PaperBLAST
PaperBLAST Hits for tr|Q9HYJ0|Q9HYJ0_PSEAE Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=PA3415 PE=3 SV=1 (370 a.a., MKHFKLPDLG...)
Show query sequence
>tr|Q9HYJ0|Q9HYJ0_PSEAE Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=PA3415 PE=3 SV=1
MKHFKLPDLGEGLQEAEIVEWHVKAGDSVRADQRLVSVETAKALVDIPAPYDGVVGKLFG
AEGDILHVGEPLVGFEGEEADAGTVVGRLEGGGSALEDRFFIGAAPSTREHLAPRATPAV
RQFARQQGVELAGLSGSGPDGLITRADVEAAAQGTRERFGGERLRGVRRSMALNMARSHA
EVVPVTIYGDADLHRWKTARDPLIRLAQALAEACRAEPTLNAWFDGASLSLKLHERLDLG
IAVDTPDGLFVPVLRDVGARSAEDLRAGMRRLREDVQARSIPPAEMLGATLTLSNFGTLF
GRYANPVVVPPQVAILGAGGIRDEVVAWRGEMAIHPILPLSLSFDHRAATGGEAARFLKV
LVNALEQPDG
Running BLASTp...
Found 333 similar proteins in the literature:
PA3415 probable dihydrolipoamide acetyltransferase from Pseudomonas aeruginosa PAO1
100% identity, 100% coverage
- Systems-wide dissection of organic acid assimilation in Pseudomonas aeruginosa reveals a novel path to underground metabolism
Dolan, 2022 - Systems-Wide Dissection of Organic Acid Assimilation in Pseudomonas aeruginosa Reveals a Novel Path To Underground Metabolism
Dolan, mBio 2022 - “...statistically significant upregulated transcripts in the wild-type following challenge with propionate were associated with ORFs PA3415 to PA3417 (2.8 FC). These ORFs are predicted to encode a pyruvate dehydrogenase (PDH) or a branched-chain amino acid dehydrogenase ( Data Set S3 ; Fig.6B ) ( 54 )....”
- “...expression of these genes ( Data Set S3 ; Fig.S5C ). Immediately adjacent to the PA3415 to PA3417 cluster is leucine dehydrogenase ( ldh , PA3418), required for BCAA catabolism, which was also significantly upregulated after propionate exposure (~3-fold change). However, given that propionyl-CoA is an...”
- ECF Sigma Factor HxuI Is Critical for In Vivo Fitness of Pseudomonas aeruginosa during Infection
Cai, Microbiology spectrum 2022 - “...acid dehydrogenase complex component 2.31 8.19E-16 PA2446 gcvH2 Glycine cleavage system protein H 2.14 3.3E-10 PA3415 Probable dihydrolipoamide acetyltransferase 3.76 3.12E-36 PA3416 Pyruvate dehydrogenase E1 component subunit beta 2.9 5.1E-10 PA3417 Pyruvate dehydrogenase E1 component subunit alpha 2.69 5.91E-22 PA3582 glpK Glycerol kinase GlpR binding site...”
- NtrBC Regulates Invasiveness and Virulence of Pseudomonas aeruginosa During High-Density Infection
Alford, Frontiers in microbiology 2020 - “...complex subunit 1.74 1.75 PA3182 pgl 6-phosphogluconolactonase 1.80 1.63 PA3183 zwf Glucose-6-phosphate 1-dehydrogenase 1.55 1.52 PA3415 Probable dihydrolipoamide acetyltransferase 2.61 2.80 PA3416 pdhB Prob. pyruvate dehydrogenase E1 component, chain 2.28 2.55 PA3417 Pyruvate dehydrogenase E1 component subunit alpha 2.39 2.53 PA3570 mmsA Methylmalonate-semialdehyde dehydrogenase 1.92 2.44...”
- The Aspergillus fumigatus Secretome Alters the Proteome of Pseudomonas aeruginosa to Stimulate Bacterial Growth: Implications for Co-infection
Margalit, Molecular & cellular proteomics : MCP 2020 - “...subunit alpha Ns 4.9 5.2 pdhA Pyruvate dehydrogenase E1 component subunit alpha 16.4 7 2.4 PA3415 Dihydrolipoamide acetyltransferase 3.4 16.4 4.7 lpdV Dihydrolipoyl dehydrogenase 1.9 15.4 8.2 Outer membrane MexE RND multidrug efflux membrane fusion protein 132.3 47.27 ns oprC Outer membrane efflux protein OprC 38.6...”
- Conceptual Model of Biofilm Antibiotic Tolerance That Integrates Phenomena of Diffusion, Metabolism, Gene Expression, and Physiology
Stewart, Journal of bacteriology 2019 (secret) - Proteomic Response of Pseudomonas aeruginosa PAO1 Adhering to Solid Surfaces
Guilbaud, Frontiers in microbiology 2017 - “...15.6 21.2 1.9E-03 urocanate hydratase PA5100 hutU 0.0 0.0 3.2 8.6E-06 1.1E-05 probable dihydrolipoamide acetyltransferase PA3415 0.8 0.0 4.6 3.0E-04 1.5E-07 quinone oxidoreductase PA0023 qor 1.6 0.6 5.2 3.2E-03 1.7E-05 isocitrate dehydrogenase PA2623 icd 22.2 28.8 32.0 5.6E-03 Fatty acid and phospholipid metabolism acetyl-CoA acetyltransferase PA2001...”
- Transcriptional and proteomic responses of Pseudomonas aeruginosa PAO1 to spaceflight conditions involve Hfq regulation and reveal a role for oxygen
Crabbé, Applied and environmental microbiology 2011 - “...PA2971 PA3001 PA3162 PA3307 PA3361 PA3369 PA3391 PA3392 PA3415 PA3416 PA3417 PA0200 PA0492 PA0493 nirM nirS norC norB PA0525 PA0534 PA0567 rpsU ostA PA0788...”
- “...PA3001 rpsA PA3307 lecB PA3369 nosR nosZ PA3415 PA3416 PA3417 Function Hypothetical protein Hypothetical protein Acetyl coenzyme A carboxylase Cytochrome c551...”
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PA14_19920 putative dihydrolipoamide acetyltransferase from Pseudomonas aeruginosa UCBPP-PA14
100% identity, 100% coverage
A0KM68 Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex from Aeromonas hydrophila subsp. hydrophila (strain ATCC 7966 / DSM 30187 / BCRC 13018 / CCUG 14551 / JCM 1027 / KCTC 2358 / NCIMB 9240 / NCTC 8049)
AHA_2865 pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide acyltransferase component from Aeromonas hydrophila subsp. hydrophila ATCC 7966
53% identity, 99% coverage
- Comprehensive analysis of the lysine acetylome in Aeromonas hydrophila reveals cross-talk between lysine acetylation and succinylation in LuxS
Sun, Emerging microbes & infections 2019 - “...A0KGR4 (polyphosphate glucokinase, AHA_0917 ), A0KIK2 (hydroxyacylglutathione hydrolase, gloB ), A0KNJ9 (glyceraldehyde-3-phosphate dehydrogenase, gap-1 ), A0KM68 (dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex, AHA_2865 ), and A0KID4 (pyruvate-flavodoxin oxidoreductase, nifJ-1 ). Overall, these findings demonstrate that lysine acetylation and succinylation are both significantly enriched and broadly...”
- Comprehensive analysis of the lysine acetylome in Aeromonas hydrophila reveals cross-talk between lysine acetylation and succinylation in LuxS
Sun, Emerging microbes & infections 2019 - “...gloB ), A0KNJ9 (glyceraldehyde-3-phosphate dehydrogenase, gap-1 ), A0KM68 (dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex, AHA_2865 ), and A0KID4 (pyruvate-flavodoxin oxidoreductase, nifJ-1 ). Overall, these findings demonstrate that lysine acetylation and succinylation are both significantly enriched and broadly distributed in central metabolic pathways, thus implying that...”
lpp1517 hypothetical protein from Legionella pneumophila str. Paris
49% identity, 99% coverage
- The Legionella pneumophila genome evolved to accommodate multiple regulatory mechanisms controlled by the CsrA-system
Sahr, PLoS genetics 2017 - “...in L . pneumophila . CsrA positively impacts the pyruvate/2-oxoglutarate dehydrogenase complex ( lpp1515 - lpp1517 ) and proteins that participate in the Entner-Dudoroff ( lpp0483 - lpp0487 ) pathway, an alternative pathway to catabolize glucose to pyruvate. Additionally, the transcript of the glycolysis protein triosephosphate...”
- Two small ncRNAs jointly govern virulence and transmission in Legionella pneumophila
Sahr, Molecular microbiology 2009 - “...synthetase - lpp3052-lpp3059 ), or proteins involved in carbohydrate metabolism ( e.g. pyruvate dehydrogenase - lpp1517 ; phosphoenolpyruvate synthase lpp0867 ) ( Table 1 ). Furthermore, in contrast to the wild type, in letA and letS mutants the biosynthesis of the lipopolyssacharide (LPS) capsule and of...”
- “...lpp1672 AstD (Succinylglutamic semialdehyde dehydrogenase) 2.46 1.96 lpp1671 AstA (Arginine N-succinyltransferase- beta chain) 2.16 2.21 lpp1517 Pyruvate dehydrogenase E2 component 3.74 2.09 lpp1516 Pyruvate dehydrogenase- (E1 beta subunit) 2.23 1.67 lpp1346 50S ribosomal subunit protein L32 2.39 2.46 lpp1247 RpoS (RNA polymerase sigma factor) - 3.11...”
VP_RS18295 dihydrolipoamide acetyltransferase family protein from Vibrio parahaemolyticus RIMD 2210633
44% identity, 96% coverage
- Identification of Antibacterial Components in the Methanol-Phase Extract from Edible Herbaceous Plant Rumex madaio Makino and Their Antibacterial Action Modes
Liu, Molecules (Basel, Switzerland) 2022 - “...For example, in the glycolysis/gluconeogenesis, except for an up-regulated 2-oxo acid dehydrogenase subunit E2 ( VP_RS18295 ), the other seven DEGs were significantly down-regulation (0.087- to 0.433-fold) ( p < 0.05); in the propanoate metabolic pathway, express of four DEGs were significantly depressed (0.051- to 0.240-fold)...”
- “...complex dihydrolipoyllysine-residue acetyltransferase VP_RS13410 0.406 Glucose-6-phosphate isomerase VP_RS10485 0.416 D-hexose-6-phosphate mutarotase VP_RS09910 0.433 Pyruvate kinase VP_RS18295 2.558 2-oxo acid dehydrogenase subunit E2 Flagellar assembly VP_RS22540 0.055 Flagellar biosynthesis protein FliQ VP_RS16540 0.064 Flagellar basal body rod protein FlgB VP_RS16565 0.086 Flagellar basal-body rod protein FlgG VP_RS22520...”
SE37_02035 dihydrolipoamide acetyltransferase family protein from Geobacter soli
41% identity, 93% coverage
- Genome sequence of a dissimilatory Fe(III)-reducing bacterium Geobacter soli type strain GSS01(T)
Yang, Standards in genomic sciences 2015 - “...two sets of genes encoding pyruvate dehydrogenase complexes (SE37_03080, SE37_02045, SE37_02040, and SE37_03100; SE37_03105 and SE37_02035) to irreversibly convert pyruvate to acetyl-CoA. The reverse reaction in G. soli from acetyl-CoA is attributed to a homodimeric pyruvate-ferredoxin/flavodoxin oxidoreductase (SE37_14040). In addition to pyruvate, ethanol is another electron...”
RHA1_ro03319 dihydrolipoyllysine-residue acetyltransferase, E2 component of pyruvate dehydrogenase complex from Rhodococcus sp. RHA1
36% identity, 89% coverage
SSPN_RS0119525 dihydrolipoamide acetyltransferase family protein from Saccharopolyspora spinosa NRRL 18395
36% identity, 88% coverage
MSMEG_4710 dihydrolipoamide acetyltransferase from Mycobacterium smegmatis str. MC2 155
37% identity, 91% coverage
- bkaR is a TetR-type repressor that controls an operon associated with branched-chain keto-acid metabolism in Mycobacteria
Balhana, FEMS microbiology letters 2013 - “...to be significantly derepressed for a P -value cut-off of 0.05 (Table 2 ). Additionally, MSMEG_4710 ( bkdC ) was also derepressed but did not meet the significance criteria. Although this gene did not meet the significance cut-off, it was 1.8-fold derepressed, and other evidence suggests...”
- “...keto-acid dehydrogenase complex MSMEG_4711 3.3 3.3E-02 bkdB Rv2496c Part of branched-chain keto-acid dehydrogenase complex * MSMEG_4710 1.8 4.9E-01 bkdC Rv2495c Part of branched-chain keto-acid dehydrogenase complex * MSMEG_4005 3.2 2.5E-02 Calcium-binding protein MSMEG_2080 3.1 3.3E-02 fadE23 Rv3140 Putative acyl-CoA dehydrogenase MSMEG_1885 3.3 2.2E-02 Rv3230c Rv3230c Ironsulphur...”
BA4182 pyruvate dehydrogenase complex E2 component, dihydrolipoamide acetyltransferase from Bacillus anthracis str. Ames
31% identity, 87% coverage
- Whole genome protein microarrays for serum profiling of immunodominant antigens of Bacillus anthracis
Kempsell, Frontiers in microbiology 2015 - “...recognized by infected or exposed groups in comparison to controls. Some of these antigens e.g., BA4182 are not recognized by vaccinated individuals, suggesting that there are proteins more specifically expressed by live Anthrax spores in vivo that are not currently found in the UK licensed Anthrax...”
- “...] (c) 3 entities DRF for the AP IVDU including PA 200 ng/l concentration and BA4182 (duplicate features) and 1990 DRF for the control [Supplementary Information S4 Figure A (iii) ] (d) 27 entities DRF for the AVPV including 27/30 of the PA, LF, and EF...”
SRIMR7_20005 dihydrolipoamide acetyltransferase family protein from Streptomyces rimosus subsp. rimosus
33% identity, 76% coverage
MAP2307c PdhC from Mycobacterium avium subsp. paratuberculosis str. k10
36% identity, 95% coverage
- Iron-sparing response of Mycobacterium avium subsp. paratuberculosis is strain dependent
Janagama, BMC microbiology 2010 - “...MAP1587c alpha amylase 2.03 0.2 2.87 0.7 MAP1554c FadE33_2 (acyl-coA synthase) 1.79 0.5 1.88 0.8 MAP2307c pdhC alpha-keto acid dehydrogenase 1.68 0.3 2.52 0.4 MAP3189 FadE23 (acyl-CoA dehydrogenase) 2.41 0.2 3.51 1.0 MAP3694c FadE5 (acyl-CoA dehydrogenase) 1.87 0.8 3.15 0.2 Cellular processes MAP3701c heat shock protein...”
- “...to SUF operon involved in Fe-S cluster assembly, fatty acid metabolism and a pyruvate dehydrogenase (MAP2307c). Transporter proteins, two component systems, and cell division associated proteins (MAP1906c, MAP0448 and MAP2997c) were also upregulated by the C strain (Table 1 and Additional file 1 , Table S8)....”
BC3971 Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex from Bacillus cereus ATCC 14579
32% identity, 85% coverage
W8Z497 Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex from Bacillus thuringiensis DB27
32% identity, 85% coverage
- Role of hsp20 in the Production of Spores and Insecticidal Crystal Proteins in Bacillus thuringiensis
Xie, Frontiers in microbiology 2019 - “...[ADP-forming] subunit alpha W8YK96 0.45 metG Methionine tRNA ligase W8Y8A7 0.45 ndk Nucleoside diphosphate kinase W8Z497 0.44 pdhC Dihydrolipoyllysine-residue acetyltransferase W8YKA7 0.44 mfd Transcription-repair-coupling factor W8YSS4 0.43 purN Phosphoribosylglycinamide formyltransferase W8Y8Z7 0.43 argD Acetylornithine aminotransferase W8YC93 0.41 ftsH ATP-dependent zinc metalloprotease W8YKA3 0.40 spoVG Putative septation...”
Q6GHZ0 Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex from Staphylococcus aureus (strain MRSA252)
32% identity, 84% coverage
NWMN_0961 branched-chain alpha-keto acid dehydrogenase subunit E2 from Staphylococcus aureus subsp. aureus str. Newman
Q8NX76 Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex from Staphylococcus aureus (strain MW2)
SAUSA300_0995 dihydrolipoamide acetyltransferase from Staphylococcus aureus subsp. aureus USA300_FPR3757
SACOL1104 pyruvate dehydrogenase complex E2 component, dihydrolipoamide acetyltransferase from Staphylococcus aureus subsp. aureus COL
32% identity, 84% coverage
- Thioredoxin Profiling of Multiple Thioredoxin-Like Proteins in Staphylococcus aureus
Peng, Frontiers in microbiology 2018 - “...Uncharacterized (glycosyl transferase family 1) 282 N 5 N NWMN_0996 Uncharacterized 95 N 1 Y/N NWMN_0961 pdhC Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex 346 N 1 Y ND e 3DUF NWMN_2028 murZ UDP- N -acetylglucosamine 1-carboxyvinyltransferase 2 376 N 5 Y/N Buried 3ZH3 Spn NWMN_0733...”
- Discovery of Furanoquinone Derivatives as a Novel Class of DNA Polymerase and Gyrase Inhibitors for MRSA Eradication in Cutaneous Infection
Yang, Frontiers in microbiology 2019 - “...via generation of an organic free radical. 7 Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex Q8NX76 46.452 17 88(44%) 0.330 0.710 The pyruvate dehydrogenase complex catalyzes the overall conversion of pyruvate to acetyl-CoA and CO(2). It contains multiple copies of three enzymatic components: pyruvate dehydrogenase (El),...”
- Defining the Roles of Pyruvate Oxidation, TCA Cycle, and Mannitol Metabolism in Methicillin-Resistant Staphylococcus aureus Catheter-Associated Urinary Tract Infection
Paudel, Microbiology spectrum 2023 - “...PDH E1 ( pdhA , SAUSA300_0993), PDH E1 ( pdhB , SAUSA300_0994), and dihydrolipoamide acetyltransferase (SAUSA300_0995) ( 17 ). The PDH complex bridges glycolysis with TCA cycle by catalyzing oxidative decarboxylation of pyruvate to acetyl-CoA and shares homology with the branched-chain -keto acid dehydrogenase (BKD) complex....”
- “...not significantly alter the transcription of the pdh gene cluster ( pdhA , pdhB , SAUSA300_0995, and lpdA ) suggests that at least at early time points, pyruvate oxidation is not needed for MRSA growth in a glucose-poor growth medium such as healthy HU ( 16...”
- Identification of Methicillin-Resistant Staphylococcus aureus (MRSA) Genetic Factors Involved in Human Endothelial Cells Damage, an Important Phenotype Correlated with Persistent Endovascular Infection
Xiao, Antibiotics (Basel, Switzerland) 2022 - “...SAUSA300_0916 hypothetical hypothetical protein 16.89 2.85 SAUSA300_1444 scpB segregation and condensation protein B 16.85 6.40 SAUSA300_0995 hypothetical branched-chain alpha-keto acid dehydrogenase subunit E2 16.83 18.68 SAUSA300_0419 hypothetical tandem lipoprotein 16.78 3.58 SAUSA300_1563 accC acetyl-CoA carboxylase, biotin carboxylase 16.73 11.04 SAUSA300_2027 alr alanine racemase 16.70 16.05 SAUSA300_2607...”
- Growth and Stress Tolerance Comprise Independent Metabolic Strategies Critical for Staphylococcus aureus Infection
Kim, mBio 2021 - “...1,288 549 *** 144,250 60,327 *** SAUSA300_0965 folD 7322 6033 7631 + + + + SAUSA300_0995 pdhC 9440 7549 937 + + + + SAUSA300_2079 fba 878 12247 7929 + + + + SAUSA300_1126 rnc 8238 13895 986 + + 4,586 1,874 332,500 148,107 * SAUSA300_0918...”
- “...**** 48.367.94 *** NA NA SAUSA300_0994 pdhB 13.4 0.560.02 **** 11.21 75.429.72 89.4935.07 NA NA SAUSA300_0995 pdhC 5.66 0.980.04 1.88 97.527.89 111.2115 31.989.28 0.580.03 SAUSA300_0996 lpdA NA 0.380.3 **** 7.64 89.6123.13 72.9018.45 * NA NA SAUSA300_2067 glyA 7.17 0.940.01 * 3.43 121.6731.52 105.8414.60 45.6122.26 10.38 ****...”
- The Spl Serine Proteases Modulate Staphylococcus aureus Protein Production and Virulence in a Rabbit Model of Pneumonia
Paharik, mSphere 2016 - “...alpha subunit PdhA Metabolism, carbohydrate metabolism 12.33 26.67 0.000044 Q2FHY5 ( Q2FHY5_STAA3 ) Dihydrolipoamide acetyltransferase SAUSA300_0995 Metabolism, carbohydrate metabolism 5.33 14.33 0.00029 Q2FKD2 ( Q2FKD2_STAA3 ) Acetoin (diacetyl) reductase SAUSA300_0129 Metabolism, carbohydrate metabolism 0.00 2.33 0.0078 Q2FIB3 ( G6PI_STAA3 ) Glucose-6-phosphate isomerase Pgi Metabolism, carbohydrate metabolism,...”
- Staphylococcus aureus Tissue Infection During Sepsis Is Supported by Differential Use of Bacterial or Host-Derived Lipoic Acid
Zorzoli, PLoS pathogens 2016 - “...species observed in immunoblots, we first generated deletion mutants of the genes encoding E2-PDH ( SAUSA300_0995) , E2-OGDH ( SAUSA300_1305) , and GcvH ( SAUSA300_0791) in S . aureus strain LAC. We identified E2-PDH and E2-OGDH as the two largest molecular weight species and GcvH as...”
- Proteomic Identification of saeRS-Dependent Targets Critical for Protective Humoral Immunity against Staphylococcus aureus Skin Infection
Zhao, Infection and immunity 2015 - “...Higher in 923sae than in WT SAUSA300_0798 SAUSA300_0995 ABC transporter, substrate-binding protein Dihydrolipoamide acetyltransferase No NDc Naive WT sae P...”
- A secreted bacterial protease tailors the Staphylococcus aureus virulence repertoire to modulate bone remodeling during osteomyelitis
Cassat, Cell host & microbe 2013 - “...0.3333 6.6667 20.0000 0.0499 Putative aldehyde dehydrogenase AldA Q2FHY5|Q2FHY5_STAA3 1.0000 19.6667 19.6667 0.0009 Dihydrolipoamide acetyltransferase; SAUSA300_0995 Q2FGI6|GCSPA_STAA3 1.3333 25.6667 19.2500 0.0084 Probable glycine dehydrogenase [decarboxylating] subunit 1; GcvPA Q2FEQ4|RL6_STAA3 7.3333 133.6667 18.2273 0.0021 50S ribosomal protein L6; RplF Q2FIM9|Q2FIM9_STAA3 5.3333 95.3333 17.8750 0.0140 Thioredoxin reductase; TrxB...”
- Identification of commonly expressed exoproteins and proteolytic cleavage events by proteomic mining of clinically relevant UK isolates of Staphylococcus aureus
Smith, Microbial genomics 2016 - “...hydratase C SACOL1092 Phosphoenolpyruvate-protein phosphotransferase C SACOL1102 Pyruvate dehydrogenase complex E1 component, alpha subunit C SACOL1104 Branched-chain alpha-keto acid dehydrogenase subunit E2 C SACOL1105 Dihydrolipoamide dehydrogenase C SACOL1329 Glutamine synthetase FemC C SACOL1516 30S ribosomal protein S1 C SACOL1637 Molecular chaperone DnaK C SACOL1722 Trigger factor...”
- Global analysis of the Staphylococcus aureus response to mupirocin
Reiss, Antimicrobial agents and chemotherapy 2012 - “...GlpD-1 GlyA-2 GuaC-2 GyrB-1 HprK HslU-1 Icd-1 MetE SACOL1966 SACOL1104 PcrA PdhC PcrA PdhC-1 1.17 0.37 1.73 1.13 1.02 0.21 0.30 0.24 0.83 0.18 SACOL1105 PdhD...”
SA0945 dihydrolipoamide S-acetyltransferase component of pyruvate dehydrogenase complex E2 from Staphylococcus aureus subsp. aureus N315
P65636 Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex from Staphylococcus aureus (strain N315)
NP_371619 dihydrolipoamide S-acetyltransferase component of pyruvate dehydrogenase complex E2 from Staphylococcus aureus subsp. aureus Mu50
32% identity, 84% coverage
- The effect of skin fatty acids on Staphylococcus aureus
Neumann, Archives of microbiology 2015 - “...Hypothetical protein 1.90 419 SA0935 PtsI Phosphoenolpyruvate-protein phosphatase 0.09 244 SA0939 Hypothetical protein 0.12 676 SA0945 PdhC Branched-chain alpha-keto acid dehydrogenase subunit E2 0.47 192 SA0946 PdhD Dihydrolipoamide dehydrogenase 1.04 287 SA1007 Hla Alpha-haemolysin 5.28 531 SA1007 Hla Alpha-haemolysin 2.71 536 SA1007 Hla Alpha-haemolysin 5.04 539...”
- “...G 0.14 162 SA0544 Putative haem peroxidase 0.21 618 SA0935 PtsI Phosphoenolpyruvate-protein phosphatase 0.09 244 SA0945 PdhC Branched-chain alpha-keto acid dehydrogenase subunit E2 0.47 192 SA1007 Hla Alpha-haemolysin 5.28 531 SA1007 Hla Alpha-haemolysin 4.60 541 SA1177 Tkt Transketolase 0.40 197 SA1499 Tig Trigger factor 0.10 231...”
- Identification of functional differences in metabolic networks using comparative genomics and constraint-based models
Hamilton, PloS one 2012 - “...ortholog deletions are lethal in only one model. For example, deletion of the ortholog pair (SA0945, Rv2495) deletes PDH from the i SB619 network, but only deletes PDHb from the i NJ661 network. The deletion is lethal only in the i SB619 model. We thus revised...”
- An RpoB mutation confers dual heteroresistance to daptomycin and vancomycin in Staphylococcus aureus
Cui, Antimicrobial agents and chemotherapy 2010 - “...SA1614 menD menE menC Citrate cycle (TCA cycle) SA0944 SA0945 phdB pdhC SA0946 pdhD SA0994 SA0995 SA0996 SA1088 SA1089 SA1131 SA1132 SA1184 SA1244 SA1245 SA1349...”
- Staphylococcal major autolysin (Atl) is involved in excretion of cytoplasmic proteins
Pasztor, The Journal of biological chemistry 2010 - “...SA1927 SA0727 SA1142 SA1836 SA1036 SA1579 SA2400 SA1245 SA0944 SA0945 00505 01683 00529 00530 00799 02366 00795 01278 02254 01159 01875 02927 01418 01041 01042...”
- Transcriptome and functional analysis of the eukaryotic-type serine/threonine kinase PknB in Staphylococcus aureus
Donat, Journal of bacteriology 2009 - “...homolog SA0823 pgi Glucose-6-phosphate isomerase A SA0945 pdhC Dihydrolipoamide S-acetyltransferase component of pyruvate dehydrogenase complex E2 SA0946 pdhD...”
- Characterizing the effect of the Staphylococcus aureus virulence factor regulator, SarA, on log-phase mRNA half-lives
Roberts, Journal of bacteriology 2006 - “...SA1904 SA1905 SA1910 SA1909 SA1906 SA1908 MW0976 SA0944 SA0945 SA0946 SA0913 SA0912 SA0911 SA0367 SA0910 SA2311 ATP synthase alpha chain FoF1-ATP synthase...”
- Reporter metabolite analysis of transcriptional profiles of a Staphylococcus aureus strain with normal phenotype and its isogenic hemB mutant displaying the small-colony-variant phenotype
Seggewiss, Journal of bacteriology 2006 - “...Mpr precursor Metabolism of carbohydrates and related molecules SA1142 SA0945 0.00 0.00 5.46 0.35 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00...”
- Differential gene expression profiling of Staphylococcus aureus cultivated under biofilm and planktonic conditions
Resch, Applied and environmental microbiology 2005 - “...SA0913 SA0911 SA0910 SA0505 SA0502 SA1075 SA0842 SA2354 SA0945 4.061 3.513 3.229 3.218 3.554 3.337 3.284 3.107 2.956 2.946 SA0731 SA2204 SA1717 SA2191 SA0802...”
- Impacts of the Type I Toxin-Antitoxin System, SprG1/SprF1, on Staphylococcus aureus Gene Expression
Chlebicka, Genes 2021 - “...Glucose-6-phosphate isomerase (Pgi) P99078 1.77 1.86 10 Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex (PdhC) P65636 2.71 2.00 11 Pyruvate dehydrogenase E1 component subunit (PdhB) P99063 1.84 2.23 12 Dihydrolipoyl dehydrogenase (PdhD) P99084 1.66 1.60 13 Fructose-bisphosphate aldolase class 1 (Fda) P99117 1.68 1.56 14 Triosephosphate...”
- Blood Serum Affects Polysaccharide Production and Surface Protein Expression in S. Aureus
Islam, Advances in biotechnology & microbiology (Newbury, Calif.) 2017 - “...precursor (MW2612) Surface Adhesin 5.81132 NP_647429 b7 1 Alpha-keto acid dehydrogenase (pdhc) Carbohydrate metabolism 4.8/46 NP_371619 2. Preprotein translocase (secA) Protein export 5_0/46 NP_371277 3. Translation initiation factor (infE) Protects of tRNA from hydrolysis 5.2/77 NP_371619 b8 1. Formate acetytansferase Anaerobic glycolysis 52184 NP_370750 2. CIpB...”
- “...Promotes protein folding 4.248 NP_372199 5. Branched-chain alpha-keto acid dehydrogenase subunit E2 Carbohydrate metabolism 4.8/46 NP_371619 b9 1. A Chain A, Crystal Structure At 2.7a Resolution Of A Complex Binding as a protein complex 8.0/23 1DEE_A Between A Staphylococcus Aureus Domain And A Fab Fragment Of...”
MAB_0895c Putative dihydrolipoamide s-acetyltransferase component of pyruvate dehydrogenase complex E2 from Mycobacterium abscessus ATCC 19977
33% identity, 89% coverage
A9VUD2 Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex from Bacillus mycoides (strain KBAB4)
31% identity, 85% coverage
SAOUHSC_01042 dihydrolipoamide S-acetyltransferase component of pyruvate dehydrogenase complex E2, putative from Staphylococcus aureus subsp. aureus NCTC 8325
32% identity, 84% coverage
- Impact of Environmental Conditions on the Protein Content of Staphylococcus aureus and Its Derived Extracellular Vesicles
da, Microorganisms 2022 - “...pyruvate dehydrogenase subunit, putative pdhA Cyt C SAOUHSC_01041 pyruvate dehydrogenase subunit, putative pdhB Cyt C SAOUHSC_01042 branched-chain -keto acid dehydrogenase pdhC Cyt C SAOUHSC_00796 phosphoglycerate kinase pgk Cyt F SAOUHSC_01002 quinol oxidase AA3, subunit II, putative qoxA PSE C SAOUHSC_01001 quinol oxidase, subunit I qoxB Memb...”
- Proteomic profiling of the endogenous peptides of MRSA and MSSA
Tu, PeerJ 2021 - “...one peptide among the MRSA-AEP is derived from the branched-chain alpha-keto acid dehydrogenase subunit E2 (SAOUHSC_01042), which is essential in the adhesion of S. aureus to host eukaryotic cells and their survival ( Khairon et al., 2016 ). Aside from proteins in the TCA cycle, we...”
- Copper stress in Staphylococcus aureus leads to adaptive changes in central carbon metabolism
Tarrant, Metallomics : integrated biometal science 2019 - “...ribosomal protein S7 rpsG SAOUHSC_00528 gi|110282992 0.7 0.00015 Branched-chain alpha-keto acid dehydrogenase subunit E2 pdhC SAOUHSC_01042 gi|88194794 0.6 <0.00010 Bifunctional autolysin atl SAOUHSC_00994 gi|110832765 0.6 0.00038 Pyruvate carboxylase pycA SAOUHSC_01064 gi|88194813 0.6 <0.00010 Phosphoribosylamine-glycine ligase purD SAOUHSC_01018 gi|88194772 0.6 0.00074 DNA-directed RNA polymerase subunit beta rpoC...”
- Genome-wide screen for genes involved in eDNA release during biofilm formation by Staphylococcus aureus
DeFrancesco, Proceedings of the National Academy of Sciences of the United States of America 2017 - “...SAOUHSC_00034 SAOUHSC_01850 SAOUHSC_02273 SAOUHSC_00798 SAOUHSC_01042 SAOUHSC_01040 SAOUHSC_01041 SAOUHSC_01743 SAOUHSC_00467 SAOUHSC_02353 SAOUHSC_02341...”
- Increased mutability of Staphylococci in biofilms as a consequence of oxidative stress
Ryder, PloS one 2012 - “...Glutamate dehydrogenase, NAD-specific, putative 2.36 up SAOUHSC_01002 qoxA Probable quinol oxidase subunit 2 2.00 up SAOUHSC_01042 Dihydrolipoamide S-acetyltransferase component of pyruvate dehydrogenase complex E2, putative 2.17 up SAOUHSC_01103 Succinate dehydrogenase cytochrome b-558 subunit, putative 2.16 up SAOUHSC_01216 sucC Succinyl-CoA synthetase subunit beta 2.44 up SAOUHSC_01389 pstS...”
- Advantage of upregulation of succinate dehydrogenase in Staphylococcus aureus biofilms
Gaupp, Journal of bacteriology 2010 - “...PdhC, pyruvate dehydrogenase component E2 (SAOUHSC_01042); CitZ, citrate synthase (SAOUHSC_01802); CitB, aconitate hydratase (SAOUHSC_01347); CitC, isocitrate...”
ING2E5A_1804 dihydrolipoamide acetyltransferase family protein from Petrimonas mucosa
29% identity, 86% coverage
SACE_3954 branched-chain alpha-keto acid dehydrogenase subunit E2 from Saccharopolyspora erythraea NRRL 2338
33% identity, 81% coverage
- Systems perspectives on erythromycin biosynthesis by comparative genomic and transcriptomic analyses of S. erythraea E3 and NRRL23338 strains
Li, BMC genomics 2013 - “...( acn ), SACE_3926/SACE_3927 ( korA ), SACE_3952 ( pdhA2 ), SACE_3953 ( pdhB1 ), SACE_3954 ( bkdC2 ), SACE_4581 ( citE3 ), SACE_6118 ( pyc ), SACE_6636 (isocitrate dehydrogenase) and SACE_6668/6669 ( sucC ), showed higher expression level, as compared to wild-type strain. It was...”
BCG_2515c putative dihydrolipoamide S-acetyltransferase E2 component pdhC from Mycobacterium bovis BCG str. Pasteur 1173P2
37% identity, 94% coverage
Q8CT13 Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex from Staphylococcus epidermidis (strain ATCC 12228 / FDA PCI 1200)
30% identity, 84% coverage
- The Extracellular Vesicles from the Commensal Staphylococcus Epidermidis ATCC12228 Strain Regulate Skin Inflammation in the Imiquimod-Induced Psoriasis Murine Model
Gómez-Chávez, International journal of molecular sciences 2021 - “...C Q8CPL2 COG1053 sdhA Succinate dehydrogenase flavoprotein subunit C Q8CQA3 COG1249 lpdA Dihydrolipoyl dehydrogenase C Q8CT13 COG0508 odp2 Dihydrolipoyllysine-residue acetyltransferase component of pyruvatedehydrogenase complex C Q8CNJ7 COG0055 atpD ATP synthase subunit beta C Q8CS25 COG1866 pckA Phosphoenolpyruvate carboxykinase (ATP) C Q8PCP2 COG1048 acnA Aconitate hydratase1 C...”
- “...Q8CPZ2 COG0653 secA1 Protein translocase subunit C Q8CNJ3 COG0711 atpF ATP synthase subunit b C Q8CT13 COG0508 pdhC Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex C Q8CPN3 COG1071 pdhA Pyruvate dehydrogenase E1 component, alpha subunit C Q8CSL9 COG0508 odhB Dihydrolipoyllysine-residue succinyltransferase, E2 component G Q8CPY5 COG0057...”
pdhC / AAC24934.1 dihydrolipoamide acetyltransferase E2 from Bacillus subtilis (see 3 papers)
P21883 Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex from Bacillus subtilis (strain 168)
BSU14600 branched-chain alpha-keto acid dehydrogenase subunit E2 from Bacillus subtilis subsp. subtilis str. 168
30% identity, 83% coverage
THTE_2674 dihydrolipoamide acetyltransferase family protein from Thermogutta terrifontis
31% identity, 82% coverage
BKDC_MYCTU / O06159 Dihydrolipoyllysine-residue acyltransferase component of branched-chain alpha-ketoacid dehydrogenase complex; Branched-chain alpha-ketoacid dehydrogenase complex component E2; BCKADH E2; Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase; EC 2.3.1.168 from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (see 2 papers)
Rv2495c dihydrolipoamide acetyltransferase from Mycobacterium tuberculosis H37Rv
36% identity, 94% coverage
- function: Component of the branched-chain alpha-ketoacid dehydrogenase (BCKADH) complex, that catalyzes the overall conversion of branched- chain alpha-ketoacids to acyl-CoA and CO(2).
catalytic activity: N(6)-[(R)-dihydrolipoyl]-L-lysyl-[protein] + 2- methylpropanoyl-CoA = N(6)-[(R)-S(8)-2-methylpropanoyldihydrolipoyl]- L-lysyl-[protein] + CoA (RHEA:18865)
cofactor: (R)-lipoate (Binds 1 lipoyl cofactor covalently.)
subunit: Forms a 24-polypeptide structural core with octahedral symmetry (By similarity). Part of the BCKADH complex, consisting of multiple copies of BkdA/BkdB (E1), BkdC (E2) and Lpd (E3). - Global-scale GWAS associates a subset of SNPs with animal-adapted variants in M. tuberculosis complex
Brenner, BMC medical genomics 2023 - “...methyltransferase) Disruption provides growth advantage (DeJesus 2017) Synonymous 2,809,318 0 0.951 4100 2100 161 1 Rv2495c BkdC Probable branched-chain keto acid dehydrogenase E2 component BkdC Arg208Trp 2,812,742 0 0.951 4100 2100 161 1 Rv2498c CitE Probable citrate (pro-3S)-lyase (beta subunit) CitE (citrase) (citratase) (citritase) (citridesmolase) (citrase...”
- Small RNA Mcr11 requires the transcription factor AbmR for stable expression and regulates genes involved in the central metabolism of Mycobacterium tuberculosis
Girardin, Molecular microbiology 2020 - “...(Spalding & Prigge, 2010 ; Venugopal et al., 2011 ). BkdC (also called PdhC or Rv2495c) is a component of the branched chain ketoacid dehydrogenase (BCKADH) complex in Mtb that also requires lipoylation for activity. Disruption of components in any of these complexes can cause growth...”
- The unfoldase ClpC1 of Mycobacterium tuberculosis regulates the expression of a distinct subset of proteins having intrinsically disordered termini
Lunge, The Journal of biological chemistry 2020 (secret) - Mycobacterium tuberculosis Complex Exhibits Lineage-Specific Variations Affecting Protein Ductility and Epitope Recognition
Yruela, Genome biology and evolution 2016 - “...proteins have mutations along their sequences. Among them only four proteins, Rv2215 (DlaT), Rv2358 (SmtB), Rv2495c (BkdC), and Rv3003c (IlvB1) have mutations inside IDRs ( table 1 ). Interestingly, SmtB of M. tuberculosis Beiijing shows five amino acid substitutions in the Phe30Pro37 motif of the N-terminal...”
- “...265 (G/E) 3141 4891 M. bovis BCG Pasteur (1) 517 (L/V) 117-160 169204 236298 307319 Rv2495c BkdC 7 M. africanum (1) 87116 14 107 (T/A) * 2331 14 Ser55 1 M. canettii (2) 67 (A/V), 107(T/A) * M. bovis (2) 107 (T/A) * , 208 (R/W)...”
- Characterization of the mycobacterial acyl-CoA carboxylase holo complexes reveals their functional expansion into amino acid catabolism
Ehebauer, PLoS pathogens 2015 - “....). Interestingly, this pattern of conservation extends into the neighboring pdhABC operon that includes genes Rv2495c to Rv2497c, which encode a lipoamide dehydrogenase-dependent keto acid dehydrogenase complex [ 23 ]. This complex acts upstream in branched amino-acid catabolism and one of its key functions is thought...”
- “...YCC enzymes. Remarkably, in addition to the conserved operon organization, the expression of most genes (Rv2495c to Rv2501c) of the citE-scoA operon and the pdhABC operon are strongly correlated (for further details see Operon Correlation Browser ( www.broadinstitute.org/annotation/tbdb/operon/ ), suggesting that the effects observed are coupled....”
- bkaR is a TetR-type repressor that controls an operon associated with branched-chain keto-acid metabolism in Mycobacteria
Balhana, FEMS microbiology letters 2013 - “...3.3 3.3E-02 bkdB Rv2496c Part of branched-chain keto-acid dehydrogenase complex * MSMEG_4710 1.8 4.9E-01 bkdC Rv2495c Part of branched-chain keto-acid dehydrogenase complex * MSMEG_4005 3.2 2.5E-02 Calcium-binding protein MSMEG_2080 3.1 3.3E-02 fadE23 Rv3140 Putative acyl-CoA dehydrogenase MSMEG_1885 3.3 2.2E-02 Rv3230c Rv3230c Ironsulphur cluster binding domain protein...”
- A multi-level multi-scale approach to study essential genes in Mycobacterium tuberculosis
Ghosh, BMC systems biology 2013 - “...to maintain original function. The perturbed path comprise 13 nodes (Rv3441c (mrsA) Rv1151c Rv3667 (acs) Rv2495c (bkdC) Rv2496c (bkdB) Rv1617 (pykA) Rv3457c (rpoA) Rv0707 (rpsC) Rv0703 (rplW) Rv2347c (esxP) Rv2346c (esxO) Rv2498c (citE) Rv1240 (mdh)), including the source and destination. Figure 3 Network topology of protein-protein...”
- Virulence of Mycobacterium tuberculosis depends on lipoamide dehydrogenase, a member of three multienzyme complexes
Venugopal, Cell host & microbe 2011 - “...E1 of PDH), pdhB (Rv2496c, annotated as the subunit of E1 of PDH) and pdhC (Rv2495c, annotated as E2 of PDH). In many organisms Lpd is also the E3 of BCKADH, so we hypothesized that the pdhABC operon may encode the E1 and E2 of BCKADH...”
- “...of metabolites and the activity of lysates. In light of these findings, Rv2497c, Rv2496c and Rv2495c can be re-annotated as bkdA, bkdB and bkdC , respectively. In contrast, WT and Lpd-deficient Mtb grown on a standard rich medium in vitro either did not express a functional...”
- More
- Actinobacteria challenge the paradigm: A unique protein architecture for a well-known, central metabolic complex
Bruch, Proceedings of the National Academy of Sciences of the United States of America 2021 (secret) - Mycobacterium tuberculosis Complex Exhibits Lineage-Specific Variations Affecting Protein Ductility and Epitope Recognition
Yruela, Genome biology and evolution 2016 - “...PyMol 1.4.1 (Schrodinger LLC). Furthermore, Rv2495c, a component of branched-chain alpha-ketoacid dehydrogenase complex (BkdC, UniProt O06159) shows mutations in Tyr103Asp and Thr107Ala in M. tuberculosis Beijing compared with M. tuberculosis H37Rv which increase the flexibility in this region as indicate IUPred/ANCHOR predictions ( supplementary fig. S3...”
Mal4_31770 dihydrolipoyllysine-residue acetyltransferase from Maioricimonas rarisocia
30% identity, 64% coverage
LMRG_00516 dihydrolipoamide acetyltransferase from Listeria monocytogenes 10403S
30% identity, 67% coverage
Q8Y863 Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex from Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)
lmo1054 highly similar to pyruvate dehydrogenase (dihydrolipoamide acetyltransferase E2 subunit) from Listeria monocytogenes EGD-e
30% identity, 67% coverage
- A Chemical Proteomic Strategy Reveals Inhibitors of Lipoate Salvage in Bacteria and Parasites
Dienemann, Angewandte Chemie (International ed. in English) 2023 (secret) - The ribonuclease PNPase is a key regulator of biofilm formation in Listeria monocytogenes and affects invasion of host cells
Quendera, NPJ biofilms and microbiomes 2023 - “...0.10 4.9410 6 0.56 lmo1053 Pyruvate dehydrogenase subunit E1 beta, PdhB 0.13 8.5410 5 0.56 lmo1054 Dihydrolipoamide acetyltransferase E2, PdhC 0.16 5.5710 4 lmo1055 Dihydrolipoamide dehydrogenase E3, PdhD 0.26 2.4010 2 Fold changes were calculated as the ratio of pnpA mutant to wild-type. Values above 1...”
- SecA2 Associates with Translating Ribosomes and Contributes to the Secretion of Potent IFN-β Inducing RNAs
Teubner, International journal of molecular sciences 2022 - “...IF-3 Translation 0.28 0.29 lmo1267 tig Trigger factor Posttranslational modification. protein turnover. chaperones 0.19 0.28 lmo1054 * pdhC Pyruvate dehydrogenase E2 component (Dihydrolipoamide acetyltransferase) Energy production and conversion 0.20 0.26 lmo2615 rpsE 30S ribosomal protein S5 Translation 0.19 0.25 lmo0135 Putative oligopeptide ABC transporter. OppA Amino...”
- Transcriptional and phenotypic responses of Listeria monocytogenes to chlorine dioxide
Pleitner, Applied and environmental microbiology 2014 - “...lmo0781 lmo0811 lmo0907 lmo0913 lmo0915 lmo0917 lmo0943 lmo1054 lmo1055 lmo1233 lmo1254 lmo1255 lmo1293 lmo1348 lmo1350 lmo1514 lmo1538 lmo1579 lmo1789 lmo1883...”
- Deep RNA sequencing of L. monocytogenes reveals overlapping and extensive stationary phase and sigma B-dependent transcriptomes, including multiple highly transcribed noncoding RNAs
Oliver, BMC genomics 2009 - “...subunit) 356.4 LMRG_00704 lmo1255 lmo1255 similar to PTS system trehalose-specific enzyme IIBC 353.6 LMRG_00516 pdhC lmo1054 highly similar to pyruvate dehydrogenase (dihydrolipoamide acetyltransferase E2 subunit) 351.3 LMRG_01480 lmo2362 lmo2362 similar to amino acid antiporter (acid resistance) 351.1 LMRG_02239 lmo2692 lmo2692 unknown 344.1 LMRG_00875 lmo1423 lmo1423 unknown...”
- Intracellular gene expression profile of Listeria monocytogenes
Chatterjee, Infection and immunity 2006 - “...pyruvate dehydrogenase, the pdhABC operon (lmo1052 to lmo1054), were down regulated, suggesting interruption of the citric acid cycle and gluconeogenesis during...”
CA54_49680 2-oxo acid dehydrogenase subunit E2 from Symmachiella macrocystis
30% identity, 84% coverage
P11961 Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex from Geobacillus stearothermophilus
30% identity, 86% coverage
- Structure of the p53 degradation complex from HPV16.
Wang, Nature communications 2024 - “...domain (Uniprot ID no. P04637, S94-T312) fused with an N-terminal 8xHis-lipoyl domain (Uniprot ID no. P11961, A2-T85)-TEV sequence, was sub-cloned into a pET21a vector (Genscript). All constructs were codon-optimized (GenSmart Codon Optimization, Version Beta 1.0) against their respective expression hosts and synthesized by Genscript. Protein expression...”
- Comparative Analysis of Symmetry Parameters in the E2 Inner Core of the Pyruvate Dehydrogenase Complex.
Kim, International journal of molecular sciences 2024 - “...was amplified by polymerase chain reaction (PCR) using suitable primers and the corresponding cDNA (UniProt: P11961) as templates, and the PCR products were digested and inserted into the pET 30a (+) vector (Merck Millipore, Darmstadt, Germany), which had been digested with the corresponding restriction enzymes. The...”
- Updated protein domain annotation of the PARP protein family sheds new light on biological function
Suskiewicz, Nucleic acids research 2023 - “...vector; the resulting plasmid contains the sequence for N-terminally His6-tagged Geobacillus stearothermophilus di-hydrolipoamide acetyltransferase (UniProt P11961) lipoyl-binding domain, followed by a TEV cleavage site, followed by the sequence for PARP1(383525). Protein was expressed and purified essentially as described previously for the uniformly [ 2 H, 13...”
- Dynamics of the HD regulatory subdomain of PARP-1; substrate access and allostery in PARP activation and inhibition
Ogden, Nucleic acids research 2021 - “...vector also containing a sequence for N-terminally His 6 -tagged Geobacillus stearothermophilus di-hydrolipoamide acetyltransferase (UniProt P11961) lipoyl-binding domain; the resultant protein contained a TEV cleavage site between the lipoyl-binding and PARP-1CAT domains. Constitutively partially active mutants (L713F, L765F, L765A) of this fragment were cloned from this...”
- HPF1 completes the PARP active site for DNA damage-induced ADP-ribosylation
Suskiewicz, Nature 2020 - “...a pET28 vector containing a sequence for N-terminally-His 6 -tagged Geobacillus stearothermophilus di-hydrolipoamide acetyltransferase (UniProt P11961) lipoyl-binding domain; the resultant protein product contained a TEV cleavage site between lipoyl-binding domain and PARP1 656-1014 . Site-directed mutagenesis was performed using QuikChange Lightning (Agilent) and Q5 (NEB) kits....”
LSA1083 Puruvate dehydrogenase complex, E2 component, dihydrolipoamide acetyltransferase from Lactobacillus sakei subsp. sakei 23K
29% identity, 68% coverage
- Global transcriptome response in Lactobacillus sakei during growth on ribose
McLeod, BMC microbiology 2011 - “...monophosphatase 0.6 0.8 LSA1082 pdhD Pyruvate dehydrogenase complex, E3 component, dihydrolipoamide dehydrogenase 2.8 2.5 2.1 LSA1083 pdhC Puruvate dehydrogenase complex, E2 component, dihydrolipoamide acetyltransferase 3.4 3.7 2.7 LSA1084 pdhB Pyruvate dehydrogenase complex, E1 component, beta subunit 3.2 3.3 2.2 LSA1085 pdhA Pyruvate dehydrogenase complex, E1 component,...”
SMc03203 Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) from Sinorhizobium meliloti 1021
SMc03203 PROBABLE LIPOAMIDE ACYLTRANSFERASE COMPONENT OF BRANCHED-CHAIN ALPHA-KETO ACID DEHYDROGENASE COMPLEX PROTEIN from Sinorhizobium meliloti 1021
33% identity, 86% coverage
- mutant phenotype: Specifically important for utilizing L-Leucine. Automated validation from mutant phenotype: the predicted function (2.3.1.168) was linked to the condition via a SEED subsystem. This annotation was also checked manually.
- Role of the Sinorhizobium meliloti global regulator Hfq in gene regulation and symbiosis
Gao, Molecular plant-microbe interactions : MPMI 2010 - “...0.4 SMc03201 ( bkdAa ) 5.4 (15.0 3.0)4 SMc03202 ( bkdAb ) 5.4 (6.0 1.0)4 SMc03203 ( bkdB ) 5.7 (9.2 0.6)4 SMc00168 ( sinI ) 1.8 (2.6 0.3) SMc02584 ( actR ) 3.1 4.8 0.6 SMc02585 ( actS ) 3.5 4.7 0.2 SMc02484 ( supA...”
Mal52_33720 2-oxo acid dehydrogenase subunit E2 from Symmachiella dynata
30% identity, 83% coverage
LSEI_1307 dihydrolipoyllysine-residue acetyltransferase from Lacticaseibacillus paracasei ATCC 334
LSEI_1307 acetoin/pyruvate dehydrogenase complex, E2 component, dihydrolipoamide succinyltransferase from Lactobacillus casei ATCC 334
30% identity, 67% coverage
- Regulatory Mechanisms of L-Lactic Acid and Taste Substances in Chinese Acid Rice Soup (Rice-Acid) Fermented With a Lacticaseibacillus paracasei and Kluyveromyces marxianus
Liu, Frontiers in microbiology 2021 - “...component alpha subunit 1.82 LSEI_1306 [EC:1.2.4.1] K00162 pyruvate dehydrogenase E1 component beta subunit 1.83 1.60 LSEI_1307 [EC:2.3.1.12] K00627 pyruvate dehydrogenase E2 component (dihydrolipoamide acetyltransferase) 1.95 1.96 LSEI_1308 [EC:1.8.1.4] K00382 dihydrolipoamide dehydrogenase 1.54 1.80 LSEI_1310 [EC:1.1.1.27] K00016 l-lactate dehydrogenase 2.17 2.64 LSEI_1446 [EC:1.8.1.4] K00382 dihydrolipoamide dehydrogenase 2.46...”
- “...component alpha subunit 1.83 LSEI_1306 [EC:1.2.4.1] K00162 pyruvate dehydrogenase E1 component beta subunit 1.83 1.60 LSEI_1307 [EC:2.3.1.12] K00627 pyruvate dehydrogenase E2 component (dihydrolipoamide acetyltransferase) 1.95 1.96 LSEI_1308 [EC:1.8.1.4] K00382 dihydrolipoamide dehydrogenase 1.54 1.80 LSEI_1315 [EC:6.4.1.1] K01958 pyruvate carboxylase 2.75 1.66 LSEI_1446 [EC:1.8.1.4] K00382 dihydrolipoamide dehydrogenase 2.46...”
Pan258_32660 2-oxo acid dehydrogenase subunit E2 from Symmachiella dynata
30% identity, 83% coverage
Pcal_1403 catalytic domain of components of various dehydrogenase complexes from Pyrobaculum calidifontis JCM 11548
31% identity, 94% coverage
blr6333 lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex E2 from Bradyrhizobium japonicum USDA 110
31% identity, 86% coverage
LCAZH_1301 dihydrolipoyllysine-residue acetyltransferase from Lacticaseibacillus paracasei
30% identity, 66% coverage
- Roles of adenine methylation in the physiology of Lacticaseibacillus paracasei
Zhao, Nature communications 2023 - “...(LCAZH_1299, pdhA ), the PDH E1 component beta subunit (LCAZH_1300, pdhB ), the dihydrolipoamide acetyltransferase (LCAZH_1301, pdhC ), and the dihydrolipoyl dehydrogenase (LCAZH_1302, pdhD ), contained a non-methylated motif that was highly similar to the CcpA binding site present in L. paracasei , according to the...”
- “...subunit alpha (LCAZH_1299, pdhA ), PDH E1 component beta subunit (LCAZH_1300, pdhB ), dihydrolipoamide acetyltransferase (LCAZH_1301, pdhC ), dihydrolipoyl dehydrogenase (LCAZH_1301, pdhD ), and L-lactate dehydrogenase (LCAZH_0554). Class II fructose-bisphosphate aldolase, triose-phosphate isomerase, and aldose 1-epimerase are enzymes of the glycolytic pathway, while acetate kinase, xylulokinase,...”
- Proteomics analysis of Lactobacillus casei Zhang, a new probiotic bacterium isolated from traditional home-made koumiss in Inner Mongolia of China
Wu, Molecular & cellular proteomics : MCP 2009 - “...LCAZH_1300; E2, dihydrolipoamide dehydrogenase transacetylase, LCAZH_1301; and E3, lipoamide dehydrogenase, LCAZH_1302) of the pyruvate dehydrogenase...”
PA14_35500 lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex E2 from Pseudomonas aeruginosa UCBPP-PA14
33% identity, 85% coverage
- Gene Expression Profiling of <i>Pseudomonas aeruginosa</i> Upon Exposure to Colistin and Tobramycin
Cianciulli, Frontiers in microbiology 2021 - “...Ornithine carbamoyltransferase 137.35 4.19 Leucin/Valine/Isoleucin degradation and biosynthesis lpdV PA14_35490 Dihydrolipoamide dehydrogenase 104.5 6.56 bkdB PA14_35500 Branched-chain alpha-keto acid dehydrogenase subunit E2 91.67 5.51 bkdA2 PA14_35520 2-oxoisovalerate dehydrogenase subunit beta 104.31 4.84 bkdA1 PA14_35530 2-oxoisovalerate dehydrogenase subunit alpha 5.23 X gnyR PA14_38430 Regulatory gene of gnyRDBHAL...”
LGG_01322 2-oxo acid dehydrogenase subunit E2 from Lacticaseibacillus rhamnosus GG
LGG_01322 brached-chain pyruvate dehydrogenase complex, E2 component, dihydrolipoamide S-acetyltransferase from Lactobacillus rhamnosus GG
29% identity, 83% coverage
PA2249 branched-chain alpha-keto acid dehydrogenase (lipoamide component) from Pseudomonas aeruginosa PAO1
Q9I1M0 Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
32% identity, 85% coverage
- Catabolite repression control protein antagonist, a novel player in Pseudomonas aeruginosa carbon catabolite repression control
Sonnleitner, Frontiers in microbiology 2023 - “...2.66 3.14E-08 bkdA1 2-oxoisovalerate dehydrogenase (alpha subunit) PA2248 2.64 3.32E-07 bkdA2 2-oxoisovalerate dehydrogenase (beta subunit) PA2249 2.51 9.12E-07 bkdB Branched-chain alpha-keto acid dehydrogenase (lipoamide component) PA2250 2.78 4.13E-06 lpdV Lipoamide dehydrogenase-Val PA2338 4.24 9.03E-16 PA 2338 Probable binding protein component of ABC maltose/mannitol transporter PA2339 4.97...”
- ECF Sigma Factor HxuI Is Critical for In Vivo Fitness of Pseudomonas aeruginosa during Infection
Cai, Microbiology spectrum 2022 - “...8E-24 PA1522 xdhC Xanthine dehydrogenase accessory protein 2.07 3.09E-15 PA2003 bdhA 3-Hydroxybutyrate dehydrogenase 2.07 7.56E-15 PA2249 bkdB Branched-chain alpha-keto acid dehydrogenase complex component 2.17 4.46E-14 PA2250 lpdV Branched-chain alpha-keto acid dehydrogenase complex component 2.31 8.19E-16 PA2446 gcvH2 Glycine cleavage system protein H 2.14 3.3E-10 PA3415 Probable...”
- The development of a new parameter for tracking post-transcriptional regulation allows the detailed map of the Pseudomonas aeruginosa Crc regulon
Corona, Scientific reports 2018 - “...3,61 1,96 5,58 Catabolism bkdA2 PA2248 2-oxoisovalerate dehydrogenase (beta subunit) 3,98 2,79 7,95 Catabolism bkdB PA2249 Branched-chain alpha-keto acid dehydrogenase (lipoamide component) 3,99 2,17 6,18 Catabolism lpdV PA2250 Lipoamide dehydrogenase-Val 4,12 2,35 6,69 Transport PA2252 Probable AGCS sodium/alanine/glycine symporter 3,32 0,89 5,85 Catabolism ansA PA2253 L-asparaginase...”
- Mitochondrial targeting increases specific activity of a heterologous valine assimilation pathway in Saccharomyces cerevisiae
Solomon, Metabolic engineering communications 2016 - “...and plasmids were maintained in E. coli XL1B. acd1 (PA0746), bkdA1 (PA2247), bkdA2 (PA2248), bkdB (PA2249), and lpdV (PA2250), encoding the acyl-CoA dehydrogenase and branched chain keto acid dehydrogenase complex, respectively, from Pseudomonas aeruginosa PA01, were PCR amplified from plasmid template (pMMA202) provided by Mitsubishi Rayon....”
- Small Colony Variants and Single Nucleotide Variations in Pf1 Region of PB1 Phage-Resistant Pseudomonas aeruginosa
Lim, Frontiers in microbiology 2016 - “...bkdA1 2-oxoisovalerate dehydrogenase (alpha subunit) -2.7 1.E-02 PA2248 bkdA2 2-oxoisovalerate dehydrogenase (beta subunit) -3.4 4.E-03 PA2249 bkdB Branched-chain alpha-keto acid dehydrogenase (lipoamide component) -3.4 1.E-03 PA2250 lpdV Lipoamide dehydrogenase-Val -3.0 4.E-03 PA2553 Probable acyl-CoA thiolase -5.6 3.E-03 PA2554 Probable short-chain dehydrogenase -2.2 1.E-02 PA3569 mmsB 3-hydroxyisobutyrate...”
- Inhibition of Pseudomonas aeruginosa swarming motility by 1-naphthol and other bicyclic compounds bearing hydroxyl groups
Oura, Applied and environmental microbiology 2015 - “...PA2007 PA2008 PA2009 PA2014 PA2015 PA2016 PA2247 PA2248 PA2249 PA2250 PA2321 PA2554 PA2555 PA3183 PA3194 PA3195 PA3559 PA3584 PA3723 PA3924 PA4022 PA5056 PA5435...”
- Comparative systems biology analysis to study the mode of action of the isothiocyanate compound Iberin on Pseudomonas aeruginosa
Tan, Antimicrobial agents and chemotherapy 2014 - “...PA1493 PA1999 PA2000 PA2008 PA2009 PA2197 PA2247 PA2248 PA2249 ahpF PA2277 PA2278 PA2310 PA2311 PA2312 PA2327 PA2359 PA2444 PA2445 PA2483 PA2490 PA2491 PA2493...”
- Novel targets of the CbrAB/Crc carbon catabolite control system revealed by transcript abundance in Pseudomonas aeruginosa
Sonnleitner, PloS one 2012 - “...2,36 3,81 3,23 2-oxoisovalerate dehydrogenase (alpha subunit) PA2248 bkdA2 2,6 3,51 2-oxoisovalerate dehydrogenase (beta subunit) PA2249 bkdB 2,48 3,22 branched-chain alpha-keto acid dehydrogenase PA2250 lpdV 2,62 3,07 lipoamide dehydrogenase-Val PA2533 2,13 probable sodium:alanine symporter AACAAGAAUAA (20 to 10) PA3038 4,13 16,75 2,11 probable porin AAUAACAA (7...”
- More
- Proteomic profiling spotlights the molecular targets and the impact of the natural antivirulent umbelliferone on stress response, virulence factors, and the quorum sensing network of Pseudomonas aeruginosa
Kasthuri, Frontiers in cellular and infection microbiology 2022 - “...ANOVA ( p ) Max fold change Q9I0A2 50S ribosomal protein L20 RplT 0.046 1.757 Q9I1M0 Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex BkdB 0.040 1.820 Q9I502 ProlinetRNA ligase ProS 0.047 1.125 Q9I2U1 ATP-dependent Clp protease proteolytic subunit 1 clpP1 0.004 3.201 P40947 Single-stranded...”
Pf6N2E2_479 Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) from Pseudomonas fluorescens FW300-N2E2
32% identity, 86% coverage
- mutant phenotype: Specifically important for utilizing L-Leucine; L-Isoleucine. Automated validation from mutant phenotype: the predicted function (2.3.1.168) was linked to the condition via a SEED subsystem. This annotation was also checked manually.
Q9RH46 dihydrolipoyllysine-residue succinyltransferase (EC 2.3.1.61) from Coxiella burnetii (see paper)
28% identity, 90% coverage
BV82_0839 dihydrolipoamide acetyltransferase family protein from Pseudomonas donghuensis
32% identity, 86% coverage
Pfl01_3465 branched-chain alpha-keto acid dehydrogenase subunit E2 from Pseudomonas fluorescens Pf0-1
33% identity, 86% coverage
Ta1436 probable lipoamide acyltransferase from Thermoplasma acidophilum DSM 1728
31% identity, 92% coverage
Q83BU7 Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex from Coxiella burnetii (strain RSA 493 / Nine Mile phase I)
CBU_1398 2-oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase from Coxiella burnetii RSA 493
28% identity, 90% coverage
- Detection of Coxiella antibodies in ruminants using a SucB recombinant antigen
Ferrara, Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc 2023 (secret) - Evaluation of a Human T Cell-Targeted Multi-Epitope Vaccine for Q Fever in Animal Models of Coxiella burnetii Immunity
Sluder, Frontiers in immunology 2022 - “...C2 9 4 *p21 IARYFMVNISQLIGEE CBU_1416 Q83BT6 repressor protein C2 14 22 p22 RLGFMSFFTKAVVEALKRF CBU_1398 Q83BU7 sucB 23 22 p23 REAVLFLVTIKELLEDP CBU_1398 Q83BU7 sucB 18 26 p24 LPPVTSSVAVKVPSS CBU_1260 Q83C69 OmpA-like transmembrane domain protein 21 26 *p26 QTQLQQSFSKRTMAT CBU_1221 Q83CA7 membrane-spanning protein 7 4 *p27 RFDLSLMLNYPNSADRY...”
- Promiscuous Coxiella burnetii CD4 Epitope Clusters Associated With Human Recall Responses Are Candidates for a Novel T-Cell Targeted Multi-Epitope Q Fever Vaccine
Scholzen, Frontiers in immunology 2019 - “...IARYFMVNISQLIGEE CBU_1416 Q83BT6 repressor protein C2 DRB1*0101, DRB1*0301, DRB1*0401, DRB1*0701, DRB1*0801, DRB1*1501 p22 RLGFMSFFTKAVVEALKRF CBU_1398 Q83BU7 sucB DRB1*0101, DRB1*0301, DRB1*0401, DRB1*0701, DRB1*0801, DRB1*1101, DRB1*1301, DRB1*1501 p23 REAVLFLVTIKELLEDP CBU_1398 Q83BU7 sucB DRB1*0301, DRB1*0401, DRB1*0701, DRB1*0801, DRB1*1301 p24 LPPVTSSVAVKVPSS CBU_1260 Q83C69 OmpA-like transmembrane domain protein DRB1*0101, DRB1*0301, DRB1*0401,...”
- “...B*0702, B*4403 p80 METPPQSPDF CBU_2052 Q83A58 T4SS B*4403 A*2402, B*0702, B*3501, B*4403 p81 GSDIIYHNY CBU_1398 Q83BU7 sucB S+ A*0101 A*0101, A*0301, A*1101, A*6801 p82 VSDATVAKWY CBU_1398 Q83BU7 sucB S+ A*0101 A*0101, A*0301, A*1101, A*6801 p83 KTEQDKLSY CBU_0630 P51752 mip S+ A*0101 A*0101, A*0301, A*1101, A*6801 p84...”
- Evaluation of a Human T Cell-Targeted Multi-Epitope Vaccine for Q Fever in Animal Models of Coxiella burnetii Immunity
Sluder, Frontiers in immunology 2022 - “...protein C2 9 4 *p21 IARYFMVNISQLIGEE CBU_1416 Q83BT6 repressor protein C2 14 22 p22 RLGFMSFFTKAVVEALKRF CBU_1398 Q83BU7 sucB 23 22 p23 REAVLFLVTIKELLEDP CBU_1398 Q83BU7 sucB 18 26 p24 LPPVTSSVAVKVPSS CBU_1260 Q83C69 OmpA-like transmembrane domain protein 21 26 *p26 QTQLQQSFSKRTMAT CBU_1221 Q83CA7 membrane-spanning protein 7 4 *p27...”
- Subunit Vaccines Using TLR Triagonist Combination Adjuvants Provide Protection Against Coxiella burnetii While Minimizing Reactogenic Responses
Fratzke, Frontiers in immunology 2021 - “...responses. All candidate vaccines, including the unadjuvanted vaccine A, induced robust IgG responses against CBU_0545, CBU_1398, and CBU_1910 by day 45. IgG production against CBU_0891 was more variable across vaccines, but all candidates induced significantly elevated serum IgG compared to Sham. Vaccine C produced the strongest...”
- Analysis of recombinant proteins for Q fever diagnostics
Miller, Scientific reports 2020 - “...Three promising antigens were identified based on receiver operating characteristic curve analysis (CBU_1718, CBU_0307, and CBU_1398). Five multiplex assays failed to outperform the individual proteins, with sensitivities and specificities ranging from 29 to 57% and 90 to 100%, respectively. Truncating the top antigen, CBU_1718, had no...”
- “...a slightly better discriminative ability (AUC 0.8786, p=0.0019) compared to CBU_0307 (AUC 0.7929, p=0.0164). Additionally, CBU_1398 had an AUC of 0.75 and showed significant discriminative ability (p<0.05); however, the sensitivity was only 57%. No other recombinant protein antigens tested had significant discriminative ability. The whole cell...”
- Promiscuous Coxiella burnetii CD4 Epitope Clusters Associated With Human Recall Responses Are Candidates for a Novel T-Cell Targeted Multi-Epitope Q Fever Vaccine
Scholzen, Frontiers in immunology 2019 - “...p21 IARYFMVNISQLIGEE CBU_1416 Q83BT6 repressor protein C2 DRB1*0101, DRB1*0301, DRB1*0401, DRB1*0701, DRB1*0801, DRB1*1501 p22 RLGFMSFFTKAVVEALKRF CBU_1398 Q83BU7 sucB DRB1*0101, DRB1*0301, DRB1*0401, DRB1*0701, DRB1*0801, DRB1*1101, DRB1*1301, DRB1*1501 p23 REAVLFLVTIKELLEDP CBU_1398 Q83BU7 sucB DRB1*0301, DRB1*0401, DRB1*0701, DRB1*0801, DRB1*1301 p24 LPPVTSSVAVKVPSS CBU_1260 Q83C69 OmpA-like transmembrane domain protein DRB1*0101, DRB1*0301,...”
- “...A*2402, B*0702, B*4403 p80 METPPQSPDF CBU_2052 Q83A58 T4SS B*4403 A*2402, B*0702, B*3501, B*4403 p81 GSDIIYHNY CBU_1398 Q83BU7 sucB S+ A*0101 A*0101, A*0301, A*1101, A*6801 p82 VSDATVAKWY CBU_1398 Q83BU7 sucB S+ A*0101 A*0101, A*0301, A*1101, A*6801 p83 KTEQDKLSY CBU_0630 P51752 mip S+ A*0101 A*0101, A*0301, A*1101, A*6801...”
- Coxiella burnetii Epitope-Specific T-Cell Responses in Patients with Chronic Q Fever
Scholzen, Infection and immunity 2019 (secret) - Potential serodiagnostic markers for Q fever identified in Coxiella burnetii by immunoproteomic and protein microarray approaches
Xiong, BMC microbiology 2012 - “...331_A2148 gi|161830152 50490 5.01 MALDI-TOF 240 2.70E-18 26 54% 21,28 A,B 5 Dihydrolipoyllysine-residue succinyltransferase sucB CBU_1398 gi|29654691 45908 5.54 MALDI-TOF 100 0.00027 16 34% 21,28 A 6 Fructose-1,6-bisphosphate aldolase fbaA CBU_1778 gi|29655066 39793 5.41 MALDI-TOF 190 2.70E-13 16 48% 21,28 A,B 7 S-adenosylmethionine Synthetase metK CBU_2030...”
- Proteomics paves the way for Q fever diagnostics
Kowalczewska, Genome medicine 2011 - “...vaccine development Phase-I-specific SP: CBU_1706, CBU_12190, CBU_0495, CBU_0780, CBU_0955, Phase-II-specific SP: CBU_1290, CBU_0235, CBU_0215, CBU_0572, CBU_1398, CBU_0236, CBU_0092, CBU_1241, CBU_1396, CBU_1227, CBU_0481, CBU_0299, CBU_0481, CBU_0495, CBU_0482, CBU_0937, CBU_0236 [ 68 ] RP-based approaches Candidate RPs for Q fever vaccine development and serodiagnosis TAP products and expression...”
- “...fever (general) Markers of Q fever (general) SP: CBU_1910, CBU_0891, CBU_0109, CBU_1143, CBU_0612, CBU_0092, CBU_0545, CBU_1398, CBU_0630, CBU_1513, CBU_1719, CBU_0229, CBU_0653 [ 69 ] Candidate RPs for Q fever vaccine development and serodiagnosis ELISA (HS), ELISPOT (AS) 11 RPs, Cb NM RSA493 I HS Q-fever (IFA-positive,...”
BCAL1214 lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex from Burkholderia cenocepacia J2315
31% identity, 84% coverage
- Burkholderia cenocepacia differential gene expression during host-pathogen interactions and adaptation to the host environment
O'Grady, Frontiers in cellular and infection microbiology 2011 - “...2.9 BCAL1212 bkdA1, 2-oxoisovalerate dehydrogenase alpha subunit 3.0 BCAL1213 bkdA2, 2-oxoisovalerate dehydrogenase beta subunit 2.9 BCAL1214 bhdB, lipoamide acyltransferase 3.7 BCAL1215 lpdV, dihydrolipoamide dehydrogenase 2.2 BCAL1749 Putative CoA-transferase 2.4 BCAL1750 Conserved hypothetical protein, pyruvate decarboxylase 2.4 BCAL1751 Glyoxalase/bleomycin resistance, amino acid transport 1.7 BCAM0047 Lysine exporter...”
- “...Hypothetical protein 1.65 BCAL1212 2-Oxoisovalerate dehydrogenase alpha subunit 3.02 BCAL1213 2-Oxoisovalerate dehydrogenase beta subunit 2.91 BCAL1214 Lipoamide acyltransferase component of 3.68 BCAL1215 Dihydrolipoamide dehydrogenase 2.22 BCAL1226 Major facilitator superfamily protein 1.52 BCAL1279 Putative exported protein 1.64 BCAL1468 Putative electron transport protein 1.51 BCAL1499 Putative exported protein...”
OEOE_0330 acetoin/pyruvate dehydrogenase complex, E2 component, dihydrolipoamide succinyltransferase from Oenococcus oeni PSU-1
28% identity, 80% coverage
PVLB_17460 dihydrolipoamide acetyltransferase family protein from Pseudomonas sp. VLB120
31% identity, 86% coverage
EF1355 pyruvate dehydrogenase complex E2 component, dihydrolipoamide acetyltransferase from Enterococcus faecalis V583
28% identity, 68% coverage
SG0468 pyruvate dehydrogenase dihydrolipoyltransacetylase component from Sodalis glossinidius str. 'morsitans'
28% identity, 69% coverage
BMEII0746 LIPOAMIDE ACYLTRANSFERASE COMPONENT OF BRANCHED-CHAIN ALPHA-KETO ACID DEHYDROGENASE COMPLEX from Brucella melitensis 16M
30% identity, 85% coverage
- Immuno-profiling of Brucella proteins for developing improved vaccines and DIVA capable serodiagnostic assays for brucellosis
Nandini, Frontiers in microbiology 2023 - “...sera. Peptidoglycan-associated lipoprotein BMEI0340 Transporter BMEI1890 Protease Do BMEI1330 Branched-chain alpha-keto acid dehydrogenase subunit E2 BMEII0746 Isopropylmalate isomerase large subunit BMEI0157 Immunogenic protein BMEI0536 Hypothetical protein BMEI0916 Periplasmic oligopeptide-binding protein precursor BMEII0735 Hypothetical protein BMEI1060 Hypothetical protein BMEI0179 Hypothetical protein BMEI0368 ATP-dependent protease ATP-binding subunit HslU...”
- Transcriptomic Analysis of the Brucella melitensis Rev.1 Vaccine Strain in an Acidic Environment: Insights Into Virulence Attenuation
Salmon-Divon, Frontiers in microbiology 2019 - “...periplasmic protein Overexpression/overexpression BMEII0633 Branched-chain amino acid ABC transporter substrate-binding protein Overexpression/overexpression BMEII0704 Bacterioferritin Overexpression/overexpression BMEII0746 2-Oxo acid dehydrogenase subunit E2 Overexpression/overexpression BMEII0747 Alpha-ketoacid dehydrogenase subunit beta Overexpression/overexpression Next, we compared the genes that we found to be DE between the two strains to a list...”
- Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits
Dessimoz, Nucleic acids research 2006 - “...the following COG identifiers: Agrobacterium tumefaciens (2: AGl2719, 3: AGc4775, 4: AGc2641), Brucella melitensis (2: BMEII0746, 3: BMEI0141, 4: BMEI0856), Buchnera sp. (1: BU206, 3: BU303), E.coli K12 (COG identifier corresponds to the gene name: aceF, sucB), E.coli H7 (1: ECs0119, 3: ECs0752), Haemophilus influenzae (1:...”
- Comparative proteome analysis of Brucella melitensis vaccine strain Rev 1 and a virulent strain, 16M
Eschenbrenner, Journal of bacteriology 2002 - “...dehydrogenase complexd Nitrogen assimilation regulatory protein NTRX BMEI0244 BMEII0746 5.25 5.72 5.69 5.77 27.5 53.8 23.7 46.5 5.1 4.5 BMEI0868 5.18 5.58 53.2...”
BruAb2_0698 2-oxoisovalerate dehydrogenase E2 component, dihydrolipamide acetyltransferase from Brucella abortus biovar 1 str. 9-941
BAB2_0713 Biotin/lipoyl attachment:Catalytic domain of components of various dehydrogenase complexes:2-oxo acid dehydrogenase, acyltran... from Brucella melitensis biovar Abortus 2308
30% identity, 85% coverage
PM0278 SucB from Pasteurella multocida subsp. multocida str. Pm70
30% identity, 91% coverage
- Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits
Dessimoz, Nucleic acids research 2006 - “...(1: HI1232, 3: HI1661), Neisseria meningitidis (1: NMB1342, 3: NMB0956), Pasteurella multocida (1: PM0894, 3: PM0278), Pseudomonas aeruginosa (1: PA5016, 2: PA2249, 3: PA1586), Rhizobium loti (2: mll4471, 3: mll4300, 4a: mlr0385, 4b: mll3627), Rhizobium meliloti (2: SMc03203, 3a: SMc02483, 3b: SMb20019, 4: SMc01032), Rickettsia conorii...”
YPO3418 dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex from Yersinia pestis CO92
31% identity, 70% coverage
RC0226 dihydrolipoamide acetyltransferase component [EC:2.3.1.61] from Rickettsia conorii str. Malish 7
28% identity, 92% coverage
- Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits
Dessimoz, Nucleic acids research 2006 - “...4b: mll3627), Rhizobium meliloti (2: SMc03203, 3a: SMc02483, 3b: SMb20019, 4: SMc01032), Rickettsia conorii (3: RC0226, 4: RC0764), Rickettsia prowazekii (3: RP179, 4: RP530), Vibrio cholerae (1: VC2413, 3: VC2086), Y.pestis (1: YPO3418, 3: YPO1114). Figure 5 Unrooted phylogenetic consensus tree for COG0513, constructed from a...”
PfGW456L13_3542 Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) from Pseudomonas fluorescens GW456-L13
32% identity, 86% coverage
- mutant phenotype: Specifically important for utilizing L-Isoleucine; L-Valine. Automated validation from mutant phenotype: the predicted function (2.3.1.168) was linked to the condition via a SEED subsystem. This annotation was also checked manually.
MSC_0267 branched-chain alpha-keto acid dehydrogenase subunit E2 from Mycoplasma mycoides subsp. mycoides SC str. PG1
29% identity, 86% coverage
- Mycoplasmas as Host Pantropic and Specific Pathogens: Clinical Implications, Gene Transfer, Virulence Factors, and Future Perspectives
Dawood, Frontiers in cellular and infection microbiology 2022 - “...specific antibody, inhibited the in vitro growth of Mmm. Also, polyclonal rabbit serum against recombinant MSC_0267 blocked the adhesion of Mmm to BoLEC by 41%. Further in vivo studies are required for exploring the immune response induced by Mmm antigens recognized by these antibodies ( Aye...”
- “...beta chain (MSC_0266) ( Naseem etal., 2010 ) PdhC, oxo acid dehydrogenase acyltransferase (Catalytic domain) (MSC_0267), ( Krasteva etal., 2014 ) PdhD, dihydrolipoamide dehydrogenase (MSC_0268). Mmm ( Jores etal., 2009 ) pyruvate dehydrogenase E1a subunit M. pneumoniae Mediate adhesion to fibronectin Essential as a structural protein...”
- Identification of targets of monoclonal antibodies that inhibit adhesion and growth in Mycoplasma mycoides subspecies mycoides
Aye, Veterinary immunology and immunopathology 2018 - “...agglutination of Mmm total cell lysate. AMMY 5, a 2-oxo acid dehydrogenase acyltransferase (Catalytic domain) (MSC_0267) specific antibody, was identified and polyclonal rabbit serum against recombinant MSC_0267 blocked adhesion of Mmm to BoLEC by 41%. Antigens recognized by these antibodies could be vaccine candidate(s) and should...”
- “...1 D9QWT6 Dihydrolipoyl dehydrogenase MSC_0268 lpdA 64.2 5.72 4 D9QWT5 c 2-oxo acid dehydrogenase acyltransferase MSC_0267 pdhC 45.8 6.67 5 D9QVZ9 DNA gyrase subunit B MSC_0006 gyrB 71.5 5.94 6 D9QX02 Aspartate--tRNA ligase MSC_0333 aspS 66.6 6.00 7 D9QYF8 glycerate mutase MSC_0825 gpmL 60.1 6.33 8...”
- Phage library screening for the rapid identification and in vivo testing of candidate genes for a DNA vaccine against Mycoplasma mycoides subsp. mycoides small colony biotype
March, Infection and immunity 2006 - “...dehydrogenase subunit of pyruvate dehydrogenase), MSC_0267 (pdhC, encoding the EII dihydrolipoamide S-acetyltransferase subunit of pyruvate dehydrogenase),...”
llmg_0072 pyruvate dehydrogenase complex E2 component from Lactococcus lactis subsp. cremoris MG1363
27% identity, 69% coverage
PP4403, PP_4403 2-oxoisovalerate dehydrogenase, lipoamide acyltransferase component from Pseudomonas putida KT2440
31% identity, 86% coverage
ABO_0623 pyruvate dehydrogenase, E2 component from Alcanivorax borkumensis SK2
31% identity, 64% coverage
PAE2648 pyruvate dehydrogenase E2 (dihydrolipoamide acetyltransferase) from Pyrobaculum aerophilum str. IM2
31% identity, 93% coverage
SSA_1140 Dihydrolipoamide acetyl transferase, E2 component, putative from Streptococcus sanguinis SK36
30% identity, 87% coverage
TTHA0184 pyruvate dehydrogenase complex, dihydrolipoamide acetyltransferase E2 component from Thermus thermophilus HB8
32% identity, 88% coverage
LLKF_0036 pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase from Lactococcus lactis subsp. lactis KF147
27% identity, 69% coverage
- Strain-Dependent Transcriptome Signatures for Robustness in Lactococcus lactis
Dijkstra, PloS one 2016 - “...yhdA 1,4-dihydroxy-2-naphthoyl-CoA thioesterase positive 2.2 LLKF_0965 yjgC amino acid ABC transporter substrate-binding protein positive 7.0 LLKF_0036 pdhC pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase positive 23.9 LLKF_1210 hypothetical protein positive 1.5 LLKF_0039 lplL lipoate-protein ligase positive 17.5 LLKF_1293 AMP-dependent synthetase and ligase family protein negative 0.6 LLKF_0381 ydcG...”
BU206 dihydrolipoamide acetyltransferase from Buchnera aphidicola str. APS (Acyrthosiphon pisum)
26% identity, 87% coverage
- Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits
Dessimoz, Nucleic acids research 2006 - “...3: AGc4775, 4: AGc2641), Brucella melitensis (2: BMEII0746, 3: BMEI0141, 4: BMEI0856), Buchnera sp. (1: BU206, 3: BU303), E.coli K12 (COG identifier corresponds to the gene name: aceF, sucB), E.coli H7 (1: ECs0119, 3: ECs0752), Haemophilus influenzae (1: HI1232, 3: HI1661), Neisseria meningitidis (1: NMB1342, 3:...”
PSPTO_2200 2-oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase from Pseudomonas syringae pv. tomato str. DC3000
29% identity, 90% coverage
- A computational model of Pseudomonas syringae metabolism unveils a role for branched-chain amino acids in Arabidopsis leaf colonization
Tubergen, PLoS computational biology 2023 - “...The search yielded one ODHC-E1 component encoded by PSPTO_2199, one ODHC-E2 component encoded by either PSPTO_2200 or PSPTO_5006, and one ODHC-E3 component encoded by PSPTO_2201 ( S1 Table ), suggesting that enzymes of the ODHC complex could be part of the leucine degradation pathway and serve...”
- “...]. In Pst DC3000, PSPTO_3860, PSPTO_5005, PSPTO_5006, and PSPTO_2201 encode the PDC enzymes, while PSPTO_2199, PSPTO_2200, and PSPTO_2201 encode the ODHC enzymes. Importantly, enzymes in these two complexes show a degree of promiscuity in substrate utilization, suggesting that they could also contribute to BCAAs catabolism in...”
P45302 Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex from Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
HI1661 2-oxoglutarate dehydrogenase E2 component, dihydrolipoamide succinyltransferase(sucB) from Haemophilus influenzae Rd KW20
27% identity, 89% coverage
- Ferritin heavy chain supports stability and function of the regulatory T cell lineage.
Wu, The EMBO journal 2024 - “...Addgene Cat#12260 pMD2.G Addgene Cat#12259 pCMV-FTH-3tag3a This paper pCMV-FTH mut -3tag3a This paper pCMV-3FLAG-TET3(human)-Neo miaolingBio P45302 Antibodies PE anti-human CD25 (Clone 2A3) BD Biosciences Cat#341011 (RRID: AB_2783790) PE-Cy7 anti-human CD45RA (Clone HI100) BD Biosciences Cat#560675 (RRID: AB_1727498) Brilliant Violet 421 Anti-human CD127 (Clone A019D5) Biolegend Cat#351309...”
- “...enzymatic activity was monitored in human HEK293T cells, transiently transfected with human TET3 (pCMV-3FLAG-TET3(human)-Neo; MiaolingBio P45302 ) plus human FTH (pCMV-FTH-3Tag3a) or FTH mutant (FTH mut ; pCMV-FTH mut -3Tag3a; Glu 62 and His 65 and Lys86 were mutated as Lys, Gly, Gln, respectively, to achieve...”
- The iron/heme regulated genes of Haemophilus influenzae: comparative transcriptional profiling as a tool to define the species core modulon
Whitby, BMC genomics 2009 - “...HI1218 L-lactate permease lldP 4.67 3.58 ns HI1444 5,10 methlyenetetrahydrofolate reductase metF 5.19 3.47 ns HI1661 2-oxoglutarate dehydrogenase E2 sucB 1.56 1.17 -1.18 HI1662 2-oxoglutarate dehydrogenase E1 sucA ns ns -1.18 HI1727 Argininosuccinate synthetase argG -2.28 ns ns HI1728 Conserved hypothetical protein ns 1.59 ns HI1730...”
- The ArcA regulon and oxidative stress resistance in Haemophilus influenzae
Wong, Molecular microbiology 2007 - “...( lldD ) 3.2 1.79E-10 4.5 1.07E-11 HI1730 Conserved hypothetical protein 3.0 1.48E-06 7.0 3.32E-08 HI1661 2-oxoglutarate dehydrogenase E2 component ( sucB ) 2.8 5.33E-07 3.0 1.14E-06 HI0026 Lipoate biosynthesis protein A ( lipA ) 2.6 4.08E-07 2.2 9.63E-06 HI1662 2-oxoglutarate dehydrogenase E1 component ( sucA...”
- “...( HI0009 ) (5-ATGAGTATCAAAATCTTATC and 5-TGCTTCTTCTGCAGGAAAAATAAATG), lldP ( HI1218 ) (5-ATGCTGTCTTTTATTCTAAG and 5-TAGATTATAAAATAAAGGTAC), sucB ( HI1661 ) (5-ATGGCAATCGAAATTCTTG and 5-GATTTCTAATAACAATCTTG), HI0592 (5-ATGCTATTTCGTACATATATAC and 5-GAGAGCCCTGTTGGATG), potE ( HI0590 ) (5-ATGAGTGCTAAAAGCAATAAAATTG and 5-TTTTTTAAGATCAAATTTGTAAG) and HI1349 (5-AACTGCAGATCTGCTCTTCAATGTCAAAAACATCAATCGGACTA and 5-AAAGATCTGCAGGCTCTTCTTTAATTATGGCAAGTTTGGCAAGC). PCR products were labelled with the Gene Images AlkPhos Direct...”
- Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits
Dessimoz, Nucleic acids research 2006 - “...gene name: aceF, sucB), E.coli H7 (1: ECs0119, 3: ECs0752), Haemophilus influenzae (1: HI1232, 3: HI1661), Neisseria meningitidis (1: NMB1342, 3: NMB0956), Pasteurella multocida (1: PM0894, 3: PM0278), Pseudomonas aeruginosa (1: PA5016, 2: PA2249, 3: PA1586), Rhizobium loti (2: mll4471, 3: mll4300, 4a: mlr0385, 4b: mll3627),...”
- Gene expression changes triggered by exposure of Haemophilus influenzae to novobiocin or ciprofloxacin: combined transcription and translation analysis
Gmuender, Genome research 2001 - “...hi0992 hi0969 hi0623 hi0625 hi0236 hi1734 hi0422 hi0537 hi1661 hi0425 hi0863 hi1434.1 hi1186 hi1676 hi1040 hi0503 hi1152 hi1193 hi0538 hi1033 hi1632 hi1227...”
- “...change No. hi0629 hi1135 hi1251 hi0508 hi0538 hi0506 hi1661 hi0546 hi0239 hi0745 hi0470 hi0008 hi1133 hi0140 hi0117 hi1154 hi1218 hi0537 hi0373 hi0142 hi1227...”
lpg1503 dihydrolipoamide acetyltransferase from Legionella pneumophila subsp. pneumophila str. Philadelphia 1
28% identity, 67% coverage
Mal52_17290 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase from Symmachiella dynata
29% identity, 91% coverage
YPTB0714 pyruvate dehydrogenase, dihydrolipoyltransacetylase component from Yersinia pseudotuberculosis IP 32953
29% identity, 68% coverage
plu3622 dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex (E2) from Photorhabdus luminescens subsp. laumondii TTO1
29% identity, 68% coverage
RP179 DIHYDROLIPOAMIDE ACETYLTRANSFERASE COMPONENT (sucB) from Rickettsia prowazekii str. Madrid E
27% identity, 91% coverage
- Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits
Dessimoz, Nucleic acids research 2006 - “...3a: SMc02483, 3b: SMb20019, 4: SMc01032), Rickettsia conorii (3: RC0226, 4: RC0764), Rickettsia prowazekii (3: RP179, 4: RP530), Vibrio cholerae (1: VC2413, 3: VC2086), Y.pestis (1: YPO3418, 3: YPO1114). Figure 5 Unrooted phylogenetic consensus tree for COG0513, constructed from a Bayesian analysis. Posterior probabilities are drawn...”
ODB2_HUMAN / P11182 Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitochondrial; 52 kDa mitochondrial autoantigen of primary biliary cirrhosis; Branched chain 2-oxo-acid dehydrogenase complex component E2; BCOADC-E2; Branched-chain alpha-keto acid dehydrogenase complex component E2; BCKAD-E2; BCKADE2; BCKDH-E2; Dihydrolipoamide acetyltransferase component of branched-chain alpha-keto acid dehydrogenase complex; Dihydrolipoamide branched chain transacylase; Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase; EC 2.3.1.168 from Homo sapiens (Human) (see 9 papers)
NP_001909 lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitochondrial isoform 1 precursor from Homo sapiens
29% identity, 76% coverage
- function: The branched-chain alpha-keto dehydrogenase complex catalyzes the overall conversion of alpha-keto acids to acyl-CoA and CO(2). It contains multiple copies of three enzymatic components: branched-chain alpha-keto acid decarboxylase (E1), lipoamide acyltransferase (E2) and lipoamide dehydrogenase (E3). Within this complex, the catalytic function of this enzyme is to accept, and to transfer to coenzyme A, acyl groups that are generated by the branched-chain alpha-keto acid decarboxylase component.
catalytic activity: N(6)-[(R)-dihydrolipoyl]-L-lysyl-[protein] + 2- methylpropanoyl-CoA = N(6)-[(R)-S(8)-2-methylpropanoyldihydrolipoyl]- L-lysyl-[protein] + CoA (RHEA:18865)
cofactor: (R)-lipoate (Binds 1 lipoyl cofactor covalently.)
subunit: Forms a 24-polypeptide structural core with octahedral symmetry that represents the E2 component of the branched-chain alpha- ketoacid dehydrogenase (BCKDH) complex. The BCKDH complex is composed of three major building blocks E1, E2 and E3. It is organized around E2, a 24-meric cubic core composed of DBT, to which are associated 6 to 12 copies of E1, and approximately 6 copies of the dehydrogenase E3, a DLD dimer (By similarity) (PubMed:22291014). Interacts with PPM1K with a 24:1 stoichiometry; the N-terminal region (residues 49-61) of PPM1K and C-terminal linker of the lipoyl domain of DBT/E2 (residues 145-160) are critical for this interaction whereas the lipoyl prosthetic group is dispensable. This interaction requires colocalization in mitochondria (PubMed:19411760, PubMed:22291014, PubMed:22589535). PPM1K competes with BCKDK for binding to DBT; this interaction is modulated by branched-chain alpha-keto acids (BCKAs). At steady state, BCKDH holoenzyme preferentially binds BCKDK and BCKDHA is phosphorylated. In response to high levels of BCKAs, BCKDK is replaced by PPM1K leading to BCKDHA dephosphorylation (PubMed:22589535, PubMed:37558654). - Multiomic analysis in fibroblasts of patients with inborn errors of cobalamin metabolism reveals concordance with clinical and metabolic variability
Wiedemann, EBioMedicine 2024 - “...cblG P32929 CTH Cystathionine gamma-lyase 607657 7.52 0.045 Cystathioninuria 219500AR Development delay (38.2%) Cystathionuria cblG P11182 DBT Dihydrolipoamide branched-chain transacylase 248610 3.17 0.033 Maple syrup urine disease, type II 248600AR Development delay (38.2%) Seizures (10.6%) Hypotonia (17.7%) Extrapyramidal syndrome (3.6%) Development delay (38.2%) Abnormal brain MRI...”
- Proteome changes of fibroblasts and endothelial cells upon incubation with human cytomegalovirus subviral Dense Bodies.
Penner, Scientific data 2023 - “...2;2;2;0;0 3 PPAN Suppressor of SWI4 1 homolog 0.611 1.632 2.353 1.532 0.019 1.729 + P11182 1;1;3;0;0 3 DBT Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitochondrial 1.502 2.267 0.420 1.396 0.029 1.534 + yes P42224 58;58;61;38;38 5 STAT1 Signal transducer and activator of...”
- Reduced symmetric dimethylation stabilizes vimentin and promotes metastasis in MTAP-deficient lung cancer.
Chang, EMBO reports 2022 - “...P06733 ENO1 Alphaenolase 47.1 2.6E+07 1.4E+07 2.6E+07 Q96P63 SERPINB12 Serpin B12 46.2 5.1E+06 8.8E+06 3.3E+06 P11182 DBT Lipoamide acyltransferase component of branchedchain alphaketo acid dehydrogenase complex, mitochondrial 53.5 9.5E+05 3.2E+07 8.0E+05 P38159 RBMX RNAbinding motif protein, X chromosome 42.3 2.4E+05 9.2E+06 3.3E+06 P08621 SNRNP70 U1 small...”
- Protective Effect of Dictyophora Polysaccharides on Sodium Arsenite-Induced Hepatotoxicity: A Proteomics Study.
Hu, Frontiers in pharmacology 2021 - “...0.71 1.85 1.33 Deoxyribonuclease-2-alpha DNASE2 O00115 1.27 0.77 0.98 Dihydrolipoamide branched chain transacylase E2 DBT P11182 1.33 0.75 1.01 DNA polymerase delta interacting protein 2 POLDIP2 Q9Y2S7 1.22 0.85 1.04 DnaJ homolog subfamily C member 9 DNAJC9 Q8WXX5 0.83 1.10 0.91 Dynein light chain roadblock-type 1...”
- ATAD3A oligomerization causes neurodegeneration by coupling mitochondrial fragmentation and bioenergetics defects.
Zhao, Nature communications 2019 - “...of 2-oxoglutarate dehydrogenase complex, mitochondrial DLST 14 O14874 [3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial BCKDK 11 P11182 Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitochondrial DBT 5 Protein kinase P67775 Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform PPP2CA 11 P12532 Creatine kinase U-type, mitochondrial CKMT1A...”
- A Combinatorial Proteomic Biomarker Assay to Detect Ovarian Cancer in Women.
Henderson, Biomarkers in cancer 2018 - “...CTAG1B P78358 Cancer/testis antigen 1 http://www.uniprot.org/uniprot/P78358 TAAb CTBP1 Q13363 C-terminal-binding protein 1 http://www.uniprot.org/uniprot/Q13363 TAAb DBT P11182 Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitochondrial http://www.uniprot.org/uniprot/P11182 TAAb DHFR P00374 Dihydrofolate reductase http://www.uniprot.org/uniprot/P00374 TAAb EIF3E P60228 Eukaryotic translation initiation factor 3 subunit E http://www.uniprot.org/uniprot/P60228 TAAb ErbB2...”
- Quantitative proteomic study of mitoxantrone-resistant NCI-H460 cell-xenograft tumors.
Su, International journal of clinical and experimental pathology 2018 - NEK1 kinase domain structure and its dynamic protein interactome after exposure to Cisplatin
Melo-Hanchuk, Scientific reports 2017 - “...C21ORF2 O43822 Chromosome 21 open reading frame2 82 KAT7 O95251 Histone acetyltransferase KAT7 B ODB2 P11182 Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex A VDAC P21796 Voltage-dependent anion-selective channel protein1 22 PRS7 P35998 26S protease regulatory subunit7 A SMBP2 P38935 DNA-binding protein SMUBP-2 B...”
- More
- Overexpression of DBT suppresses the aggressiveness of renal clear cell carcinoma and correlates with immune infiltration.
Zhang, Frontiers in immunology 2023 - GeneRIF: Overexpression of DBT suppresses the aggressiveness of renal clear cell carcinoma and correlates with immune infiltration.
- Three novel mutations of the BCKDHA, BCKDHB and DBT genes in Chinese children with maple syrup urine disease.
Yang, Journal of pediatric endocrinology & metabolism : JPEM 2022 (PubMed)- GeneRIF: Three novel mutations of the BCKDHA, BCKDHB and DBT genes in Chinese children with maple syrup urine disease.
- Pathogenic Homozygous Mutations in the DBT Gene (c.1174A>C) Result in Maple Syrup Urine Disease in a rs12021720 Carrier.
Alijanpour, Laboratory medicine 2022 (PubMed)- GeneRIF: Pathogenic Homozygous Mutations in the DBT Gene (c.1174A>C) Result in Maple Syrup Urine Disease in a rs12021720 Carrier.
- Different gene preferences of maple syrup urine disease in the aboriginal tribes of Taiwan.
Hou, Pediatrics and neonatology 2014 (PubMed)- GeneRIF: The novel DBT mutation c.650-651insT was more prevalent than the deleted 4.7-kb heterozygote in the Amis population. The reported 4.7-kb deletion indicating a possible founder mutation may be preserved.
- Molecular characterization of maple syrup urine disease patients from Tunisia.
Jaafar, Gene 2013 (PubMed)- GeneRIF: Deletion in DBT gene is associated with maple syrup urine disease.
- Four novel mutations identified in Norwegian patients result in intermittent maple syrup urine disease when combined with the R301C mutation.
Brodtkorb, Molecular genetics and metabolism 2010 (PubMed)- GeneRIF: 4 novel mutations in DBT gene resulting in intermittent maple syrup urine disease in 7 Norwegian patients; pathogenic effect of the mutations is depletion of cellular protein; intermittent form of MSUD appears to be due to residual R301C mutant protein
- Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
Hendrickson, PloS one 2010 - GeneRIF: Observational study of gene-disease association. (HuGE Navigator)
- Molecular and structural analyses of maple syrup urine disease and identification of a founder mutation in a Portuguese Gypsy community.
Quental, Molecular genetics and metabolism 2008 (PubMed)- GeneRIF: 30 Maple syrup urine disease Portuguese patients studied; 17 putative mutations have been identified (6 in BCKDHA, 5 in BCKDHB and 6 in DBT); 7 of are described for the first time.
- More
Pnuc_0735 pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase from Polynucleobacter sp. QLW-P1DMWA-1
30% identity, 66% coverage
JHW33_RS12725 pyruvate dehydrogenase complex dihydrolipoyllysine-residue acetyltransferase from Rahnella aceris
28% identity, 58% coverage
SO1931 2-oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase from Shewanella oneidensis MR-1
SO_1931 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase from Shewanella oneidensis MR-1
30% identity, 92% coverage
- Shewanella oneidensis MR-1 sensory box protein involved in aerobic and anoxic growth
Sundararajan, Applied and environmental microbiology 2011 - “...SO1927 (sdhC) SO1928 (sdhA) SO1929 (sdhB) SO1930 (sucA) SO1931 (sucB) SO1932 (sucC) SO2097 (hydC) SO2098 (hyaB) SO3285 (cydB) SO3286 (cydA) SO4047 SO4048 Log2...”
- Fnr (EtrA) acts as a fine-tuning regulator of anaerobic metabolism in Shewanella oneidensis MR-1
Cruz-García, BMC microbiology 2011 - “...1.26) succinate dehydrogenase, cytochrome b556 subunit SO1930 sucA 3.02 ( 1.22) 2-oxoglutarate dehydrogenase, E1 component SO1931 sucB 3.60 ( 1.58) 2-oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase SO1932 sucC 3.29 ( 0.98) succinyl-CoA synthase, beta subunit SO1933 sucD 3.28 ( 1.24) succinyl-CoA synthase, alpha subunit SO2361 ccoP...”
- An empirical strategy for characterizing bacterial proteomes across species in the absence of genomic sequences
Turse, PloS one 2010 - “...2 SO1926 gltA 6 4 2 SO1928 sdhA 5 4 2 SO1929 sdhB SO1930 sucA SO1931 sucB 9 SO1932 sucC 5 2 SO1933 sucD 6 4 SO2222 SO2222 12 2 SO2629 icd 50 12 4 SO4118 SO4118 4 Data represented here are from highly conserved central...”
- “...CN32_2270 sdh B SO1930 CN32_2269 suc A 6 4 9 4 2 4 4 4 SO1931 CN32_2268 suc B 4 4 6 4 4 3 3 4 SO1932 CN32_2267 suc C 3 2 4 3 2 2 2 SO1933 CN32_2266 suc D 4 2 4 2...”
- Constraint-based model of Shewanella oneidensis MR-1 metabolism: a tool for data analysis and hypothesis generation
Pinchuk, PLoS computational biology 2010 - “...using a previously described method [57] , [58] . The sucrose selection step for obtaining SO1931 and SO4606/SO2361 deletion mutants was performed under anaerobic conditions at 25C using plates containing modified M1 medium supplemented with 20 mM D, L-lactate, 30 mM sodium fumarate, 10% LB, and...”
- The influence of cultivation methods on Shewanella oneidensis physiology and proteome expression
Elias, Archives of microbiology 2008 - “...10634 172 b 6.3 SO4349 Ketol-acid reductoisomerase 636 1148 3150 0.003 0.4 226 13926 0.2 SO1931 2-Oxoglutarate dehydrogenase 763 495 a 951 0.024 a 0.5 361 464 0.8 SO3237 Flagellin 999 2711 1223 9.9E-05 2.2 10836 7314 1.5 ND 1048 1196 196 8.8E-04 6.1 SO3549 Hypothetical...”
- Profiling the membrane proteome of Shewanella oneidensis MR-1 with new affinity labeling probes
Tang, Journal of proteome research 2007 - “...SO1798 SO1825 SO1826 SO1827 SO1829 SO1896 SO1928 SO1930 SO1931 SO2001 SO2361 SO2363 SO2397 SO2427 SO2469 60469 44635 56190 48709 45291 72323 34624 129383 47189...”
- Supplementation with Amino Acid Sources Facilitates Fermentative Growth of Shewanella oneidensis MR-1 in Defined Media
Ikeda, Applied and environmental microbiology 2023 (secret) - Electrochemically active bacteria sense electrode potentials for regulating catabolic pathways
Hirose, Nature communications 2018 - “...cytochrome b subunit 1.94 TCA cycle SO_1930 sucA 2-Oxoglutarate dehydrogenase complex dehydrogenase E1 component 1.75 SO_1931 sucB 2-Oxoglutarate dehydrogenase complex succinyl-CoA:dihydrolipoate S-succinyltransferase E2 component 1.77 SO_1933 sucD Succinyl-CoA synthase alpha subunit 1.66 NADH oxidation SO_1010 nuoM NADH-ubiquinone oxidoreductase subunit M 2.85 SO_1012 nuoK NADH-ubiquinone oxidoreductase subunit...”
Tfu_0182 putative dihydrolipoamide acyltransferase component from Thermobifida fusca YX
29% identity, 83% coverage
- The Effects of Carbon Source and Growth Temperature on the Fatty Acid Profiles of Thermobifida fusca
Winkelman, Frontiers in molecular biosciences 2022 - “...chain amino acid aminotransferase Tfu_0616, Tfu_2112 BCAD Branched Chain alpha keto acid dehydrogenase Tfu_0180, Tfu_0181, Tfu_0182 Des1 Delta-9 acyl-CoA desaturase Tfu_0413 BfaB 9 unsaturated fatty acid methyl transferase Tfu_2160 BfaA 10-methylene BCFA reductase Tfu_2161 PDH Pyruvate Dehydrogenase Complex Tfu_3049, Tfu_3050, Tfu_3051 ACK Acetate Kinase Tfu_2971 ACS-AMP...”
- “...both the branched chain aminotransferase (Tfu_0616, Tfu_2112) and branched chain -keto acid dehydrogenase (Tfu_0180, Tfu_0181, Tfu_0182) enzymes required to generate isobutyryl-CoA and 2-methylbutyryl-CoA from valine, leucine, or isoleucine. Alternatively, these branched chain acyl-CoAs may be generated from the -keto acids that are intermediates of branched chain...”
ODB2_BOVIN / P11181 Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitochondrial; Branched-chain alpha-keto acid dehydrogenase complex component E2; BCKAD-E2; BCKADE2; Dihydrolipoamide acetyltransferase component of branched-chain alpha-keto acid dehydrogenase complex; Dihydrolipoamide branched chain transacylase; Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase; EC 2.3.1.168 from Bos taurus (Bovine) (see 2 papers)
30% identity, 76% coverage
- function: The branched-chain alpha-keto dehydrogenase complex catalyzes the overall conversion of alpha-keto acids to acyl-CoA and CO(2). It contains multiple copies of three enzymatic components: branched-chain alpha-keto acid decarboxylase (E1), lipoamide acyltransferase (E2) and lipoamide dehydrogenase (E3). Within this complex, the catalytic function of this enzyme is to accept, and to transfer to coenzyme A, acyl groups that are generated by the branched-chain alpha-keto acid decarboxylase component.
catalytic activity: N(6)-[(R)-dihydrolipoyl]-L-lysyl-[protein] + 2- methylpropanoyl-CoA = N(6)-[(R)-S(8)-2-methylpropanoyldihydrolipoyl]- L-lysyl-[protein] + CoA (RHEA:18865)
cofactor: (R)-lipoate (Binds 1 lipoyl cofactor covalently.)
subunit: Forms a 24-polypeptide structural core with octahedral symmetry that represents the E2 component of the branched-chain alpha- ketoacid dehydrogenase (BCKDH) complex. The BCKDH complex is composed of three major building blocks E1, E2 and E3. It is organized around E2, a 24-meric cubic core composed of DBT, to which are associated 6 to 12 copies of E1, and approximately 6 copies of the dehydrogenase E3, a DLD dimer (By similarity). Interacts with PPM1K with a 24:1 stoichiometry; the N-terminal region (residues 49-61) of PPM1K and C- terminal linker of the lipoyl domain of DBT/E2 (residues 145-160) are critical for this interaction whereas the lipoyl prosthetic group is dispensable. This interaction requires colocalization in mitochondria (By similarity). PPM1K competes with BCKDK for binding to DBT; this interaction is modulated by branched-chain alpha-keto acids (BCKAs). At steady state, BCKDH holoenzyme preferentially binds BCKDK and BCKDHA is phosphorylated. In response to high levels of BCKAs, BCKDK is replaced by PPM1K leading to BCKDHA dephosphorylation (By similarity). - Elucidation of molecular mechanisms of physiological variations between bovine subcutaneous and visceral fat depots under different nutritional regimes.
Romao, PloS one 2013 - “...E1B8H0 PEAK1 NKF3 kinase family member 0.594 0.015 A6QR11 NELL2 NEL-like 2 (chicken) 0.581 0.018 P11181 DBT dihydrolipoamide branched chain transacylase E2 0.559 0.025 P00129 UQCRB ubiquinol-cytochrome c reductase binding protein 0.544 0.029 F1MHQ4 FABP4 fatty acid binding protein 4, adipocyte 0.541 0.031 G5E5C8 TALDO1 transaldolase...”
DBT / P11182 branched-chain α-keto acid dehydrogenase complex E2 component subunit (EC 2.3.1.168) from Homo sapiens (see 9 papers)
P11182 dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) from Homo sapiens (see 3 papers)
29% identity, 76% coverage
NJ56_RS02590 pyruvate dehydrogenase complex dihydrolipoyllysine-residue acetyltransferase from Yersinia ruckeri
29% identity, 57% coverage
SG0877 2-oxoglutarate dehydrogenase E2 component from Sodalis glossinidius str. 'morsitans'
30% identity, 92% coverage
Q8ZRT1 Acetyltransferase component of pyruvate dehydrogenase complex from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
29% identity, 58% coverage
- Effects of 1,8-cineole on Carbohydrate Metabolism Related Cell Structure Changes of Salmonella
Sun, Frontiers in microbiology 2018 - “...related to carbohydrate metabolism (Figure 5 ). Protein aceF (Acetyltransferase component of pyruvate dehydrogenase complex, Q8ZRT1), aceE (Pyruvate dehydrogenase E1 component, V1HP36), and pgk (Phosphoglycerate kinase, V1H0S6) take an interrelation in carbohydrate metabolism pathway. Figure 5 Establishment of protein-protein interaction networks for differential proteins. Validation of...”
Q8Z9E9 Acetyltransferase component of pyruvate dehydrogenase complex from Salmonella typhi
STY0176 dihydrolipoamide acetyltransferase component (E2) of pyruvate dehydrogenase from Salmonella enterica subsp. enterica serovar Typhi str. CT18
29% identity, 58% coverage
STM0153 pyruvate dehydrogenase, dihydrolipoyltransacetylase component from Salmonella typhimurium LT2
29% identity, 58% coverage
SPA0157 dihydrolipoamide acetyltransferase component (E2) of pyruvate dehydrogenase from Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150
29% identity, 58% coverage
S0114 pyruvate dehydrogenase (dihydrolipoyltransacetylase component) from Shigella flexneri 2a str. 2457T
29% identity, 58% coverage
SPC_0164 dihydrolipoamide acetyltransferase from Salmonella enterica subsp. enterica serovar Paratyphi C strain RKS4594
29% identity, 58% coverage
- Antibacterial Components and Modes of the Methanol-Phase Extract from Commelina communis Linn
Liu, Plants (Basel, Switzerland) 2023 - “...acetyltransferase SPC_0736 0.25 Succinyl-CoA synthetase alpha subunit SPC_3569 0.296 Phosphoenolpyruvate carboxykinase SPC_0727 0.5 Citrate synthase SPC_0164 3.325 Dihydrolipoamide acetyltransferase SPC_0163 4.714 Pyruvate dehydrogenase E1 component Glycolysis/Gluconeogenesis SPC_3760 0.06 Aldehyde dehydrogenase B SPC_4566 0.241 Fructose-1-bisphosphatase SPC_4282 0.417 Glucose-6-phosphate isomerase SPC_1226 2.146 Glucose-specific PTS system enzyme IIA component...”
Pan258_17100 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase from Symmachiella dynata
28% identity, 91% coverage
PPUBIRD1_1664 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase from Pseudomonas putida BIRD-1
28% identity, 90% coverage
- Understanding butanol tolerance and assimilation in Pseudomonas putida BIRD-1: an integrated omics approach
Cuenca, Microbial biotechnology 2016 - “...of these also presented insertions in TCA cyclerelated genes; namely, we found an insertion in PPUBIRD1_1664, which is a gene that is homologous to kgdB that encodes the E2 component of the branchedchain keto acid dehydrogenase. We also identified another mutant with an insertion in sucC...”
- “...lpdG (as mentioned before, a gene that when mutated led to compromised butanol tolerance) and PPUBIRD1_1664, suggesting that the insertions exert a polar effect on the operon that interferes with the ability of the strain to assimilate butanol. Two mutants had insertions in genes related to...”
swp_2948 2-oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase from Shewanella piezotolerans WP3
29% identity, 92% coverage
- Condition-Specific Molecular Network Analysis Revealed That Flagellar Proteins Are Involved in Electron Transfer Processes of Shewanella piezotolerans WP3
Ding, Genetics research 2021 - “...swp_2462, swp_1221 3 7 0.52 1.90 E 03 Oxidative phosphorylation swp_0794, swp_4826, swp_4824, swp_2950, swp_2059, swp_2948, swp_5156 4 5 0.50 3.54 E 03 Molybdenum cofactor biosynthesis swp_5032, swp_5036, swp_4980, swp_4983, swp_0101 5 5 0.50 7.98 E 03 Propanoate metabolism swp_3440, swp_4179, swp_3386, swp_0423, swp_1949 6 5...”
ESA_02621 hypothetical protein from Enterobacter sakazakii ATCC BAA-894
28% identity, 89% coverage
CA54_02340 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase from Symmachiella macrocystis
29% identity, 92% coverage
Z0125 pyruvate dehydrogenase (dihydrolipoyltransacetylase component) from Escherichia coli O157:H7 EDL933
ECs0119 pyruvate dehydrogenase dihydrolipoyltransacetylase component from Escherichia coli O157:H7 str. Sakai
29% identity, 58% coverage
- Disruption of rcsB by a duplicated sequence in a curli-producing Escherichia coli O157:H7 results in differential gene expression in relation to biofilm formation, stress responses and metabolism
Sharma, BMC microbiology 2017 - “...Z3959 Succinate-semialdehyde dehydrogenase I 4.12 5.0E-03 gabT Z3960 4-aminobutyrate aminotransferase 5.66 5.0E-03 Carbohydrate/Energy metabolism aceF Z0125 Dihydrolipoamide acetyltransferase 2.00 0.02 yaeM Z0184 1-deoxy-D-xylulose 5-phosphate reductoisomerase 1.33 0.03 malZ Z0501 Maltodextrin glucosidase 2.13 0.041 ybdR Z0752 Zn-dependent oxidoreductase 2.70 3.0E-04 sdhA Z0877 Succinate dehydrogenase flavoprotein subunit 3.11...”
- Analysis of promoter targets for Escherichia coli transcription elongation factor GreA in vivo and in vitro
Stepanova, Journal of bacteriology 2007 - “...subunit protein S20 aceE aceF b0114 Z0125 4.9 4.9 Pyruvate dehydrogenase (decarboxylase component) (EDL933) pyruvate dehydrogenase (dihydrolipoyltransacetylase...”
- Global transcriptional response of Escherichia coli O157:H7 to growth transitions in glucose minimal medium
Bergholz, BMC microbiology 2007 - “...guaC -2.45 1 ECs0656 citD 2.79 2 ECs0118 aceE -3.27 1 ECs0864 ybhL 2.61 2 ECs0119 aceF -2.55 1 ECs0866 ybhN 2.27 2 ECs0123 yacL 3.17 2 ECs0881 ybiI 3.35 2 ECs0128 gcd 2.69 2 ECs0896 ybiS -2.07 1 ECs0168 dapD -3.16 1 ECs0915 yliG -2.77...”
- Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits
Dessimoz, Nucleic acids research 2006 - “...BU303), E.coli K12 (COG identifier corresponds to the gene name: aceF, sucB), E.coli H7 (1: ECs0119, 3: ECs0752), Haemophilus influenzae (1: HI1232, 3: HI1661), Neisseria meningitidis (1: NMB1342, 3: NMB0956), Pasteurella multocida (1: PM0894, 3: PM0278), Pseudomonas aeruginosa (1: PA5016, 2: PA2249, 3: PA1586), Rhizobium loti...”
KPN_00119 dihydrolipoamide acetyltransferase from Klebsiella pneumoniae subsp. pneumoniae MGH 78578
28% identity, 58% coverage
MCA1953 2-oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase from Methylococcus capsulatus str. Bath
29% identity, 96% coverage
P53395 Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitochondrial from Mus musculus
29% identity, 76% coverage
- Neurodegenerative Disorder Risk in Krabbe Disease Carriers
Vantaggiato, International journal of molecular sciences 2022 - “...# 0.73 NS 1.45 11 Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitochondrial P53395 BCKD-E2 127 3.4 10 9 12/18 17 0.32 # 1.69 NS 0.54 NS 12 2,3-cyclic-nucleotide 3-phosphodiesterase P16330 CNP1 210 1.7 10 17 16/25 41 2.47 # 0.47 # 1.14 NS...”
- iTRAQ‑based proteomic analysis of endotoxin tolerance induced by lipopolysaccharide
Zhang, Molecular medicine reports 2019 - “...1.253 32 Q8BSY0 Asph Aspartyl/asparaginyl -hydroxylase 1.249 33 Q9QUJ7 Acsl4 Long-chain-fatty-acid-CoA ligase 4 1.247 34 P53395 Dbt Lipoamide acyltransferase component of branched-chain -keto acid 1.237 dehydrogenase complex, mitochondrial 35 P61620 Sec61a1 Protein transport protein Sec61 subunit isoform 1 1.221 36 Q6NZF1 Zc3h11a Zinc finger CCCH domain-containing...”
- Subproteomic profiling of sarcolemma from dystrophic mdx-4cv skeletal muscle.
Murphy, Data in brief 2018 - “...Pdha1 Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1 1 70.6 1.89E-03 2.5 P53395 Dbt Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitochondrial 1 1 69.0 3.34E-04 2.4 Q64105 Spr Sepiapterin reductase 1 1 51.0 1.18E-03 2.4 P10493 Nid1 Nidogen-1 1 1...”
- Native KCC2 interactome reveals PACSIN1 as a critical regulator of synaptic inhibition
Mahadevan, eLife 2017 - “...X X X ADGRL2 Q8JZZ7 1.5 0.89 X BSN O88737 1.5 0.72 X X DBT P53395 1.5 0.86 X X X GTF2I Q9ESZ8 1.5 0.89 X HELB Q6NVF4 1.5 0.89 X HK1 P17710 1.5 0.89 X X HMCN2 A2AJ76 1.5 0.89 X LGI3 Q8K406 1.5 0.89...”
- Functional proteomic analysis of corticosteroid pharmacodynamics in rat liver: Relationship to hepatic stress, signaling, energy regulation, and drug metabolism.
Ayyar, Journal of proteomics 2017 - “...UP P18298 Mat2a S-adenosylmethionine synthase isoform type-2 Formation of S-adenosylmethionine from methionine and ATP UP P53395 Dbt Dihydrolipoamide branched chain transacylase Mitochondrial breakdown of the branched-chain amino acids isoleucine, leucine, and valine UP Table 2B MPL-regulated proteins related to carbohydrate metabolism. UProt_ID Gene Name Protein Name...”
- Delineation of Molecular Pathways Involved in Cardiomyopathies Caused by Troponin T Mutations.
Gilda, Molecular & cellular proteomics : MCP 2016 - Simultaneous Pathoproteomic Evaluation of the Dystrophin-Glycoprotein Complex and Secondary Changes in the mdx-4cv Mouse Model of Duchenne Muscular Dystrophy
Murphy, Biology 2015 - “...P09542 Myosin light chain 3 7 435.9 0.021966 4.68 P82348 Gamma-sarcoglycan 3 139.3 0.013191 4.08 P53395 Lipoamide acyltransferase of branched alpha-keto acid dehydrogenase 12 531.9 3.36E-05 3.97 P68134 Actin, alpha skeletal muscle 2 67.6 0.019843 3.85 Q9WUB3 Glycogen phosphorylase, muscle form 4 58.3 0.006224 3.85 P70695...”
- CypD(-/-) hearts have altered levels of proteins involved in Krebs cycle, branch chain amino acid degradation and pyruvate metabolism
Menazza, Journal of molecular and cellular cardiology 2013 - “...20 (Q791V5) Mitochondrial carrier homolog 2 MTCH2_MOUSE 33.00 22 0.984 0.006 0.797 0.033 0.001 19 (P53395) Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitochondrial ODB2_MOUSE 6.43 3 0.877 0.053 0.718 0.018 0.031 18 (Q9CQA3) Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial DHSB_MOUSE 51.06 77 1.079...”
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AceF / b0115 pyruvate dehydrogenase, E2 subunit (EC 2.3.1.12) from Escherichia coli K-12 substr. MG1655 (see 48 papers)
aceF / P06959 pyruvate dehydrogenase E2 subunit (EC 2.3.1.12) from Escherichia coli (strain K12) (see 48 papers)
P06959 pyruvate dehydrogenase system (EC 1.2.1.104); prephenate dehydrogenase (EC 1.3.1.12); dihydrolipoyllysine-residue acetyltransferase (EC 2.3.1.12) from Escherichia coli (see 6 papers)
AceF-lipoate / ECOCYC|ACEF-LIPOATE pyruvate dehydrogenase, dihydrolipoyltransacetylase component E2 from Escherichia coli K12 (see 2 papers)
aceF / PDB|1QJO dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex; EC 2.3.1.12 from Escherichia coli K12 (see 23 papers)
b0115 dihydrolipoamide acetyltransferase from Escherichia coli str. K-12 substr. MG1655
NP_414657 pyruvate dehydrogenase, E2 subunit from Escherichia coli str. K-12 substr. MG1655
29% identity, 58% coverage
- Medium-Chain-Length Fatty Acid Catabolism in Cupriavidus necator H16: Transcriptome Sequencing Reveals Differences from Long-Chain-Length Fatty Acid β-Oxidation and Involvement of Several Homologous Genes
Strittmatter, Applied and environmental microbiology 2023 (secret) - Functional genomics analysis of free fatty acid production under continuous phosphate limiting conditions
Youngquist, Journal of industrial microbiology & biotechnology 2017 - “...efflux system Acetyl-CoA Flux b0114 aceE 1.2 4.210 2 pyruvate dehydrogenase, decarboxylase component E1, thiamin-binding b0115 aceF 1.2 5.510 4 pyruvate dehydrogenase, dihydrolipoyltransacetylase component E2 b4015 aceA 2.0 5.510 4 isocitrate lyase b4014 aceB 2.4 5.910 5 malate synthase A Respiration b0430 cyoC 1.8 7.810 4...”
- The Streptomyces coelicolor lipoate-protein ligase is a circularly permuted version of the Escherichia coli enzyme composed of discrete interacting domains
Cao, The Journal of biological chemistry 2015 - “...E. coli pyruvate dehydrogenase E2 component (locus_tag b0115) and the S. coelicolor branched-chain 2-oxoacid dehydrogenase E2 component (KEGG entry SCO3815)....”
- More than just a metabolic regulator--elucidation and validation of new targets of PdhR in Escherichia coli
Göhler, BMC systems biology 2011 - “...b1109 ndh * 2.913 7.803 b0091 murC $ -0.030 5.958 b0114 aceE * 2.250 5.866 b0115 aceF * 2.008 5.883 b4467 glcF $ 2.181 0.275 b0114 aceE * 2.250 5.866 b0115 aceF * 2.008 5.883 b0088 murD $ -0.013 5.623 b2579 yfiD * 1.973 0.805 b0090...”
- Reconstitution of the Mycobacterium tuberculosis pupylation pathway in Escherichia coli
Cerda-Maira, EMBO reports 2011 (secret) - The HU regulon is composed of genes responding to anaerobiosis, acid stress, high osmolarity and SOS induction
Oberto, PloS one 2009 - “...1 1.37 1.51 0.35 1 0.78 0.75 1.02 FR, FRec pyruvate dehydrogenase (decarboxylase component) aceF b0115 pdhR-aceEF-lpd 1 0.46 1.35 0.65 1 1.51 1.58 0.41 1 0.74 0.73 1.04 FR, FRec pyruvate dehydrogenase (dihydrolipoyltransacetylase component) ybcW b0559 ybcW 1 0.27 0.97 1.46 1 0.89 1.94 0.29...”
- Protein disorder is positively correlated with gene expression in Escherichia coli
Paliy, Journal of proteome research 2008 - “...segment. NIH-PA Author Manuscript AceF (b0115) - dihydrolipoyl acetyltransferase component of pyruvate dehydrogenase--The pyruvate dehydrogenase (PDH)...”
- “...to the disordered regions discussed in the text. A) AceB (b0115); B) HlpA (b0178); C) SucB (b0727); D) Pal (b0741); E) InfA (b0884); F) AcpP (b1094); G) HNS...”
- Dimerization of a 5-kDa domain defines the architecture of the 5-MDa gammaproteobacterial pyruvate dehydrogenase complex.
Meinhold, Science advances 2024 - GeneRIF: Dimerization of a 5-kDa domain defines the architecture of the 5-MDa gammaproteobacterial pyruvate dehydrogenase complex.
- Structure and function of the catalytic domain of the dihydrolipoyl acetyltransferase component in Escherichia coli pyruvate dehydrogenase complex.
Wang, The Journal of biological chemistry 2014 - GeneRIF: The inclusion of each additional domain of E2p strengthened the interaction with E1p, and the interaction was strongest with intact E2p.
- The role of loop and beta-turn residues as structural and functional determinants for the lipoyl domain from the Escherichia coli 2-oxoglutarate dehydrogenase complex.
Jones, The Biochemical journal 2008 (PubMed)- GeneRIF: The surface loop of E1o is important to the structural integrity of the protein and together with Thr42 plays an important role in specifying the interaction of the lipoyl domain with its partner E1o in the E. coli 2OGDH complex.
- A dynamic loop at the active center of the Escherichia coli pyruvate dehydrogenase complex E1 component modulates substrate utilization and chemical communication with the E2 component.
Kale, The Journal of biological chemistry 2007 (PubMed)- GeneRIF: the dynamic loop at the active center of the Escherichia coli pyruvate dehydrogenase complex E1 component modulates substrate utilization and chemical communication with the E2 component
- Amino-terminal residues 1-45 of the Escherichia coli pyruvate dehydrogenase complex E1 subunit interact with the E2 subunit and are required for activity of the complex but not for reductive acetylation of the E2 subunit.
Park, Biochemistry 2004 (PubMed)- GeneRIF: Pyruvate dehydrogenase complex E2 (PDHc-E2)subunit protects N-terminal residues 1-55 of PDHc-E1 subunit selectively from trypsin digestion.
- Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12.
Link, Electrophoresis 1997 (PubMed)- GeneRIF: N-terminus verified by Edman degradation on mature peptide
- Identification of novel microRNAs: Biomarkers for pathogenesis of hepatocellular carcinoma in mice model.
Priya, Biochemistry and biophysics reports 2025 - “...(GO:0097136), Wnt Signalosome (GO:1990909), and Pathways like Gonadotropin-releasing hormone receptor pathway (P06664), CCKR signalling map (P06959), Apoptosis signalling pathway (P00006), Inflammation mediated by chemokine and cytokine signalling pathway (P00031), Wnt signalling pathway (P00057), shows indirectly the functional role of these miRNAs targeting these particular genes. The...”
- “...Structure (GO:0005622), Neuron Projection (GO:0043005), and Pathways like Cadherin Signaling Pathway (P00012), CCKR signalling map (P06959), Wnt Signaling Pathway (P00057), Angiogenesis (P00005). 4 Discussion The functional significance of the gene targets was examined. Gene ontology and pathway analyses aid in comprehending the significance of these miRNAs....”
- Pectolinarigenin regulates the tumor-associated proteins in AGS-xenograft BALB/c nude mice.
Lee, Molecular biology reports 2024 - “...pathway P00031 8 8.14E-15 ARPC2, ARPC4, ACTB, RHOA, MAPK1, MYH6, ARPC3, CAMK2D CCKR signaling map P06959 7 2.43E-10 ELAVL1, RHOA, MAPK1, GNB1, RPS6, EIF4E, YES1 Cadherin signaling pathway P00012 4 1.64E-08 ACTB, CSNK2B, YES1, CSNK2A2 Cell cycle P00013 3 8.92E-08 PSMD3, PSMD13, PSMD7 Wnt signaling pathway...”
- “...PI3K/AKT/mTOR pathway [ 23 , 24 ]. In PANTHER pathway analysis, the CCKR pathway map (P06959) included seven proteins: ELAVL1, RHOA, MAPK1, GNB1, RPS6, EIF4E, and YES1. CCKR is a cholecystokinin receptor that has been linked to gastrin [ 25 ], a circulating hormone that maintains...”
- Potential Role of Protein Kinase FAM20C on the Brain in Raine Syndrome, an In Silico Analysis.
Palma-Lara, International journal of molecular sciences 2023 - “...coagulation (P00011) 5 1.90% 5.80% 23 B-cell activation (P00010) 2 0.70% 2.30% 24 CCKR-signaling map (P06959) 5 1.90% 5.80% 25 Salvage pyrimidine deoxyribonucleotides (P02774) 1 0.40% 1.20% 26 p53 pathway (P00059) 1 0.40% 1.20% 27 Wnt-signaling pathway (P00057) 3 1.10% 3.50% 28 VEGF-signaling pathway (P00056) 2...”
- A zebrafish model of growth hormone insensitivity syndrome with immune dysregulation 1 (GHISID1).
Heidary, Cellular and molecular life sciences : CMLS 2023 - “...1 Downregulated pathways in Stat5.1 LOF embryos Gonadotrophin-releasing hormone receptor pathway (P06664) CCKR signalling pathway (P06959) PDGF signalling pathway (P00047) Huntington's disease (P00029) Angiogenesis (P00005) Apoptosis (P00006) Insulin/IGF pathway-protein kinase B signalling cascade (P00033) Inflammation mediated by chemokine and cytokine signalling pathway (P00031) Ras Pathway (P04393)...”
- Mass spectrometry-based proteomic strategy for ecchymotic skin examination in forensic pathology.
Toma, Scientific reports 2023 - “...PAK1 Angiogenesis (P00005) PTPN11, CTNNB1, PAK1 Alzheimer disease-presenilin pathway (P00004) CTNNB1, MLLT4 CCKR signaling map (P06959) PTPN11, CTNNB1, PAK1 Proteins involved in cytoskeletal regulation by Rho GTPase, angiogenesis and CCKR signalling were found only in wounds that predated death by at least 1h, suggesting that their...”
- The combined impact of testosterone and Western-style diet on endometriosis severity and progression in rhesus macaques†.
Bishop, Biology of reproduction 2023 - The Expression of Signaling Genes in Breast Cancer Cells
Rzymowska, Biology 2022 - “...pathway. Alzheimer disease-presenilin pathway (P00004) -WNT3, CTNNB1, WNT10B, Angiogenesis (P00005) -WNT10B, CTNNB1, CCKR signaling map (P06959) -CTNNB1, RGS2, Cadherin signaling pathway (P00012) -WNT10B, CTNNB1, WNT3, Gonadotropin-releasing hormone receptor pathway (P06664) -CTNNB1, Heterotrimeric G-protein signaling pathway-Gi alpha and Gs alpha mediated pathway (P00026) -RGS16, RGS2, Heterotrimeric G-protein...”
- Toxocara canis- and Toxocara cati-Induced Neurotoxocarosis Is Associated with Comprehensive Brain Transcriptomic Alterations.
Waindok, Microorganisms 2022 - “...signaling pathway (P00036) 13 3.44 0.005 Ras Pathway (P04393) 10 3.33 0.030 CCKR signaling map (P06959) 21 3.08 0.001 Inflammation mediated by chemokine and cytokine signaling pathway (P00031) 23 2.08 0.034 Unclassified 790 0.93 <0.001 Cerebellum Apoptosis signaling pathway (P00006) 25 2.54 0.006 Inflammation mediated by...”
- “...signaling pathway (P00006), Axon guidance mediated by Slit/Robo (P00008), B-cell activation (P00010), CCKR signaling map (P06959), FAS signaling pathway (P00020), Inflammation mediated by chemokine and cytokine signaling pathway (P00031), Interleukin signaling pathway (P00036), JAK/STAT signaling pathway (P00038), Ras Pathway (P04393), T-cell activation (P00053) down 434 Cholesterol...”
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B488_RS03580 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase from Liberibacter crescens BT-1
27% identity, 93% coverage
- Osmotic stress induces long-term biofilm survival in Liberibacter crescens
Padgett-Pagliai, BMC microbiology 2022 - “...dihydrolipoamide dehydrogenase, 2-oxoglutarate dehydrogenase, two succinyl-CoA synthetases and malate dehydrogenase ( B488_RS03575 , ldpC ; B488_RS03580 , sucA ; B488_RS03590 , sucD ; B488_RS03595, sucC ; and B488_RS03600 , mdh , respectively) were also down-regulated. Of note, some of the genes from the last putative operons...”
LOC116207451 lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitochondrial from Punica granatum
27% identity, 72% coverage
- Two major chromosome evolution events with unrivaled conserved gene content in pomegranate
Akparov, Frontiers in plant science 2023 - “...LOC116206080 16,562,644 16,563,970 secoisolariciresinol dehydrogenase-like Chr5 11,360,872 to 11,495,723 LOC116207452 11,374,356 11,377,493 epoxide hydrolase A-like LOC116207451 11,383,152 11,386,479 lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex LOC116208343 11,442,930 11,449,322 peroxisomal fatty acid beta-oxidation multifunctional protein MFP2 LOC116208154 11,485,969 11,487,326 probable 3-ketoacyl-CoA synthase 21 Chr6 5,174,766...”
VC2413 pyruvate dehydrogenase, E2 component, dihydrolipoamide acetyltransferase from Vibrio cholerae O1 biovar eltor str. N16961
29% identity, 57% coverage
- Transient Glycolytic Complexation of Arsenate Enhances Resistance in the Enteropathogen Vibrio cholerae
Bueno, mBio 2022 - “...III oxidase; Icd, VC1141 isocitrate dehydrogenase; FrdA, VC2656 fumarate reductase; IspH, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; AceF, VC2413 pyruvate dehydrogenase, E2 component; UbiE, VC0083 ubiquinone/menaquinone biosynthesis methyltransferase. (E) Representative dot plots from V. cholerae WT and var mutant cells stained with DiOC2 following growth in the presence of...”
- Aerobic Metabolism in Vibrio cholerae Is Required for Population Expansion during Infection
Van, mBio 2020 - “...of the pyruvate dehydrogenase (PDH) complex were identified in our screen, aceE (VC2414) and aceF (VC2413) (Table S1 at https://doi.org/10.5281/zenodo.3966283 ). The third component of the PDH complex, lpdA (VC2414), was also defective for growth in our screen; however, growth of this transposon mutant was also...”
- A novel phase variant of the cholera pathogen shows stress-adaptive cryptic transcriptomic signatures
Lambert, BMC genomics 2016 - “...the smooth derivative compared to rugose (Additional file 14 : Table S10). Moreover, two genes, VC2413 ( aceF ) and VC2414 ( aceE ), encoding components of the pyruvate dehydrogenase complex that converts pyruvate to acetyl-CoA, were also up-regulated approximately 3-fold in the N16961SD variants (Additional...”
- High-throughput sequencing reveals suppressors of Vibrio cholerae rpoE mutations: one fewer porin is enough
Davis, Nucleic acids research 2009 - “...followed by patching to plates containing kanamycin, led to similar conclusions.) Point mutations in vca0199, vc2413 and the ompU ( vc0633 ) promoter and 5UTR were introduced using plasmids pBD2038, pBD2036, pBD2049 and pBD2088, respectively. Deletions in ompU and ompT were introduced using the previously described...”
- “...process we verified the presence of five candidate suppressor mutations, located in the vca0199 and vc2413 -coding regions (one each, in strains BD1965 and BD1963 respectively) and in the intergenic region between vc0633 and vc0634 (three distinct mutations, in strains BD1962, BD1956 and BD1987). The effects...”
- Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits
Dessimoz, Nucleic acids research 2006 - “...Rickettsia conorii (3: RC0226, 4: RC0764), Rickettsia prowazekii (3: RP179, 4: RP530), Vibrio cholerae (1: VC2413, 3: VC2086), Y.pestis (1: YPO3418, 3: YPO1114). Figure 5 Unrooted phylogenetic consensus tree for COG0513, constructed from a Bayesian analysis. Posterior probabilities are drawn to the right of the nodes...”
- Transcriptional profiling of Vibrio cholerae recovered directly from patient specimens during early and late stages of human infection
Larocque, Infection and immunity 2005 - “...9.7 106 5.0 104 1.1 105 Energy metabolism VC2413 VC2447 VCA0897 Pyruvate dehydrogenase, E2 component, dihydrolipoamide Enolase DevB protein 3.24 3.05 2.04 3.5...”
- Sequence analysis of TnphoA insertion sites in Vibrio cholerae mutants defective in rugose polysaccharide production
Ali, Infection and immunity 2000 - “...lpd and odp genes (ORFs VC2412 and VC2413), which encode the dihydrolipoamide dehydrogenase and acetyltransferase enzymes, respectively. In Downloaded from...”
Q7TND9 Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex from Mus musculus
29% identity, 76% coverage
YPK_2967 2-oxoglutarate dehydrogenase, E2 subunit, dihydrolipoamide succinyltransferase from Yersinia pseudotuberculosis YPIII
YPO1114 dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex from Yersinia pestis CO92
y3066 2-oxoglutarate dehydrogenase (dihydrolipoyltranssuccinase E2 component) from Yersinia pestis KIM
YPTB1148 dihydrolipoamide succinyltransferase component of 2-oxoglutar... from Yersinia pseudotuberculosis IP 32953
27% identity, 90% coverage
- Genome-Scale Mapping Reveals Complex Regulatory Activities of RpoN in Yersinia pseudotuberculosis
Mahmud, mSystems 2020 - “...YPK_2901 YPK_2902 7, 24, 44, 146 IrGS29 3266581 3.4 NA NA CTGGAACGTTATTTGCAG 10.4 38,32,54,24,70 YPK_2968 YPK_2967 1, 13, 20, 148 IrGS30 3276693 3.3 NA 3.1 TTGGCATCAAAGTTGCCG + 10.3 54,38,24 YPK_2976 YPK_2977 67, 147 IrGS31 3386998 4.7 NA 2.9 TCGGCCCGTTTATTGCTC 10.4 54,28,32,38,28 YPK_3080 YPK_3079 44, 86, 91...”
- The cyclic AMP receptor protein, CRP, is required for both virulence and expression of the minimal CRP regulon in Yersinia pestis biovar microtus
Zhan, Infection and immunity 2008 - “...2 sdhB 3.21 YPO1112 2 sucA 3.04 YPO1113 2 sucB 3.30 YPO1114 2 sucC 3.17 YPO1115 2 sucD 3.12 YPO1116 2 cydA 3.24 cydB 2.03 gntT 5.88 A AAACTGTGATTTGACTC ACTCTG...”
- Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
Rosso, BMC microbiology 2008 - “...0.001) YPTB1150 YPO1116 sucD putative succinyl-CoA synthetase alpha chain 0.525 (< 0.001) 0.236 (0.001) YPTB1148 YPO1114 sucB putative dihydrolipoamide succinyltransferase component 0.610 (0.014) 0.267 (0.003) YPTB1147 YPO1113 sucA putative 2-oxoglutarate dehydrogenase E1 component 0.516 (0.007) 0.193 (< 0.001) YPTB0716 YPO3415 acnB putative aconitate hydratase 2 0.510...”
- “...iron-sulfur protein 0.592 (0.003) YPTB1147 (sucA) YPO1113 2-oxoglutarate dehydrogenase E1 component 0.515 (0.006) YPTB1148 (sucB) YPO1114 dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydro 0.61 (0.013) 0.671 (0.04) YPTB1149 (sucC) YPO1115 succinyl-CoA synthetase beta chain 0.419 (< 0.001) YPTB1150 (sucD) YPO1116 succinyl-CoA synthetase alpha chain 0.524 (< 0.001)...”
- Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits
Dessimoz, Nucleic acids research 2006 - “...prowazekii (3: RP179, 4: RP530), Vibrio cholerae (1: VC2413, 3: VC2086), Y.pestis (1: YPO3418, 3: YPO1114). Figure 5 Unrooted phylogenetic consensus tree for COG0513, constructed from a Bayesian analysis. Posterior probabilities are drawn to the right of the nodes and clan-supporting bootstrap values are below the...”
- Proteomic analysis of iron acquisition, metabolic and regulatory responses of Yersinia pestis to iron starvation
Pieper, BMC microbiology 2010 - “...ybtT yersiniabactin thioesterase U Fur 123 34389 5.88 0.10 - > 20 N.D. 12.08 111 y3066 sucB 2-oxoglutarate dehydrogenase (dihydrolipoyltranssuccinase E2 component) CY 789 58844 5.38 0.29 0.76 0.38 0.0468 0.38 a) spot number as denoted in Figure 4; b) protein accession number and locus tag...”
- IscR is essential for yersinia pseudotuberculosis type III secretion and virulence
Miller, PLoS pathogens 2014 - “...deacetylase nagA 4.1 YPTB1119 putative glucosamine-6-phosphate isomerase nagB 5.9 YPTB1120 N-acetylglucosamine-specific IIABC component nagE 5.2 YPTB1148 dihydrolipoamide succinyltransferase sucB 2.1 YPTB1149 succinyl-CoA synthetase beta chain sucC 3.0 YPTB1150 succinyl-CoA synthetase alpha chain sucD 3.1 YPTB1358 glutaredoxin 1 grxA 2.3 YPTB1418 integration host factor beta-subunit ihfB 2.7...”
- Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
Rosso, BMC microbiology 2008 - “...(< 0.001) YPTB1150 YPO1116 sucD putative succinyl-CoA synthetase alpha chain 0.525 (< 0.001) 0.236 (0.001) YPTB1148 YPO1114 sucB putative dihydrolipoamide succinyltransferase component 0.610 (0.014) 0.267 (0.003) YPTB1147 YPO1113 sucA putative 2-oxoglutarate dehydrogenase E1 component 0.516 (0.007) 0.193 (< 0.001) YPTB0716 YPO3415 acnB putative aconitate hydratase 2...”
- “...succinate dehydrogenase iron-sulfur protein 0.592 (0.003) YPTB1147 (sucA) YPO1113 2-oxoglutarate dehydrogenase E1 component 0.515 (0.006) YPTB1148 (sucB) YPO1114 dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydro 0.61 (0.013) 0.671 (0.04) YPTB1149 (sucC) YPO1115 succinyl-CoA synthetase beta chain 0.419 (< 0.001) YPTB1150 (sucD) YPO1116 succinyl-CoA synthetase alpha chain 0.524...”
G4234_16835 pyruvate dehydrogenase complex dihydrolipoyllysine-residue acetyltransferase from Serratia marcescens
28% identity, 58% coverage
- Whole genome sequence of Serratia marcescens 39_H1, a potential hydrolytic and acidogenic strain
Obi, Biotechnology reports (Amsterdam, Netherlands) 2020 - “...including CspE (G4234_01545), CspC (G4234_10320), CspD (G4234_04250), hupB (G4234_01000), gyrA (G4234_13035), aceE (G4234_16840) and aceF (G4234_16835) indicating its potential to be used as an inoculum to augment psychrophilic AD in low-cost, non-heated rural anaerobic digesters [ [40] , [41] , [42] ]. Serratia marcescens strain 39_H1...”
DR0083, DR_0083 2-oxoglutarate dehydrogenase, dihydrolipoamide succinyltransferase E2 component from Deinococcus radiodurans R1
28% identity, 88% coverage
- Proteometabolomic response of Deinococcus radiodurans exposed to UVC and vacuum conditions: Initial studies prior to the Tanpopo space mission
Ott, PloS one 2017 - “...are citrate synthase (gltA), aconitate hydratase (acn), isocitrate dehydrogenase (DR_1540), 2-oxoglutarate dehydrogenase (sucA), dihydrolipoamide succinyltransferase (DR_0083), succinate-CoA ligase (sucC), succinyl-CoA synthetase (sdhB), fumarate hydratase (fumC) and malate dehydrogenase (mdh). 10.1371/journal.pone.0189381.g007 Fig 7 Main components of the TCA cycle in Deinococcus radiodurans connected to related pathways under...”
- Oxidative stress resistance in Deinococcus radiodurans
Slade, Microbiology and molecular biology reviews : MMBR 2011 - “...Isocitrate lyase (AceA) DR0757 DR1720 DR1540 DR0287 DR0083 DR1247 DR1248 DR0700 DR0701 DR0698 DR0702 DR0697 DR0699 DR0695 DR0696 Sulfur metabolism...”
- Predicted highly expressed and putative alien genes of Deinococcus radiodurans and implications for resistance to ionizing radiation damage
Karlin, Proceedings of the National Academy of Sciences of the United States of America 2001 - “...1.05 DR1720 DR0828 DR1540 DR0325 DR1247 DR0287 DR2627 DR1248 DR1674 DR0757 DR0083 905 463 430 329 385 955 812 300 332 410 416 2.56 2.19 2.07 1.80 1.71 1.70 1.69...”
C7W88_RS10070 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase from Novosphingobium sp. THN1
30% identity, 89% coverage
Mfl041 dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex (E2) from Mesoplasma florum L1
26% identity, 87% coverage
- Genome-scale metabolic modeling reveals key features of a minimal gene set
Lachance, Molecular systems biology 2021 - “...the protein expression levels compared with genes of the pyruvate dehydrogenase complex (PDH: Mfl039, Mfl040, Mfl041, and Mfl042). We thus used an 8:1 initial ratio (lactate:acetate) for further phenotypic phase plane analysis (Materials and Methods). For lactate production, this analysis revealed a positive linear relationship between...”
YP_856459 2-oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase from Aeromonas hydrophila subsp. hydrophila ATCC 7966
27% identity, 93% coverage
- Directed culturing of microorganisms using metatranscriptomics
Bomar, mBio 2011 - “...YP_856906 1.37 10 180 Glycolysis 138 Fructose-1,6 bisphosphatase YP_001141703 0 Gluconeogenesis 350 2-Oxoglutarate dehydrogenase E2 YP_856459 0 TCA cycle 282 CcoN YP_856818 0 Aerobic respiration 301 Ribosomal protein S19 YP_854843 7.78 10 47 Translation 6,926 Ribosome modulation factor YP_856804 4.76 10 28 Stationary phase 40,628 RpoD...”
VpaChn25_0843, WU75_19790 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase from Vibrio parahaemolyticus
27% identity, 91% coverage
- Identification of Antibacterial Components and Modes in the Methanol-Phase Extract from a Herbal Plant Potentilla kleiniana Wight et Arn
Tang, Foods (Basel, Switzerland) 2023 - “...1 from P. kleiniana Wight et Arn. For instance, the DEGs ( sucABCD, WU75_19785 and WU75_19790 , WU75_19795, and WU75_19800 ), encoding a 2-oxoglutarate dehydrogenase, a dihydrolipoamide succinyltransferase, and succinyl-CoA synthetase subunits alpha and beta, respectively, were highly inhibited (0.146-fold, 0.133-fold, 0.134-fold, and 0.16-fold) ( p...”
- “...Change Gene Description Citrate cycle WU75_19785 sucA 0.146 2-oxoglutarate dehydrogenase WU75_07425 pckA 0.465 Phosphoenolpyruvate carboxykinase WU75_19790 sucB 0.133 Dihydrolipoamide succinyltransferase WU75_11550 acnB 0.143 Bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase WU75_19795 sucC 0.134 Succinyl-CoA synthetase subunit beta WU75_19800 sucD 0.16 Succinyl-CoA synthetase subunit alpha WU75_19770 sdhD 0.199 Succinate...”
- Genomic and transcriptomic analyses reveal distinct biological functions for cold shock proteins (VpaCspA and VpaCspD) in Vibrio parahaemolyticus CHN25 during low-temperature survival
Zhu, BMC genomics 2017 - “...large membrane subunit VpaChn25_0840 0.402 Succinate dehydrogenase flavoprotein subunit VpaChn25_0841 0.3554 Succinate dehydrogenase iron-sulfur subunit VpaChn25_0843 0.3915 Dihydrolipoamide succinyltransferase VpaChn25_0844 0.3535 Succinyl-CoA synthetase subunit beta VpaChn25_0845 0.3009 Succinyl-CoA synthetase subunit alpha VpaChn25_1035 0.4921 Isocitrate dehydrogenase VpaChn25_2762 0.478 Fumarate reductase flavoprotein subunit VpaChn25_2763 0.4836 Fumarate reductase iron-sulfur...”
LT988_19205 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase from Thiocapsa bogorovii
27% identity, 85% coverage
- The Complete Genome of a Novel Typical Species Thiocapsa bogorovii and Analysis of Its Central Metabolic Pathways
Petushkova, Microorganisms 2024 - “...[EC:1.2.4.2] LT988_19210 2-oxoglutarate dehydrogenase E1 component 8 K00658 2-oxoglutarate dehydrogenase E2 component (dihydrolipoamide succinyltransferase) [EC:2.3.1.61] LT988_19205 odhB ; 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase 9 K00382 dihydrolipoyl dehydrogenase [EC:1.8.1.4] LT988_13640 dihydrolipoyl dehydrogenase 9 K00382 dihydrolipoyl dehydrogenase [EC:1.8.1.4] LT988_22720 lpdA ; dihydrolipoyl dehydrogenase 9 K00382 dihydrolipoyl dehydrogenase [EC:1.8.1.4]...”
ABO_1495 dihydrolipoamide succinyltransferase from Alcanivorax borkumensis SK2
27% identity, 87% coverage
plu1431 Dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex (E2) from Photorhabdus luminescens subsp. laumondii TTO1
30% identity, 89% coverage
- Photorhabdus luminescens genes induced upon insect infection
Münch, BMC genomics 2008 - “...(histidase) sucABCD 1.5-fold ( 0.4) sucA ( plu1430 ) -oxoglutarate dehydrogenase E1 component sucB ( plu1431 ) dihydrolipoamid succinyltransferase component of -oxoglutarate dehydrogenase complex (E2) sucC ( plu1432 ) succinyl-CoA synthetase chain sucD ( plu1433 ) succinyl-CoA synthetase -chain plu1864 similarities to phosphoenolpyruvat phosphomutase 1.0-fold (...”
SCLAV_2979 dihydrolipoamide acetyltransferase family protein from Streptomyces clavuligerus
35% identity, 50% coverage
Lreu_0633 dihydrolipoyllysine-residue succinyltransferase from Lactobacillus reuteri DSM 20016
A5VJ74 Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex from Limosilactobacillus reuteri (strain DSM 20016)
Lreu_0633 2-oxo acid dehydrogenase subunit E2 from Limosilactobacillus reuteri subsp. reuteri
26% identity, 82% coverage
SO2341 alpha keto acid dehydrogenase complex, E2 component from Shewanella oneidensis MR-1
30% identity, 69% coverage
PVX_122850 Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase from Plasmodium vivax
26% identity, 88% coverage
- Clinical proteomics of the neglected human malarial parasite Plasmodium vivax
Acharya, PloS one 2011 - “...mentioned above, which may relate to different physiological states [5] , [6] . These are PVX_122850 (Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex, putative), PVX_099275 (hypothetical protein), PVX_080555 (hypothetical protein), PVX_086990 (vacuolar ATP synthase subunit E), PVX_095195 (ATP-dependent RNA helicase, putative), PVX_099095 (elongation factor 1B, putative),...”
Abu_1473 dihydrolipoamide acetyltransferase from Arcobacter butzleri RM4018
26% identity, 66% coverage
Rta_10500 dihydrolipoamide acetyltransferase family protein from Ramlibacter tataouinensis TTB310
31% identity, 84% coverage
HMPREF1120_04123 2-oxoisovalerate dehydrogenase E2 component (dihydrolipoyl transacylase) from Exophiala dermatitidis NIH/UT8656
27% identity, 75% coverage
ESA_03222 hypothetical protein from Enterobacter sakazakii ATCC BAA-894
28% identity, 58% coverage
BPSL2300 dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex from Burkholderia pseudomallei K96243
28% identity, 65% coverage
- Transcriptional landscape of Burkholderia pseudomallei cultured under environmental and clinical conditions
Kong, Microbial genomics 2023 - “...phosphorylation ( Fig. 3a ). Among the nine carbohydrate and lipid metabolism genes, bpsl2299 , bpsl2300 , bpss0804 and bpss1918 encode for proteins involved in glycolysis or gluconeogenesis, implying that the bacteria undergo active cellular metabolic processes when present under infection conditions by oxidizing the nutrients...”
- Transcriptional profiles of Burkholderia pseudomallei reveal the direct and indirect roles of Sigma E under oxidative stress conditions
Jitprasutwit, BMC genomics 2014 - “...2.33 3.52 bpsl3419 Putative GMC oxidoreductase 2.27 1.22 bpss1252 Inner membrane transport protein 2.20 1.11 bpsl2300 PdhB 2.19 1.34 bpsl2301 PdhA 1.89 1.68 bpss0175-0184 T6SS-4 BPSS0175 1.89 3.67 BPSS0176 1.77 3.55 BPSS 0177 1.70 3.78 BPSS 0178 1.99 2.92 BPSS 0179 1.94 2.56 BPSS 0180 1.70...”
- “...and metabolism included bpsl0320 - 0321 (sugar kinase and N-acyl-D-glucosamine 2-epimerase), bpsl2931 (KHG/KDPG aldolase) and bpsl2300 - l2301 (pyruvate dehydrogenase complex). The absence of a functional E under oxidative stress affected the expression of bpss1838-1839 (encoding ferredoxin and rubrerythrin proteins), genes that play important roles in...”
FTH_1719 dihydrolipoyllysine-residue succinyltransferase from Francisella tularensis subsp. holarctica OSU18
FTT_0077 dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex from Francisella tularensis subsp. tularensis SCHU S4
28% identity, 75% coverage
- Use of magnetic hydrazide-modified polymer microspheres for enrichment of Francisella tularensis glycoproteins
Horák, Soft matter 2012 - “...cyt cyt FTH_1696 Glycerol-3-phosphate dehydrogenase 57.78/8.36 ?, MLS cyt FTH_1708 Aconitate hydratase 102.70/5.30 cyt cyt FTH_1719 Dihydrolipoyllysine-residue succinyltransferase 52.75/4.89 cyt cyt FTH_1720 Oxoglutarate dehydrogenase (succinyl-transferring) 105.67/6.01 cyt cyt FTH_1721 Succinate dehydrogenase 27.2/8.42 CM cyt FTH_1722 Succinate dehydrogenase 65.86/6.14 CM cyt FTH_1726 MFS family major facilitator transporter...”
- “...cyt cyt FTH_1696 Glycerol-3-phosphate dehydrogenase 57.78/8.36 ?, MLS cyt FTH_1708 Aconitate hydratase 102.70/5.30 cyt cyt FTH_1719 Dihydrolipoyllysine-residue succinyltransferase 52.75/4.89 cyt cyt FTH_1720 Oxoglutarate dehydrogenase (succinyl-transferring) 105.67/6.01 cyt cyt FTH_1721 Succinate dehydrogenase 26.57/8.18 CM cyt FTH_1722 Succinate dehydrogenase 65.86/6.14 CM cyt FTH_1731 ATP synthase epsilon chain (ATP...”
- Multimethodological approach to identification of glycoproteins from the proteome of Francisella tularensis, an intracellular microorganism
Balonova, Journal of proteome research 2010 - “...phosphodiesterase (FTH_1463), chaperonin GroEL (FTH_1651), succinate dehydrogenase (FTH_1722), acetyl-CoA carboxylase alpha subunit (FTH_0295), dihydrolipoyllysine-residue succinyltransferase (FTH_1719), DNA-binding protein HU-beta (FTH_0880), 17 kDa lipoprotein TUL4 precursor (FTH_0414), aconitate hydratase (FTH_1708), cell division protein FtsZ (FTH_1830), LemA-like protein (FTH_0357), dihydrolipoamide dehydrogenase (FTH_0312), bacterioferritin (FTH_0620), thioredoxin family protein (FTH_1071),...”
- “...- cyt - FTH_0295 ConA, DSA, PNA, SBA, SNA 35.44 8.07 1 - ? - FTH_1719 ConA, DSA, PNA, SBA, SNA 52.75 4.89 2 - cyt - FTH_0384 ConA, DSA, PNA, SBA, SNA 13.48 9.22 2 - ? SPI FTH_1732 ConA, DSA, PNA, SBA, SNA 49.87...”
- A ΔclpB mutant of Francisella tularensis subspecies holarctica strain, FSC200, is a more effective live vaccine than F. tularensis LVS in a mouse respiratory challenge model of tularemia
Golovliov, PloS one 2013 - “...sera from mice immunised with LVS vs FSC200 clpB . Immunoreactive proteins included dihydrolipoamide succinyltransferase (FTT_0077), 30S ribosomal protein S1 (FTT_0183), chaperonin protein, GroEL (FTT_1696) and hypothetical protein FTT_1747. One of the serum pools from mice immunised with FSC200 clpB , recognised nine proteins that were...”
- Immunoproteomic analysis of the human antibody response to natural tularemia infection with Type A or Type B strains or LVS vaccination
Fulton, International journal of medical microbiology : IJMM 2011 - “...reactivity with the Chaperonin GroEL (FTT_1696). The protein dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex (FTT_0077) was immunoreactive with 11 of the 12 patient sera screened but none of the control sera. Due to limited volumes or sera, a single serum sample from patient 1671 was...”
- “...of the twelve sera studied. In addition, the proteins dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase (FTT_0077) and chaperonin protein DnaK (FTT_1269c) were reactive with 8 of the total 12 sera. Representative Western blots probed using sera from LVS vaccinated Swedish laboratory workers (LVS NDBR101 Lot 11)...”
- The francisella tularensis proteome and its recognition by antibodies
Kilmury, Frontiers in microbiology 2010 - “...Succinate dehydrogenase iron-sulfur subunit sdhB Mouse 2D-Western blot Cytoplasmic Twine et al. ( 2006b ) FTT_0077 Dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex sucB Human, type A; human, presumed type B; mouse Proteome microarray/2D-Western blot Cytoplasmic Twine et al. ( 2006b ), Eyles et al. (...”
- “...were reactive with six or more of the sera screened. Of note, although the protein FTT_0077 was reactive with eight of the nine patient sera screened, no single protein was observed to be reactive with all of the patient sera in this study. Figure 3 Frequency...”
FTL_1783 dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex from Francisella tularensis subsp. holarctica
28% identity, 75% coverage
- Francisella tularensis LVS surface and membrane proteins as targets of effective post-exposure immunization for tularemia
Chandler, Journal of proteome research 2015 - “...43 T, 35 , 41 S 25 dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex (SucB) FTL_1783 Cyto(9.97) ( 21 , 40 , 45 , 46 , 50 ) M 21 , 37 , 50 a NCBI reference sequence identification codes matching each loci are listed in...”
- Possible links between stress defense and the tricarboxylic acid (TCA) cycle in Francisella pathogenesis
Dieppedale, Molecular & cellular proteomics : MCP 2013 - “...fusions to T25, respectively) (16). The genes FTL_1783, FTL_0309, FTL_0310, FTL_0311, and FTL_0295, were cloned into pUT18C vector (C-terminal fusion to...”
- “...E2 components of the two complexes were also detected (FTL_1783, OGDH E2; and FTL_0310, PDH E2) as well as the E3 component common to both complexes (FTL_0311,...”
- Francisella tularensis infection-derived monoclonal antibodies provide detection, protection, and therapy
Savitt, Clinical and vaccine immunology : CVI 2009 - “...YP_169209.1 FTT0504c YP_169539.1 FTL_0617 FTL_0421 FTL_1191 FTL_1783 FTT1441 YP_170379.1 FTT0901 YP_169898.1 FTT1269c YP_170225.1 FTT0077 YP_169152.1 312/6 98/2...”
XF0869 dihydrolipoamide acetyltranferase from Xylella fastidiosa 9a5c
27% identity, 66% coverage
- Xylella fastidiosa gene expression analysis by DNA microarrays
Travensolo, Genetics and molecular biology 2009 - “...= 0.27 for all genes). Gene ID Gene name Description Log ratio b Energy metabolism XF0869 pdhB Dihydrolipoamide acetyltransferase 0.98 c XF0824 pykA Piruvate kinase typo II 0.72 XF1855 fumB Fumarate hydratase -2.02 d XF0274 pfkA 6-phosphofrutokinase -1.78 XF0457 gapA Glyceraldehyde-3-phosphate dehydrogenase -1.74 XF0292 acnB Aconitate...”
A0A024B875 Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex from Solanum tuberosum
28% identity, 72% coverage
Q6FYD4 dihydrolipoyllysine-residue succinyltransferase (EC 2.3.1.61) from Bartonella quintana (see paper)
BQ13410 Dihydrolipoamide succinyltransferase from Bartonella quintana str. Toulouse
28% identity, 89% coverage
Q8DTD0 Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex from Streptococcus mutans serotype c (strain ATCC 700610 / UA159)
SMU_1421 dihydrolipoamide acetyltransferase family protein from Streptococcus mutans UA159
30% identity, 87% coverage
- Staphylococcus aureus Interferes with Streptococci Spatial Distribution and with Protein Expression of Species within a Polymicrobial Oral Biofilm
Schnurr, Antibiotics (Basel, Switzerland) 2021 - “...upregulated. Two S. mutans proteins were detected only in the 6S + USA300-MRSA MSCRAMM samples: Q8DTD0, related to acyl-groups transferase, and Q8DUL2, glutamate dehydrogenase. As no uniquely or overlapped protein was characterized from S. mutans while in the 6S + USA300-MRSA WT, we assume that the...”
- Cnm of Streptococcus mutans is important for cell surface structure and membrane permeability
Naka, Frontiers in cellular and infection microbiology 2022 - “...ABC transporter ATP-binding protein 1029549 SMU_1068c 2.328 pdhC Branched-chain alpha-keto acid dehydrogenase E2 subunit 1028680 SMU_1421 2.319 lacE PTS system lactose-specific transporter subunit IIBC 1028733 SMU_1491 2.306 oadB Oxaloacetate decarboxylase, sodium ion pump subunit 1028350 SMU_1017 2.285 SMU_1934c Cobalt ABC transporter ATP-binding protein 1029130 SMU_1934c 2.216...”
- Understanding the Streptococcus mutans Cid/Lrg System through CidB Function
Ahn, Applied and environmental microbiology 2016 - “...SMU_574c SMU_1396 SMU_1914c SMU_423 SMU_490 SMU_1752 SMU_191 SMU_40 SMU_1421 SMU_609 SMU_41 SMU_82 SMU_925 SMU_508 SMU_940c tpn lrgB gbpC cipB nlmD pflC NA NA...”
- A five-species transcriptome array for oral mixed-biofilm studies
Redanz, PloS one 2011 - “...Metabolism SMU_1140c conserved hypothetical protein 2.11 down SMU_1322 budC - putative acetoin dehydrogenase 2.78 down SMU_1421 pdhC - putative dihydrolipoamide acetyltransferase, E2 component 2.78 up SMU_1422 pdhB - putative pyruvate dehydrogenase E1 component subunit beta 2.32 up SMU_1424 pdhD - putative dihydrolipoamide dehydrogenase 2.54 up SMU_1493...”
DR_0256 pyruvate dehydrogenase complex, dihydrolipoamide acetyltransferase E2 component from Deinococcus radiodurans R1
28% identity, 59% coverage
BCAL2208 dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex from Burkholderia cenocepacia J2315
29% identity, 65% coverage
SPC_0734 dihydrolipoamide acetyltransferase from Salmonella enterica subsp. enterica serovar Paratyphi C strain RKS4594
STM0737 2-oxoglutarate dehydrogenase (dihydrolipoyltranssuccinase E2 component) from Salmonella typhimurium LT2
STY0780 dihydrolipoamide succinyltransferase component (E2) from Salmonella enterica subsp. enterica serovar Typhi str. CT18
t2139 dihydrolipoamide succinyltransferase component from Salmonella enterica subsp. enterica serovar Typhi Ty2
28% identity, 90% coverage
- Antibacterial Components and Modes of the Methanol-Phase Extract from Commelina communis Linn
Liu, Plants (Basel, Switzerland) 2023 - “...cytochrome b556 large membrane subunit SPC_2506 0.119 Isocitrate dehydrogenase SPC_0735 0.217 Succinyl-CoA synthetase subunit beta SPC_0734 0.227 Dihydrolipoamide acetyltransferase SPC_0736 0.25 Succinyl-CoA synthetase alpha subunit SPC_3569 0.296 Phosphoenolpyruvate carboxykinase SPC_0727 0.5 Citrate synthase SPC_0164 3.325 Dihydrolipoamide acetyltransferase SPC_0163 4.714 Pyruvate dehydrogenase E1 component Glycolysis/Gluconeogenesis SPC_3760 0.06...”
- Transcriptomic Responses of Salmonella enterica Serovars Enteritidis in Sodium Hypochlorite
Wang, Frontiers in cellular and infection microbiology 2022 - “...transporter ATP-binding protein LivF Carbohydrate and energy metabolism STM0736 sucA -1.9 2-oxoglutarate dehydrogenase E1 component STM0737 sucB -1.4 2-oxoglutarate dehydrogenase STM0730 gltA -2.5 type II citrate synthase STM1238 icdA -1.9 NADP-dependent isocitrate dehydrogenase STM1468 fumA -1.8 fumarate hydratase STM0738 sucC -1.4 ADP-forming succinateCoA ligase subunit beta...”
- Comparative proteomic analysis of Salmonella enterica serovar Typhimurium ppGpp-deficient mutant to identify a novel virulence protein required for intracellular survival in macrophages
Haneda, BMC microbiology 2010 - “...0.044 EC 115 STM3415 rpoA 1.5 0.043 EC 116 STM4184 aceA 1.6 0.007 ND 118 STM0737 sucB 1.7 0.006 ND 119 STM2660 clpB 3.7 0.035 ND 135 STM0735 sdhB 2.1 0.002 ND 142 STM3063 rpiA 1.8 0.022 ND 145 STM4190 pepE 1.5 0.003 ND 155 STM0734...”
- Comparative proteomic analysis of the PhoP regulon in Salmonella enterica serovar Typhi versus Typhimurium
Charles, PloS one 2009 - “...t3669 STM3854 pstB phosphate ABC transporter, ATP-binding protein STY2710 t0257 STM2473 talA transaldolase STY0780 t2139 STM0737 sucB ** 2-oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase STY3930 t3670 STM3853 phoU phosphate transport system regulatory protein STY0231 t0210 STM0209 htrA Heat shock protein * These proteins were either not...”
- Comparative proteomic analysis of the PhoP regulon in Salmonella enterica serovar Typhi versus Typhimurium
Charles, PloS one 2009 - “...transporter STY3929 t3669 STM3854 pstB phosphate ABC transporter, ATP-binding protein STY2710 t0257 STM2473 talA transaldolase STY0780 t2139 STM0737 sucB ** 2-oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase STY3930 t3670 STM3853 phoU phosphate transport system regulatory protein STY0231 t0210 STM0209 htrA Heat shock protein * These proteins were...”
- Comparative proteomic analysis of the PhoP regulon in Salmonella enterica serovar Typhi versus Typhimurium
Charles, PloS one 2009 - “...STY3929 t3669 STM3854 pstB phosphate ABC transporter, ATP-binding protein STY2710 t0257 STM2473 talA transaldolase STY0780 t2139 STM0737 sucB ** 2-oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase STY3930 t3670 STM3853 phoU phosphate transport system regulatory protein STY0231 t0210 STM0209 htrA Heat shock protein * These proteins were either...”
ODB2_ARATH / Q9M7Z1 Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitochondrial; Branched-chain alpha-keto acid dehydrogenase complex component E2; BCE2; BCKAD-E2; BCKADE2; Dihydrolipoamide acetyltransferase component of branched-chain alpha-keto acid dehydrogenase complex; Dihydrolipoamide branched chain transacylase; Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase; Protein DARK INDUCIBLE 3; EC 2.3.1.168 from Arabidopsis thaliana (Mouse-ear cress) (see 8 papers)
AT3G06850 BCE2; acetyltransferase/ alpha-ketoacid dehydrogenase/ dihydrolipoamide branched chain acyltransferase from Arabidopsis thaliana
27% identity, 75% coverage
- function: The branched-chain alpha-keto dehydrogenase complex catalyzes the overall conversion of alpha-keto acids to acyl-CoA and CO(2). It contains multiple copies of three enzymatic components: branched-chain alpha-keto acid decarboxylase (E1), lipoamide acyltransferase (E2) and lipoamide dehydrogenase (E3). Within this complex, the catalytic function of this enzyme is to accept, and to transfer to coenzyme A, acyl groups that are generated by the branched-chain alpha-keto acid decarboxylase component (By similarity). Required during sugar starvation and acts under the control of a sugar-sensing mechanism involving Ser/Thr kinases and phosphatases.
catalytic activity: N(6)-[(R)-dihydrolipoyl]-L-lysyl-[protein] + 2- methylpropanoyl-CoA = N(6)-[(R)-S(8)-2-methylpropanoyldihydrolipoyl]- L-lysyl-[protein] + CoA (RHEA:18865)
cofactor: (R)-lipoate (Binds 1 lipoyl cofactor covalently.)
subunit: Forms a 24-polypeptide structural core with octahedral symmetry. - Identification and Characterization of Plant-Interacting Targets of Tomato Spotted Wilt Virus Silencing Suppressor
Zhai, Pathogens (Basel, Switzerland) 2021 - “...LOC107830934 Solyc05g024290 AT5G13160 Cysteine proteinase aleurain type LOC107784768 Solyc07g041900 AT5G60360 Lipoamide acetyltransferase component LOC107820956 Solyc01g066520 AT3G06850 Calcium-transporting ATPase LOC107814306 Solyc04g016260 AT3G57330 Calcium-dependent protein kinase LOC107805386 Solyc07g064610 AT3G20410 Glutamyl-tRNA synthetase LOC107774917 Solyc01g112290 AT5G64050 Histone H3 LOC107759185 Solyc01g073970 AT5G65360 Ubiquitin-conjugating enzyme variant LOC107831808 Solyc04g007960 AT1G70660 pathogens-10-00027-t003_Table 3 Table...”
- HSFA2 Functions in the Physiological Adaptation of Undifferentiated Plant Cells to Spaceflight
Zupanska, International journal of molecular sciences 2019 - “...was downregulated in HSFA2 KO cells on the ground. In accordance, DIN3 DARK INDUCIBLE 3 (AT3G06850) and MCCB 3-methylcrotonyl-CoA carboxylase (AT4G34030), both mitochondrial proteins involved in valine, leucine, and isoleucine degradation during sugar starvation [ 87 , 88 ] were also down-regulated. Glucose level may influence...”
- “...expression level in WT cells in the spaceflight environment. The dark inducible 3, DIN3 gene (At3g06850) coding the subunits of the branched-chain -ketoacid dehydrogenase complex (BCKDC), and two other genes important to small amino acid degradation, MCCB (At4g34030) coding for subunit of methylcrotonyl-CoA carboxylase participating in...”
- In vivo evidence for a regulatory role of phosphorylation of Arabidopsis Rubisco activase at the Thr78 site
Kim, Proceedings of the National Academy of Sciences of the United States of America 2019 (secret) - A user-friendly platform for yeast two-hybrid library screening using next generation sequencing
Erffelinck, PloS one 2018 - “...Scientific, Waltham, MA, USA). The full-length coding sequence of IAA17 , AT4G36480 , AT1G34340 , AT3G06850 , AT4G05553 , AT3G50000 , AT3G54390 , AT2G40260 , AT3G05670 , AT2G33550 and AT3G19860 were PCR-amplified (for primers, see S1 Table ) using cDNA of Arabidopsis seedlings and recombined in...”
- “...<100 8 AT4G36480 2058 0,282 28,960 102,697 ATLCB1/EMB2779 9 AT1G34340 1833 0,950 47,346 49,847 10 AT3G06850 1730 1,342 33,645 25,074 BCE2/DIN3/LTA1 11 AT4G05553 336 1,727 36,306 21,020 Y 12 AT5G47810 1684 4,480 64,989 14,506 PFK2 Y 13 AT3G03680 3308 0,175 2,213 12,612 14 AT3G15760 843 0,688...”
- Activation of senescence-associated Dark-inducible (DIN) genes during infection contributes to enhanced susceptibility to plant viruses
Fernández-Calvino, Molecular plant pathology 2016 (secret) - Microgravity induces changes in microsome-associated proteins of Arabidopsis seedlings grown on board the international space station
Mazars, PloS one 2014 - “...(Extracellular lipase At1g33811) Q8LPS1 At3G05970 2.7547 Long chain acyl-CoA synthetase 6, peroxisomal (EC 6.2.1.3) Q9M7Z1 AT3G06850 1.7488 2-oxoisovalerate dehydrogenase E2 component (Dihydrolipoyl transacylase) (AT3G06850 protein) (Branched chain alpha-keto acid dehydrogenase E2 subunit) Q9SJD4 At2G04350 1.7513 Long chain acyl-CoA synthetase 8 (EC 6.2.1.3) Stress Defence P50700 AT4G11650...”
- From dusk till dawn: the Arabidopsis thaliana sugar starving responsive network
Arias, Frontiers in plant science 2014 - “...al., 2007 BCAA degradation At3g13450 BCKDH E1 BC -keto acid dehydrogenase Binder et al., 2007 At3g06850 BCKDH E2 BC -keto acid dehydrogenase Binder et al., 2007 At1g03090 MCCA sub1 3-methylcrotonyl-CoA carboxylase Binder et al., 2007 At4g34030 MCCB sub2 3-methylcrotonyl-CoA carboxylase Binder et al., 2007 Glutamate metabolism...”
- Microsome-associated proteome modifications of Arabidopsis seedlings grown on board the International Space Station reveal the possible effect on plants of space stresses other than microgravity
Mazars, Plant signaling & behavior 2014 - “...cycloartenol-c-24-methyltransferase Q9LTV6 AT3G12800 1.914 peroxisomal 2,4-dienoyl-CoA reductase Q9LSQ0 AT3G16910 1.874 acyl-activating enzyme 7 C0Z3A0 1.793 AT3G06850 Q9ZPI5 AT3G06860 1.688 enoyl-CoA hydratase/3-hydroxyacyl-CoA dehydrogenase Q8LAZ1 1.681 very-long-chain fatty acid condensing enzyme CUT1 Auxin metabolism and trafficking Q9FZ33 AT1G54990 2.909 protein auxin RESPONSE 4 Q9SRU2 AT3G02260 2.471 Auxin transport...”
- More
- Identification of the Candidate Proteins Related to Oleic Acid Accumulation during Peanut (Arachis hypogaea L.) Seed Development through Comparative Proteome Analysis
Liu, International journal of molecular sciences 2018 - “...1.62 Q9SW21 ACP4 fatty acid biosynthetic process Araip.10014644.1 1.62 Q9SS98 At3g01570 lipid storage Araip.10014038.1 1.34 Q9M7Z1 BCE2 fatty acid biosynthetic process Araip.10039882.1 1.33 Q8L9C4 KCR1 fatty acid biosynthetic process Araip.10004625.1 1.26 Q9FVS9 CYP96A15 fatty acid derivative metabolic process Araip.10034912.1 1.25 Q9FLH8 At5g51830 lipid metabolic process Araip.10032969.1...”
- Microgravity induces changes in microsome-associated proteins of Arabidopsis seedlings grown on board the international space station
Mazars, PloS one 2014 - “...3.1.1.-) (Extracellular lipase At1g33811) Q8LPS1 At3G05970 2.7547 Long chain acyl-CoA synthetase 6, peroxisomal (EC 6.2.1.3) Q9M7Z1 AT3G06850 1.7488 2-oxoisovalerate dehydrogenase E2 component (Dihydrolipoyl transacylase) (AT3G06850 protein) (Branched chain alpha-keto acid dehydrogenase E2 subunit) Q9SJD4 At2G04350 1.7513 Long chain acyl-CoA synthetase 8 (EC 6.2.1.3) Stress Defence P50700...”
PP4188 2-oxoglutarate dehydrogenase, dihydrolipoamide succinyltransferase from Pseudomonas putida KT2440
PP_4188 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase from Pseudomonas putida KT2440
28% identity, 90% coverage
- Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology
Puchałka, PLoS computational biology 2008 - “...that is composed of proteins expressed from the genes knocked-out in the two false positives PP4188 and PP 4189 catalyzes the decarboxylation of -ketoglutarate to succinyl-CoA in the TCA cycle, concurrently producing succinyl-CoA for anabolic purposes. In the model, this functionality is not needed as this...”
- Regulatory tasks of the phosphoenolpyruvate-phosphotransferase system of Pseudomonas putida in central carbon metabolism
Chavarría, mBio 2012 - “...aconitate hydratase 2 (PP_2339); Icd, isocitrate dehydrogenase (PP_4011); Kgd, alpha-ketoglutarate decarboxylase (PP_4189); KgdB, dihydrolipoamide acetyltransferase (PP_4188); SucA, 2-oxoglutarate dehydrogenase E1 component (PP_4189); SucC, succinyl-CoA synthetase beta subunit (PP_4186); SucD, succinyl-CoA synthetase (PP_4185); SdhA, succinate dehydrogenase flavoprotein subunit (PP_4191); SdhB, succinate dehydrogenase iron sulfur subunit (PP_4190); SdhC,...”
ETAE_2583 2-oxoglutarate dehydrogenase, E2 subunit, dihydrolipoamide succinyltransferase from Edwardsiella tarda EIB202
29% identity, 90% coverage
P20708 dihydrolipoyllysine-residue succinyltransferase (EC 2.3.1.61) from Azotobacter vinelandii (see paper)
27% identity, 91% coverage
pdhC / P75392 pyruvate dehydrogenase (EC 1.2.1.104) from Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1) (see 3 papers)
MPN391 dihydrolipoamide acetyltransferase component (E2) from Mycoplasma pneumoniae M129
P75392 Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex from Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)
27% identity, 91% coverage
- Exploring the adaptability and robustness of the central carbon metabolism of Mycoplasma pneumoniae
Zondervan, 2022 - Subunits of the Pyruvate Dehydrogenase Cluster of Mycoplasma pneumoniae Are Surface-Displayed Proteins that Bind and Activate Human Plasminogen
Gründel, PloS one 2015 - “...are encoded by the genes pdhA ( mpn393 ), pdhB ( mpn392 ), pdhC ( mpn391 ) and pdhD ( mpn390 ) [ 4 ]. These are organized in two operons encoding for the E1 and E1 subunits and the other for the E2 and E3...”
- Network of Surface-Displayed Glycolytic Enzymes in Mycoplasma pneumoniae and Their Interactions with Human Plasminogen
Gründel, Infection and immunity 2015 - “...Yes Yes Yes Internal helix* mpn392 1 35.9 Yes mpn391 0 42.4 Yes Surface displayed, binds human Plg and fibronectin (25-27) Surface displayed, binds human Plg...”
- Systematic Structural Analyses of Attachment Organelle in Mycoplasma pneumoniae
Nakane, PLoS pathogens 2015 - “...proteins, we detected the fusion proteins for P200 (MPN567), TopJ (MPN119), MPN295, MPN390 (PdhD), and MPN391 (PdhC) by Western blotting using an antibody against EYFP ( S3 Fig ). The major bands were detected around the positions expected from the amino acid sequences. These observations suggest...”
- Comprehensive methylome characterization of Mycoplasma genitalium and Mycoplasma pneumoniae at single-base resolution
Lluch-Senar, PLoS genetics 2013 - “...of the mpn390 gene that codifies for the dihydrolipoamide dehydrogenase (PdhD). This gene together with mpn391 (PdhC, dihydrolipoamide acetyltransferase) constitute an operon involved in pyruvate metabolism. Also, three 5-G A N 7 TAY-3/3-CTN 7 A TR-5 unmethylated sites were detected. One is located in an intergenic...”
- The phosphoproteome of the minimal bacterium Mycoplasma pneumoniae: analysis of the complete known Ser/Thr kinome suggests the existence of novel kinases
Schmidl, Molecular & cellular proteomics : MCP 2010 - “...MPN303 MPN311b MPN322 MPN324 MPN331 MPN349 MPN389 MPN390 MPN391 MPN392 MPN393 MPN394 MPN420 MPN425 MPN428 MPN429 MPN430 MPN434 MPN452b MPN470 MPN474b MPN495...”
- Quantitative proteomics analysis of Mycoplasma pneumoniae identifies potential macrolide resistance determinants
Li, AMB Express 2021 - “...1.14223E05 2.268532831 2.22037E05 P75121 MPN_670 1.766381125 0.028324373 1.266310644 3.47397E05 P75603 MPN_090 1.654676801 0.021731425 1.231982961 0.000180854 P75392 pdhC 1.549656015 0.009815993 1.240981292 5.22141E05 P75527 def 1.514331423 0.036288214 1.302137569 0.000302493 P75236 MPN_542 1.37969945 0.098842902 1.493066835 0.000621553 Discussion Mycoplasma pneumoniae is one of the main pathogens to cause community-acquired respiratory...”
MG_272 dihydrolipoamide acetyltransferase from Mycoplasma genitalium G37
P47514 Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex from Mycoplasma genitalium (strain ATCC 33530 / DSM 19775 / NCTC 10195 / G37)
24% identity, 95% coverage
- Designing minimal genomes using whole-cell models
Rees-Garbutt, Nature communications 2020 - “...single gene (MG_270), creating the in silico minimal genome GAMA_237. MG_270 (lipoate-protein ligase A) modifies MG_272 (Supplementary Note mmc1, pg. 65) 18 , one of four genes (MG_271274) that form the pyruvate dehydrogenase complex. This provides acetyl-CoA for the Krebs cycle, producing ATP. Reintroducing MG_270 repairs...”
- Subtractive Genomics Approach for Identification of Novel Therapeutic Drug Targets in Mycoplasma genitalium
Fatoba, Pathogens (Basel, Switzerland) 2021 - “...kinase K11753 mge01110-Biosynthesis-of-secondary-metabolites P47416 Protein translocase subunit K03076 mge02024-Quorum-sensing, mge03070-Bacterial-secretion-system P47489 Glycerol-3-phosphate acyltransferase K08591 mge01110-Biosynthesis-of-secondary-metabolites P47514 Dihydrolipoyllysine-residue acetyltransferase K00627 mge01110-Biosynthesis-of-secondary-metabolites, mge01120-Microbial-metabolism-in-diverse-environments P47515 Pyruvate dehydrogenase E1 component subunit beta K00162 mge01110-Biosynthesis-of-secondary-metabolites, mge01120-Microbial-metabolism-in-diverse-environments P47516 Pyruvate dehydrogenase E1 component subunit alpha K00161 mge01110-Biosynthesis-of-secondary-metabolites, mge01120-Microbial-metabolism-in-diverse-environments P47529 Acyl carrier protein homolog...”
- “...P47287 Dexfosfoserine DB04522 Experimental Cytoplasmic P47357 N-Bromoacetyl-aminoethyl Phosphate DB02257 Experimental Cytoplasmic 5-Phosphoarabinonic acid DB03042 Experimental P47514 NADH DB00157 Approved Cytoplasmic Radicicol DB03758 Experimental Dihydrolipoic acid DB03760 Experimental P47515 Pyruvic acid DB00119 Approved Cytoplasmic NADH DB00157 Approved P47516 NADH DB00157 Approved Cytoplasmic P47541 Acetylphosphate DB02897 Experimental Cytoplasmic...”
HD1624 dihydrolipoamide acetyltransferase from Haemophilus ducreyi 35000HP
27% identity, 68% coverage
Q98UJ6 dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) from Gallus gallus (see paper)
29% identity, 74% coverage
TTHA0232 pyruvate dehydrogenase complex, dihydrolipoamide acetyltranferase E2 component from Thermus thermophilus HB8
27% identity, 80% coverage
S0583 2-oxoglutarate dehydrogenase (dihydrolipoyltranssuccinase E2 component) from Shigella flexneri 2a str. 2457T
27% identity, 90% coverage
TTC1754 No description from Thermus thermophilus HB27
27% identity, 80% coverage
FE46_RS12380 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase from Flavobacterium psychrophilum
28% identity, 91% coverage
ODB2_CAEEL / Q23571 Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitochondrial; Branched-chain alpha-keto acid dehydrogenase complex component E2; Dihydrolipoamide branched-chain transacylase E2; EC 2.3.1.168 from Caenorhabditis elegans (see paper)
NP_495670 Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitochondrial from Caenorhabditis elegans
29% identity, 82% coverage
- function: The branched-chain alpha-keto dehydrogenase complex catalyzes the overall conversion of alpha-keto acids to acyl-CoA and CO(2) (By similarity). It contains multiple copies of three enzymatic components: branched-chain alpha-keto acid decarboxylase (E1), lipoamide acyltransferase (E2) and lipoamide dehydrogenase (E3) (By similarity). Within this complex, the catalytic function of this enzyme is to accept, and to transfer to coenzyme A, acyl groups that are generated by the branched-chain alpha-keto acid decarboxylase component (By similarity). Required for the catabolism of branched-chain amino acids and the subsequent synthesis of monomethyl branched-chain fatty acids, which are important for regulating postembryonic growth (PubMed:26683372).
catalytic activity: N(6)-[(R)-dihydrolipoyl]-L-lysyl-[protein] + 2- methylpropanoyl-CoA = N(6)-[(R)-S(8)-2-methylpropanoyldihydrolipoyl]- L-lysyl-[protein] + CoA (RHEA:18865)
cofactor: (R)-lipoate (Binds 1 lipoyl cofactor covalently.)
disruption phenotype: RNAi-mediated knockdown results in reduced monomethyl branched-chain fatty acid generation and also results in larval arrest in the subsequent generation. - Natural variation in C. elegans arsenic toxicity is explained by differences in branched chain amino acid metabolism.
Zdraljevic, eLife 2019 - GeneRIF: This study implicates the branched-chain alpha-keto acid dehydrogenase complex and branched-chain amino acid metabolism in arsenic responses, demonstrating the power of Caenorhabditis elegans natural genetic diversity to identify novel mechanisms by which environmental toxins affect organismal physiology.
VF_0824 dihydrolipoamide acetyltransferase from Vibrio fischeri ES114
VF_0824 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase from Aliivibrio fischeri ES114
28% identity, 90% coverage
E2(o) subunit / b0727 dihydrolipoyltranssuccinylase (EC 2.3.1.61) from Escherichia coli K-12 substr. MG1655 (see 4 papers)
sucB / P0AFG6 2-oxoglutarate dehydrogenase E2 subunit (EC 2.3.1.61) from Escherichia coli (strain K12) (see paper)
ODO2_ECOLI / P0AFG6 Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex; 2-oxoglutarate dehydrogenase complex component E2; OGDC-E2; Dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex; EC 2.3.1.61 from Escherichia coli (strain K12) (see 3 papers)
P0AFG6 2-oxoglutarate dehydrogenase system (EC 1.2.1.105); dihydrolipoyllysine-residue succinyltransferase (EC 2.3.1.61) from Escherichia coli (see 6 papers)
SucB-lipoate / ECOCYC|SUCB-LIPOATE dihydrolipoyltranssuccinase from Escherichia coli K12 (see 3 papers)
sucB / PDB|1PMR dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex; EC 2.3.1.61 from Escherichia coli K12 (see 14 papers)
NP_415255 dihydrolipoyltranssuccinylase from Escherichia coli str. K-12 substr. MG1655
P0AFG7 Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex from Escherichia coli O157:H7
b0727 dihydrolipoamide acetyltransferase from Escherichia coli str. K-12 substr. MG1655
Z0881 2-oxoglutarate dehydrogenase (dihydrolipoyltranssuccinase E2 component) from Escherichia coli O157:H7 EDL933
ECB_00686 dihydrolipoamide acetyltransferase from Escherichia coli B str. REL606
ECO26_0787 dihydrolipoyltranssuccinase from Escherichia coli O26:H11 str. 11368
ECs0752 2-oxoglutarate dehydrogenase dihydrolipoyltranssuccinase E2 component from Escherichia coli O157:H7 str. Sakai
BC33_RS19235, Z_RS03890 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase from Escherichia coli ATCC 700728
27% identity, 90% coverage
- function: E2 component of the 2-oxoglutarate dehydrogenase (OGDH) complex which catalyzes the second step in the conversion of 2- oxoglutarate to succinyl-CoA and CO(2).
catalytic activity: N(6)-[(R)-dihydrolipoyl]-L-lysyl-[2-oxoglutarate dehydrogenase complex component E2] + succinyl-CoA = N(6)-[(R)-S(8)- succinyldihydrolipoyl]-L-lysyl-[2-oxoglutarate dehydrogenase complex component E2] + CoA (RHEA:15213)
cofactor: (R)-lipoate Note=Binds 1 lipoyl cofactor covalently
subunit: Forms a 24-polypeptide structural core with octahedral symmetry (PubMed:10739245, PubMed:9677295). Part of the 2-oxoglutarate dehydrogenase (OGDH) complex composed of E1 (2-oxoglutarate dehydrogenase), E2 (dihydrolipoamide succinyltransferase) and E3 (dihydrolipoamide dehydrogenase); the complex contains multiple copies of the three enzymatic components (E1, E2 and E3) (Probable). Interacts with SucA (via N-terminus), the E1 component of OGDH complex (PubMed:17367808). - BEAN and HABAS: Polyphyletic insertions in the DNA-directed RNA polymerase
Alvarez-Carreño, Protein science : a publication of the Protein Society 2024 - “...D8 (Q0AUH3), psd (A0L627), cytochrome f (A2BPU4), peptidase M23 (A0A0E3QUJ6), RND (A0A1T5M7J5), BCC (O59021), OGDCE2 (P0AFG6), NusG (C5CGE4), rsxC (P77611) and uD5 (P11512). The structurederived multiple sequence alignment and the structure superimposition are colored by Scorecons conservation. Residues below 0.4 are gray. The location and number...”
- The Thioredoxin Fold Protein (TFP2) from Extreme Acidophilic Leptospirillum sp. CF-1 Is a Chaperedoxin-like Protein That Prevents the Aggregation of Proteins under Oxidative Stress
Muñoz-Villagrán, International journal of molecular sciences 2024 - “...YkgE ykgE 4.59 0.021 P0AFG3 subunit of E1(0) component of 2-oxoglutarate dehydrogenase sucA 1.08 0.034 P0AFG6 dihydrolipoyltranssuccinylase sucB 6.63 0.045 P09373 pyruvate formate-lyase pflB 7.94 0.000 P0AC33 fumarase A fumA 9.99 0.002 P0A9C0 anaerobic glycerol-3-phosphate dehydrogenase subunit A glpA 2.34 0.037 P33602 NADH:quinone oxidoreductase subunit G...”
- Quantitative proteomic analysis reveals the influence of plantaricin BM-1 on metabolic pathways and peptidoglycan synthesis in Escherichia coli K12
Wang, PloS one 2020 - “...P0AC47 1.26 0.006763 FrdB Fumarate reductase (anaerobic), Fe-S subunit Enzyme; Energy metabolism, carbon: Anaerobic respiration P0AFG6 1.40 0.0003 SucB Dihydrolipoyltranssuccinase Enzyme; Energy metabolism, carbon: TCA cycle P0AFG3 1.47 0.001002 SucA Enzyme; Energy metabolism, carbon: TCA cycle 2-oxoglutarate decarboxylase,thiamine triphosphate-binding Effect of plantaricin BM-1 on E ....”
- Structure of the dihydrolipoamide succinyltransferase catalytic domain from Escherichia coli in a novel crystal form: a tale of a common protein crystallization contaminant
Andi, Acta crystallographica. Section F, Structural biology communications 2019 - “...Expression vector pNYCOMPSC-23 N/A Expression host E. coli E. coli Amino-acid sequence UniProt Q9FR37 UniProt P0AFG6 (residues 173405) C-terminal 10His tag. Table 2 Crystallization of dihydrolipoamide succinyltransferase Method Hanging-drop vapour diffusion Plate type VDX plate Temperature (K) 298 Protein concentration 0.10.2mgml 1 (in a 254mgml 1...”
- Identification of enzymes and regulatory proteins in Escherichia coli that are oxidized under nitrogen, carbon, or phosphate starvation
Noda, Proceedings of the National Academy of Sciences of the United States of America 2007 - “...Accession no. P36683 P35340 P00509 P00968 P63268 Q8FBM1 P0AFG6 P0A6M9 P0A6N2 P0A6Q0 P0A8G6 P09373 P0AB71 Q8FBT4 P64294 P0A9C6 P00961 P0A3B3 Q8FL75 P05793 P0A956...”
- The Escherichia coli proteome: past, present, and future prospects
Han, Microbiology and molecular biology reviews : MMBR 2006 - “...E1 component 6.04/105,061.72 6.01/103,036 SucB P0AFG6 Dihydrolipoyllysine residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex...”
- Energy production genes sucB and ubiF are involved in persister survival and tolerance to multiple antibiotics and stresses in Escherichia coli.
Ma, FEMS microbiology letters 2010 (PubMed)- GeneRIF: sucB and ubiF mutants deficient in energy production were identified from the mutant screens to have defective persister survival as demonstrated by higher susceptibility to various antibiotics and different stresses.
- sucAB and sucCD are mutually essential genes in Escherichia coli.
Yu, FEMS microbiology letters 2006 (PubMed)- GeneRIF: sucAB and sucCD are mutually essential genes for production of succinyl Coa that is essential for cell viability
- Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12.
Link, Electrophoresis 1997 (PubMed)- GeneRIF: N-terminus verified by Edman degradation on mature peptide
- Determination of the Near-Atomic Structure of Non-Purified Oligomeric E. coli Proteins.
Pichkur, Crystallography reports 2021 - “...chaperonin (CH60_ECOLI) 396 57.46 15 0.65 P0A9H3 Inducible lysine decarboxylase (LDCI_ECOLI) 275 81.61 7 0.54 P0AFG7 Succinyltransferase component of 2-oxoglutarate dehydrogenase complex (ODO2_ECOLI) 311 43.98 6 0.34 P0AES4 DNA gyrase subunit A (GYRA_ECOLI) 41 97.13 3 0.07 After precipitation and washing, the protein mixture was instantly...”
- Metabolomic and proteomic investigations of impacts of titanium dioxide nanoparticles on Escherichia coli
Planchon, PloS one 2017 - “...cycle u 105 Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex E . coli O157:H7 44 P0AFG7 TCA cycle u 113 30S ribosomal protein S1 E . coli O157:H7 61.1 P0AG69 Protein synthesis u 122 Chaperone protein skp E . coli O157:H7 17.7 P0AEU9 Protein synthesis u...”
- Identification of Modules With Similar Gene Regulation and Metabolic Functions Based on Co-expression Data
Galán-Vásquez, Frontiers in molecular biosciences 2019 - “...module 15, which is enriched with enzymes, the genes with the highest connectivity were sucB (b0727), sucC (b0728), and sucD (b0729), which are associated with the citrate cycle, an important aerobic pathway for the final steps of the oxidation of carbohydrates and fatty acids (Buck et...”
- Accurate estimation of nucleic acids by amplification efficiency dependent PCR
Chatterjee, PloS one 2012 - “...2-oxoglutarate dehydrogenase 1.94 1.87 3.14 1.33 1.40 b0116 dihydrolipoamide dehydrogenase 1.92 1.84 0.26 0.13 1.13 b0727 dihydrolipoamide succinyl transferase 1.95 1.98 0.57 0.67 1.42 b0728 succinyl CoA synthetase,sucC 1.91 1.93 1.13 1.31 1.65 b0729 succinyl CoA synthetase,sucD 1.91 1.92 2.74 2.59 1.55 b0721 succinate dehydrogenase 1.99...”
- On the accessibility of adaptive phenotypes of a bacterial metabolic network
Ndifon, PLoS computational biology 2009 - “...in the E. coli metabolic network. The protein products of the genes b0116, b0726, and b0727 combine to form a protein complex that catalyzes production of succinate coenzyme A (SUCCOA) from alpha-ketoglutarate (AKG) and coenzyme A, with the concomitant reduction of nicotinamide adenine dinucleotide (NAD) and...”
- Control and benefits of CP4-57 prophage excision in Escherichia coli biofilms
Wang, The ISME journal 2009 - “...sdhD b0722 1.7 Succinate dehydrogenase, hydrophobic subunit sucA b0726 1.9 Succinate dehydrogenase (decarboxylase component) sucB b0727 1.6 Dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex sucC b0728 1.9 Succinyl-CoA synthetase, -subunit sucD b0729 1.7 Succinyl-CoA synthetase, -subunit aceA b4015 1.7 Isocitrate lyase aceB b4014 1.5 Malate synthetase...”
- The HU regulon is composed of genes responding to anaerobiosis, acid stress, high osmolarity and SOS induction
Oberto, PloS one 2009 - “...2.28 1 0.15 0.22 0.74 1 0.26 0.56 0.45 FRec 2-oxoglutarate dehydrogenase (decarboxylase component) sucB b0727 sdhCDAB-b0725-sucABCD 1 1.83 0.67 1.79 1 0.15 0.2 0.7 1 0.29 0.6 0.62 FRec 2-oxoglutarate dehydrogenase (dihydrolipoyltranssuccinase E2 component) sucC b0728 sdhCDAB-b0725-sucABCD 1 1.81 0.63 1.97 1 0.16 0.19 0.84...”
- Protein disorder is positively correlated with gene expression in Escherichia coli
Paliy, Journal of proteome research 2008 - “...long enough. NIH-PA Author Manuscript SucB (b0727) - dihydrolipoyl succinyltransferase chain of 2-oxoglutarate dehydrogenase--Three classes of the dehydrogenase...”
- “...the text. A) AceB (b0115); B) HlpA (b0178); C) SucB (b0727); D) Pal (b0741); E) InfA (b0884); F) AcpP (b1094); G) HNS (b1237); H) PtsI (b2416); I) GcvH (b2904);...”
- Analysis of promoter targets for Escherichia coli transcription elongation factor GreA in vivo and in vitro
Stepanova, Journal of bacteriology 2007 - “...protease La; heat shock K protein b0725 b0726 b0727 2.6 3.7 4.1 4.0 4.4 3.7 ORF, hypothetical protein in sdh-suc operon 2-Oxoglutarate dehydrogenase...”
- Identification of genome-scale metabolic network models using experimentally measured flux profiles
Herrgård, PLoS computational biology 2006 - “...tpi (b3919), ppc (b3956), pgi (b4025), pfkA (b3916), pta (b2297), lpdA (b0116), sucA (b0726), sucB (b0727), pgl (b0767), galU (b1236), fdnG (b1474), fdnH (b1475), fdnI (b1476), edd (b1851), nuoN (b2276), nuoM (b2277), nuoL (b2278), nuoK (b2279), nuoJ (b2280), nuoI (b2281), nuoH (b2282), nuoG (b2283), nuoF (b2284),...”
- More
- Transcriptomic analysis reveals specific metabolic pathways of enterohemorrhagic Escherichia coli O157:H7 in bovine digestive contents
Segura, BMC genomics 2018 - “...2.04 2.05E-03 NDE Z0880 sucA 2-oxoglutarate dehydrogenase E1 component NDE NDE NDE 2.60 6.80E-04 NDE Z0881 sucB 2-oxoglutarate dehydrogenase E2 component NDE NDE NDE 2.91 3.11E-04 NDE Z0882 sucC Succinyl-CoA synthetase ( subunit) NDE NDE NDE 2.93 2.18E-04 NDE Z0883 sucD Succinyl-CoA synthetase ( subunit) NDE...”
- Disruption of rcsB by a duplicated sequence in a curli-producing Escherichia coli O157:H7 results in differential gene expression in relation to biofilm formation, stress responses and metabolism
Sharma, BMC microbiology 2017 - “...Z0877 Succinate dehydrogenase flavoprotein subunit 3.11 0.044 sucA Z0880 2-oxoglutarate dehydrogenase E1 2.73 0.047 sucB Z0881 Dihydrolipoamide succinyltransferase 2.62 0.039 sucC Z0882 Succinyl-CoA synthetase subunit beta 2.64 0.029 sucD Z0883 Succinyl-CoA synthetase subunit alpha 2.37 0.054 nadA Z0919 Quinolate synthetase 1.82 0.002 galM Z0926 Galactose-1-epimerase 1.33...”
- The gluconeogenesis pathway is involved in maintenance of enterohaemorrhagic Escherichia coli O157:H7 in bovine intestinal content
Bertin, PloS one 2014 - “...sdhD Succinate dehydrogenase (hydrophobic subunit) 5.14 2.5E-03 Z0880 sucA 2-oxoglutarate dehydrogenase (decarboxylase component) 3.58 2.3E-03 Z0881 sucB 2-oxoglutarate dehydrogenase (E2 component) 2.37 3.6E-03 Z0882 sucC Succinyl-CoA synthetase (b subunit) 3.00 5.6E-03 Z0883 sucD Succinyl-CoA synthetase (a subunit) 2.70 6.8E-03 Glycerol and glycerol-3P Z4786 glpD Glycerol-3-phosphate dehydrogenase...”
- Large-scale analysis of post-translational modifications in E. coli under glucose-limiting conditions
Brown, BMC genomics 2017 - “...coli Locus E. coli Peptide P. aeruginosa P. aeruginosa Peptide Description Locus Tag Locus Tag ECB_00686 sucB SSVDILVPDLPESVADATVATWHKK PA14_44000 MAIEIK Dihydrolipoamide Succinyltransferase ECB_03391 dppF STQEATLQQPLLQAIDLKK PA14_58490 METVLTAR Dipeptide transporter ATP-binding subunit ECB_00915 rpsA TESFAQLFEESLKE PA14_23330 SESFAELFEESLK 30S ribosomal protein S1 ECB_00155 yadR SDDVALPLEFTDAAANKV PA14_08510 SIETFTPTPLLFTPGAANK Iron-sulfur...”
- Evolution of enterohemorrhagic escherichia coli O26 based on single-nucleotide polymorphisms
Bletz, Genome biology and evolution 2013 - “...Nonsynonymous (Lys Thr) 89.17 ECO26_0785 sdhB (1) 841192 C G d Nonsynonymous (Asp Glu) 6.67 ECO26_0787 sucB (1) 844779 T G Synonymous 10.00 ECO26_0968 ybjG (1) 1020736 T A d Synonymous 6.67 ECO26_1012 cydC (1) 1066493 G C c Nonsynonymous (Arg Thr) 56.67 ECO26_1062 ssuD (1)...”
- Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits
Dessimoz, Nucleic acids research 2006 - “...K12 (COG identifier corresponds to the gene name: aceF, sucB), E.coli H7 (1: ECs0119, 3: ECs0752), Haemophilus influenzae (1: HI1232, 3: HI1661), Neisseria meningitidis (1: NMB1342, 3: NMB0956), Pasteurella multocida (1: PM0894, 3: PM0278), Pseudomonas aeruginosa (1: PA5016, 2: PA2249, 3: PA1586), Rhizobium loti (2: mll4471,...”
- Transcriptomic analysis reveal differential gene expressions of Escherichia coli O157:H7 under ultrasonic stress
Li, Ultrasonics sonochemistry 2021 - “...aconitate hydratase BC33_RS22310 acnB 1.5 aconitate hydratase 2 BC33_RS19240 sucA 2.4 2-oxoglutarate dehydrogenase E1 component BC33_RS19235 sucB 2.2 2-oxoglutarate dehydrogenase E2 component BC33_RS19230 sucC 2.5 succinyl-CoA synthetase beta subunit BC33_RS19225 sucD 2.8 succinyl-CoA synthetase alpha subunit BC33_RS19250 sdhA 2.4 succinate dehydrogenase, flavoprotein subunit BC33_RS19245 sdhB 2.2...”
- Transcriptomic Analysis of Viable but Non-Culturable Escherichia coli O157:H7 Formation Induced by Low Temperature
Zhong, Microorganisms 2019 - “...Z_RS23610, Z_RS23465, Z_RS22905, Z_RS21350, Z_RS21150, Z_RS21140, Z_RS21025, Z_RS19885, Z_RS18625, Z_RS16005, Z_RS12610, Z_RS12490, Z_RS09475, Z_RS09120, Z_RS04060, Z_RS03890, Z_RS02910, Z_RS02490, Z_RS01960, sec F, pst S, pst A, nep I, lam B, gld A, gcv T, gcv H, fuc I, fgh A, fad E IT, SMCP, SSTTA IT =...”
NGO0564 Odp2 from Neisseria gonorrhoeae FA 1090
28% identity, 68% coverage
- Epitope determination of immunogenic proteins of Neisseria gonorrhoeae
Connor, PloS one 2017 - “...split evenly between Fig 1 and Fig 2 . The former covers epitopes of NGO0326, NGO0564, NGO0592, NGO0777, NGO1429, and NGO1577, while the latter summarizes epitope mappings of NGO1656, NGO1852, NGO2094, NGO2095 polypeptides 1 and 2, NGO2095 polypeptide 4 as well as NGO0170, which was the...”
- “...10.1371/journal.pone.0180962.g001 Fig 1 Epitope mapping (n = 9) of the polypeptides of A) NGO0326, B) NGO0564, C) NGO0592, D) NGO0777, E) NGO1429, F) NGO1577. The boxes embody 50% of the values, while the whiskers comprise 98% of the data. Outliers are marked with a small x....”
- Identification of Novel Immunogenic Proteins of Neisseria gonorrhoeae by Phage Display
Connor, PloS one 2016 - “...by affinity chromatography using the polyhistidine-tag of the proteins ( Fig 2B and 2C ). NGO0564 was applied as a positive control, since it was also found in outer membrane vesicle vaccines of N . lactamica and N . meningitidis [ 49 ]. NGO1043 was expressed...”
- “...1.5% agarose gel: M Hyperladder I (bioline, Bio-33025-26), 1 NGO0170, 2 NGO0326, 3 NGO0451, 4 NGO0564 (+ control), 5 NGO0642, 6 NGO0777, 7 NGO0916, 8 NGO1043, 9 NGO1500 (- control), 10 NGO1634, 11 NGO1656, 12 NGO1657, 13 NGO1796, 14 NGO1852. B SDS-PAGE (15%) of 0.5 g...”
- The NarE protein of Neisseria gonorrhoeae catalyzes ADP-ribosylation of several ADP-ribose acceptors despite an N-terminal deletion
Rodas, FEMS microbiology letters 2016 - “...was located between genes NGO0562 and NGO0564, which encode the putative proteins dihydrolipoamide acetyltransferase and dihydrolipoamide dehydrogenase,...”
- Proteomic analysis of Neisseria gonorrhoeae biofilms shows shift to anaerobic respiration and changes in nutrient transport and outermembrane proteins
Phillips, PloS one 2012 - “...0.668 (2) Energy metabolism NGO1769 CcpR; cytochrome c peroxidase Electron transport 3.271 (1) 1.547 (2) NGO0564 dihydrolipoamide acetyltransferase Pyruvate dehydrogenase 1.724 (3) NGO1812 d major outer membrane protein porin P.IB Electron transport 1.669 (3) 0.908 (3) 0.697 (3) NGO2146 F0F1 ATP synthase subunit B; F-type H+-transporting...”
- “...upregulated in the transcriptomic experiment. The only upregulated proteins on the pathway were dihydrolipoamide acetyltransferase (NGO0564), a putative phosphotransacetylase (NGO0214), and pyruvate kinase (PykA). From our proteomic and transcriptomic datasets, we found 8 entries that mapped onto the KEGG pathway for the TCA cycle (Supplementary Figure...”
- Manganese regulation of virulence factors and oxidative stress resistance in Neisseria gonorrhoeae
Wu, Journal of proteomics 2010 - “...TufA tufA B 2.10.44 NGO1227 Cytosol leucyl aminopeptidase, LAP (aminopeptidase A) ampA/pepA /lap B 1.9 NGO0564 dihydrolipoamide S-acetyltransferase complex, E2 component of pyruvate dehydrogenase aceF I 1.810.45 NGO0249 acetyl-CoA carboxylase, beta subunit accD S 2.75 NGO0200 phosphoenolpyruvate (PEP) synthase ~ ppsA T 2.21.05 NGO0223 inorganic pyrophosphatase...”
VP_RS12210 pyruvate dehydrogenase complex dihydrolipoyllysine-residue acetyltransferase from Vibrio parahaemolyticus RIMD 2210633
29% identity, 58% coverage
- Identification of Antibacterial Components in the Methanol-Phase Extract from Edible Herbaceous Plant Rumex madaio Makino and Their Antibacterial Action Modes
Liu, Molecules (Basel, Switzerland) 2022 - “...p < 0.05). For example, the DEG encoding a pyruvate dehydrogenase complex dihydrolipoyllysine-residue acetyltransferase ( VP_RS12210 ) was significantly down-regulated (0.331-fold), which connects glycolysis with tricarboxylic acid cycle (TCA) and plays a key role in glucose metabolism [ 19 ]. The down-regulation of this enzyme led...”
- “...VP_RS05640 0.342 6-phosphofructokinase Glycolysis/Gluconeogenesis VP_RS23260 0.087 6-phospho-beta-glucosidase VP_RS12915 0.272 6-phospho-beta-glucosidase VP_RS12215 0.310 Pyruvate dehydrogenase (acetyl-transferring) VP_RS12210 0.331 Pyruvate dehydrogenase complex dihydrolipoyllysine-residue acetyltransferase VP_RS13410 0.406 Glucose-6-phosphate isomerase VP_RS10485 0.416 D-hexose-6-phosphate mutarotase VP_RS09910 0.433 Pyruvate kinase VP_RS18295 2.558 2-oxo acid dehydrogenase subunit E2 Flagellar assembly VP_RS22540 0.055 Flagellar...”
SAR11_0430 dihydrolipoamide S-acetyltransferase from Candidatus Pelagibacter ubique HTCC1062
26% identity, 84% coverage
TTE0690 Dihydrolipoamide acyltransferases from Thermoanaerobacter tengcongensis MB4
29% identity, 92% coverage
PSLF89_899 dihydrolipoyllysine-residue succinyltransferase from Piscirickettsia salmonis LF-89 = ATCC VR-1361
28% identity, 96% coverage
VC2086 2-oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase from Vibrio cholerae O1 biovar eltor str. N16961
28% identity, 90% coverage
- A novel phase variant of the cholera pathogen shows stress-adaptive cryptic transcriptomic signatures
Lambert, BMC genomics 2016 - “...acnA ), VC0604 ( acnB ) and VC1141 ( icd ), or TCA only genes VC2086 ( sucB ) and VC2085 ( sucC ), were not significantly changed from N16961 to N16961R but then were all reduced by 3-fold or greater in N16961SD (Additional file 13...”
- Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits
Dessimoz, Nucleic acids research 2006 - “...(3: RC0226, 4: RC0764), Rickettsia prowazekii (3: RP179, 4: RP530), Vibrio cholerae (1: VC2413, 3: VC2086), Y.pestis (1: YPO3418, 3: YPO1114). Figure 5 Unrooted phylogenetic consensus tree for COG0513, constructed from a Bayesian analysis. Posterior probabilities are drawn to the right of the nodes and clan-supporting...”
- Characterization of Vibrio cholerae RyhB: the RyhB regulon and role of ryhB in biofilm formation
Mey, Infection and immunity 2005 - “...dehydrogenase E2 E1b .............................................................................VC2086 (2.0), VC2087 (2.0) NADH-ubiquinone oxidoreductaseb,c,d...”
PMI_RS02805 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase from Proteus mirabilis HI4320
PMI0570 dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex from Proteus mirabilis HI4320
28% identity, 90% coverage
- Organ agar serves as physiologically relevant alternative for in vivo bacterial colonization
Pearson, Infection and immunity 2023 - “...PMI_RS01770 208 E11 0.727 U Gamma-glutamyl phosphate reductase Amino acid metabolism n/a PMI0570 d sucB PMI_RS02805 207 F6 0.863 UKL Dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex TCA cycle e Y PMI0641 sanA PMI_RS03160 215 C10 0.854 K Putative transport protein Y PMI0711 serC PMI_RS03500 219...”
- Organ agar serves as physiologically relevant alternative for in vivo bacterial colonization
Pearson, Infection and immunity 2023 - “...n/a PMI0370 proA PMI_RS01770 208 E11 0.727 U Gamma-glutamyl phosphate reductase Amino acid metabolism n/a PMI0570 d sucB PMI_RS02805 207 F6 0.863 UKL Dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex TCA cycle e Y PMI0641 sanA PMI_RS03160 215 C10 0.854 K Putative transport protein Y PMI0711...”
- “...in vivo mutant phenotypes Gene Name Organ a CBA/J agar b In vivo c Function PMI0570 sucB UKL UKLBS UBK Dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex PMI0641 sanA K KS US Putative transport protein PMI0711 serC UK KS UBKS Phosphoserine aminotransferase PMI1545 guaA UKL UKLBS...”
O31550 Dihydrolipoyllysine-residue acetyltransferase component of acetoin cleaving system from Bacillus subtilis (strain 168)
28% identity, 91% coverage
- Probabilistic annotation of protein sequences based on functional classifications
Levy, BMC bioinformatics 2005 - “...top and to the right) marks the limit of the sampling regions used to annotate O31550 with the multivariate (univariate) Bayesian method [See Additional file 1 , Fig. S1]. (b): EC 1.6.5.3 (black triangles) and EC 1.6.99.5 (grey circles). (c): EC 1.2.1.59 (black triangles) and EC...”
- “...CI space for EC classes 2.3.1.61 (Dihydrolipoamide S-succinyltransferase) and 2.3.1.12 (Dihydrolipoamide S-acetyltransferase) Focusing on protein O31550 [Swiss-Prot: O31550 ] from EC 2.3.1.12, we note Figure 3(a) that its CIs (best bit-scores) with both EC classes are similar (231 on the Y-coordinate with EC2.3.1.12 and 225 on...”
LIMLP_12355 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase from Leptospira interrogans serovar Manilae
28% identity, 87% coverage
- Leptospira interrogans biofilm transcriptome highlights adaption to starvation and general stress while maintaining virulence
Davignon, NPJ biofilms and microbiomes 2024 - “...2.0), a succinate-CoA ligase (LIMLP_12885, FC 2.1), a succinyl transferase of the 2-oxoglutarate dehydrogenase complex (LIMLP_12355, FC 1.4), an isocitrate dehydrogenase (LIMLP_01230, FC 2.0), a citrate synthase (LIMLP_02815, FC 1.7), and a 2-methylisocitrate lyase (LIMLP_11605, FC 2.3). Consistently, our data revealed a downregulation of several components...”
FTN_1634 2-oxoglutarate dehydrogenase complex, E2 component, dihydrolipoyltranssuccinase from Francisella tularensis subsp. novicida U112
27% identity, 75% coverage
VAA_RS05360 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase from Vibrio anguillarum 775
27% identity, 90% coverage
- Characterization of the <i>Vibrio anguillarum Va</i>RyhB regulon and role in pathogenesis
Li, Frontiers in cellular and infection microbiology 2024 - “...-0.01 0.906 -1.51 0.024 Negative frdD VAA_RS02605 Fumarate reductase -0.43 0.183 -1.31 0.045 Negative susB VAA_RS05360 -ketoglutarate dehydrogenase -0.12 0.560 -2.32 0.004 Negative susC VAA_RS05365 -ketoglutarate dehydrogenase 0.95 0.066 -1.70 0.0002 Negative susD VAA_RS05370 Succinate-CoA synthetase -0.12 0.640 -2.54 0.0005 Negative sdhC VAA_RS05335 Succinate dehydrogenase -0.71...”
JHW33_RS09930 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase from Rahnella aceris
27% identity, 89% coverage
PVX_119310 dihydrolipoamide acyltransferase, putative from Plasmodium vivax
25% identity, 80% coverage
- A systems-based analysis of Plasmodium vivax lifecycle transcription from human to mosquito
Westenberger, PLoS neglected tropical diseases 2010 - “...ATP-specific succinyl-CoA synthetase beta subunit (PVX_084960, PF14_0295); 2-oxoglutarate dehydrogenase E1 component (PVX_089325, PF08_0045); dihydrolipoamide acyltransferase (PVX_119310, PFC0170c); succinyl-CoA synthetase alpha subunit (PVX_091100, PF11_0097); iron-sulfur subunit of succinate dehydrogenase (PVX_123345, PFL0630w); cytochrome C oxidase (PVX_099845, PFI1375w); cytochrome c oxidase copper chaperone (PVX_111430, PF10_0252); cytochrome c oxidase subunit...”
PMCN03_0914 pyruvate dehydrogenase complex dihydrolipoyllysine-residue acetyltransferase from Pasteurella multocida subsp. multocida str. HB03
PM0894 AceF from Pasteurella multocida subsp. multocida str. Pm70
27% identity, 58% coverage
- Genomic and transcriptomics analysis reveal putative secreted proteins expressed of <i>Pasteurella multocida</i> during 18β-glycyrrhetinic acid treatment
Wu, Frontiers in veterinary science 2024 - “...study. Gene name Forward (53) Reverse (53) PMCN03_0121 (galT) TAGCGGTGGTGCCTTATTGG TAAAAGGCGCCGCATGAAAC PMCN03_0319 (sel1L) CAGACAGCACCAACTGCAAC AGCTTGTGCCTGGTAATCCC PMCN03_0914 (aceF) CGGATATGCAAGGGGGTTGT AATGAAACGTGCGCCATCTG PMCN03_1217 (gdhA) GTGGCTGAAGGGGCTAACAT TTACCCGGACCAAAGAGCAC PMCN03_1641 (xynC) CTGGGGGATTAGTGCAGTCG GGTGTAATGCTCGGTTTGGC PMCN03_1741 (hpaG) ACGCGTGAAAAATCGTGTGG ACTCGCCATTGACCCATGTT 16S rRNA GAATGTTGCGGTGAATAC GGTTACCTTGTTACGACTTC 2.6 Molecular modelling methods The protein structure of bacterial secreted proteins...”
- “...9 PMCN03_0606 50S ribosomal protein L20, rpl20 10 PMCN03_0622 Phohoribosylaminoimidazole carboxylase catalytic subunit, purE 11 PMCN03_0914 Dihydrolipoamide acetyltransferase, aceF 12 PMCN03_1019 50S ribosomal protein L31 type B, rpl31 13 PMCN03_1064 UDP-N-acetylglucosamine 1-carboxyvinyltransferase, murA 14 PMCN03_1092 Ribokinase, menG 15 PMCN03_1108 ftsI 16 PMCN03_1127 HflK protein, hflK 17...”
- Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits
Dessimoz, Nucleic acids research 2006 - “...Haemophilus influenzae (1: HI1232, 3: HI1661), Neisseria meningitidis (1: NMB1342, 3: NMB0956), Pasteurella multocida (1: PM0894, 3: PM0278), Pseudomonas aeruginosa (1: PA5016, 2: PA2249, 3: PA1586), Rhizobium loti (2: mll4471, 3: mll4300, 4a: mlr0385, 4b: mll3627), Rhizobium meliloti (2: SMc03203, 3a: SMc02483, 3b: SMb20019, 4: SMc01032),...”
LIC_12476 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase from Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130
LIC12476 dihydrolipoamide succinyltransferase from Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130
27% identity, 87% coverage
- Pathogenic Leptospires Modulate Protein Expression and Post-translational Modifications in Response to Mammalian Host Signals
Nally, Frontiers in cellular and infection microbiology 2017 - “...) LipL32 (LIC_11352) 537, 546 0.00014, 0.00041 2.50, 2.14 gi|45601560 ( AAS71041.1 ) Dihydrolipoamide succinyltransferase (LIC_12476) 459, 227, 457 0.012, 0.03, 0.046 2.40, 1.69, 1.56 gi|30652620 (Q72SY1.2 ) ATP synthase subunit alpha (LIC_11241) 1,612 0.00042 2.38 gi|45602544 ( AAS72021.1 ) Cell shape determination protein (LIC_13483) 814...”
- Global transcriptomic response of Leptospira interrogans serovar Copenhageni upon exposure to serum
Patarakul, BMC microbiology 2010 - “...production and conversion (C) LIC12002 (LA1897) sdhA -1.72 succinate dehydrogenase/fumarate reductase subunit A - - LIC12476 (LA1222) aceF -1.63 dihydrolipoyllysine-residue acetyl transferase and succinyltransferase - - LIC12217 (LA1553) petE -1.62 plastocyanin - LIC12829 (LA0790) gltA -1.53 citrate (Si)-synthase - - - carbohydrate transport and metabolism (G)...”
- “...encoding citrate synthase and sdhA (LIC12002), encoding a flavoprotein subunit of succinate dehydrogenase, and aceF (LIC12476), encoding a subunit of the pyruvate dehydrogenase complex were down-regulated. The results suggest that acetyl-CoA derived from fatty acid oxidation was less likely to feed into the TCA cycle. In...”
BP0994 dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex from Bordetella pertussis Tohama I
29% identity, 64% coverage
BTH_I1865 pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase from Burkholderia thailandensis E264
28% identity, 64% coverage
- Molecular Mechanisms of AhpC in Resistance to Oxidative Stress in Burkholderia thailandensis
Zhang, Frontiers in microbiology 2019 - “...Construction Genes encoding B. thailandensis E264 AhpC (BTH_I2092), dihydrolipoamide dehydrogenases Lpd (BTH_I2554), dihydrolipoamide acyltransferase SucB (BTH_I1865), TrxC (BTH_I2218), and thioredoxin reductase TrxR (BTH_I1560) were amplified using PCR with B. thailandensis E264 genomic DNA as the template. These DNA fragments were digested using corresponding restriction enzymes and...”
GL4_0109 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase from Methyloceanibacter caenitepidi
27% identity, 84% coverage
- Possible cross-feeding pathway of facultative methylotroph Methyloceanibacter caenitepidi Gela4 on methanotroph Methylocaldum marinum S8
Takeuchi, PloS one 2019 - “...icd 346 185 -0.90 0.000 GL4_0108 2-oxoglutarate dehydrogenase E1 component sucA 386 652 0.75 0.000 GL4_0109 2-oxoglutarate dehydrogenase E2 component sucB 265 585 1.14 0.000 GL4_0107 Succinyl-CoA ligase alpha chain sucD 132 700 2.40 0.000 GL4_0106 Succinyl-CoA ligase beta chain sucC 217 673 1.63 0.000 GL4_0100...”
- “...sucC and sucD ; GL4_0106 and GL4_0107) and 2-oxoglutarate dehydrogenase (sucA and sucB; GL4_0108 and GL4_0109) were upregulated ( Fig 3 , Table 1 ). The TCA cycle was also found to be upregulated according to the pathway enrichment analysis ( Fig 5 and S4 Fig...”
PDIP_86090 Biotin-dependent 2-oxo acid dehydrogenases acyltransferase, putative from Penicillium digitatum
29% identity, 76% coverage
- Effects of Peptide Thanatin on the Growth and Transcriptome of Penicillium digitatum
Feng, Frontiers in microbiology 2020 - “...(Ssc70), putative 1.42 (up) Amino acid metabolism 26236295 PDIP_79790 3-methyl-2-oxobutanoate dehydrogenase, putative 0.33 (down) 26236923 PDIP_86090 Biotin-dependent 2-oxo acid dehydrogenases acyltransferase, putative 0.37 (down) Effect of Thanatin on P. digitatum DNA and RNA Synthesis To identify potential effect of thanatin on nucleic acid synthesis of P....”
NP_001013533 lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitochondrial from Danio rerio
28% identity, 74% coverage
PA14_66310 dihydrolipoamide acetyltransferase from Pseudomonas aeruginosa UCBPP-PA14
31% identity, 66% coverage
PMI2045 dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex from Proteus mirabilis HI4320
27% identity, 58% coverage
LT988_22725 dihydrolipoyllysine-residue acetyltransferase from Thiocapsa bogorovii
29% identity, 61% coverage
- The Complete Genome of a Novel Typical Species Thiocapsa bogorovii and Analysis of Its Central Metabolic Pathways
Petushkova, Microorganisms 2024 - “...[EC:1.8.1.4] LT988_22720 lpdA ; dihydrolipoyl dehydrogenase 15 K00627 pyruvate dehydrogenase E2 component (dihydrolipoamide acetyltransferase) [EC:2.3.1.12] LT988_22725 aceF ; dihydrolipoyllysine-residue acetyltransferase microorganisms-12-00391-t007_Table 7 Table 7 The genes encoding the enzymes of the pentosophosphate pathway (17) in T. bogorovii BBS. Function Number, Enzyme Annotation, and Number (According to...”
- “...[EC:1.8.1.4] LT988_22720 lpdA ; dihydrolipoyl dehydrogenase 15 K00627 pyruvate dehydrogenase E2 component (dihydrolipoamide acetyltransferase) [EC:2.3.1.12] LT988_22725 aceF ; dihydrolipoyllysine-residue acetyltransferase microorganisms-12-00391-t008_Table 8 Table 8 The genes encoding the enzymes involved in Sox system thiosulfate oxidation (15), sulfide oxidation (sulfide/quinone oxidoreductase (SQR (6)), and flavocytochrome c sulfide...”
Cenrod_2157 2-oxo acid dehydrogenase subunit E2 from Candidatus Symbiobacter mobilis CR
33% identity, 86% coverage
A4W92_RS13735 dihydrolipoyllysine-residue acetyltransferase from Pseudomonas aeruginosa
31% identity, 66% coverage
ATEG_03862 uncharacterized protein from Aspergillus terreus NIH2624
28% identity, 83% coverage
TTHA0288 2-oxoglutarate dehydrogenase E2 component (dihydrolipoamide succinyltransferase) from Thermus thermophilus HB8
27% identity, 91% coverage
Mal48_24080 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase from Thalassoglobus polymorphus
27% identity, 93% coverage
ODP2_PSEAE / Q59638 Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex; Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex; E2; EC 2.3.1.12 from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (see paper)
PA5016 dihydrolipoamide acetyltransferase from Pseudomonas aeruginosa PAO1
NP_253703 dihydrolipoamide acetyltransferase from Pseudomonas aeruginosa PAO1
31% identity, 66% coverage
- function: The pyruvate dehydrogenase complex catalyzes the overall conversion of pyruvate to acetyl-CoA and CO(2). It contains multiple copies of three enzymatic components: pyruvate dehydrogenase (E1), dihydrolipoamide acetyltransferase (E2) and lipoamide dehydrogenase (E3)
catalytic activity: N(6)-[(R)-dihydrolipoyl]-L-lysyl-[protein] + acetyl-CoA = N(6)-[(R)-S(8)-acetyldihydrolipoyl]-L-lysyl-[protein] + CoA (RHEA:17017)
cofactor: (R)-lipoate (Binds 2 lipoyl cofactors covalently.)
subunit: Forms a 24-polypeptide structural core with octahedral symmetry
disruption phenotype: Disruption inactivates the pyruvate dehydrogenase complex and causes an increase in pyruvate concentration and acidity of the culture medium. - Distinct transcriptome and traits of freshly dispersed <i>Pseudomonas aeruginosa</i> cells
Kalia, mSphere 2024 - “...0.966 0.87 PA4899 Probable aldehyde dehydrogenase 0.422 0.113 1.51 PA5015 Pyruvate dehydrogenase 0.87 0.625 0.305 PA5016 Dihydrolipoamide acetyltransferase 0.644 0.346 0.117 PA5110 Fructose-1,6-bisphosphatase 0.526 0.269 110 PA5131 Phosphoglycerate mutase 0.629 0.15 0.18 PA5192 Phosphoenolpyruvate carboxykinase 0.52 0.284 1.59 TCA cycle PA4333 Probable fumarase 1.15 1.16 0.32...”
- Identification of complex III, NQR, and SDH as primary bioenergetic enzymes during the stationary phase of Pseudomonas aeruginosa cultured in urine-like conditions
Hu, Frontiers in microbiology 2024 - “...Krebs cycle and glyoxylate cycle PA5015 NP_253702 2,649 aceE Pyruvate dehydrogenase Pyruvate dehydrogenase subunit E1 PA5016 NP_253703 1,644 aceF Dihydrolipoamide acetyltransferase PA1587 NP_250278 1,437 lpd 2-oxoglutarate dehydrogenase complex dihydrolipoyl dehydrogenase PA1787 NP_250478 2,610 acnB Aconitate synthase Aconitate hydratase B PA2623 NP_251313 1,257 icd Isocitrate dehydrogenase Isocitrate...”
- Discovery of coordinately regulated pathways that provide innate protection against interbacterial antagonism
Ting, eLife 2022 - “...Fold change (VSV-G/Ctrl ) Arc3B-VSV-G sample PA5113 (Arc3B ) 5.86 > 200 PA4385 1.62 2.29 PA5016 1.45 0.82 PA0090 1.17 0.72 PA3729 1.12 1.30 PA4761 1.12 0.71 PA5114 (Arc3A ) 1.12 N.D . PA5239 1.06 1.10 PA3861 1.00 1.10 PA4269 1.00 1.10 PA1092 0.95 0.78 PA0141...”
- “...PA5114 (Arc3A ) 1.44 N.D . PA4751 1.30 12.87 PA5556 1.26 3.55 PA3729 1.10 1.28 PA5016 1.10 0.62 PA4429 0.99 N.D. PA4942 0.96 6.36 PA2493 0.92 2.60 PA3160 0.90 N.D. PA4246 0.87 0.79 PA0090 0.85 0.53 PA1552 0.83 N.D. PA0077 0.81 5.33 PA2494 0.81 ND PA2976...”
- Feeding behaviour of Caenorhabditis elegans is an indicator of Pseudomonas aeruginosa PAO1 virulence
Lewenza, PeerJ 2014 - “...rRNA methylase B 26_C3 Gene PA4983 PA4983 Two-component response regulator A, C 80_B7 Gene aceF PA5016 Dihydrolipoamide acetyltransferase B 47_B5 Gene typA PA5117 Regulatory GTPase A 18_H10 Gene dctD PA5166 Two-component response regulator A, C 12_B5 Gene gcvT1 PA5215 Glycine-cleavage system protein T1 B 68_G8 Gene...”
- A theoretical and experimental proteome map of Pseudomonas aeruginosa PAO1
Lecoutere, MicrobiologyOpen 2012 - “...151 PA4974 Outer membrane protein MU OM 53.4 52 5.80 5.40 0.721 0.518 152 * PA5016 aceF Dihydrolipoamide acetyltransferase C C 56.7 67 5.23 5.11 0.694 0.046 153 PA5040 pilQ Fimbrial biogenesis U OM 77.4 74 5.48 5.25 0.621 0.257 154 PA5046 Malic enzyme C CM...”
- Analysis of Pseudomonas aeruginosa cell envelope proteome by capture of surface-exposed proteins on activated magnetic nanoparticles
Vecchietti, PloS one 2012 - “...Aspartyl-tRNA synthetase AspS 2 C,2 - P,1 lon PA1803 Lon protease 2 C,2 aceF aceB PA5016 Dihydrolipoyllysine-residue acetyltransferase 1 C,3 - P,1 rpoD PA0576 RNA polymerase sigma factor RpoD 1 C,3 ccoO1 PA1553 Cytochrome c oxidase 1 C,3 ftsY PA0373 Signal recognition particle receptor FtsY 2...”
- Microcolony formation by the opportunistic pathogen Pseudomonas aeruginosa requires pyruvate and pyruvate fermentation
Petrova, Molecular microbiology 2012 - “...PA2623, icd 4.44 PA1984 (Ad-DH) 4.52 PA1789, uspL 7.24 PA0836 (AckA) 4.40 PA4328, uspM 9.05 PA5016, aceF 2.55 PA1553, ccoQ1 24.7 PA1554, ccoN1 8.5 PA1555, ccoP2 6.9 PA1556, ccoQ2 6.1 PA1557, ccoN2 11.1 Fold changes refer to mifR versus wild-type. a respective transcripts have previously been...”
- Comparisons of Two Proteomic Analyses of Non-Mucoid and Mucoid Pseudomonas aeruginosa Clinical Isolates from a Cystic Fibrosis Patient
Rao, Frontiers in microbiology 2011 - “...1.01 0.9193 0.83 273 PA5253 Regulatory protein AlgP 1 0.86 0.7890 0.66 0.1443 0.76 47 PA5016 Dihydrolipoamide acetyltransferase AceF 8 0.75 0.0127 0.80 0.0273 0.77 2 PA4385 GroEL protein 49 0.75 0.0000 0.69 0.0000 0.72 181 PA2853 Outer-membrane lipoprotein OprI precursor 3 0.69 0.1906 0.69 0.0376...”
- More
- Identification of complex III, NQR, and SDH as primary bioenergetic enzymes during the stationary phase of Pseudomonas aeruginosa cultured in urine-like conditions
Hu, Frontiers in microbiology 2024 - “...cycle and glyoxylate cycle PA5015 NP_253702 2,649 aceE Pyruvate dehydrogenase Pyruvate dehydrogenase subunit E1 PA5016 NP_253703 1,644 aceF Dihydrolipoamide acetyltransferase PA1587 NP_250278 1,437 lpd 2-oxoglutarate dehydrogenase complex dihydrolipoyl dehydrogenase PA1787 NP_250478 2,610 acnB Aconitate synthase Aconitate hydratase B PA2623 NP_251313 1,257 icd Isocitrate dehydrogenase Isocitrate dehydrogenase...”
- Protein Interaction Networks of Catalytically Active and Catalytically Inactive PqsE in Pseudomonas aeruginosa
Taylor, mBio 2022 - “...thrB thrB 1.365692537 Q02FF4 ureA ureA 1.264836648 Q9I3F5 acnA acnA 1.002888279 Q02V73 glyS glyS 1.008682243 Q59638 aceF aceF 1.067938829 B7UZY2 cysD cysD 1.092340172 Q02H29 murC murC 1.224317298 P27726 gap gapA 1.354759487 Q51363 nadB nadB 1.354759487 Q9I6M4 davT PA14_03450 1.411195433 B7UYA0 ackA ackA 1.486004021 P30718 groL groL...”
- “...aceE aceA 1.392137097 P30718 groL groL 1.415037499 Q02H54 groS groS 1.60823228 Q9I3D2 sucB sucB 1.694321257 Q59638 aceF aceF 1.805912948 Q51481 nirQ nirQ 5.158429363 10.1128/mbio.01559-22.2 FIGS2 Specificity-filtered interactions with eGFP-PqsE(WT) (a) and eGFP-PqsE(D73A) (b) in either WT or rhlR P. aeruginosa . Shapes indicate whether the interaction...”
- Proteomic Analysis of Resistance of Gram-Negative Bacteria to Chlorhexidine and Impacts on Susceptibility to Colistin, Antimicrobial Peptides, and Ceragenins
Hashemi, Frontiers in microbiology 2019 - “...(AceE) Catalyzes conversion of pyruvate to acetyl-CoA and CO 2 . Glycolytic process 3014.55 21 Q59638 Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex (AceF) Catalyzes acetyl-CoA and enzyme N 6 -(dihydrolipoyl)lysine to CoA and enzyme N 6 -( S -acetyldihydrolipoyl)lysine. Glycolytic process 40.67 22 Q9HZA7 Acetyl-coenzyme...”
AMUC_RS09035 dihydrolipoyllysine-residue succinyltransferase from Akkermansia muciniphila ATCC BAA-835
28% identity, 99% coverage
BU303 dihydrolipoamide succinyltransferase from Buchnera aphidicola str. APS (Acyrthosiphon pisum)
24% identity, 86% coverage
- Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits
Dessimoz, Nucleic acids research 2006 - “...4: AGc2641), Brucella melitensis (2: BMEII0746, 3: BMEI0141, 4: BMEI0856), Buchnera sp. (1: BU206, 3: BU303), E.coli K12 (COG identifier corresponds to the gene name: aceF, sucB), E.coli H7 (1: ECs0119, 3: ECs0752), Haemophilus influenzae (1: HI1232, 3: HI1661), Neisseria meningitidis (1: NMB1342, 3: NMB0956), Pasteurella...”
acoC TPP-dependent acetoin dehydrogenase complex, E2 component, dihydrolipoyllysine-residue acetyltransferase; EC 2.3.1.12 from Clostridium magnum (see paper)
AAA21747.1 dihydrolipoamide acetyltransferase from Clostridium magnum (see paper)
24% identity, 82% coverage
RSP_0964 Dihydrolipoamide transsuccinylase from Rhodobacter sphaeroides 2.4.1
27% identity, 72% coverage
Q8QHL7 dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) from Oncorhynchus mykiss (see paper)
29% identity, 74% coverage
Mal33_37980 2-oxo acid dehydrogenase subunit E2 from Rosistilla oblonga
32% identity, 54% coverage
CA51_39160 2-oxo acid dehydrogenase subunit E2 from Rosistilla oblonga
32% identity, 54% coverage
PF3D7_1320800, XP_001349947 dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex from Plasmodium falciparum 3D7
24% identity, 88% coverage
- Metabolic changes that allow <i>Plasmodium falciparum</i> artemisinin-resistant parasites to tolerate oxidative stress
Bonive-Boscan, Frontiers in parasitology 2024 - “...on transcript level changes. For example, citrate synthase (PF3D7_1022500, PF3D7_0609200) is upregulated, and oxoglutarate dehydrogenase (PF3D7_1320800), succinate dehydrogenase (PF3D7_1010300), and succinate CoA ligase (PF3D7_1108500) are downregulated ( Figure1B ). These changes in the transcript levels may be related to changes in the metabolites influx and efflux...”
- The mitochondrion of Plasmodium falciparum is required for cellular acetyl-CoA metabolism and protein acetylation
Nair, Proceedings of the National Academy of Sciences of the United States of America 2023 - “...subunits in other species ( 49 ). Therefore, we tested whether the KDH E2 subunit (PF3D7_1320800) is essential. Similar to the E1 knockout, kdh E2 parasites did not display a noticeable growth phenotype compared to parental parasites ( SIAppendix , Fig.S2 ). Taken together, the results...”
- “...Knockdown Lines. For deletion of mpdh E1 (PF3D7_1312600), mpdh E2 (PF3D7_0303700), e3 (PF3D7_1232200), kdh E2 (PF3D7_1320800), and lipl2 (PF3D7_0923600), 300 L red blood cells were electroporated with 75g each of gene-specific pRSng and pCasG plasmids. For the generation of acs (PF3D7_0627800)- and mpdh E2 (PF3D7_1314600)-inducible knockdown...”
- The acquisition of humoral immune responses targeting Plasmodium falciparum sexual stages in controlled human malaria infections
de, Frontiers in immunology 2022 - “...3 (EMP3) SPZ and BS/36 and 51** Early giRBC membrane antigen, putative ( 6 ) PF3D7_1320800 dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex SPZ and BS/36 and 51** PF3D7_1302000 PTP6 EMP1-trafficking protein (PTP6) SPZ and BS/36 and 51* / ** Early giRBC membrane antigen, putative (...”
- Insights into the intracellular localization, protein associations and artemisinin resistance properties of Plasmodium falciparum K13
Gnädig, PLoS pathogens 2020 - “...in the ER, component of chaperone complexes that interact with BiP 0.69% 3 5 (2,3) PF3D7_1320800 Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex -- Mitochondrial TCA cycle 0.68% 4 7 (3,4) PF3D7_1408600 40S ribosomal protein S8e, putative -- Ribosome 0.68% 3 6 (2,4) PF3D7_0816600 Chaperone protein...”
- A novel lipoate attachment enzyme is shared by Plasmodium and Chlamydia species
Afanador, Molecular microbiology 2017 - “...been localized to the mitochondrion: the branched chain dehydrogenase (BCDH) (PF3D7_0303700), the -ketoglutarate dehydrogenase (KDH) (PF3D7_1320800), and the H-protein (PF3D7_1132900) of the GCV ( Spalding et al. , 2010 ; Afanador et al. , 2014 ). These three mitochondrial proteins are lipoylated through two distinct routes...”
- “...Cloning, expression and purification of the lipoylation domains of Pf BCDH (PF3D7_0303700) and Pf KDH (PF3D7_1320800), the H-protein (PF3D7_1132900), as well as LipL1 (PF3D7_1314600) and LipL2 (PF3D7_0923600) were previously described ( Afanador et al. , 2014 ). The genes encoding the lipoylation enzymes were cloned into...”
- Crystal structure of lipoate-bound lipoate ligase 1, LipL1, from Plasmodium falciparum
Guerra, Proteins 2017 - “...chain a-ketoacid dehydrogenase complex (BCDH, PF3D7_0303700), the E2 component of the -ketoglutarate dehydrogenase complex (KDH, PF3D7_1320800), and the H-protein of the glycine cleavage system (PF3D7_1132900). 9 , 14 , 15 The lipoylation of these three proteins occurs via a complex mechanism that involves two enzymes, Pf...”
- Redox-dependent lipoylation of mitochondrial proteins in Plasmodium falciparum
Afanador, Molecular microbiology 2014 - “...was used to identify the genes encoding the E2 subunits of BCDH (PF3D7_0303700) and KDH (PF3D7_1320800). Nucleotides encoding the first 30 amino acids of both proteins were amplified from cDNA extracted from erythrocytic stage Plasmodium falciparum 3D7 parasites using primers BCDH 30 .AvrII.F and BCDH 30...”
- Apicoplast lipoic acid protein ligase B is not essential for Plasmodium falciparum
Günther, PLoS pathogens 2007 - “...P. falciparum enoyl-ACP reductase (FabI) (XP_966137; CAG25389), P. falciparum H-protein (XP_001348010; AAN35923), P. falciparum KGDH-E2 (XP_001349947; CAD52355), P. falciparum LipA (XP_001350160; CAD52569), P. falciparum LipB (XP_001349288; CAD51137), P. falciparum LplA1 (XP_001349882; CAD52290), P. falciparum LplA2 (XP_001352107; CAD51918), P. falciparum PDH-E2 (XP_001347486; AAN35399), P. knowlesi LplA2 (gene...”
NMB1342 dihydrolipoamide acetyltransferase from Neisseria meningitidis MC58
27% identity, 67% coverage
- The NarE protein of Neisseria gonorrhoeae catalyzes ADP-ribosylation of several ADP-ribose acceptors despite an N-terminal deletion
Rodas, FEMS microbiology letters 2016 - “...meningitidis MC58 these genes were annotated as aceF (NMB1342) and lpdA2 (NMB1344), respectively, which correspond to the flanking genes of narE (NMB1143)...”
- Identification of Novel Immunogenic Proteins of Neisseria gonorrhoeae by Phage Display
Connor, PloS one 2016 - “...DNA helicase 1 76 52.18 NMB0885 Cytoplasm No - NGO0564* dihydrolipoamide acetyltransferase 1 310 54.69 NMB1342 Cytoplasm Yes [ 46 ] NGO0584 50S ribosomal protein L9 2 130/148 15.07 NMB1320 Cytoplasm Yes [ 47 ] NGO0592 trigger factor 3 115208 48.37 NMB1313 Cytoplasm Yes [ 48...”
- Identification of an iron-sulfur cluster that modulates the enzymatic activity in NarE, a Neisseria meningitidis ADP-ribosyltransferase
Del, The Journal of biological chemistry 2009 - “...always located at the same genome locus between nmb1342 and nmb1344 (9), which code for the dihydrolipoyl acetyltransferase (E2) and the dihydrolipoyl...”
- Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits
Dessimoz, Nucleic acids research 2006 - “...E.coli H7 (1: ECs0119, 3: ECs0752), Haemophilus influenzae (1: HI1232, 3: HI1661), Neisseria meningitidis (1: NMB1342, 3: NMB0956), Pasteurella multocida (1: PM0894, 3: PM0278), Pseudomonas aeruginosa (1: PA5016, 2: PA2249, 3: PA1586), Rhizobium loti (2: mll4471, 3: mll4300, 4a: mlr0385, 4b: mll3627), Rhizobium meliloti (2: SMc03203,...”
PA14_44000 dihydrolipoamide succinyltransferase E2 subunit from Pseudomonas aeruginosa UCBPP-PA14
26% identity, 89% coverage
- Gene Expression Profiling of <i>Pseudomonas aeruginosa</i> Upon Exposure to Colistin and Tobramycin
Cianciulli, Frontiers in microbiology 2021 - “...sucC PA14_43950 Succinyl-CoA synthetase subunit beta 3.73 ND lpdG PA14_43970 Dihydrolipoamide dehydrogenase 16.47 5.26 sucB PA14_44000 Dihydrolipoamide succinyltransferase 10.98 9.15 sucA PA14_44010 2-oxoglutarate dehydrogenase E1 4.27 4.12 PA14_53970 PA14_53970 Aconitate hydratase 18.05 8.09 Phenylalanine/Tyrosine catabolism fahA PA14_38530 Fumarylacetoacetase 30.98 2.32 maiA PA14_38550 Maleylacetoacetate isomerase 48.44 3.57...”
- Large-scale analysis of post-translational modifications in E. coli under glucose-limiting conditions
Brown, BMC genomics 2017 - “...coli Peptide P. aeruginosa P. aeruginosa Peptide Description Locus Tag Locus Tag ECB_00686 sucB SSVDILVPDLPESVADATVATWHKK PA14_44000 MAIEIK Dihydrolipoamide Succinyltransferase ECB_03391 dppF STQEATLQQPLLQAIDLKK PA14_58490 METVLTAR Dipeptide transporter ATP-binding subunit ECB_00915 rpsA TESFAQLFEESLKE PA14_23330 SESFAELFEESLK 30S ribosomal protein S1 ECB_00155 yadR SDDVALPLEFTDAAANKV PA14_08510 SIETFTPTPLLFTPGAANK Iron-sulfur cluster insertion protein...”
BAS1176 2-oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase from Bacillus anthracis str. Sterne
28% identity, 88% coverage
EF1658 branched-chain alpha-keto acid, E2 component, dihydrolipoamide acetyltransferase from Enterococcus faecalis V583
Q834J2 Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex from Enterococcus faecalis (strain ATCC 700802 / V583)
27% identity, 83% coverage
- Genes Contributing to the Unique Biology and Intrinsic Antibiotic Resistance of Enterococcus faecalis
Gilmore, mBio 2020 - “...antimicrobial peptides. Finally, nearby is a cluster of genes related to branched-chain fatty acid biosynthesis (EF1658 to EF1690). This pathway is known to serve E. faecalis as a temporary electron sink, helping the cell achieve electron balance in the absence of the electron transport chain (...”
- “...of five genes in this cluster (EF1665, EF1669, EF1680, EF1682, and EF1683), with two more (EF1658 and EF1666) barely missing the conservative dVal cutoff of <0.100 to be called daptomycin affected. (Another dense array of genes nearby [EF1531 and EF1592] broadly affects antibiotic susceptibility. These genes...”
- Using a genome-scale metabolic model of Enterococcus faecalis V583 to assess amino acid uptake and its impact on central metabolism
Veith, Applied and environmental microbiology 2015 - “...the alpha-keto acid dehydrogenase complex (bkdABCD; EF1660, EF1659, EF1658, and EF1661) (53, 54). Thereby, one ATP is formed per branched-chain amino acid and...”
- Comparative genomics of enterococci: variation in Enterococcus faecalis, clade structure in E. faecium, and defining characteristics of E. gallinarum and E. casseliflavus
Palmer, mBio 2012 - “...is specific to E . faecalis , as are genes ( bkdDABC ; EF1661 to EF1658) encoding a previously characterized branched-chain -keto acid dehydrogenase complex ( 53 ). The eutBC genes (EF1629 and EF1627, respectively) directing ethanolamine catabolism and the formate dehydrogenase gene fdhA (EF1390) are...”
- Transcriptional responses of Enterococcus faecalis V583 to bovine bile and sodium dodecyl sulfate
Solheim, Applied and environmental microbiology 2007 - “...exact test; data not shown). The bkd operon (EF1658 to -63), which encodes the branched-chain -keto acid dehydrogenase complex in V583, was downregulated at...”
- Comparison of OG1RF and an isogenic fsrB deletion mutant by transcriptional analysis: the Fsr system of Enterococcus faecalis is more than the activator of gelatinase and serine protease
Bourgogne, Journal of bacteriology 2006 - “...ATP:cob(I)alamin adenosyltransferase pduv Valine, leucine, and isoleucine degradation EF1658 EF1659 EF1660 EF1661 EF1662 EF1663 bkdC bkdB bkdA bkdD buk ptb 5 6...”
- “...fsrB (Fig. 2B). For the second set of genes (ef1658 to -1663), expression was only partially repressed in the parent strain. However, the level of regulation...”
- Comparative analysis of proteomic adaptations in Enterococcus faecalis and Enterococcus faecium after long term bile acid exposure
Dreyer, BMC microbiology 2024 - “...citrate- and folate metabolism, e.g. the dihydrolipoamide acetyltransferase component BkdC of the pyruvate dehydrogenase complex (Q834J2), the citrate ligase CitC (Q82YW0), the dihydrofolate reductase FolA (Q834R2), or the 5-formyltetrahydrofolate cyclo-ligase (Q830J1), was only observed in E. faecalis , but not in E. faecium . Together, our...”
NP_250277 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase from Pseudomonas aeruginosa PAO1
Q9I3D2 Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
PA1586 dihydrolipoamide acetyltransferase from Pseudomonas aeruginosa PAO1
27% identity, 89% coverage
- Identification of complex III, NQR, and SDH as primary bioenergetic enzymes during the stationary phase of Pseudomonas aeruginosa cultured in urine-like conditions
Hu, Frontiers in microbiology 2024 - “...2,226 idh Isocitrate dehydrogenase PA1585 NP_250276 2,832 sucA 2-Ketoglutarate dehydrogenase 2-oxoglutarate dehydrogenase subunit E1 PA1586 NP_250277 1,230 sucB 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase PA1588 NP_250279 1,167 sucC Succinyl-coenzyme A synthetase Succinyl-CoA ligase subunit beta PA1589 NP_250280 888 sucD Succinyl-CoA ligase subunit alpha PA1583 NP_250274 1773 sdhA...”
- Proteomic approach to identify host cell attachment proteins provides protective Pseudomonas aeruginosa vaccine antigen FtsZ
Jurado-Martín, NPJ vaccines 2024 - “...47.7 5.95 P47204 Cell division protein (FtsZ) LES 431, 57P31PA, A5803 4 39.119.0 41.2 4.91 Q9I3D2 Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase (SucB) LES 431, 57P31PA, A5803 4 35.526.4 42.9 5.4 P09591 Elongation factor Tu (EF-Tu) LES 431, 57P31PA, A5803 4 53.424.2 43.4 5.22 Q9I1N7 Mannose-1-phosphate...”
- Protein Interaction Networks of Catalytically Active and Catalytically Inactive PqsE in Pseudomonas aeruginosa
Taylor, mBio 2022 - “...pqsE pqsE 1.373327247 Q59637 aceE aceA 1.392137097 P30718 groL groL 1.415037499 Q02H54 groS groS 1.60823228 Q9I3D2 sucB sucB 1.694321257 Q59638 aceF aceF 1.805912948 Q51481 nirQ nirQ 5.158429363 10.1128/mbio.01559-22.2 FIGS2 Specificity-filtered interactions with eGFP-PqsE(WT) (a) and eGFP-PqsE(D73A) (b) in either WT or rhlR P. aeruginosa . Shapes...”
- Label-Free Quantitative Proteomics Distinguishes General and Site-Specific Host Responses to Pseudomonas aeruginosa Infection at the Ocular Surface
Yeung, Proteomics 2020 - “...1 Translation, post-translational modification, degradation Q9HZ71 rpsA 30S ribosomal protein S1 Translation, post-translational modification, degradation Q9I3D2 sucB Dihydrolipoyllysine-residue succinyltransferase Energy metabolism Q9I4Z4 pal Peptidoglycan-associated lipoprotein Transport of small molecules; membrane proteins Q9I690 PA0423 UPF0312 protein PA0423 Secreted factors (toxins, enzymes, alginate) Q9I6Z3 ahpC Alkyl hydroperoxide reductase...”
- Identification of complex III, NQR, and SDH as primary bioenergetic enzymes during the stationary phase of Pseudomonas aeruginosa cultured in urine-like conditions
Hu, Frontiers in microbiology 2024 - “...NP_251314 2,226 idh Isocitrate dehydrogenase PA1585 NP_250276 2,832 sucA 2-Ketoglutarate dehydrogenase 2-oxoglutarate dehydrogenase subunit E1 PA1586 NP_250277 1,230 sucB 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase PA1588 NP_250279 1,167 sucC Succinyl-coenzyme A synthetase Succinyl-CoA ligase subunit beta PA1589 NP_250280 888 sucD Succinyl-CoA ligase subunit alpha PA1583 NP_250274 1773...”
- Comparisons of Two Proteomic Analyses of Non-Mucoid and Mucoid Pseudomonas aeruginosa Clinical Isolates from a Cystic Fibrosis Patient
Rao, Frontiers in microbiology 2011 - “...0.2466 1.40 0.0001 1.26 45 PA4386 GroES protein 11 0.98 0.8852 0.84 0.0355 0.91 91 PA1586 Dihydrolipoamide succinyltransferase SucB 6 1.00 0.9967 0.77 0.0230 0.88 120 PA4315 Transcriptional regulator MvaT, P16 subunit 5 1.00 0.9881 0.70 0.0003 0.85 11 PA1596 Heat shock protein HtpG 20 0.84...”
- Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits
Dessimoz, Nucleic acids research 2006 - “...3: NMB0956), Pasteurella multocida (1: PM0894, 3: PM0278), Pseudomonas aeruginosa (1: PA5016, 2: PA2249, 3: PA1586), Rhizobium loti (2: mll4471, 3: mll4300, 4a: mlr0385, 4b: mll3627), Rhizobium meliloti (2: SMc03203, 3a: SMc02483, 3b: SMb20019, 4: SMc01032), Rickettsia conorii (3: RC0226, 4: RC0764), Rickettsia prowazekii (3: RP179,...”
BC1251 Dihydrolipoamide succinyltransferase component (E2) of 2-oxoglutarate dehydrogenase complex from Bacillus cereus ATCC 14579
28% identity, 88% coverage
HD73_3216 dihydrolipoamide acetyltransferase family protein from Bacillus thuringiensis serovar kurstaki str. HD73
28% identity, 92% coverage
- Identification of metabolism pathways directly regulated by sigma(54) factor in Bacillus thuringiensis
Peng, Frontiers in microbiology 2015 - “...alpha 25.424 HD73_3214 TPP-dependent acetoin dehydrogenase E1 alpha-subunit 19.979 HD73_3215 Acetoin:2,6-dichlorophenolindophenol oxidoreductase subunit beta 9.610 HD73_3216 Dihydrolipoyllysine-residue acetyltransferase component of acetoin cleaving system 9.326 HD73_3217 Dihydrolipoyl dehydrogenase 4.337 HD73_4161 Proline dipeptidase 103.525 HD73_4468 Phosphate butyryltransferase 6.110 HD73_4467 Leucine dehydrogenase - HD73_4466 Branched-chain-fatty-acid kinase 2.728 HD73_4465 Dihydrolipoamide...”
Pnuc_0841 2-oxoglutarate dehydrogenase, E2 subunit, dihydrolipoamide succinyltransferase from Polynucleobacter sp. QLW-P1DMWA-1
29% identity, 93% coverage
Q8GCY1 dihydrolipoyllysine-residue succinyltransferase (EC 2.3.1.61) from Bartonella vinsonii (see paper)
26% identity, 89% coverage
BC1G_03362 hypothetical protein from Botrytis cinerea B05.10
28% identity, 77% coverage
Afu1g00490 biotin-dependent 2-oxo acid dehydrogenases acyltransferase, putative from Aspergillus fumigatus Af293
28% identity, 76% coverage
- Evolutionary Analysis of Sequence Divergence and Diversity of Duplicate Genes in Aspergillus fumigatus
Yang, Evolutionary bioinformatics online 2012 - “...2.05 [2.19, 1.37] Afu1g14380 1.45 [2.37, 2.34] Afu7g00840 2.58 [2.11, 0.66] Afu4g12010 1.46 [1.53, 0.66] Afu1g00490 4.07 [1.97, 0.91] Afu4g13310 1.49 [1.57, 0.69] Afu5g12770 2.20 [2.17, 1.20] Afu1g00540 1.54 [1.78, 1.00] Afu8g04060 1.74 [1.85, 0.86] Afu2g10920 1.57 [2.32, 2.09] Afu3g03410 1.95 [2.24, 1.52] Afu8g04070 1.66 [1.85,...”
B7PEH7 Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex (Fragment) from Ixodes scapularis
30% identity, 87% coverage
lp_2152 pyruvate dehydrogenase complex, E2 component; dihydrolipoamide S-acetyltransferase from Lactobacillus plantarum WCFS1
F9UQ91 Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex from Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)
29% identity, 85% coverage
- Transcriptional Reprogramming at Genome-Scale of Lactobacillus plantarum WCFS1 in Response to Olive Oil Challenge
Esteban-Torres, Frontiers in microbiology 2017 - “...( fabZ, fabI ) phases. Among the repressed genes, two coded for the E2 ( lp_2152 ) and E3 ( lp_2151 ) subunits of the pyruvate dehydrogenase (PDH) complex, which produces acetyl-coA to feed the FAB pathway. Further related with the PDH complex, the gene coding...”
- Functional analysis of the role of CggR (central glycolytic gene regulator) in Lactobacillus plantarum by transcriptome analysis
Rud, Microbial biotechnology 2011 - “...oxidase 2.3 lp_1112 fum Fumarate hydratase 0.8 lp_2151 pdhD Pyruvate dehydrogenase complex, E3 component 2.8 lp_2152 pdhC Pyruvate dehydrogenase complex, E2 component 3.0 lp_2153 pdhB Pyruvate dehydrogenase complex, E1 component, beta subunit 3.7 1.0 lp_2154 pdhA Pyruvate dehydrogenase complex, E1 component, alpha subunit 4.1 0.9 1.1...”
- Identification of prebiotic fructooligosaccharide metabolism in Lactobacillus plantarum WCFS1 through microarrays
Saulnier, Applied and environmental microbiology 2007 - “...lp_1398 lp_1481 lp_1498 lp_1499 lp_2096 lp_2097 lp_2151 lp_2152 lp_2153 lp_2154 lp_2371 lp_2757 lp_2684 lp_2776 lp_2794 lp_2920 lp_2969 lp_3010 lp_3011 lp_3045...”
- Inorganic phosphate modifies stationary phase fitness and metabolic pathways in Lactiplantibacillus paraplantarum CRL 1905
Araoz, Frontiers in microbiology 2024 - “...dehydrogenase complex, E1 component, alpha subunit * pdhB F9UQ92 Pyruvate dehydrogenase complex, E1 2.8 pdhC F9UQ91 Component, beta subunit Pyruvate dehydrogenase complex, 4.9 pox3 F9URC8 Dihydrolipoamide acetyltransferase * ack2 F9UTR4 Pyruvate oxidase * glpK1 Q88ZF1 Acetate kinase 1.8 pflB F9UTJ5 Glycerol kinase 1 * lp_2150 F9UQ89...”
- Identification of key proteins and pathways in cadmium tolerance of Lactobacillus plantarum strains by proteomic analysis.
Zhai, Scientific reports 2017 - “...F9UMS1 fum; fumarate hydratase 3.81 F9UQ90 pdhD; pyruvate dehydrogenase complex, E3 component; dihydrolipoamide dehydrogenase 1.90 F9UQ91 pdhC; pyruvate dehydrogenase complex, E2 component; dihydrolipoamide S-acetyltransferase 2.30 F9UQ92 pdhB; pyruvate dehydrogenase complex, E1 component, beta subunit 2.21 F9UQ93 pdhA; pyruvate dehydrogenase complex, E1 component, alpha subunit 2.12 Pyruvate...”
FRAAL3226 putative dihydrolipoamide acyltransferase component E2 from Frankia alni ACN14a
36% identity, 53% coverage
- The Proteogenome of Symbiotic Frankia alni in Alnus glutinosa Nodules
Pujic, Microorganisms 2022 - “...C1, C1c, C4 0.000 WP_041938916.1 FRAAL1429 hpnD Phytoene synthase HpnD 8.40 I A 0.003 WP_011604375.1 FRAAL3226 bkdC Branched-chain alpha-keto acid dehydrogenase subunit BkdC 8.14 C A 0.000 WP_041940119.1 FRAAL0708 Lipid esterase 7.91 R C1, C2, C3, C4 0.000 WP_011602626.1 FRAAL1431 fppS Farnesyl diphosphate synthase 7.75 H...”
TC0518 pyruvate dehydrogenase, E2 component, dihydrolipoamide acetyltransferase, putative from Chlamydia muridarum Nigg
26% identity, 86% coverage
- Outer membrane proteins preferentially load MHC class II peptides: implications for a Chlamydia trachomatis T cell vaccine
Karunakaran, Vaccine 2015 - “...I Q TD V D 75% CT237 (FabG) G SPGQTNYAAAKAGIIGFS TC0508 SPGQTNYAAAKAGIIGFS 90% CT247(PdhC) GTKTPIGTPIAVFSTEQ TC0518 E GTK I PIGTPIAVFSTEQ N 87% CT424 (RsbV) KLDGVSSPAVQESISE SL TC0707 KLDGVSSPAVQESISE 96% CT375 YDHIIVTPGANADIL PE TC0654 YDHIIVTPGANADIL 85% CT505 (GapA) DSTHGSFAPQATFSDG TC0792 MTTVHAATATQSVVD 95% CT514 (RplF) VKGNEVFV T PAAH...”
- Immunization with live and dead Chlamydia muridarum induces different levels of protective immunity in a murine genital tract model: correlation with MHC class II peptide presentation and multifunctional Th1 cells
Yu, Journal of immunology (Baltimore, Md. : 1950) 2011 - “...organisms for 24 h ( 18 ). Thus 10 new C. muridarum T cell epitopes (TC0518, FusA, TC0884, Tuf, TC0654, TC0190, Tsf, PmpE/F-1, AtpE; Table I ) were identified in the current study. Explanation for the different Ag repertoires presented by live and dead C. muridarum...”
- “...Polymorphic membrane protein F PmpE/F-2 GRDLNVTGPKIQTDVDL (7) Hypothetical protein TC0420 TC0420 EGTKIPIGTPIAVFSTEQN (4) Pyruvate dehydrogenase TC0518 GANAIPVHCPIGAESQ (3) Elongation factor G FusA VFWLGSKINIIDTPG (1) Elongation factor G FusA SVPSYVYYPSGNRAPVV (2) Thiol-disulfide interchange protein TC0884 FEVQLISPVALEEGMR (2) Elongation factor Tu Tuf YDHIIVTPGANADIL (1) Oxidoreductase TC0654 LPLMIVSSPKASESGAA (1)...”
SMU_129 dihydrolipoamide acetyltransferase from Streptococcus mutans UA159
26% identity, 80% coverage
EY04_RS01835 dihydrolipoyllysine-residue acetyltransferase from Pseudomonas chlororaphis
30% identity, 56% coverage
SPO0343, YP_165606 2-oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase from Silicibacter pomeroyi DSS-3
27% identity, 91% coverage
- An Updated genome annotation for the model marine bacterium Ruegeria pomeroyi DSS-3
Rivers, Standards in genomic sciences 2014 - “...ORF position YP_165330 SPO0056 Hypothetical protein ORF position YP_165481 SPO0212 Hypothetical protein ORF position YP_165606 SPO0343 2-oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase sucB ORF position YP_165666 SPO0403 Conserved domain protein ORF position YP_165678 SPO0415 D-isomer specific 2-hydroxyacid dehydrogenase family protein ORF position YP_165703 SPO0440 Thioesterase family...”
- “...protein ORF position YP_165330 SPO0056 Hypothetical protein ORF position YP_165481 SPO0212 Hypothetical protein ORF position YP_165606 SPO0343 2-oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase sucB ORF position YP_165666 SPO0403 Conserved domain protein ORF position YP_165678 SPO0415 D-isomer specific 2-hydroxyacid dehydrogenase family protein ORF position YP_165703 SPO0440 Thioesterase...”
SPO0343 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase from Ruegeria pomeroyi DSS-3
27% identity, 72% coverage
- An Updated genome annotation for the model marine bacterium Ruegeria pomeroyi DSS-3
Rivers, Standards in genomic sciences 2014 - “...ORF position YP_165330 SPO0056 Hypothetical protein ORF position YP_165481 SPO0212 Hypothetical protein ORF position YP_165606 SPO0343 2-oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase sucB ORF position YP_165666 SPO0403 Conserved domain protein ORF position YP_165678 SPO0415 D-isomer specific 2-hydroxyacid dehydrogenase family protein ORF position YP_165703 SPO0440 Thioesterase family...”
Tfu_3051 pyruvate dehydrogenase complex, E2 component, dihydrolipoamide acetyltransferase from Thermobifida fusca YX
28% identity, 85% coverage
- The Effects of Carbon Source and Growth Temperature on the Fatty Acid Profiles of Thermobifida fusca
Winkelman, Frontiers in molecular biosciences 2022 - “...acid methyl transferase Tfu_2160 BfaA 10-methylene BCFA reductase Tfu_2161 PDH Pyruvate Dehydrogenase Complex Tfu_3049, Tfu_3050, Tfu_3051 ACK Acetate Kinase Tfu_2971 ACS-AMP AMP-Forming Acetyl-CoA Synthetase Tfu_1546, Tfu_2808, Tfu_2856 ACS-ADP ADP-Forming Acetyl-CoA Synthetase Tfu_1302, Tfu_1473 CCL Citryl-CoA lyase Tfu_0341, Tfu_1285, Tfu_1313 ALS Acetolactate synthase Tfu_0611, Tfu_0612 FIGURE 4...”
- “...including the oxidative decarboxylation of pyruvate catalyzed by the pyruvate dehydrogenase complex (PDH) (Tfu_3049, Tfu_3050, Tfu_3051). Alternatively, acetyl-CoA can be generated through the activation of acetate catalyzed by: 1) an acetate kinase (Tfu_2971); 2) an AMP-forming acetyl-CoA synthetase (Tfu_1546, Tfu_2808, Tfu_2856); or 3) an ADP-forming acetyl-CoA...”
U876_02130 pyruvate dehydrogenase complex dihydrolipoyllysine-residue acetyltransferase from Aeromonas hydrophila NJ-35
29% identity, 58% coverage
ACIAD2875 dihydrolipoamide succinyltransferase, component of 2-oxoglutarate dehydrogenase complex (E2) from Acinetobacter sp. ADP1
27% identity, 91% coverage
GYA98_RS08685 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase from Bacillus velezensis
27% identity, 89% coverage
- Comparative transcriptome analysis reveals the biocontrol mechanism of Bacillus velezensis E68 against Fusarium graminearum DAOMC 180378, the causal agent of Fusarium head blight
Liang, PloS one 2023 - “...the TCA cycle: 2 citrate synthases (GYA98_RS03820, 12240), aconitase (GYA98_RS08030), isocitrate dehydrogenase (GYA98_RS12235), 2-oxoglutarate dehydrogenase (GYA98_RS08685, 08690), succinate dehydrogenase (GYA98_RS11900, 11905), succinyl-CoA ligase (GYA98_RS07090, 07095) and fumarate dehydrogenase (GYA98_RS14210), as well as a citrate/malate transporter (GYA98_RS17095) ( S2 Table ). Malate dehydrogenase (GYA98_RS12230), which was not...”
PF3D7_0303700, XP_001351112 lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex from Plasmodium falciparum 3D7
O97227 Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex from Plasmodium falciparum (isolate 3D7)
24% identity, 81% coverage
- The mitochondrion of Plasmodium falciparum is required for cellular acetyl-CoA metabolism and protein acetylation
Nair, Proceedings of the National Academy of Sciences of the United States of America 2023 - “...the decarboxylation reaction is conjugated to a lipoate cofactor covalently attached to the E2 subunit (PF3D7_0303700) and is then transferred to CoA to form acetyl-CoA. To prepare for the next catalytic cycle, the E3 subunit oxidizes the lipoate cofactor, reforming the dithiolane ring ( 34 )...”
- “...Transfections to Generate Knockout and Knockdown Lines. For deletion of mpdh E1 (PF3D7_1312600), mpdh E2 (PF3D7_0303700), e3 (PF3D7_1232200), kdh E2 (PF3D7_1320800), and lipl2 (PF3D7_0923600), 300 L red blood cells were electroporated with 75g each of gene-specific pRSng and pCasG plasmids. For the generation of acs (PF3D7_0627800)-...”
- A novel lipoate attachment enzyme is shared by Plasmodium and Chlamydia species
Afanador, Molecular microbiology 2017 - “...). Three lipoylated substrates have been localized to the mitochondrion: the branched chain dehydrogenase (BCDH) (PF3D7_0303700), the -ketoglutarate dehydrogenase (KDH) (PF3D7_1320800), and the H-protein (PF3D7_1132900) of the GCV ( Spalding et al. , 2010 ; Afanador et al. , 2014 ). These three mitochondrial proteins are...”
- “...Protein expression and purification Cloning, expression and purification of the lipoylation domains of Pf BCDH (PF3D7_0303700) and Pf KDH (PF3D7_1320800), the H-protein (PF3D7_1132900), as well as LipL1 (PF3D7_1314600) and LipL2 (PF3D7_0923600) were previously described ( Afanador et al. , 2014 ). The genes encoding the lipoylation...”
- Crystal structure of lipoate-bound lipoate ligase 1, LipL1, from Plasmodium falciparum
Guerra, Proteins 2017 - “...in the parasite mitochondrion: the E2 component of the branched chain a-ketoacid dehydrogenase complex (BCDH, PF3D7_0303700), the E2 component of the -ketoglutarate dehydrogenase complex (KDH, PF3D7_1320800), and the H-protein of the glycine cleavage system (PF3D7_1132900). 9 , 14 , 15 The lipoylation of these three proteins...”
- Biochemical and structural characterization of the apicoplast dihydrolipoamide dehydrogenase of Plasmodium falciparum
Laine, Bioscience reports 2015 - “...Procedure. The levels of mitochondrial proteins such as branched chain -keto acid dehydrogenase E2 (BCDH-E2; PF3D7_0303700) were elevated in all mutant parasite clones although this particularly pronounced in clone 21. This tendency correlated well with increased levels of mitochondrial NADP + -dependent ICDH (isocitrate dehydrogenase; PF3D7_1345700)...”
- Genome-wide transcriptome profiling reveals functional networks involving the Plasmodium falciparum drug resistance transporters PfCRT and PfMDR1
Adjalley, BMC genomics 2015 - “...S14). Interestingly, the two clusters also contained PF3D7_0823300 that encodes the histone acetyltransferase GCN5 and PF3D7_0303700, a gene involved in lipoamide synthesis, which is in concordance with a recent study reporting the co-expression of pfcrt with lipoamide synthesis genes [ 59 ]. Altogether these observations suggest...”
- Redox-dependent lipoylation of mitochondrial proteins in Plasmodium falciparum
Afanador, Molecular microbiology 2014 - “..., 2003 ) was used to identify the genes encoding the E2 subunits of BCDH (PF3D7_0303700) and KDH (PF3D7_1320800). Nucleotides encoding the first 30 amino acids of both proteins were amplified from cDNA extracted from erythrocytic stage Plasmodium falciparum 3D7 parasites using primers BCDH 30 .AvrII.F...”
- Apicoplast lipoic acid protein ligase B is not essential for Plasmodium falciparum
Günther, PLoS pathogens 2007 - “...P. falciparum ACP (XP_001349595; AAC71866), P. falciparum apicoplast lipoamide dehydrogenase (XP_001349365; CAD51214), P. falciparum BCDH-E2 (XP_001351112; CAB38991), P. falciparum enoyl-ACP reductase (FabI) (XP_966137; CAG25389), P. falciparum H-protein (XP_001348010; AAN35923), P. falciparum KGDH-E2 (XP_001349947; CAD52355), P. falciparum LipA (XP_001350160; CAD52569), P. falciparum LipB (XP_001349288; CAD51137), P. falciparum...”
- Plasmodium falciparum immunodominant IgG epitopes in subclinical malaria
Azcárate, Scientific reports 2020 - “...SC (very high) ALL (MR predominant) 33 Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex BCKDH-E2 O97227 707 43 60 9 Mitochondrion/acetyltransferase activity Metabolism Sexual & Asexual Early TR-Early SC MR, GM, TR (GM predominant) 30 Ferredoxin reductase-like protein Q8IBP8 279 36 60 8 Oxidoreductase Metabolism Sexual...”
APL_0772 dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex (E2) from Actinobacillus pleuropneumoniae L20
25% identity, 57% coverage
P10802 Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex from Azotobacter vinelandii
31% identity, 56% coverage
Dshi_2884 2-oxoglutarate dehydrogenase, E2 subunit, dihydrolipoamide succinyltransferase from Dinoroseobacter shibae DFL 12
27% identity, 73% coverage
PPA0693 dihydrolipoamide acyltransferase from Propionibacterium acnes KPA171202
28% identity, 80% coverage
- Vitamin B12 modulates the transcriptome of the skin microbiota in acne pathogenesis
Kang, Science translational medicine 2015 - “...B12 with differential expression between Day0 and Day14 samples ( table S6 ). Among them, PPA0693 encodes the E2 component of the 2-oxoglutarate dehydrogenase complex, which functions in the tricarboxylic acid (TCA) cycle. It was down-regulated in all the healthy subjects after vitamin B12 supplementation (fold...”
- “...vitamin B12 and is involved in acne pathogenesis. We further investigated the potential role of PPA0693 in acne pathogenesis. Based on the metabolic pathways in P. acnes ( Fig. 2 ), 2-oxoglutarate dehydrogenase complex converts 2-oxoglutarate to succinyl-CoA. 2-oxoglutarate is a substrate for the biosynthesis of...”
- A combination of improved differential and global RNA-seq reveals pervasive transcription initiation and events in all stages of the life-cycle of functional RNAs in Propionibacterium acnes, a major contributor to wide-spread human disease
Lin, BMC genomics 2013 - “...IF-2 (PPA1493) and IF-3 (PPA1414) and central metabolism enzymes, e.g. alanine dehydrogenase (PPA2274), dihydrolipoamide acyltransferase (PPA0693), uridylate kinase (PPA1519), 3-oxoacyl-(acyl-carrier-protein) reductase (PPA1533), cytochrome d ubiquinol oxidase subunit I (PPA0176), fructose-1,6-bisphosphate aldolase (PPA2024), isopentenyl diphosphate delta isomerase (PPA2115), nitric-oxide reductase subunit B (PPA1975), and polynucleotide phosphorylase (PPA1471)....”
SO_0425 pyruvate dehydrogenase complex, E2 component, dihydrolipoamide acetyltransferase from Shewanella oneidensis MR-1
27% identity, 53% coverage
A0A075R422 Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex from Brevibacillus laterosporus LMG 15441
26% identity, 80% coverage
MXAN_2668 pyruvate dehydrogenase complex , E2 component, dihydrolipoamide acetyltransferase from Myxococcus xanthus DK 1622
29% identity, 69% coverage
- Peripheral rods: a specialized developmental cell type in Myxococcus xanthus
Whitfield, Genomics 2020 - “...MxDK1622 tag Stationary/Peripheral PdhC dehydrogenase MXAN_2666 2.47 PdhC dihydrolipoate dehydrogenase MXAN_2667 2.21 PdhC dihydrolipoamide acetyltransferase MXAN_2668 3.29 Malate dehydrogenase MXAN_3538 3.01 Succinate CoA ligase MXAN_3542 2.21 Cytochrome c MXAN_5560 2.20 The numbers in the final column represent log2FoldChange. Positive values demonstrate an upregulation of transcripts....”
BC2777 Dihydrolipoamide acetyltransferase component of acetoin dehydrogenase complex from Bacillus cereus ATCC 14579
28% identity, 91% coverage
TpMuguga_01g00262 dihydrolipoyllysine-residue succinyltransferase from Theileria parva strain Muguga
26% identity, 81% coverage
- Characterization of the Theileria parva sporozoite proteome
Nyagwange, International journal for parasitology 2018 - “...(TpMuguga_01g01182); PC, pyruvate carboxylase; ACH, aconitate hydratase-1 (TpMuguga_01g01050); IDH, isocitrate dehydrogenase (TpMuguga_04g00620); OGDH, oxoglutarate dehydrogenase (TpMuguga_01g00262); SCL, succinyl coenzyme A ligase (TpMuguga_04g00660); SDH, succinate dehydrogenase (TpMuguga_01g00210); FH, fumarate hydratase-1 (TpMuguga_03g00078); MDH, malate dehydrogenase; MQOR, Malate: quinone oxidoreductase (TpMuguga_03g00758); CS, citrate synthase (TpMuguga_02g00666); PEPC, phosphoenolpyruvate carboxylase; PEPCK,...”
Q8CSL9 Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex from Staphylococcus epidermidis (strain ATCC 12228 / FDA PCI 1200)
24% identity, 88% coverage
- The Extracellular Vesicles from the Commensal Staphylococcus Epidermidis ATCC12228 Strain Regulate Skin Inflammation in the Imiquimod-Induced Psoriasis Murine Model
Gómez-Chávez, International journal of molecular sciences 2021 - “...O Q8CTA6 COG0396 - ABC transporter (ATP-binding protein) C Q8CN04 COG1012 rocA 1-Pyrroline-5-carboxylate dehydrogenase C Q8CSL9 COG0508 odhB Dihydrolipoyllysine-residue succinyltransferase C Q8CPH5 COG0045 sucC Succinyl-CoA ligase (ADP-forming) subunit beta C Q8CNX4 COG0538 Icd Isocitrate dehydrogenase (NADP) C Q8CP83 COG0567 odhA 2-Oxoglutarate dehydrogenase E1 component C Q8CPL2...”
- “...of pyruvate dehydrogenase complex C Q8CPN3 COG1071 pdhA Pyruvate dehydrogenase E1 component, alpha subunit C Q8CSL9 COG0508 odhB Dihydrolipoyllysine-residue succinyltransferase, E2 component G Q8CPY5 COG0057 gapA1 Glyceraldehyde-3-phosphate dehydrogenase, type I E Q8CSR8 COG0174 glnA Putative uncharacterized protein F Q7CCJ0 COG0503 purR Purine operon repressor F Q8CRN4...”
SERP0985 2-oxoglutarate dehydrogenase, E2 component, dihydroipoamide succinyltransferase from Staphylococcus epidermidis RP62A
SERP_RS04930 dihydrolipoyllysine-residue succinyltransferase from Staphylococcus epidermidis RP62A
24% identity, 88% coverage
P16263 dihydrolipoyllysine-residue succinyltransferase (EC 2.3.1.61) from Bacillus subtilis (see paper)
BSU19360 dihydrolipoamide succinyltransferase from Bacillus subtilis subsp. subtilis str. 168
26% identity, 88% coverage
- Prediction of prkC-mediated protein serine/threonine phosphorylation sites for bacteria
Zhang, PloS one 2018 - “...serine/threonine residues. 10.1371/journal.pone.0203840.t001 Table 1 Experimentally identified prkC-specific phosphorylation sites. Acc Position Gene Organism PMID(s) P16263 182 odhB Bacillus subtilis 24390483 P38494 365 ypfD Bacillus subtilis 24390483 P37561 88 yabS Bacillus subtilis 24390483 P37561 90 yabS Bacillus subtilis 24390483 P45740 565 thiC Bacillus subtilis 24390483 P42974...”
- “...prkC-PSP predictor. Here, we presented the Bacillus subtilis odhB, ypfD and tal proteins (UniProt accessions: P16263, P38494 and P12425) as examples to demonstrate the simplicity and precision of the prkC-PSP. These sequences were pasted into the text box, and the high threshold was chosen; then, we...”
- Arginine phosphorylation marks proteins for degradation by a Clp protease
Trentini, Nature 2016 - “...O34645 melA Alpha-galactosidase R56 R56 O34338 mntB Mn transport ATP-binding prot. MntB R132, (R73) R132 P16263 odhB 2-oxoglutarate dehydrogenase E2 R300 P12875 rplN 50S ribosomal prot. L14 R17 R17 P42060 rplV 50S ribosomal prot. L22 R11 P12879 rpsH 30S ribosomal prot. S8 R47, R72, R79 R47,...”
- Correction: Comprehensive Analysis of Temporal Alterations in Cellular Proteome of Bacillus subtilis under Curcumin Treatment
Reddy, PloS one 2015 - “...P23129 2-oxoglutarate dehydrogenase E1 component OdhA 35.28 27 1.37 2.90 1.96 14 1.113 1.911 1.634 P16263 Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex OdhB 54.44 18 1.18 2.51 3.30 13 1.101 1.669 2.818 P80865 Succinyl-CoA ligase [ADP-forming] subunit alpha SucD 33.00 6 1.12 2.73 3.39 4...”
- Comprehensive analysis of temporal alterations in cellular proteome of Bacillus subtilis under curcumin treatment
Reddy, PloS one 2015 - “...P23129 2-oxoglutarate dehydrogenase E1 component OdhA 35.28 27 1.37 2.90 1.96 14 1.286 2.223 1.744 P16263 Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex OdhB 54.44 18 1.18 2.51 3.30 13 2.203 4.063 3.053 P80865 Succinyl-CoA ligase [ADP-forming] subunit alpha SucD 33.00 6 1.12 2.73 3.39 4...”
- Biochemical and molecular characterization of the Alcaligenes eutrophus pyruvate dehydrogenase complex and identification of a new type of dihydrolipoamide dehydrogenase
Hein, Journal of bacteriology 1994 - “...Pseudomonas putida Rat Bovine Human P06959 P10802 P21883 P20708 P16263 P07016 P09062 Q01205 P11181 P11182 58.3 53.2 37.7 34.9 33.1 33.0 32.7 29.2 28.7 28.5 549...”
- Identification of an RNA sponge that controls the RoxS riboregulator of central metabolism in Bacillus subtilis
Durand, Nucleic acids research 2021 - “...acid degradation, CitZ BSU29140 0.95 RoxS and FsrA RoxS Citrate synthase 2 TCA Cycle OdhB BSU19360 0.87 RoxS TCA Cycle 2-oxoglutarate dehydrogenase complex OdhA BSU19370 0.85 RoxS TCA Cycle 2-oxoglutarate dehydrogenase (E1 subunit) SucC BSU16090 0.84 RoxS RoxS Succinyl-CoA synthetase (beta subunit) TCA Cycle YvyI/Pmi BSU35790...”
- Secondary structural entropy in RNA switch (Riboswitch) identification
Manzourolajdad, BMC bioinformatics 2015 - “...665425 665581 forward BSU06130 ydjC -677 0.3439 1963 gutB BSU06150 0.846 58 2106272 2106428 reverse BSU19360 odhB -1154 0.3949 79 yocR BSU19340 0.846 59 226409 226565 forward BSU02050 ybdO -82 0.3885 79 ybxG BSU02060 0.844 60 2106333 2106489 forward BSU19330 sodF -1353 0.3885 79 yocS BSU19350...”
- “...665425 665581 forward BSU06130 ydjC -677 0.3439 1963 gutB BSU06150 0.846 33 2106272 2106428 reverse BSU19360 odhB -1154 0.3949 79 yocR BSU19340 0.846 34 226409 226565 forward BSU02050 ybdO -82 0.3885 79 ybxG BSU02060 0.844 35 2106333 2106489 forward BSU19330 sodF -1353 0.3885 79 yocS BSU19350...”
C1G4D1 Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex from Paracoccidioides brasiliensis (strain Pb18)
PADG_01797 uncharacterized protein from Paracoccidioides brasiliensis Pb18
28% identity, 74% coverage
- Effect of Nitrosative Stress on the S-Nitroso-Proteome of Paracoccidioides brasiliensis
Navarro, Frontiers in microbiology 2020 - “...ribosomal protein S5 700.02 PADG_00446 C1G0Q6 Uncharacterized protein 459.28 PADG_05032 C1GBN1 Uncharacterized protein 458.46 PADG_01797 C1G4D1 Uncharacterized protein 279.19 PADG_00443 C1G0Q3 Dihydropteroate synthase 188.75 PADG_07627 C1GK41 Uncharacterized protein 180.29 PADG_07370 C1GJD4 Uncharacterized protein 172.67 PADG_00210 C1G020 Glycine dehydrogenase 156.30 PAD.G_04192 C1GAA6 Uncharacterized protein 122.04 PADG_01100 C1FZ74...”
- Effect of Nitrosative Stress on the S-Nitroso-Proteome of Paracoccidioides brasiliensis
Navarro, Frontiers in microbiology 2020 - “...40S ribosomal protein S5 700.02 PADG_00446 C1G0Q6 Uncharacterized protein 459.28 PADG_05032 C1GBN1 Uncharacterized protein 458.46 PADG_01797 C1G4D1 Uncharacterized protein 279.19 PADG_00443 C1G0Q3 Dihydropteroate synthase 188.75 PADG_07627 C1GK41 Uncharacterized protein 180.29 PADG_07370 C1GJD4 Uncharacterized protein 172.67 PADG_00210 C1G020 Glycine dehydrogenase 156.30 PAD.G_04192 C1GAA6 Uncharacterized protein 122.04 PADG_01100...”
Poly24_28990 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase from Rosistilla carotiformis
27% identity, 90% coverage
- Rosistilla oblonga gen. nov., sp. nov. and Rosistilla carotiformis sp. nov., isolated from biotic or abiotic surfaces in Northern Germany, Mallorca, Spain and California, USA
Waqqas, Antonie van Leeuwenhoek 2020 - “...aceE CA51_39170 Mal33_37970 Poly24_43390 Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex 2.3.1.12 aceF CA51_39160 Mal33_37980 Poly24_28990 Gluconeogenesis Phosphoenolpyruvate carboxylase 4.1.1.31 ppc CA51_23330 Mal33_54740 Poly24_29970 Pyruvate, phosphate dikinase 2.7.9.1 ppdK CA51_24710 Mal33_53210 Poly24_24110 Pyruvate carboxylase 6.4.1.1 pyc CA51_17250 Mal33_20070 Poly24_16690 Phosphoenolpyruvate carboxykinase (ATP) 4.1.1.49 pckA CA51_25590 Mal33_52570...”
- “...sucA CA51_08330 Mal33_06250 Poly24_05710 Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex 2.3.1.61 sucB CA51_18830 Mal33_19360 Poly24_28990 SuccinateCoA ligase [ADP-forming] subunit alpha 6.2.1.5 sucD CA51_28020 Mal33_49450 Poly24_21030 SuccinateCoA ligase [ADP-forming] subunit beta 6.2.1.5 sucC CA51_28010 Mal33_49460 Poly24_21040 Succinate dehydrogenase flavoprotein subunit 1.3.5.1 sdhA CA51_43190 Mal33_34540 Poly24_44610 Succinate...”
Q9L6H8 dihydrolipoyllysine-residue succinyltransferase (EC 2.3.1.61) from Brucella melitensis (see paper)
BMEI0141 DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE COMPONENT (E2) OF 2-OXOGLUTARATE DEHYDROGENASE COMPLEX from Brucella melitensis 16M
27% identity, 90% coverage
- Immuno-profiling of Brucella proteins for developing improved vaccines and DIVA capable serodiagnostic assays for brucellosis
Nandini, Frontiers in microbiology 2023 - “...dehydrogenase subunit beta BMEI0855 VirB8 BMEII0032 Hypothetical protein BMEI0563 Outer membrane lipoprotein BMEI0135 Dihydrolipoamide succinyltransferase BMEI0141 Flagellar hook-associated protein FlgL BMEII0161 Hypothetical protein BMEI0178 Hypothetical protein BMEI0805 Hypothetical protein BMEI0051 DNA gyrase subunit A BMEI0884 Thiol:disulfide interchange protein DsbA BMEI1440 Transcriptional regulatory protein MUCR BMEI1364 Molecular...”
- High-Resolution Melting PCR as Rapid Genotyping Tool for Brucella Species
Girault, Microorganisms 2022 - “...1010775-1010794 NR NR 99 T G B. melitensis Rev 1 139509 cttcacgccatgcttctttt 139556-139575 atgctcaccaccttcaacg 139483-139501 BMEI0141 dihydrolipoamide succinyltransferase component (e2) of 2-oxoglutarate dehydrogenase complex 93 T C microorganisms-10-00336-t002_Table 2 Table 2 Results of inclusivity tests. Expected SNP Profile (Inclusivity Test) Reference DNA Field DNA Total Expected...”
- Proteomic and Antibody Profiles Reveal Antigenic Composition and Signatures of Bacterial Ghost Vaccine of Brucella abortus A19
He, Frontiers in immunology 2022 - “...BMEII0032 0.223 3.04 BMEII1048 0.584 4.17 BMEI0587 0.5929 2.45 BMEI0587 0.459 4.52 BMEI0340 0.6625 1.92 BMEI0141 0.247 2.21 BMEI1236 0.5283 1.79 BMEI0340 0.466 2.05 BMEI0094 0.3343 1.51 BMEI1184 0.440 2.66 BMEII0735 0.0004 1.48 BMEI0339 0.281 1.76 BMEI1796 0.1411 0.91 BMEI0613 0.522 1.17 BMEI0668 0.0663 1.01 BMEI0135...”
- Antigen-specific acquired immunity in human brucellosis: implications for diagnosis, prognosis, and vaccine development
Cannella, Frontiers in cellular and infection microbiology 2012 - “...BMEI0856 Dihydrolipoamide acetyltransferase component of PyDH complex 46,721 BMEI1980 DNA protection during starvation protein 19,903 BMEI0141 Dihydrolipoamide succinyltransferase 42,911 BMEI0135 Outer membrane lipoprotein omp19 17,604 BMEI1060 Outer membrane protein 27,290 BMEI0786 Outer membrane protein (integral) 24,423 BMEI0587 Competence lipoprotein 34,770 BMEII0497 Enoyl-CoA hydratase/3-hydroxyacyl-CoA dehydrogenase/3-hydroxybutyryl-CoA epimerase 80,197...”
- Large scale immune profiling of infected humans and goats reveals differential recognition of Brucella melitensis antigens
Liang, PLoS neglected tropical diseases 2010 - “...BAB1_0522 BR0497 0.715 Chromosome Segregation Protein SMC BMEI0340 BAB1_1707 BR1695 0.889 Omp16 lipoprotein {Tibor, 1994} BMEI0141 BAB1_1922 BR1922 0.734 2-oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase BMEII0032 BAB2_0061 BRA0062 0.849 VirB8 BMEI0228 BAB1_1830 BR1822 0.719 Hypothetical protein BMEI1890 BAB1_0051 BR0054 0.866 Transporter BMEI0810 BAB1_1199 BR1177 0.918 COG1434...”
- “...patients. Three metabolic enzymes, acetyl coA carboxylase, (BMEI0503), Acetyl CoA carboxylase (BMEI0039 and 2-oxoglutarate dehydrogenase (BMEI0141) also represent novel serodiagnostic antigens for human brucellosis. The finding that these proteins are immunogenic suggests that they are expressed during B. melitensis infection of humans. A group of 16...”
- Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits
Dessimoz, Nucleic acids research 2006 - “...COG identifiers: Agrobacterium tumefaciens (2: AGl2719, 3: AGc4775, 4: AGc2641), Brucella melitensis (2: BMEII0746, 3: BMEI0141, 4: BMEI0856), Buchnera sp. (1: BU206, 3: BU303), E.coli K12 (COG identifier corresponds to the gene name: aceF, sucB), E.coli H7 (1: ECs0119, 3: ECs0752), Haemophilus influenzae (1: HI1232, 3:...”
- Selection of protective epitopes for Brucella melitensis by DNA vaccination
Yang, Infection and immunity 2005 - “...BMEII0036 BMEII0083 BMEII0017 BMEI0826 BMEII1003 BMEI1895 BMEI0141 BMEI0328 BMEI1954 BMEI1934 BMEII0885 BMEII0679 BMEII0702 BMEII0681 BMEI0748 a , Unnamed...”
Q7NZ50 Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex from Chromobacterium violaceum (strain ATCC 12472 / DSM 30191 / JCM 1249 / CCUG 213 / NBRC 12614 / NCIMB 9131 / NCTC 9757 / MK)
24% identity, 89% coverage
- The influence of iron on the proteomic profile of Chromobacterium violaceum
Lima, BMC microbiology 2014 - “...2.52323856021444 0.1701 Citrate synthase (GtlA) 30 Q7NQM5 3.90695002871913 0.2484 Fumarate hydratase class II (AspA) 35 Q7NZ50 3.90695002871913 0.2054 Dihydrolipoamide succinyltransferase E2 component (SucB) 21 Proteins of unknown function Q7NZQ3 3.32090752441126 0.3605 Putative uncharacterized protein (CV_0868) 26 Q7NQ40 3.71160252728317 0.4051 Putative uncharacterized protein (CV_4300) 20 Oxidative metabolism...”
FTA_0329 dihydrolipoamide acetyltransferase component / pyruvate dehydrogenase complex E2 component from Francisella tularensis subsp. holarctica FTA
25% identity, 67% coverage
ODO2_YEAST / P19262 Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial; DLST; 2-oxoglutarate dehydrogenase complex component E2; OGDC-E2; OGDHC subunit E2; Alpha-ketoglutarate dehydrogenase subunit E2; alpha-KGDHC subunit E2; Dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex; EC 2.3.1.61 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 4 papers)
P19262 dihydrolipoyllysine-residue succinyltransferase (EC 2.3.1.61) from Saccharomyces cerevisiae (see paper)
YDR148C Dihydrolipoyl transsuccinylase, component of the mitochondrial alpha-ketoglutarate dehydrogenase complex, which catalyzes the oxidative decarboxylation of alpha-ketoglutarate to succinyl-CoA in the TCA cycle; phosphorylated from Saccharomyces cerevisiae
25% identity, 79% coverage
- function: The 2-oxoglutarate dehydrogenase complex catalyzes the overall conversion of 2-oxoglutarate to succinyl-CoA and CO(2). It contains multiple copies of three enzymatic components: 2-oxoglutarate dehydrogenase (E1), dihydrolipoamide succinyltransferase (E2) and lipoamide dehydrogenase (E3).
catalytic activity: N(6)-[(R)-dihydrolipoyl]-L-lysyl-[2-oxoglutarate dehydrogenase complex component E2] + succinyl-CoA = N(6)-[(R)-S(8)- succinyldihydrolipoyl]-L-lysyl-[2-oxoglutarate dehydrogenase complex component E2] + CoA (RHEA:15213)
cofactor: (R)-lipoate Note=Binds 1 lipoyl cofactor covalently
subunit: Component of the 2-oxoglutarate dehydrogenase complex (OGDC), also called alpha-ketoglutarate dehydrogenase (KGDH) complex. The copmplex is composed of the catalytic subunits OGDH (2-oxoglutarate dehydrogenase KGD1; also called E1 subunit), DLST (dihydrolipoamide succinyltransferase KGD2; also called E2 subunit) and DLD (dihydrolipoamide dehydrogenase LPD1; also called E3 subunit), and the assembly factor KGD4. - Improving Identification of In-organello Protein-Protein Interactions Using an Affinity-enrichable, Isotopically Coded, and Mass Spectrometry-cleavable Chemical Crosslinker
Makepeace, Molecular & cellular proteomics : MCP 2020 - “...13 9 4 33 P07253 CBP6 P21560 CBP3 41 Yes Yes 13 0 27 14 P19262 KGD2 P20967 KGD1 40 Yes Yes 9 19 3 18 P05626 ATP4 P07251 ATP1 38 No Yes 6 2 22 14 P09624 LPD1 P16451 PDX1 35 Yes Yes 10 7...”
- Proteomic analysis reveals a novel function of the kinase Sat4p in Saccharomyces cerevisiae mitochondria
Gey, PloS one 2014 - “...Q12031 Mitochondrial 2-methylisocitrate lyase 0.28 MALDI-TOF-MS 159 20/51 32 65.3 7.21 62 6.2 6 KGD2 P19262 Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial 0.33 nanoLC-MS/MS 7132 17 58 50.5 8.88 55 5.4 7 LYS4 P49367 Homoaconitase, mitochondrial 0.39 MALDI-TOF-MS 180 15/25 24 68.0 6.12 74...”
- “...P36112 Formation of crista junctions protein 1 nanoLC-MS/MS 2219 26 58 61.1 6.60 11 KGD2 P19262 Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial 3.62 nanoLC-MS/MS 3659 19 59 50.5 8.88 54 5.5 12 KGD2 P19262 Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial 3.65 MALDI-TOF-MS...”
- Mitochondrial enzymes are protected from stress-induced aggregation by mitochondrial chaperones and the Pim1/LON protease
Bender, Molecular biology of the cell 2011 - “...75 53 20 8 Kgd1 -Ketoglutarate dehydrogenase P20967 114 58 19 9 Kgd2 Dihydrolipoyl transsuccinylase P19262 50 60 20 10 Lat1 Dihydrolipoylamide acetyltransferase, subunit E2 P12695 52 46 16 11 Leu4 -Isopropylmalate synthase P06208 68 83 24 12 Lsc2 Succinyl-CoA ligase, subunit P53312 47 93 25...”
- Plant mitochondrial 2-oxoglutarate dehydrogenase complex: purification and characterization in potato
Millar, The Biochemical journal 1999 (secret) - Loss of function of Hog1 improves glycerol assimilation in Saccharomyces cerevisiae
Sone, World journal of microbiology & biotechnology 2023 - “...kinase involved in osmoregulation Frameshift mutation corresponding to Lys65 Chr IV 753,916 T A KGD2 (YDR148C) 2-Oxoglutarate dehydrogenase E2 component Asn384 (A A T) Ile (A T T) Chr XII 1,019,484 A T SIR3 (YLR442C) Chromatin-silencing protein Leu923 (C T A) Gln (C A A) Chr...”
- Data integration uncovers the metabolic bases of phenotypic variation in yeast
Petrizzelli, PLoS computational biology 2021 - “...protein complexes with an AND Boolean relationship. Proteins Reactions (YOR136W AND YNL037C) Icit_Akg_m_nad (YIL125W AND YDR148C AND YFL018C ) Akg_Succoa_m ( YGR240C AND YMR205C ) F6p_Fdp (YBR221C AND YER178W AND YFL018C AND YGR193C AND YNL071W ) Pyr_Accoa_m ( YGR244C AND YOR142W ) Succoa_Succ_m ( YGL080W AND...”
- Central Metabolism in Mammals and Plants as a Hub for Controlling Cell Fate
Selinski, Antioxidants & redox signaling 2021 - “...(EC 1.1.2.4) 2-Oxoglutarate dehydrogenase complex OGDH-E1 AT3G55410 (EC 1.2.4.2) HGNC:8124 (EC 1.2.4.2) YIL125W (EC 1.2.4.2) YDR148C (EC 1.2.4.2) YFR049W (EC 1.2.4.2) OGDH-E1 AT5G65750 (EC 1.2.4.2) OGDH-E2 AT4G26910 (EC 1.2.4.2) OGDH-E2 AT5G55070 (EC 1.2.4.2) OGDH-E3 AT3G17240 (EC 1.2.4.2) OGDH-E3 AT1G48030 (EC 1.2.4.2) OGDH-E3 AT3G13930 (EC 1.2.4.2) The...”
- Systematic analysis of nuclear gene function in respiratory growth and expression of the mitochondrial genome in S. cerevisiae
Stenger, Microbial cell (Graz, Austria) 2020 - “...COQ4 YDR204W ISA1 YLL027W SOM1 YEL059C-A COQ5 YML110C ISA2 YPR067W SSQ1 YLR369W COQ6 YGR255C KGD2 YDR148C SUV3 YPL029W COQ9 YLR201C LIP2 YLR239C YTA12 YMR089C DSS1 YMR287C LPD1 YFL018C ETR1 YBR026C MCT1 YOR221C Vacuolar proteins DID4 YKL002W VMA21 YGR105W VMA6 YLR447C VMA1 YDL185W VMA22 YHR060W VMA8 YEL051W...”
- Adjustment of trehalose metabolism in wine Saccharomyces cerevisiae strains to modify ethanol yields
Rossouw, Applied and environmental microbiology 2013 - “...YCR005c YPR001w YLR304c YJL200C YNL037c YOR136w YIL125w YDR148c YOR142w YGR244c Y15376 Y13485 Y12828 Y15212 Y17022 Y15362 Y12392 Y12284 Y13506 Y12398 Y15897...”
- High hydrostatic pressure activates gene expression that leads to ethanol production enhancement in a Saccharomyces cerevisiae distillery strain
Bravim, Applied microbiology and biotechnology 2013 - “...2.39 3.53 4.18 High-affinity glucose transporter YDR342C HXT7 2.72 2.49 3.78 4.52 High-affinity glucose transporter YDR148C KGD2 0.86 0.68 1.55 2.05 Dihydrolipoyl transsuccinylase, which catalyses the oxidative decarboxylation of -ketoglutarate to succinyl-CoA in the TCA cycle YFR030W MET10 1.76 0.44 0.93 1.02 Subunit alpha of assimilatory...”
- Inaccurately assembled cytochrome c oxidase can lead to oxidative stress-induced growth arrest
Bode, Antioxidants & redox signaling 2013 - “...Strong None Strong None Minor YHR067W HTD2 Poor Poor YDR148C KGD2 None Poor Minor None Minor None YIL125W KGD1 None Poor Minor None Minor None Function Twin...”
- Systematic genetic array analysis links the Saccharomyces cerevisiae SAGA/SLIK and NuA4 component Tra1 to multiple cellular processes
Hoke, BMC genetics 2008 - “...5, 9 ER 19 MDM34 YGL219C S 6 mitochondrial outer membrane E, R 10 KGD2 YDR148C S 6, 5 mitochondrion 0 MDM10 YAL010C s 6, 9 Mdm10/Mdm12/Mmm1 complex, mitochondrial outer membrane T, E 11 BEM1 YBR200W S 7, 3, 1 bud neck E 33 BEM4 YPL161C...”
- More
DJ41_3574 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
28% identity, 92% coverage
- Metabolic Responses to Polymyxin Treatment in Acinetobacter baumannii ATCC 19606: Integrating Transcriptomics and Metabolomics with Genome-Scale Metabolic Modeling
Zhu, mSystems 2019 - “...at 1h, including citrate synthase (DJ41_3568, 1.5-fold), aconitate hydratase (DJ41_1103, 2.7-fold), 2-oxoglutarate dehydrogenase (DJ41_3573 and DJ41_3574, 1.9 and 2.5-fold, respectively), succinyl-CoA ligase (DJ41_3576 and DJ41_3577, 2.1-fold for both), fumarate hydratase (DJ41_227, 2.6-fold), and malate dehydrogenase (DJ41_3006, 1.8-fold). However, the fluxes and metabolites throughout the TCA cycle...”
PSLF89_3189 dihydrolipoyllysine-residue acetyltransferase from Piscirickettsia salmonis LF-89 = ATCC VR-1361
28% identity, 57% coverage
- Nutrient Scarcity in a New Defined Medium Reveals Metabolic Resistance to Antibiotics in the Fish Pathogen Piscirickettsia salmonis
Ortiz-Severín, Frontiers in microbiology 2021 - “...TCA cycle was also observed. Genes encoding pyruvate kinase (PYK, PSLF89_1027), pyruvate dehydrogenase (PDH, PSLF89_3190, PSLF89_3189, PSLF89_3188, PSLF89_2098, PSLF89_3189, and PSLF89_3190), and malic enzymes (ME1, PSLF89_3304, ME2, and PSLF89_234) showed lower expression levels in the CMMAB medium with or without amp compared to Austral-SRS medium. For...”
ABBFA_RS03900 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase from Acinetobacter baumannii AB307-0294
28% identity, 92% coverage
Bd2729 2-oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase from Bdellovibrio bacteriovorus HD100
24% identity, 88% coverage
- An Extended Cyclic Di-GMP Network in the Predatory Bacterium Bdellovibrio bacteriovorus
Rotem, Journal of bacteriology 2016 - “...effectors (Bd0025, Bd0407, Bd1608, Bd1833, Bd2174, Bd2611, and Bd2729) specifically binding in AP and assigned to metabolism (thereby encoded by GP expressed...”
- “...amino acid degradation (Bd1835, Bd2070, Bd2728, and Bd2729). In addition, 2-methylcitrate dehydratase (Bd2500) provides a modulation point in the...”
Rmet_2049 2-oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase from Ralstonia metallidurans CH34
Rmet_2049 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase from Cupriavidus metallidurans CH34
27% identity, 87% coverage
CT247 Dihydrolipoamide Acetyltransferase from Chlamydia trachomatis D/UW-3/CX
26% identity, 85% coverage
- Remodeling of host phosphatidylcholine by Chlamydia acyltransferase is regulated by acyl-CoA binding protein ACBD6 associated with lipid droplets
Soupene, MicrobiologyOpen 2015 - “...2005 ). The PDH complex of C. trachomatis is PdhA (CT245), PdhB (CT246), and PdhC (CT247). bAAs are imported into the inclusion by the bacterial ABC transporter BrnQ (CT554) (Braun etal. 2008 ). Deamination of valine, leucine and isoleucine by CT773 (Ldh) generates the branched keto...”
- “...(2-methylbutyryl-CoA, isobutyryl-CoA, isovaleryl-CoA) are produced by the Branched Keto Dehydrogenase complex (PdhA_B, PdhC, LpdA; CT340, CT247, CT557) from the b( -keto) intermediates. The extender malonyl-CoA is produced by the acetyl-CoA carboxylase complex (AccA, AccB, AccC, AccD; CT123-124-265-293) from acetyl-CoA. Acetyl-CoA is produced from pyruvate by the...”
- Outer membrane proteins preferentially load MHC class II peptides: implications for a Chlamydia trachomatis T cell vaccine
Karunakaran, Vaccine 2015 - “...protein 33 CT143 GKLIVTNPKSDISFGG CT144 Hypothetical protein 60 CT144 GSPGQTNYAAAKAGIIGFS CT237 3-Ketoacyl-(acyl-carrier-protein) reductase FabG GTKTPIGTPIAVFSTEQ CT247 Dihydrolipoamide acetyltransferase 51 PdhC SPKEAAIAAARASLSPEEKR CT289 Hypothetical protein CT289 YDHIIVTPGANADILPE CT375 Predicted d -amino acid dehydrogenase CT375 FDGEKASVGAPTVGNAVVKG CT420 50S ribosomal protein L21 33 Rl21 KLDGVSSPAVQESISESL CT424 Sigma regulatory factor...”
- Chlamydia trachomatis lacks an adaptive response to changes in carbon source availability
Nicholson, Infection and immunity 2004 - “...1.61 0.03 Pyruvate dehydrogenase CT245 pdhA CT246 pdhB CT247 pdhC CT285 lplA CT340 pdhA Pyruvate dehydrogenase E1 alpha Pyruvate dehydrogenase E1 beta...”
PAAG_02769 pyruvate dehydrogenase protein X component from Paracoccidioides lutzii Pb01
28% identity, 74% coverage
- The Response of Paracoccidioides lutzii to the Interaction with Human Neutrophils
Silva, Journal of fungi (Basel, Switzerland) 2023 - “...valine, leucine and isoleucine, producing acetyl-CoA, together with 2-oxoisovalerate dehydrogenase and pyruvate dehydrogenase X component (PAAG_02769), which was exclusively found at both neutrophil interaction times. Most of the cited enzymes had their expression increased over time, suggesting a need for acetyl-CoA production during neutrophil internalization. 3.4....”
- “...E1 component subunit beta # 1.55 PAAG_00050 pyruvate dehydrogenase protein X component # 1.15 ** PAAG_02769 pyruvate dehydrogenase protein X component * * a Accession number from FungiDB Database ( https://fungidb.org/fungidb/app , accessed on 26 September 2022). b Protein description according to FungiDB Database ( https://fungidb.org/fungidb/app...”
- Interacting with Hemoglobin: Paracoccidioides spp. Recruits hsp30 on Its Cell Surface for Enhanced Ability to Use This Iron Source
de, Journal of fungi (Basel, Switzerland) 2021 - “...component 1 (PAAG_01861; XP_002795973.1), protein disulfide-isomerase domain (PAAG_11504; XP_015703276.1) and pyruvate dehydrogenase protein X component (PAAG_02769; XP_002795293.1). Figure 1 A presents the heatmap of upregulated proteins predicted as secreted in the presence of hemoglobin. In order to correlate protein and transcript levels, firstly, we analyzed the...”
- “...cells submitted to hemoglobin treatment: disulfide-isomerase domain protein (PAAG_11504; XP_015703276.1), pyruvate dehydrogenase protein X component (PAAG_02769; XP_002795293.1) and HSP30 (PAAG_00871; XP_002797012.2). In order to confirm the increase in the adhesion capacity of P. lutzii , we pretreated yeast cells with hemoglobin and assessed the ability of...”
- Interaction of Isocitrate Lyase with Proteins Involved in the Energetic Metabolism in Paracoccidioides lutzii
Freitas, Journal of fungi (Basel, Switzerland) 2020 - “...pyruvate dehydrogenase E1 component subunit beta 13,649.55 PAAG_08295 pyruvate dehydrogenase E1 component subunit alpha 13,423.09 PAAG_02769 pyruvate dehydrogenase protein X component 14,287.29 PAAG_03330 dihydrolipoyl dehydrogenase 11,642.86 PAAG_08915 dihydrolipoamide succinyltransferase 14,385.67 PAAG_01725 succinate dehydrogenase flavoprotein subunit 9554.287 PAAG_04238 succinate dehydrogenase flavoprotein subunit 9647.347 PAAG_06103 succinate dehydrogenase iron-sulfur...”
- Transcriptional and proteomic responses to carbon starvation in Paracoccidioides
Lima, PLoS neglected tropical diseases 2014 - “...and methionine biosynthesis C-compound and carbohydrate metabolism PAAG_02975 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase * phenylacetate catabolic process PAAG_02769 pyruvate dehydrogenase protein X component * carbohydrate metabolism PAAG_03774 S-(hydroxymethyl)glutathione dehydrogenase * C-compound and carbohydrate metabolism/metane metabolism PAAG_00799 uroporphyrinogen decarboxylase * porphyrin biosynthesis Lipid, fatty acid and isoprenoid metabolism PAAG_02211...”
NGO0916 Odo2 from Neisseria gonorrhoeae FA 1090
26% identity, 93% coverage
- Epitope determination of immunogenic proteins of Neisseria gonorrhoeae
Connor, PloS one 2017 - “...The epitope mappings of the remaining proteins featured in Table 1 , namely NGO0584, NGO0642, NGO0916, NGO0983, NGO1043, NGO1634, NGO1796, and NGO2139 resulted either in very low signal intensities in the range of the negative control or high variance. Thus, the results are not shown here...”
- “...B Cytoplasm 188 (306) - NGO0777 DNA-binding protein Hu Cytoplasm 437 (89) Peptide 1_6 KALDATTNAVTNALK NGO0916 dihydrolipoamide succinyltransferase Cytoplasm 191 (393) - NGO0983 outer membrane protein H.8 Outer membrane 2380 (88) - NGO1043 hypothetical protein Periplasm 3588 (114) - NGO1429 molecular chaperone DnaK Cytoplasm 144166; 209269;...”
- Identification of Novel Immunogenic Proteins of Neisseria gonorrhoeae by Phage Display
Connor, PloS one 2016 - “...and positive clones were identified by colony PCR and sequencing after transformation. All proteins except NGO0916 (selected as a positive control that was isolated from outer membrane vesicle vaccines of N . lactamica and N . meningitidis [ 49 ]) were expressed and purified by affinity...”
- “...1 NGO0170, 2 NGO0326, 3 NGO0451, 4 NGO0564 (+ control), 5 NGO0642, 6 NGO0777, 7 NGO0916, 8 NGO1043, 9 NGO1500 (- control), 10 NGO1634, 11 NGO1656, 12 NGO1657, 13 NGO1796, 14 NGO1852. B SDS-PAGE (15%) of 0.5 g each of produced proteins: M Spectra Multicolor Low...”
- MpeR regulates the mtr efflux locus in Neisseria gonorrhoeae and modulates antimicrobial resistance by an iron-responsive mechanism
Mercante, Antimicrobial agents and chemotherapy 2012 - “...NGO0393 NGO0678 NGO0679 NGO0754 NGO0795 NGO0863 NGO0891 NGO0916 NGO1046 NGO1273 NGO1368 NGO1416 NGO1418 NGO1422 NGO1428 NGO1494 NGO1600 NGO1665 NGO1685 NGO1749...”
- MtrR modulates rpoH expression and levels of antimicrobial resistance in Neisseria gonorrhoeae
Folster, Journal of bacteriology 2009 - “...NGO0309 NGO0658 NGO0756 NGO0795 NGO0846 NGO0863 NGO0891 NGO0916 NGO0927 NGO1002 NGO1029 NGO1046 NGO1069 NGO1084 NGO1189 NGO1244 NGO1293 NGO1294 NGO1314 NGO1325...”
GRMZM2G033644 dihydrolipoyllysine-residue acetyltransferase component of pyruvatedehydrogenase complex from Zea mays
27% identity, 70% coverage
NMB0956 dihydrolipoamide acetyltransferase from Neisseria meningitidis MC58
26% identity, 93% coverage
- Identification of Novel Immunogenic Proteins of Neisseria gonorrhoeae by Phage Display
Connor, PloS one 2016 - “...protein Hu 1 100 9.38 NMB1230 Cytoplasm No - NGO0916* dihydrolipoamide succinyltransferase 1 272 41.69 NMB0956 Cytoplasm Yes [ 49 ] NGO0983 outer membrane protein H.8 1 174 8.02 NMB1523 Outer membrane Yes [ 50 ] NGO1043* hypothetical protein 2 160/217 11.41 NMB1468 Periplasm Yes [...”
- Host iron binding proteins acting as niche indicators for Neisseria meningitidis
Jordan, PloS one 2009 - “...according to manufacturer specifications (Stratagene). The relative transcript level of each gene was normalized to nmb0956 ( sucB ), on the basis of the microarray data which showed it to be invariant between all conditions tested. Quantitative values were obtained by using the comparative threshold cycle...”
- Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits
Dessimoz, Nucleic acids research 2006 - “...(1: ECs0119, 3: ECs0752), Haemophilus influenzae (1: HI1232, 3: HI1661), Neisseria meningitidis (1: NMB1342, 3: NMB0956), Pasteurella multocida (1: PM0894, 3: PM0278), Pseudomonas aeruginosa (1: PA5016, 2: PA2249, 3: PA1586), Rhizobium loti (2: mll4471, 3: mll4300, 4a: mlr0385, 4b: mll3627), Rhizobium meliloti (2: SMc03203, 3a: SMc02483,...”
- Diversity in coding tandem repeats in related Neisseria spp
Jordan, BMC microbiology 2003 - “...second protein that functions in the cytoplasm has been identified in this study, SucB (TR8, NMB0956). This is the dihydrolipoamide succinyltransferase (E2o) of the 2-oxogluterate dehydrogenase complex, a component of the TCA cycle. Although the sequence of this gene in E. coli contains no repeats, the...”
- “...XNG0120 aluminium resistance protein, putative no TR7 NMA0789 NMB0586 XNG0151 adhesin, putative no TR8 NMA1150 NMB0956 XNG0849 SucB protein ( sucB ) no TR9 NMA1461 NMB1027 XNG0526 DnaJ protein, truncation ( dnaJ ) no TR10 NMA1491 NMB1281 XNG0596 transcription-repair coupling factor ( mfd ) no TR11...”
CA51_18830 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase from Rosistilla oblonga
27% identity, 90% coverage
CTL0499 dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex from Chlamydia trachomatis 434/Bu
26% identity, 85% coverage
Mal33_19360 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase from Rosistilla oblonga
27% identity, 90% coverage
NWMN_1325 dihydrolipoamide acetyltransferase from Staphylococcus aureus subsp. aureus str. Newman
Q2FH26 Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex from Staphylococcus aureus (strain USA300)
SAOUHSC_01416 2-oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase from Staphylococcus aureus subsp. aureus NCTC 8325
SAUSA300_1305 2-oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase from Staphylococcus aureus subsp. aureus USA300_FPR3757
SACOL1448 2-oxoglutarate dehydrogenase, E2 component, dihydroipoamide succinyltransferase from Staphylococcus aureus subsp. aureus COL
RDJ18_RS08040, SAUSA300_RS07100 dihydrolipoyllysine-residue succinyltransferase from Staphylococcus aureus
24% identity, 87% coverage
- Essential Fitness Repertoire of Staphylococcus aureus during Co-infection with Acinetobacter baumannii In Vivo
Li, mSystems 2022 - “...lysine degradation were identified, which include genes encoding aldehyde dehydrogenase AldA (NWMN_0113), dihydrolipoamide succinyltransferase SucB (NWMN_1325), 2-oxoglutarate dehydrogenase SucA (NWMN_1326), d-alanine aminotransferase (NWMN_1643), and acetyl-CoA C-acetyltransferase VraB (NWMN_0539) ( Fig.4 ). Four genes were identified to be related to base excision repair, including endonuclease III (NWMN_1363),...”
- CodY in Staphylococcus aureus: a regulatory link between metabolism and virulence gene expression
Pohl, Journal of bacteriology 2009 - “...NWMN_1110 NWMN_1111 NWMN_1112 NWMN_1249 NWMN_0163 NWMN_0162 NWMN_0979 NWMN_1325 NWMN_2294 NWMN_0167 Gene Newman vs codY mutant agr mutant vs agr codY mutant...”
- The Spl Serine Proteases Modulate Staphylococcus aureus Protein Production and Virulence in a Rabbit Model of Pneumonia
Paharik, mSphere 2016 - “...translation 0.00 2.33 0.007 Q2FJU4 ( Q2FJU4_STAA3 ) Triacylglycerol lipase GehB/SAL2 Lipase 8.67 32.33 1.2E11 Q2FH26 ( ODO2_STAA3 ) Dihydrolipoyllysine residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex OdhB Metabolism, amino acid degradation 0.00 2.33 0.007 Q2FHD0 ( Q2FHD0_STAA3 ) Glutamine synthetase GlnA Metabolism, amino acid metabolism,...”
- The conserved regulatory RNA RsaE down-regulates the arginine degradation pathway in Staphylococcus aureus
Rochat, Nucleic acids research 2018 - “...SAOUHSC_01218 sucD Succinyl-CoA synthetase, alpha subunit 2.40 0.63 SAOUHSC_01347 citB Aconitate hydratase 1 1.82 0.38 SAOUHSC_01416 sucB 2-oxoglutarate dehydrogenase, E2 component 1.35 0.53 SAOUHSC_01418 sucA 2-oxoglutarate dehydrogenase, E1 component 1.36 0.48 SAOUHSC_01983 fumC Fumarate hydratase 1.49 0.42 Malate metabolism SAOUHSC_00698 Putative malate transporter 2.31 0.59 SAOUHSC_02647...”
- Bacterial Hypoxic Responses Revealed as Critical Determinants of the Host-Pathogen Outcome by TnSeq Analysis of Staphylococcus aureus Invasive Infection
Wilde, PLoS pathogens 2015 - “...genes), and the TCA cycle (5 genes). In the TCA cycle, mutations in genes sucB (SAOUHSC_01416), sucC (SAOUHSC_01216), and sucD (SAOUHSC_01218), which encode enzymes responsible for the conversion of -ketoglutarate to succinate, each resulted in compromised growth during osteomyelitis. Moreover, genes encoding enzymes in pathways that...”
- Advantage of upregulation of succinate dehydrogenase in Staphylococcus aureus biofilms
Gaupp, Journal of bacteriology 2010 - “...dehydrogenase E2 component/dihydrolipoamide acetyltransferase (SAOUHSC_01416); SucC, succinyl-CoA synthetase subunit beta (SAOUHSC_01216); SucD, succinyl-CoA...”
- Human Urine Alters Methicillin-Resistant Staphylococcus aureus Virulence and Transcriptome
Paudel, Applied and environmental microbiology 2021 (secret) - Novel Regulation of Alpha-Toxin and the Phenol-Soluble Modulins by Peptidyl-Prolyl cis/trans Isomerase Enzymes in Staphylococcus aureus
Keogh, Toxins 2019 - “...Energy metabolism SAUSA300_0226 FadB 13.36 Fatty acid and phospholipid metabolism SAUSA300_2581 SasA 7.36 Cell envelope SAUSA300_1305 OdhB 4.93 Energy metabolism SAUSA300_0912 FabI 4.78 Fatty acid and phospholipid metabolism SAUSA300_1594 YajC 4.71 Protein fate SAUSA300_2061 AtpH 3.70 Energy metabolism SAUSA300_2060 AtpA 3.44 Energy metabolism SAUSA300_0547 SdrD 3.37...”
- Identification of Staphylococcus aureus Factors Required for Pathogenicity and Growth in Human Blood
Connolly, Infection and immunity 2017 - “...regulatory protein (AraC) Reduced hemolysis SAUSA300_0899 NE1315 Adaptor protein (MecA) Reduced hemolysis Slightly reduced hemolysis SAUSA300_1305 NE1391 Dihydrolipoamide succinyltransferase (OdhB) Slightly reduced growth Slightly reduced growth Increased hemolysis Increased hemolysis SAUSA300_0320 NE1775 Triacylglycerol lipase (LipA) Slightly reduced growth Increased hemolysis B SAUSA300_1989 NE95 Accessory gene regulator...”
- Staphylococcus aureus Tissue Infection During Sepsis Is Supported by Differential Use of Bacterial or Host-Derived Lipoic Acid
Zorzoli, PLoS pathogens 2016 - “...we first generated deletion mutants of the genes encoding E2-PDH ( SAUSA300_0995) , E2-OGDH ( SAUSA300_1305) , and GcvH ( SAUSA300_0791) in S . aureus strain LAC. We identified E2-PDH and E2-OGDH as the two largest molecular weight species and GcvH as the smallest ( S5...”
- Investigating the genetic regulation of the ECF sigma factor σS in Staphylococcus aureus
Burda, BMC microbiology 2014 - “...biosynthesis SACOL0168 NE595 Glutamate N-acetyltransferase/amino-acid acetyltransferase argJ 2 1 SACOL1349 NE809 Threonine aldolase 1 1 SACOL1448 NE1391 Dihydroipoamide succinyltransferase sucB 1 1 SACOL1449 NE547 2-Oxoglutarate dehydrogenase, E1 component sucA 3 1 SACOL1478 NE1136 Alanine dehydrogenase 1 1 SACOL2045 NE1177 Ketol-acid reductoisomerase 1 1 Protein synthesis and...”
- The Staphylococcus aureus LytSR two-component regulatory system affects biofilm formation
Sharma-Kuinkel, Journal of bacteriology 2009 - “...University of California, Berkeley SACOL1741 SACOL1449 SACOL1448 SACOL1262 SACOL1782 SACOL2198 SACOL2199 SACOL2553 SACOL2146 SACOL2149 SACOL0175 SACOL0543 Fold...”
- Genetic changes that correlate with the pine-oil disinfectant-reduced susceptibility mechanism of Staphylococcus aureus
Lamichhane-Khadka, Journal of applied microbiology 2008 - “...nucleoside phosphorylase 1.87 SACOL0426 acetyl-CoA acetyltransferase 1.81 SACOL1897 putative protein export protein PrsA, 1.77 sucB SACOL1448 dihydrolipoamide succinyltransferase 1.76 gltA SACOL1742 citrate synthase 1.73 SACOL2569 delta-1-pyrroline-5-carboxylate dehydrogenase 1.72 SACOL1447 conserved hypothetical protein 1.67 SACOL2140 lytic regulatory protein, authentic frameshift 1.62 SACOL1114 Mn2 + /Fe2 + transporter,...”
- Complete and SOS-mediated response of Staphylococcus aureus to the antibiotic ciprofloxacin
Cirz, Journal of bacteriology 2007 - “...encode components of the pyruvate dehydrogenase complex (SACOL1448 and SACOL1449), which converts pyruvate to succinyl-coenzyme A (succinyl-CoA) and funnels it...”
- “...SACOL1158 SACOL1159 SACOL1160 SACOL1262 SACOL1263 SACOL1385 SACOL1448 SACOL1449 SACOL1741 SACOL1908 SACOL2424 SACOL2426 SACOL2427 SACOL2428 Gene S. AUREUS SOS...”
- Multiomics analysis of Staphylococcus aureus ST239 strains resistant to virulent Herelleviridae phages
Kornienko, Scientific reports 2024 - “...data confirmed alterations in the tricarboxylic acid cycle, evidenced by reduced abundance of dihydrolipoyllysine-residue succinyltransferase (RDJ18_RS08040) and succinateCoA ligase subunit alpha (RDJ18_RS08935), along with changes in gluconeogenesis attributed to underrepresentation of the key enzyme, phosphoenolpyruvate carboxykinase (RDJ18_RS06075). Compensating for decreased energy production through the tricarboxylic acid...”
- Metabolic diversity of human macrophages: potential influence on Staphylococcus aureus intracellular survival
Bertrand, Infection and immunity 2024 - “...HMDMs, which included polA (SAUSA300_RS08925), pgcA (SAUSA300_RS13475), atpD (SAUSA300_RS11335), atpA (SAUSA300_RS11345), mprF (SAUSA300_RS06820), and sucB (SAUSA300_RS07100) ( Fig. 3A ; Table 1 ). The full list of essential genes for each condition is presented in Data Set S1. Fig 3 Tn-seq identifies pathways important for S....”
- Accumulation of Succinyl Coenzyme A Perturbs the Methicillin-Resistant Staphylococcus aureus (MRSA) Succinylome and Is Associated with Increased Susceptibility to Beta-Lactam Antibiotics
Campbell, mBio 2021 - “...SNV A T 100 36.9 hflX Ile 53 Phe 1436058 SNV A G 100 33.1 SAUSA300_RS07100, sucB Ile 361 Thr sucC suppressor 3 12470991247100 INS TA T- Tn -A 100 NA Bursa aurealis transposon NA 14361861436231 DEL T-A 46bp h 100 NA SAUSA300_RS07100, sucB NA a...”
- Network-based genetic investigation of virulence-associated phenotypes in methicillin-resistant Staphylococcus aureus
Kim, Scientific reports 2018 - “...(3) FALSE 4 SAUSA300_RS11410 20.84 FALSE Not tested 5 SAUSA300_RS11425 20.64 TRUE (4) FALSE 6 SAUSA300_RS07100 19.34 TRUE (5) FALSE 7 SAUSA300_RS11990 18.85 FALSE Not tested 8 SAUSA300_RS01250 18.38 TRUE (6) FALSE 9 SAUSA300_RS11355 18.36 TRUE (7) FALSE 10 SAUSA300_RS02850 18.23 FALSE Not tested 11 SAUSA300_RS07405...”
SA1244 dihydrolipoamide acetyltransferase from Staphylococcus aureus subsp. aureus N315
Q7A5N4 Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex from Staphylococcus aureus (strain N315)
SAV1412 dihydrolipoamide acetyltransferase from Staphylococcus aureus subsp. aureus Mu50
24% identity, 87% coverage
- Exposure of clinical MRSA heterogeneous strains to β-lactams redirects metabolism to optimize energy production through the TCA cycle
Keaton, PloS one 2013 - “...SA1184 citB 6.3 aconitate hydratase Involved in the TCA cycle (conversion of citrate to isocitrate). SA1244 odhB 2.2 Dihydrolipo-amide acetyltrans-ferase Involved in the TCA cycle and lysine degradation. SA1518 citZ 8.9 citrate synthase Catalyzes the first step in the TCA cycle. SAS1622 citC 11 isocitrate dehydro-genase...”
- “...SA11884), isocitrate dehydrogenase ( citC, SAS1622), and a subunit of -ketoglutarate dehydrogenase ( odhB , SA1244). Another gene related to the TCA cycle also found to be up-regulated was acsA (SA1554); this gene codes for the enzyme responsible of converting acetate into acetyl-CoA, which can be...”
- An RpoB mutation confers dual heteroresistance to daptomycin and vancomycin in Staphylococcus aureus
Cui, Antimicrobial agents and chemotherapy 2010 - “...SA0994 SA0995 SA0996 SA1088 SA1089 SA1131 SA1132 SA1184 SA1244 SA1245 SA1349 SA1517 SA1518 SA1609 sdhC sdhA sdhB sucC sucD Cell envelope and cellular processes...”
- Characterizing the effects of inorganic acid and alkaline shock on the Staphylococcus aureus transcriptome and messenger RNA turnover
Anderson, FEMS immunology and medical microbiology 2010 - “...sa_c9605s8367_a_at * 6.6 2.5 15 cdsA SA1280 phosphatidate cytidylyltransferase sa_c1260s1035_a_at * 5.4 2.5 30 fabD SA1244 malonyl CoA-acyl transacylase sa_c318s157_a_at * 2.7 2.5 30 fabF SA0988 acyl-carrier-protein synthase II sa_c4695s4014_a_at 5.8 2.5 2.5 SA0207 hypothetical protein sa_c6975s6099_a_at 6.3 2.5 2.5 SA0317 lipase precursor sa_c10609s11066_s_at 3.3 2.5...”
- “...synthetase sa_c4357s3707_at 2.7 2.5 2.5 cls2 SA2079 cardiolipin synthetase sa_c1260s1035_a_at * 12.0 2.5 2.5 fabD SA1244 malonyl CoA-acyl carrier protein transacylase sa_c318s157_a_at * 5.5 2.5 2.5 fabF SA0988 3-oxoacyl-(acyl-carrier-protein) synthase II sa_c9967s8662_at 6.4 2.5 5 fabG1 SA1245 3-oxoacyl-reductase, acyl-carrier sa_c312s155_a_at 20.3 2.5 2.5 fabH SA0987 3-oxoacyl-(acyl-carrier-protein)...”
- Transcriptome and functional analysis of the eukaryotic-type serine/threonine kinase PknB in Staphylococcus aureus
Donat, Journal of bacteriology 2009 - “...pknB mutant strain N315 ORF Gene Citrate cycle SA1244 SA1245 odhB odhA Change (fold)a Description or predicted function 2.4 2.2 Two-component system SA0252 lrgA...”
- Reporter metabolite analysis of transcriptional profiles of a Staphylococcus aureus strain with normal phenotype and its isogenic hemB mutant displaying the small-colony-variant phenotype
Seggewiss, Journal of bacteriology 2006 - “...of California, Berkeley SA1245 SA2008 SA0730 SA1184 SA1244 SA1141 SA0728 SA2007 SA0729 SA0182 SA1553 SA1089 SA2327 SA1554 SA0232 SA0219 Description 7770...”
- “...changes, respectively), odhAB (dihydrolipoamide succinyltransferase, SA1244, 0.20fold), and 2-oxoglutarate dehydrogenase E1 (SA1245, 0.26fold). Interestingly,...”
- Staphylococcus aureus virulence factors identified by using a high-throughput Caenorhabditis elegans-killing model
Begun, Infection and immunity 2005 - “...name/function SA1245 odhAc,d,e 2-Oxoglutarate dehydrogenase SA1244 SA1669 odhBc,d,e citG Dihydrolipoamide succinyltransferase Fumarate hydratase, class II...”
- Differential gene expression profiling of Staphylococcus aureus cultivated under biofilm and planktonic conditions
Resch, Applied and environmental microbiology 2005 - “...SA2203 2.62 Physiological proteins SA0171 SA0996 SA2427 SA2204 SA1244 SA2007 SA0995 SA1245 16.161 4.37 3.965 3.842 3.706 3.274 2.694 2.634 SA2424 4.967 SA1984...”
- Transcription profiling-based identification of Staphylococcus aureus genes regulated by the agr and/or sarA loci
Dunman, Journal of bacteriology 2001 - “...SA1450 SA1844 SA1842 SA1843 SAS066 SA1245 SA1244 SA2424 Lipid metabolism Miscellaneous Miscellaneous Miscellaneous Miscellaneous Signal transduction Signal...”
- Impacts of the Type I Toxin-Antitoxin System, SprG1/SprF1, on Staphylococcus aureus Gene Expression
Chlebicka, Genes 2021 - “...2,3-bisphosphoglycerate-independent phosphoglycerate mutase (GpmI) P64270 1.53 10 Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex (OdhB) Q7A5N4 1.53 11 Catalase (KatA) Q7A5T2 1.66 1.90 12 Cell division protein FtsA (FtsA) P63765 1.53 13 ATP-dependent Clp protease ATP-binding subunit ClpL (ClpL) Q7A3F4 1.53 14 Fructose-bisphosphate aldolase class 1...”
- The SAV1322 gene from Staphylococcus aureus: genomic and proteomic approaches to identification and characterization of gene function
Kim, BMC microbiology 2016 - “...Gene Locus b Expression change Carbohydrate metabolism and transport A023 gi|15924402 Dihydrolipoamide succinyltransferase 714 odhB SAV1412 Down A025 gi|15924086 Dihydrolipoamide dehydrogenase 1153 pdhD SAV1096 Down A277 gi|15924841 Fumarate hydratase 601 fumC SAV1851 Down A043 gi|15924684 Isocitrate dehydrogenase 845 citC SAV1694 Down A286 gi|15924412 Glucose-specific enzyme II,...”
FTL_0310 pyruvate dehydrogenase, E2 component from Francisella tularensis subsp. holarctica
25% identity, 67% coverage
- Francisella tularensis LVS surface and membrane proteins as targets of effective post-exposure immunization for tularemia
Chandler, Journal of proteome research 2015 - “...21 , 23 , 50 T, 35 , 41 S 25 29 dihydrolipoamide acetyltransferase (AceF) FTL_0310 NC(SP) Cyto(9.97) Y ( 21 , 40 , 45 , 50 ) M 21 , 37 , 47 , 50 outer membrane associated protein FopA1 f FTL_1328 SpI OM(9.93) (...”
- Possible links between stress defense and the tricarboxylic acid (TCA) cycle in Francisella pathogenesis
Dieppedale, Molecular & cellular proteomics : MCP 2013 - “...to T25, respectively) (16). The genes FTL_1783, FTL_0309, FTL_0310, FTL_0311, and FTL_0295, were cloned into pUT18C vector (C-terminal fusion to T18 domain)....”
- “...two complexes were also detected (FTL_1783, OGDH E2; and FTL_0310, PDH E2) as well as the E3 component common to both complexes (FTL_0311, PDH/OGDH E3). Only...”
Q5NEX3 Acetyltransferase component of pyruvate dehydrogenase complex from Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4)
FTT_1484c dihydrolipoamide acetyltransferase from Francisella tularensis subsp. tularensis SCHU S4
25% identity, 56% coverage
- Shotgun Immunoproteomic Approach for the Discovery of Linear B-Cell Epitopes in Biothreat Agents Francisella tularensis and Burkholderia pseudomallei
D'haeseleer, Frontiers in immunology 2021 - “...Aminotransferase AspC1 Q5NGG1 LPIDDAEK 2 Glutamate dehydrogenase Gdh Q5NHR7 a FHPSVYSGIIK Pyruvate dehydrogenase acetyltransferase AceF Q5NEX3 a VSQGSLILK 2 60 kDa chaperonin GroL Q5NEE1 a DRVDDALHATR 2 Chaperone protein DnaK Q5NFG7 a NTADNLIHSSR Chaperone protein DnaK Q5NFG7 a SSSGLSEEDIEK 60 kDa chaperonin GroL Q5NEE1 a DNTTIIDGAGEK...”
- Immunoproteomic analysis of the human antibody response to natural tularemia infection with Type A or Type B strains or LVS vaccination
Fulton, International journal of medical microbiology : IJMM 2011 - “...immunoreactive with all Type A tularemia patient sera screened, although the proteins pyruvate dehydrogenase E2 (FTT_1484c) and ribosomal protein L7/L12 (FTT_0143) were observed to be reactive with ten of the twelve sera studied. In addition, the proteins dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase (FTT_0077) and chaperonin...”
- “...membrane associated protein, FopA (FTT_0583), Peroxidase/catalase (FTT_0721c), Chaperone protein DnaK (FTT_1269c), Pyruvate dehydrogenase E2 component (FTT_1484c), Chaperone protein groEL (FTT1696), and Hypothetical membrane protein (FTT_1778c). DISCUSSION There is a need for a safe and effective tularemia vaccine, which can be licensed for general use to address...”
- The francisella tularensis proteome and its recognition by antibodies
Kilmury, Frontiers in microbiology 2010 - “...Dihydrolipoamide dehydrogenase Human, presumed type B 2D-Western blot Cytoplasmic Janovska et al. ( 2007a ) FTT_1484c Pyruvate dehydrogenase, E2 component aceF Human, type A; human, presumed type B; mouse 2D-Western blot/proteome microarray Cytoplasmic membrane Eyles et al. ( 2007 ), Janovska et al. ( 2007a ,...”
- “...half of the studies (FTT_1696, FTT_1269c, FTT_1696, FTT_0077, FTT_0137, FTT_0472, FTT_0583, FTT_0721c, FTT_0143, FTT_1103, FTT_0863, FTT_1484c). Of these proteins, FTT_2369c, FTT_1696, FTT_0583, FTT_0721c, and FTT_1103 were also noted to be components of LVS and SCHU S4 outer membrane preparations (Huntley et al., 2007 ). Examining the...”
ECH_1065 2-oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase from Ehrlichia chaffeensis str. Arkansas
26% identity, 89% coverage
SAMCCGM7_Ch3374 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase from Sinorhizobium americanum CCGM7
26% identity, 89% coverage
BAB1_1922 Biotin/lipoyl attachment:Antifreeze protein, type I:Catalytic domain of components of various dehydrogenase complexes:Ribosom... from Brucella melitensis biovar Abortus 2308
26% identity, 90% coverage
- Iron-dependent reconfiguration of the proteome underlies the intracellular lifestyle of Brucella abortus
Roset, Scientific reports 2017 - “...82699969 BAB1_1152 E1 dehydrogenase, E1 component C NO 1.77 0.23 Oxoglutarate dehydrogenase complex GI: 82700688 BAB1_1922 sucB dihydrolipoamide acetyltransferase C NO 1.61 0.35 GI: 82700689 BAB1_1923 sucA alpha-ketoglutarate decarboxylase C NO 1.25 0.02 Others GI: 82698965 BAB1_0036 cytochrome c heme-binding site:cytochrome c, class IA/ IB CM...”
- Large scale immune profiling of infected humans and goats reveals differential recognition of Brucella melitensis antigens
Liang, PLoS neglected tropical diseases 2010 - “...BR0497 0.715 Chromosome Segregation Protein SMC BMEI0340 BAB1_1707 BR1695 0.889 Omp16 lipoprotein {Tibor, 1994} BMEI0141 BAB1_1922 BR1922 0.734 2-oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase BMEII0032 BAB2_0061 BRA0062 0.849 VirB8 BMEI0228 BAB1_1830 BR1822 0.719 Hypothetical protein BMEI1890 BAB1_0051 BR0054 0.866 Transporter BMEI0810 BAB1_1199 BR1177 0.918 COG1434 Uncharacterized...”
- Intracellular adaptation of Brucella abortus
Lamontagne, Journal of proteome research 2009 - “...tricarboxylic acid (TCA) cycle components, such as aconitate hydratase (BAB1_0090), 2-oxoglutarate dehydrogenase (BAB1_1923), dihydrolipoamide acetyltransferase (BAB1_1922), succinyl-CoA synthetase (BAB1_1925) and malate dehydrogenase (BAB1_1927), were all reduced at similar rates 3 hours after infection. Similarly, transketolase (BAB1_1740) and enolase (BAB1_1155), enzymes committed to the pentose phosphate shunt...”
- “...of the coordinated expression changes occurred in proteins that form continuous genetic arrangements. For example BAB1_1922, BAB1_1923, BAB1_1925, as well as BAB1_1149, BAB1_1150, BAB1_1151, and BAB1_1645, BAB1_1646, BAB1_1648. These proteins may be transcribed as a single message and subsequently translated as has been observed in other...”
SDRG_01993 hypothetical protein from Saprolegnia diclina VS20
26% identity, 69% coverage
AL01_00925 pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase from Bombella intestini
26% identity, 87% coverage
- Whole-Genome Sequence Analysis of Bombella intestini LMG 28161T, a Novel Acetic Acid Bacterium Isolated from the Crop of a Red-Tailed Bumble Bee, Bombus lapidarius
Li, PloS one 2016 - “...(AL01_00625); 11, malate dehydrogenase (AL01_05845); 12, pyruvate dehydrogenase (AL01_00915, AL01_00920, AL01_03860); 13, pyruvate dehydrogenase E2 (AL01_00925); 14, dihydrolipoamide dehydrogenase (AL01_00930); 15, lactate dehydrogenase (AL01_06935); 16, hydroxyacylglutathione hydrolase (AL01_04950); 17, lactoylgluthathione lyase (AL01_00090); 18, pyruvate decarboxylase (AL01_08375); 19, alcohol dehydrogenase (AL01_01980, AL01_07015); 20, citrate synthase (AL01_06255); 21,...”
ODO2_BOVIN / P11179 Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial; 2-oxoglutarate dehydrogenase complex component E2; OGDC-E2; Dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex; E2K; EC 2.3.1.61 from Bos taurus (Bovine) (see 2 papers)
27% identity, 80% coverage
- function: Dihydrolipoamide succinyltransferase (E2) component of the 2- oxoglutarate dehydrogenase complex (By similarity). The 2-oxoglutarate dehydrogenase complex catalyzes the overall conversion of 2- oxoglutarate to succinyl-CoA and CO(2) (By similarity). The 2- oxoglutarate dehydrogenase complex is mainly active in the mitochondrion. A fraction of the 2-oxoglutarate dehydrogenase complex also localizes in the nucleus and is required for lysine succinylation of histones: associates with KAT2A on chromatin and provides succinyl- CoA to histone succinyltransferase KAT2A (By similarity).
catalytic activity: N(6)-[(R)-dihydrolipoyl]-L-lysyl-[2-oxoglutarate dehydrogenase complex component E2] + succinyl-CoA = N(6)-[(R)-S(8)- succinyldihydrolipoyl]-L-lysyl-[2-oxoglutarate dehydrogenase complex component E2] + CoA (RHEA:15213)
cofactor: (R)-lipoate (Binds 1 lipoyl cofactor covalently.)
subunit: The 2-oxoglutarate dehydrogenase complex is composed of OGDH (2-oxoglutarate dehydrogenase; E1), DLST (dihydrolipoamide succinyltransferase; E2), DLD (dihydrolipoamide dehydrogenase; E3) and the assembly factor KGD4 (PubMed:36854377). It contains multiple copies of the three enzymatic components (E1, E2 and E3). In the nucleus, the 2-oxoglutarate dehydrogenase complex associates with KAT2A. Interacts with ABHD11; this interaction maintains the functional lipoylation of the 2-oxoglutarate dehydrogenase complex (By similarity). - Comparative Analysis of Erythrocyte Proteomes of Water Buffalo, Dairy Cattle, and Beef Cattle by Shotgun LC-MS/MS
Guo, Frontiers in veterinary science 2019 - “...protein 1 1 47895.71 9.63 L8IKB7 26S protease regulatory subunit 7 9 8 48633.3 5.71 P11179 Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial 1 1 48971.98 9.1 L8IG31 Uncharacterized protein 1 1 50072.82 6.58 Q3SX22 BSD domain-containing protein 1 1 1 50342.11 4.47 E1BKY9 Uncharacterized...”
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 793,807 different protein sequences to 1,259,118 scientific articles. Searches against EuropePMC were last performed on March 13 2025.
PaperBLAST builds a database of protein sequences that are linked
to scientific articles. These links come from automated text searches
against the articles in EuropePMC
and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot,
BRENDA,
CAZy (as made available by dbCAN),
BioLiP,
CharProtDB,
MetaCyc,
EcoCyc,
TCDB,
REBASE,
the Fitness Browser,
and a subset of the European Nucleotide Archive with the /experiment tag.
Given this database and a protein sequence query,
PaperBLAST uses protein-protein BLAST
to find similar sequences with E < 0.001.
To build the database, we query EuropePMC with locus tags, with RefSeq protein
identifiers, and with UniProt
accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use
queries of the form "locus_tag AND genus_name" to try to ensure that
the paper is actually discussing that gene. Because EuropePMC indexes
most recent biomedical papers, even if they are not open access, some
of the links may be to papers that you cannot read or that our
computers cannot read. We query each of these identifiers that
appears in the open access part of EuropePMC, as well as every locus
tag that appears in the 500 most-referenced genomes, so that a gene
may appear in the PaperBLAST results even though none of the papers
that mention it are open access. We also incorporate text-mined links
from EuropePMC that link open access articles to UniProt or RefSeq
identifiers. (This yields some additional links because EuropePMC
uses different heuristics for their text mining than we do.)
For every article that mentions a locus tag, a RefSeq protein
identifier, or a UniProt accession, we try to select one or two
snippets of text that refer to the protein. If we cannot get access to
the full text, we try to select a snippet from the abstract, but
unfortunately, unique identifiers such as locus tags are rarely
provided in abstracts.
PaperBLAST also incorporates manually-curated protein functions:
- Proteins from NCBI's RefSeq are included if a
GeneRIF
entry links the gene to an article in
PubMed®.
GeneRIF also provides a short summary of the article's claim about the
protein, which is shown instead of a snippet.
- Proteins from Swiss-Prot (the curated part of UniProt)
are included if the curators
identified experimental evidence for the protein's function (evidence
code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that
describe the protein's function are shown (with bold headings).
- Proteins from BRENDA,
a curated database of enzymes, are included if they are linked to a paper in PubMed
and their full sequence is known.
- Every protein from the non-redundant subset of
BioLiP,
a database
of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself
does not include descriptions of the proteins, those are taken from the
Protein Data Bank.
Descriptions from PDB rely on the original submitter of the
structure and cannot be updated by others, so they may be less reliable.
(For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every
ligand is represented among a group of structures with similar sequences, but for
PaperBLAST, we use the non-redundant set provided by BioLiP.)
- Every protein from EcoCyc, a curated
database of the proteins in Escherichia coli K-12, is included, regardless
of whether they are characterized or not.
- Proteins from the MetaCyc metabolic pathway database
are included if they are linked to a paper in PubMed and their full sequence is known.
- Proteins from the Transport Classification Database (TCDB)
are included if they have known substrate(s), have reference(s),
and are not described as uncharacterized or putative.
(Some of the references are not visible on the PaperBLAST web site.)
- Every protein from CharProtDB,
a database of experimentally characterized protein annotations, is included.
- Proteins from the CAZy database of carbohydrate-active enzymes
are included if they are associated with an Enzyme Classification number.
Even though CAZy does not provide links from individual protein sequences to papers,
these should all be experimentally-characterized proteins.
- Proteins from the REBASE database
of restriction enzymes are included if they have known specificity.
- Every protein with an evidence-based reannotation (based on mutant phenotypes)
in the Fitness Browser is included.
- Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators)
with experimentally-determined DNA binding sites from the
PRODORIC database of gene regulation in prokaryotes.
- Putative transcription factors from RegPrecise
that have manually-curated predictions for their binding sites. These predictions are based on
conserved putative regulatory sites across genomes that contain similar transcription factors,
so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
- Coding sequence (CDS) features from the
European Nucleotide Archive (ENA)
are included if the /experiment tag is set (implying that there is experimental evidence for the annotation),
the nucleotide entry links to paper(s) in PubMed,
and the nucleotide entry is from the STD data class
(implying that these are targeted annotated sequences, not from shotgun sequencing).
Also, to filter out genes whose transcription or translation was detected, but whose function
was not studied, nucleotide entries or papers with more than 25 such proteins are excluded.
Descriptions from ENA rely on the original submitter of the
sequence and cannot be updated by others, so they may be less reliable.
Except for GeneRIF and ENA,
the curated entries include a short curated
description of the protein's function.
For entries from BioLiP, the protein's function may not be known beyond binding to the ligand.
Many of these entries also link to articles in PubMed.
For more information see the
PaperBLAST paper (mSystems 2017)
or the code.
You can download PaperBLAST's database here.
Changes to PaperBLAST since the paper was written:
- November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
- February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
- June 2022: incorporated some coding sequences from ENA with the /experiment tag.
- March 2022: incorporated BioLiP.
- April 2020: incorporated TCDB.
- April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
- February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
- January 2018: incorporated BRENDA.
- December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
- September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.
Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.
PaperBLAST cannot provide snippets for many of the papers that are
published in non-open-access journals. This limitation applies even if
the paper is marked as "free" on the publisher's web site and is
available in PubmedCentral or EuropePMC. If a journal that you publish
in is marked as "secret," please consider publishing elsewhere.
Many important articles are missing from PaperBLAST, either because
the article's full text is not in EuropePMC (as for many older
articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an
article that characterizes a protein's function but is missing from
PaperBLAST, please notify the curators at UniProt
or add an entry to GeneRIF.
Entries in either of these databases will eventually be incorporated
into PaperBLAST. Note that to add an entry to UniProt, you will need
to find the UniProt identifier for the protein. If the protein is not
already in UniProt, you can ask them to create an entry. To add an
entry to GeneRIF, you will need an NCBI Gene identifier, but
unfortunately many prokaryotic proteins in RefSeq do not have
corresponding Gene identifers.
References
PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.
Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.
Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.
UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.
BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.
The MetaCyc database of metabolic pathways and enzymes.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.
CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.
The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.
The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.
REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
R. J. Roberts et al (2015). Nucleic Acids Research, 10.1093/nar/gku1046.
Deep annotation of protein function across diverse bacteria from mutant phenotypes.
M. N. Price et al (2016). bioRxiv, 10.1101/072470.
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory