYILaPGEP--------LPLALLDEPTLDRRAALAALDAAGIPWRIAYAASSLSGLRAAVRAGLGI 136
PBP2_GcdR_like cd08481
The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, ...
 112-256 9.16e-04

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: 39.59  E-value: 9.16e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 112 LERFHREYPHIRLVIQNGtsIEAVEmLAEHSVDLAFVNSPVRDQRVEEHRFFRVHDVFLAGPRYpLPQRPLAAAE-VAAL 190
Cdd:cd08481   19 LPDFLARHPDITVNLVTR--DEPFD-FSQGSFDAAIHFGDPVWPGAESEYLMDEEVVPVCSPAL-LAGRALAAPAdLAHL 94

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 972349739 191 PLILLERKSNARRlvdDWFAAQGL-----PISPEIELGShdLLLDFARIGLGVCCAIEEFAEDYLRRG-LVV 256
Cdd:cd08481   95 PLLQQTTRPEAWR---DWFEEVGLevptaYRGMRFEQFS--MLAQAAVAGLGVALLPRFLIEEELARGrLVV 161
PBP2_DntR_like_4 cd08463
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 96-262 9.35e-04

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


Pssm-ID: 176152 [Multi-domain]  Cd Length: 203  Bit Score: 39.60  E-value: 9.35e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  96 RVGVSDTISRFVILGQLERFHREYPHIRLVIQN-GTSIEAVEMLAEHSVDLAFVNSPVRDQRVEEHRFFRVHDVFLAGPR 174
Cdd:cd08463    3 RIAAPDYLNALFLPELVARFRREAPGARLEIHPlGPDFDYERALASGELDLVIGNWPEPPEHLHLSPLFSDEIVCLMRAD 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 175 YPLPQRP-------LAAAEVAALPLIllerkSNARRLVDDWFAAQGLP-----ISPEIELGSH-----DLLLDFARiglg 237
Cdd:cd08463   83 HPLARRGlmtlddyLEAPHLAPTPYS-----VGQRGVIDSHLARLGLKrnivvTVPYFGLAPYmlaqsDLVFTTGR---- 153

                        170       180
                 ....*....|....*....|....*..
gi 972349739 238 vccaieEFAEDYLRR--GLVVKLPVDF 262
Cdd:cd08463  154 ------HFAEHYAKLlpLAVVDAPIEF 174
MarR COG1846
DNA-binding transcriptional regulator, MarR family [Transcription];
7-79 1.41e-03

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


Pssm-ID: 441451 [Multi-domain]  Cd Length: 142  Bit Score: 38.41  E-value: 1.41e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739   7 HYRVFREVARQGGFSAA--AGKLFVSQSAVSQTVKHLEsQLG------VPLfDRRGKRLSLTSEGELLYGYVDAALKTLE 78
Cdd:COG1846   40 QFRVLAALAEAGGLTQSelAERLGLTKSTVSRLLDRLE-EKGlverepDPE-DRRAVLVRLTEKGRALLEEARPALEALL 117


                 .
gi 972349739  79 Q 79
Cdd:COG1846  118 A 118
PBP2_ToxR cd08465
The C-terminal substrate binding domain of LysR-type transcriptional regulator ToxR regulates ...
 95-237 1.72e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulator ToxR regulates the expression of the toxoflavin biosynthesis genes; contains the type 2 periplasmic bindinig fold; In soil bacterium Burkholderia glumae, ToxR regulates the toxABCDE and toxFGHI operons in the presence of toxoflavin as a coinducer. Additionally, the expression of both operons requires a transcriptional activator, ToxJ, whose expression is regulated by the TofI or TofR quorum-sensing system. The biosynthesis of toxoflavin is suggested to be synthesized in a pathway common to the synthesis of riboflavin. 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: 176154  Cd Length: 200  Bit Score: 38.83  E-value: 1.72e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  95 LRVGVSDTISRFVILGQLERFHREYPHIRLVIQNGTSIEAVEMLAEHSVDLAFVNSPVRDQRVEEHRFFRVHDVFLAGPR 174
Cdd:cd08465    2 FRLAMSDYGARLVLPALMRQLRAEAPGIDLAVSQASREAMLAQVADGEIDLALGVFPELPEELHAETLFEERFVCLADRA 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 972349739 175 YpLPQR-PLAAAEVAALPLILLERKSNARRLVDDWFAAQGLP-----------ISPEIELGShDLLLDFARIGLG 237
Cdd:cd08465   82 T-LPASgGLSLDAWLARPHVLVAMRGDAANEIDRALAARGLRrrvaltlphwgVAPELIAGT-DLILTVARRALD 154
PBP2_LTTR_aromatics_like_2 cd08448
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-197 2.33e-03

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


Pssm-ID: 176139 [Multi-domain]  Cd Length: 197  Bit Score: 38.40  E-value: 2.33e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  94 QLRVG-VSDTISRfVILGQLERFHREYPHIRLVIQNGTSIEAVEMLAEHSVDLAFVNSPVRDQRVEEHRFFRVHDVFLAG 172
Cdd:cd08448    1 RLRIGfVGSMLYR-GLPRILRAFRAEYPGIEVALHEMSSAEQIEALLRGELDLGFVHSRRLPAGLSARLLHREPFVCCLP 79

                         90       100
                 ....*....|....*....|....*.
gi 972349739 173 PRYPLPQRP-LAAAEVAALPLILLER 197
Cdd:cd08448   80 AGHPLAARRrIDLRELAGEPFVLFSR 105
PBP2_CrgA cd08478
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains ...
 92-290 3.61e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains the type 2 periplasmic binding domain; This CD represents the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA. 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: 176167 [Multi-domain]  Cd Length: 199  Bit Score: 37.70  E-value: 3.61e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  92 QGQLRVGVSDTISRFVILGQLERFHREYPHIRLVIQNGtsiEAVEMLAEHSVDLAFVNSPVRDQRVEEHRFFRVHDVFLA 171
Cdd:cd08478    2 SGLLRVDAATPFVLHLLAPLIAKFRERYPDIELELVSN---EGIIDLIERKTDVAIRIGELTDSTLHARPLGKSRLRILA 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739 172 GP----RYPLPQRPlaaAEVAALPLILLERKSNarrlVDDW--FAAQG--LPISPEIELGSHDLLLDFARIGLGVCCaIE 243
Cdd:cd08478   79 SPdylaRHGTPQSI---EDLAQHQLLGFTEPAS----LNTWpiKDADGnlLKIQPTITASSGETLRQLALSGCGIAC-LS 150

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 972349739 244 EFAEDY-LRRGLVVKLPVDFSLPPRH-ISWCKLRDVSLSPSAKRFVDFI 290
Cdd:cd08478  151 DFMTDKdIAEGRLIPLFAEQTSDVRQpINAVYYRNTALSLRIRCFIDFL 199
PBP2_CrgA_like_10 cd08480
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-238 9.47e-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 10. 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: 176169  Cd Length: 198  Bit Score: 36.55  E-value: 9.47e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349739  93 GQLRVGVSDTISRFVILGQLERFHREYPHIRLVIQngTSIEAVEMLAEHSvDLAFVNSPVRDQRVEEHRFFRVHDVFLAG 172
Cdd:cd08480    1 GRLRVNASVPFGTHFLLPLLPAFLARYPEILVDLS--LTDEVVDLLAERT-DVAIRVGPLPDSSLVARKLGESRRVIVAS 77

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 972349739 173 P----RYPLPQRPlaaAEVAALPLIllerKSNARRLVDDW-FAAQG----LPISPEIELGSHDLLLDFARIGLGV 238
Cdd:cd08480   78 PsylaRHGTPLTP---QDLARHNCL----GFNFRRALPDWpFRDGGrivaLPVSGNILVNDGEALRRLALAGAGL 145
 
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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