PaperBLAST

PaperBLAST Hits for reanno::Cup4G11:RR42_RS17300 D-lactate dehydrogenase, FAD-linked subunit GlcD (EC 1.1.99.6) (Cupriavidus basilensis FW507-4G11) (497 a.a., MNAPHEVSLV...)

Show query sequence

>reanno::Cup4G11:RR42_RS17300 D-lactate dehydrogenase, FAD-linked subunit GlcD (EC 1.1.99.6) (Cupriavidus basilensis FW507-4G11)
MNAPHEVSLVADDARRSALLAGLAKILPDAALLWKPEDTVPYECDGLAAYRQVPMAVALP
DNEDQVCAILRLCHSLQVPVVPRGAGTSLSGGAMPIATGLVLSLAKFKRIVSVDVRSRTA
VVQPGVRNLAISEAAAQYNLYYAPDPSSQIACTIGGNVSENSGGVHCLKYGLTVHNVLRV
RAVTMEGDVVEFGSEAPDAPGLDLLAAVIGSEGMLAVVTEVSVKLIPKPQLAQVIMASFD
DVAKGGNAVADVIGAGIIPAGLEMMDKPATAAVEEFVRAGYDLDAAAILLCESDGTPEEV
AEEVERMSEVLRASGASRIQVSQSEPERLRFWSGRKNAFPAAGRISPDYYCMDGTIPRKH
IGTLLKRIEEMERKYGLRCMNVFHAGDGNMHPLILFDGADQDEWHRAELFGSDILESCVE
LGGTVTGEHGVGVEKLNSMCVQFSAQERDLFFGVKAAFDPARLLNPDKAIPTLARCAEYG
RMHVKRGLLPHPDLPRF

Running BLASTp...

Found 258 similar proteins in the literature:

RR42_RS17300 D-lactate dehydrogenase, FAD-linked subunit GlcD (EC 1.1.99.6) from Cupriavidus basilensis FW507-4G11
100% identity, 100% coverage

• mutant phenotype: Specifically important for: Sodium D-Lactate.

Pnuc_1781 D-lactate dehydrogenase (cytochrome) from Polynucleobacter sp. QLW-P1DMWA-1
75% identity, 98% coverage

• The passive yet successful way of planktonic life: genomic and experimental analysis of the ecology of a free-living polynucleobacter population
  Hahn, PloS one 2012
  • “...shown). The genome of strain QLW-P1DMWA-1 encoded a putative glycolate oxidase consisting of three subunits (Pnuc_1781, 1782, 1783). The encoded enzyme, however, could also represent a lactate dehydrogenase. In addition, a glycolate permease gene as found in Ralstonia / Cupriavidus strains is missing in QLW-P1DMWA-1. 10.1371/journal.pone.0032772.g012...”
  • “...percent of the glcD sequences obtained from five lakes clustered with the putative glcD gene (Pnuc_1781) of strain QLW-P1DMWA-1 [36] . Altogether, our results do not indicate that P.n. ssp. asymbioticus strains affiliated with the F10 lineage are specially adapted to utilization of algal exudation products....”

BP2905 glycolate oxidase subunit from Bordetella pertussis Tohama I
68% identity, 96% coverage

• Avirulent phenotype promotes Bordetella pertussis adaptation to the intramacrophage environment
  Farman, Emerging microbes & infections 2023
  • “...On the other hand, the expression of glcDEF genes involved in glycolate/glyoxylate metabolism ( BP2903 BP2905 ) and the glyoxalase gene BP2863 was strongly upregulated. Similarly, the expression of genes responsible for the biosynthesis (acetolactate synthase BP0467 ) and transport (ABC transporters BP0619BP0622 and BP3573BP3577 )...”

Psest_3841 D-lactate/glycolate dehydrogenase, FAD-linked subunit GlcD (EC 1.1.99.6; EC 1.1.99.14) from Pseudomonas stutzeri RCH2
62% identity, 97% coverage

• mutant phenotype: Specifically important for: Sodium D-Lactate; Glycolic Acid. This is the first step in both D-lactate and glycolate oxidation.

PP_3745 glycolate oxidase, subunit GlcD from Pseudomonas putida KT2440
63% identity, 96% coverage

• Genome analysis of the metabolically versatile Pseudomonas umsongensis GO16: the genetic basis for PET monomer upcycling into polyhydroxyalkanoates
  Narancic, Microbial biotechnology 2021
  • “...Glc operon transcriptional regulator 98 73 PP_3744 glcD F6476_01185 Glycolate oxidase FADlinked subunit 100 86 PP_3745 glcE F6476_01180 Glycolate oxidase FADbinding subunit 100 72 PP_3746 glcF F6476_01175 Glycolate oxidase FeS subunit 100 77 PP_3747 glcG F6476_01170 Uncharacterized protein 90 73 PP_3748 glcB F6476_01165 Malate synthase 99...”
• The Cellular Response to Lanthanum Is Substrate Specific and Reveals a Novel Route for Glycerol Metabolism in Pseudomonas putida KT2440
  Wehrmann, mBio 2020
  • “...NCS1 nucleoside transporter family 3.65 2.46 PP_2440 AhpF Alkyl hydroperoxide reductase subunit F 3.13 3.08 PP_3745 GlcD Glycolate oxidase, putative FAD-linked subunit 3.12 3.32 PP_3747 GlcF Glycolate oxidase, iron-sulfur subunit 2.67 3.50 PP_3746 GlcE Glycolate oxidase, putative FAD-binding subunit 2.64 2.98 PP_4922 ThiC Phosphomethylpyrimidine synthase 2.21...”
  • “...upstream and downstream of the calA (PP_2426), garK (PP_3178), glpFKRD (PP_1076 to PP_1973), and glcDEF (PP_3745 to PP_3747) genes were amplified from genomic DNA of P. putida KT2440 using primer pairs PcalA1/2 and PcalA3/4, PgarK1/2 and PgarK3/4, Pglp1/2 and Pglp3/4, and MWH03/04 and MWH05/06, respectively (...”
• FinR Regulates Expression of nicC and nicX Operons, Involved in Nicotinic Acid Degradation in Pseudomonas putida KT2440
  Xiao, Applied and environmental microbiology 2018
  • “...PP_2453 PP_2454 PP_3073 PP_3074 PP_3191 PP_3589 PP_3661 PP_3745 PP_3940 PP_3941 PP_3942 PP_3943 PP_3944 PP_3945 PP_4232 PP_4233 PP_4434 PP_4435 PP_4548 PP_4625...”

F6476_01185 glycolate oxidase subunit GlcD from Pseudomonas umsongensis
61% identity, 97% coverage

• Genome analysis of the metabolically versatile Pseudomonas umsongensis GO16: the genetic basis for PET monomer upcycling into polyhydroxyalkanoates
  Narancic, Microbial biotechnology 2021
  • “...Pyruvate kinase 99 79 PP_4301 glcC F6476_01190 Glc operon transcriptional regulator 98 73 PP_3744 glcD F6476_01185 Glycolate oxidase FADlinked subunit 100 86 PP_3745 glcE F6476_01180 Glycolate oxidase FADbinding subunit 100 72 PP_3746 glcF F6476_01175 Glycolate oxidase FeS subunit 100 77 PP_3747 glcG F6476_01170 Uncharacterized protein 90...”

PA5355 glycolate oxidase subunit GlcD from Pseudomonas aeruginosa PAO1
62% identity, 97% coverage

• ECF Sigma Factor HxuI Is Critical for In Vivo Fitness of Pseudomonas aeruginosa during Infection
  Cai, Microbiology spectrum 2022
  • “...glcF Glycolate oxidase iron-sulfur subunit 2.53 2.42E-15 PA5354 glcE Glycolate oxidase FAD-binding subunit 2.49 3.83E-14 PA5355 glcD Glycolate oxidase subunit 2.02 0.0000669 Iron response PA0471 fiuR Anti-sigma factor Fur box 2.13 0.000138 PA0472 fiuI ECF sigma factor; ferric uptake Fur box 2.01 6.87E-05 PA1302 hxuA TonB-dependent...”
• A previously uncharacterized gene, PA2146, contributes to biofilm formation and drug tolerance across the ɣ-Proteobacteria
  Kaleta, NPJ biofilms and microbiomes 2022
  • “...PA2146 ymdF 19.70 73.33 (11.63) 38.90 (9.99) PA3531; bfrB Bfr 9.65 5.64 (3.30) 3.36 (0.33) PA5355; glcD glcD 4.89 3.00 (1.41) 1.74 (0.25) PA3584; glpD glpD 7.88 15.56 (10.45) 16.99 (1.77) PA3581; glpF glpF 2.01 8.49 (1.46) 12.72 (3.11) PA2184 yciE 3.58 6.19 (0.56) 91.89 (17.63)...”
• NtrBC Regulates Invasiveness and Virulence of Pseudomonas aeruginosa During High-Density Infection
  Alford, Frontiers in microbiology 2020
  • “...glcF Glycolate oxidase subunit GlcF 15.6 20.0 PA5354 glcE Glycolate oxidase subunit GlcE 25.5 16.5 PA5355 glcD Glycolate oxidase subunit GlcD 9.09 8.42 PA5415 glyA1 serine hydroxymethyltransferase 4.76 4.96 PA5421 fdhA Glutathione-independent formaldehyde dehydrogenase 1.45 1.79 PA5445 Coenzyme A transferase 1.87 3.38 C. Pathogenicity genes required...”
• 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
  • “...PA5054 PA5067 PA5069 PA5078 PA5117 PA5128 PA5276 PA5316 PA5355 PA5460 PA5490 PA5491 PA5555 PA5557 PA5569 PA5570 ispB glyA3 PA4608 PA4610 PA4633 PA4671 PA4692...”
• Host and invader impact of transfer of the clc genomic island into Pseudomonas aeruginosa PAO1
  Gaillard, Proceedings of the National Academy of Sciences of the United States of America 2008
  • “...or aco genes) and in glycolate catabolism (PA5351 to PA5355, or glcDEF) (Table S1). None of these operons has known links to the 3-chlorocatechol or...”
  • “...acetoin catabolism PA4153 PA4151 PA5353 PA5352 PA5355 glycolate catabolism PAO1-clc1 stationary phase PAO1-rif PAO1-clc1 exponential phase PAO1-rif PAO1-clc1...”
• Identification, timing, and signal specificity of Pseudomonas aeruginosa quorum-controlled genes: a transcriptome analysis
  Schuster, Journal of bacteriology 2003
  • “...PA5161 PA5162 PA5164 PA5220 PA5352 PA5353 PA5354 PA5355 PA5356 PA5415 PA5481 PA5482 Description b VOL. 185, 2003 TRANSCRIPTOME ANALYSIS OF QUORUM-CONTROLLED...”

BPHY_RS36905, Bphy_7454 glycolate oxidase subunit GlcD from Paraburkholderia phymatum STM815
61% identity, 97% coverage

• Metabolomics and Dual RNA-Sequencing on Root Nodules Revealed New Cellular Functions Controlled by Paraburkholderia phymatum NifA
  Bellés-Sancho, Metabolites 2021
  • “...protein Bphy_7752 11.54 BPHY_RS40755 IS66 family transposase Bphy_7404 NA BPHY_RS37010 IS3 family transposase Bphy_7482 NA BPHY_RS36905 glycolate oxidase subunit G Bphy_7454 glcD NA BPHY_RS41325 diaminobutyrate-2-oxoglutarate transaminase Bphy_7273 NA BPHY_RS38360 nitrogen fixation protein Bphy_7776 nifZ NA BPHY_RS37060 hypothetical protein NA BPHY_RS38235 hypothetical protein NA BPHY_RS35970 HypC/HybG/HupF family...”
  • “...family transposase Bphy_7404 NA BPHY_RS37010 IS3 family transposase Bphy_7482 NA BPHY_RS36905 glycolate oxidase subunit G Bphy_7454 glcD NA BPHY_RS41325 diaminobutyrate-2-oxoglutarate transaminase Bphy_7273 NA BPHY_RS38360 nitrogen fixation protein Bphy_7776 nifZ NA BPHY_RS37060 hypothetical protein NA BPHY_RS38235 hypothetical protein NA BPHY_RS35970 HypC/HybG/HupF family hydrogenase formation chaperone Bphy_7253 hypC...”

PSPPH_3252 glycolate oxidase, GlcD subunit from Pseudomonas syringae pv. phaseolicola 1448A
60% identity, 97% coverage

• Transcriptional profile of P. syringae pv. phaseolicola NPS3121 at low temperature: physiology of phytopathogenic bacteria
  Arvizu-Gómez, BMC microbiology 2013
  • “...protein 1.55 PSPPH_2847 general secretion pathway protein GspK, putative 1.89 PSPPH_3045 transporter, AcrB/AcrD/AcrF family 1.64 PSPPH_3252 glycolate oxidase, GlcD subunit 1.97 PSPPH_3291 oxidoreductase, molybdopterin-binding 1.88 PSPPH_3294 DNA-binding heavy metal response regulator 1.81 PSPPH_3654 transcriptional regulator, TetR family 1.51 PSPPH_3906 sensor histidine kinase 1.65 PSPPH_3946 DNA repair...”

b2979 glycolate dehydrogenase, putative FAD-linked subunit from Escherichia coli BW25113
YghM / b2979 glycolate dehydrogenase, putative FAD-linked subunit (EC 1.1.99.14) from Escherichia coli K-12 substr. MG1655 (see 9 papers)
glcD / P0AEP9 glycolate dehydrogenase, putative FAD-linked subunit (EC 1.1.99.14) from Escherichia coli (strain K12) (see 7 papers)
GLCD_ECOLI / P0AEP9 Glycolate oxidase subunit GlcD; Glycolate dehydrogenase subunit GlcD; EC 1.1.99.14 from Escherichia coli (strain K12) (see 4 papers)
glcD / RF|NP_417453 glycolate oxidase subunit glcD from Escherichia coli K12 (see paper)
glcD / AAB02530.1 glycolate oxidase subunit from Escherichia coli (see paper)
b2979 glycolate oxidase subunit, FAD-linked from Escherichia coli str. K-12 substr. MG1655
D1792_12370, ECHMS174_03014 glycolate oxidase subunit GlcD from Escherichia coli
59% identity, 97% coverage

• mutant phenotype: Specific phenotype: utilization of Glycolic Acid
• function: Component of a complex that catalyzes the oxidation of glycolate to glyoxylate (PubMed:4557653, PubMed:8606183). Is required for E.coli to grow on glycolate as a sole source of carbon (PubMed:8606183). Is also able to oxidize D-lactate ((R)-lactate) with a similar rate (PubMed:4557653). Does not link directly to O(2), and 2,6-dichloroindophenol (DCIP) and phenazine methosulfate (PMS) can act as artificial electron acceptors in vitro, but the physiological molecule that functions as a primary electron acceptor during glycolate oxidation is unknown (PubMed:4557653).
  catalytic activity: glycolate + A = glyoxylate + AH2 (RHEA:21264)
  catalytic activity: (R)-lactate + A = pyruvate + AH2 (RHEA:15089)
  cofactor: FAD
  subunit: The glycolate oxidase likely consists of three subunits, GlcD, GlcE and GlcF.
  disruption phenotype: Abolishes glycolate oxidase activity. Is unable to grow on glycolate as the sole source of carbon, in contrast to wild type.
• The catabolism of ethylene glycol by <i>Rhodococcus jostii</i> RHA1 and its dependence on mycofactocin
  Roccor, Applied and environmental microbiology 2024 (secret)
• Effect of Global Regulators RpoS and Cyclic-AMP/CRP on the Catabolome and Transcriptome of Escherichia coli K12 during Carbon- and Energy-Limited Growth
  Franchini, PloS one 2015
  • “...3.6 glcB b2976 malate synthase G 4.1 glcF b2978 glycolate oxidase iron-sulfur subunit 7.1 glcD b2979 glycolate oxidase subunit D 7.0 mdh f , g , i b3236 malate dehydrogenase 4.1 pckA g b3403 phosphoenolpyruvate carboxykinase 8.7 atpD g b3732 membrane-bound ATP synthase, F1 sector, beta-subunit...”
• More than just a metabolic regulator--elucidation and validation of new targets of PdhR in Escherichia coli
  Göhler, BMC systems biology 2011
  • “...b0088 murD $ -0.013 5.623 b2579 yfiD * 1.973 0.805 b0090 murG $ -0.015 4.773 b2979 glcD $ 1.853 1.709 b0089 ftsW $ 0.073 4.664 b4467 glcF $ 1.163 0.275 b0084 ftsI $ 0.140 4.556 b2975 glcA $ 1.144 0.400 b0082 mraW $ -0.056 4.297 b2977...”
• EFICAz: a comprehensive approach for accurate genome-scale enzyme function inference
  Tian, Nucleic acids research 2004
  • “...approaches, the two genes whose annotations disagree are b2979 (glcD) and b3583 (sgbE). KEGG annotation for b2979 is `glycolate oxidase subunit glcD [EC...”
  • “...catalytic (36). In contrast, the EFICAz prediction for b2979 is EC 1.1.2.4 (D-lactate dehydrogenase). Indeed, the glycolate oxidase complex of E.coli can act as...”
• A New EBS2b-IBS2b Base Paring (A_-8/T_-8) Improved the Gene-Targeting Efficiency of Thermotargetron in Escherichia coli
  Cui, Microbiology spectrum 2023
  • “...sites in fliC (flagellin C, ECHMS174_01916), lacZ (eta-galactosidase, ECHMS174_00351), dctA (C4-dicarboxylate, ECHMS174_03796), glcD (glycolate oxidase, ECHMS174_03014), and constructed 152 gene-targeting plasmids (random gene-targeting plasmids pool, RGPP). All plasmids met the following criteria: A (15) A (14) nnnnnnnnnnnnnA (+1) (n represents 13 arbitrary nucleotides) (Tables S1, S2,...”
• Genomic and Transcriptomic Analysis of Colistin-Susceptible and Colistin-Resistant Isolates Identify Two-Component System EvgS/EvgA Associated with Colistin Resistance in Escherichia coli
  Wan, Infection and drug resistance 2021
  • “...transcriptional regulator 6 glcB 3.6 Malate synthase B 7 D1792_24740 3.4 Succinyl-CoA ligase subunit 8 D1792_12370 3.2 Glycolate oxidase 9 D1792_16520 3.0 Low affinity typtophan permease 10 D1792_12360 -2.6 Glycolate oxidase iron-sulfur subunit In E. coli ATCC 25922-R and its counterpart treated with 2 mg/L colistin...”

AYM39_RS13600 FAD-linked oxidase C-terminal domain-containing protein from Methylomonas sp. DH-1
60% identity, 95% coverage

• Boosting the acetol production in methanotrophic biocatalyst Methylomonas sp. DH-1 by the coupling activity of heteroexpressed novel protein PmoD with endogenous particulate methane monooxygenase
  Chau, Biotechnology for biofuels and bioproducts 2022
  • “...into lactate by hydroxyacylglutathione hydrolase (AYM39_RS06120) and then to pyruvate by putative lactate dehydrogenase (AYM39_RS04895, AYM39_RS13600). The generated pyruvate can be either converted to acetyl-CoA to enter the TCA cycle or to phosphoenolpyruvate (PEP) by PEP-synthase (AYM39_RS13170). The related genes are shown using their locus tags...”

bll7543 glycolate oxidase subunit from Bradyrhizobium japonicum USDA 110
54% identity, 97% coverage

• A link between arabinose utilization and oxalotrophy in Bradyrhizobium japonicum
  Koch, Applied and environmental microbiology 2014
  • “...Cowpea Siratro BVM plus arabinose PSY plus arabinose Blr3205 Blr3207 Bll7540 Bll7541 Bll7543 23 31 114 9 38 55 81 47 5 42 13 91 34 11 522 555 98 73 46 502 458...”
  • “...80 Number 7 and glycolate oxidase (Bll7540-41, Bll7543), the enzymes glyoxylate carboligase (Blr3166) as well as the tartronate semialdehyde reductase (Blr3168)...”

BMEII1064 (S)-2-hydroxy-acid oxidase chain D from Brucella melitensis 16M
53% identity, 89% coverage

• Integrated Bioinformatics-Based Subtractive Genomics Approach to Decipher the Therapeutic Drug Target and Its Possible Intervention against Brucellosis
  Khan, Bioengineering (Basel, Switzerland) 2022
  • “...involved in the glycolate utilization (glcB); aconitate hydratase (BMEI1855), (BMEII0009), (BMEI1952), (BMEII1061), (BMEI1939), (BMEII1060), (BMEII1062), (BMEII1064); and ureidoglycolate lyase (allA) and (BMEI0799). The PPI results showed that isocitrate lyase had a total number of nodes 11, average node numbers 7.09, average local clustering coefficient 0.95, the...”

BOV_RS11160 FAD-linked oxidase C-terminal domain-containing protein from Brucella ovis ATCC 25840
53% identity, 97% coverage

• Mining the Flavoproteome of Brucella ovis, the Brucellosis Causing Agent in Ovis aries
  Minjárez-Sáenz, Microbiology spectrum 2022
  • “...(lhgO) ABQ62911.1 FAD NADH 3DME (37) 51 1.1.99.14 Glycolate dehydrogenase GlcD subunit FAD_binding_4 (PF01565) 55-193 BOV_RS11160 (glcD) ABQ62237.1 FAD 3PM9 (29) FAD-oxidase_C (PF02913) 229-470 52 1.3.1.- b /1.7.1.B1 Predicted alkene reductase: N-ethylmaleimide reductase, glycerol trinitrate reductase or xenobiotic reductase B Oxidored_FMN (PF00724) 3-349 BOV_RS14625 ABQ62490.1 FMN...”

NGR_c03920 FAD-binding oxidoreductase from Sinorhizobium fredii NGR234
NGR_c03920 glycolate oxidase, subunit GlcD from Rhizobium sp. NGR234
49% identity, 93% coverage

• High-resolution transcriptomic analyses of Sinorhizobium sp. NGR234 bacteroids in determinate nodules of Vigna unguiculata and indeterminate nodules of Leucaena leucocephala
  Li, PloS one 2013
  • “...the glyoxylate cycle were not impaired in nodulation and nitrogen fixation on alfalfa [85] . NGR_c03920- NGR_c03950 expressed higher in V. unguiculata bacteroids (RPKM=254401) than in L. leucocephala bacteroids (RPKM=55105) and the free-living condition (RPKM=2440). They encode glycolate oxidase which catalyses the oxidation from glycolate and...”

Atu0665 glycolate oxidase subunit from Agrobacterium tumefaciens str. C58 (Cereon)
48% identity, 93% coverage

• Discrete Responses to Limitation for Iron and Manganese in Agrobacterium tumefaciens: Influence on Attachment and Biofilm Formation
  Heindl, Journal of bacteriology 2015
  • “...or more iron-sulfur clusters include glycolate oxidase (Atu0665 to Atu0667), a gene annotated as an electrotransfer ubiquinone oxidoreductase (Atu0994), a...”

SMc00832 D-lactate dehydrogenase, FAD-linked subunit GlcD (EC 1.1.99.6) from Sinorhizobium meliloti 1021
SMc00832 PROBABLE GLYCOLATE OXIDASE SUBUNIT PROTEIN from Sinorhizobium meliloti 1021
49% identity, 93% coverage

• mutant phenotype: Specifically important for: Sodium D,L-Lactate. This is the first step in D-lactate oxidation.
• Role of the regulatory gene rirA in the transcriptional response of Sinorhizobium meliloti to iron limitation
  Chao, Applied and environmental microbiology 2005
  • “...SMc00591 SMc00592 SMc00764 SMc00784 SMc00819 SMc00830 SMc00832 SMc00922 SMc01016 SMc01022 SMc01095 SMc01169 SMc01266 SMc01267 SMc01471 SMc01489 SMc01512...”

glcD1 / Q55124 glycolate dehydrogenase 1 (EC 1.1.99.14) from Synechocystis sp. (strain PCC 6803 / Kazusa) (see 4 papers)
Q55124 glycolate dehydrogenase (EC 1.1.99.14) from Synechocystis sp. PCC 6803 (see paper)
sll0404 glycolate oxidase subunit; GlcD from Synechocystis sp. PCC 6803
44% identity, 93% coverage

• Expression of cyanobacterial genes enhanced CO₂ assimilation and biomass production in transgenic Arabidopsis thaliana
  Abbasi, PeerJ 2021
  • “...growth conditions The cyanobacterial glycolate decarboxylation pathway genes i.e . glycolate dehydrogenase (GDH; Accession No. sll0404 ), hydroxyacid dehydrogenase (HDH; Accession No. slr1556 ), and oxalate decarboxylase (ODC; Accession No. sll1358 ) in cyanobacteria Synechocystis sp. strain PCC 6803 as reported by Eisenhut et al. (2008)...”
• Chirality Matters: Synthesis and Consumption of the d-Enantiomer of Lactic Acid by Synechocystis sp. Strain PCC6803
  Angermayr, Applied and environmental microbiology 2016
  • “...the presence of glycolate dehydrogenase GlcD1 (encoded by sll0404). Accordingly, this report highlights the need to match a product of interest of a...”
  • “...but the glycolate dehydrogenase glcD1 gene (carried by sll0404) is primarily responsible for the consumption of D-lactic acid. It appears that a significantly...”
• Computational metabolic engineering strategies for growth-coupled biofuel production by Synechocystis
  Shabestary, Metabolic engineering communications 2016
  • “...sll1484 NDH2_2p NdbA, NdbB, NdbC (periplasm) h[c]+nadh[c]+pq[p]nad[c]+pqh2[p] slr0851, slr1743, and sll1484 GLYCTO1 Glycolate oxidase o2[c]+glyclt[c]h2o2[c]+glx[c] sll0404 (glcD2) GLUSx Glutamate synthase GOGAT (NADH-dependent) h[c]+nadh[c]+akg[c]+ gln-L[c]nad[c]+2 glu-L[c] sll1502 MDH Malate dehydrogenase nad[c]+mal-L[c]h[c]+nadh[c]+oaa[c] sll0891 POR_syn Pyruvate: ferredoxin oxidoreductase coa[c]+pyr[c]+2 fdxo-2:2[c]h[c]+co2[c]+accoa[c]+2 fdxr-2:2[c] sll0741 FPK Phosphoketolase f6p[c]+pi[c]actp[c]+e4p[c]+h2o[c] slr0453 NADTRHD *** NAD...”
  • “...(flv3) Cyo1b_syn Cytochrome c oxidase 4h[c]+2 focytc6[u]+0.5 o2[u]2h[u]+2 ficytc6[u]+ h2o[u] slr1137 GLYCTO1 Glycolate oxidase o2[c]+glyclt[c]h2o2[c]+glx[c] sll0404 (glcD2) GLUSx Glutamate synthase GOGAT (NADH-dependent) h[c]+nadh[ c ]+akg[ c ]+gln-L[ c ]nad[ c ]+2 glu-L[c] sll1502 ACKr Acetate kinase atp[c]+ac[c]adp[c]+actp[c] sll1299 H2ase_syn [NiFe] Hydrogenase h[c]+ nadph[c]nadp[c]+h2[c] sll1224 (hoxY) ATPS4rpp...”
• Recent applications of metabolomics toward cyanobacteria
  Schwarz, Metabolites 2013
  • “...Figure 3 Mapping of metabolite profiles from the glycolate dehydrogenase 1 ( glcD1 ) ( sll0404 ) and the glycine decarboxylase ( gcvT ) ( sll0171 ) mutants to primary metabolism of Synechocystis 6803 wild type. The pathway mapping was customized to the current coverage of...”
• Proteomic analysis reveals resistance mechanism against biofuel hexane in Synechocystis sp. PCC 6803
  Liu, Biotechnology for biofuels 2012
  • “...1.68 1.63 Glutathione peroxidase Slr1171 1.54 1.59 Glutathione peroxidase Slr0879 1.50 Glycine decarboxylase complex H-protein Sll0404 1.54 1.79 Glycolate oxidase subunit GlcD Sll0057 1.94 1.75 1.52 1.59 Heat shock protein GrpE Slr0298 1.80 1.75 Heterocyst to vegetative cell connection protein Ssl3044 2.08 Hydrogenase component Slr0689 1.68...”
• The photorespiratory glycolate metabolism is essential for cyanobacteria and might have been conveyed endosymbiontically to plants
  Eisenhut, Proceedings of the National Academy of Sciences of the United States of America 2008
  • “...of Slr0806 shares 46% similarity with GlcD1 (Sll0404) from Synechocystis and from Escherichia coli. Also, Slr0806 harbors a conserved consensus sequence...”
  • “...sll1349 alr4944 At5 g36790* Cyano origin? (At5g06580) sll0404 slr0806 sll1559 alr5269 all4443 all0170 alr1004 At4g18360 At2g13360 At4 g18360 slr0293 sll0171...”

AM1_1070 glycolate oxidase, subunit GlcD from Acaryochloris marina MBIC11017
43% identity, 96% coverage

• New insights into iron acquisition by cyanobacteria: an essential role for ExbB-ExbD complex in inorganic iron uptake
  Jiang, The ISME journal 2015
  • “...SynRCC307_1279 SynWH7803_0707 Tery_4448 AM1_B0121 AM1_3410 AM1_1070 AM1_4902 AM1_A0164 AM1_0169 cce_3053 cce_1115 cce_1160 Unnamed (gb: EEE41044.1)...”

PGA1_c29720 D-lactate dehydrogenase, FAD-linked subunit GlcD (EC 1.1.99.6) from Phaeobacter inhibens DSM 17395
45% identity, 92% coverage

• mutant phenotype: Specifically important for: Sodium D,L-Lactate; Sodium D-Lactate.

SPO3478 FAD-linked oxidase C-terminal domain-containing protein from Ruegeria pomeroyi DSS-3
45% identity, 92% coverage

• Diel investments in metabolite production and consumption in a model microbial system
  Uchimiya, The ISME journal 2022
  • “...(n.s.) SPO0325 phbB acetoacetyl-CoA reductase 1.9 SPO0326 phbA acetyl-CoA acetyltransferase 1.1 (n.s.) Organic acid Glycolate SPO3478 glcD glycolate oxidase, GlcD subunit 18.6 [ 25 ] SPO3479 glcE glycolate oxidase, GlcE subunit 19.9 SPO3480 glcF glycolate oxidase, iron-sulfur subunit 21.6 Phosphonate Phosphonate SPO0780 phnC ABC transporter, ATP-binding...”

alr5269 glycolate oxidase subunit from Nostoc sp. PCC 7120
45% identity, 83% coverage

• Proteogenomic Analysis Provides Novel Insight into Genome Annotation and Nitrogen Metabolism in Nostoc sp. PCC 7120
  Yu, Microbiology spectrum 2021
  • “...N terminus. Eight unique peptides were mapped to the upstream region of the existing gene alr5269 , and one GSSP spanned the initiation site of the N terminus of alr5269 . It is worth noting that the correction model of alr5269 was also reported by other...”
  • “...gene model. Eight novel peptides partially mapped to the upstream region of an annotated gene (alr5269). 2019 annotation and 2020 annotation represented that the sequence existed in the Nostoc 7120 genome annotation of the 2019 version or the 2020 version in NCBI database, respectively. Validation of...”
• The photorespiratory glycolate metabolism is essential for cyanobacteria and might have been conveyed endosymbiontically to plants
  Eisenhut, Proceedings of the National Academy of Sciences of the United States of America 2008
  • “...g36790* Cyano origin? (At5g06580) sll0404 slr0806 sll1559 alr5269 all4443 all0170 alr1004 At4g18360 At2g13360 At4 g18360 slr0293 sll0171 slr0879 slr1096 sll1931...”

Caur_2132 D-lactate dehydrogenase (cytochrome) from Chloroflexus aurantiacus J-10-fl
39% identity, 93% coverage

• Temporal metatranscriptomic patterning in phototrophic Chloroflexi inhabiting a microbial mat in a geothermal spring
  Klatt, The ISME journal 2013
  • “...encode homologs of glycolate oxidase (glcD, RoseRS_3360, Caur_2132), which oxidizes glycolate to produce glyoxylate. Transcripts for glcD in both FAPs showed...”
• Complete genome sequence of the filamentous anoxygenic phototrophic bacterium Chloroflexus aurantiacus
  Tang, BMC genomics 2011
  • “...genes are distant from the C p operon (Caur_0621 to Caur_0627) and C r operon (Caur_2132 to Caur_2144). In addition to auraA and auraB , two more genes encoding auracyanin-like proteins (or type I blue-copper proteins) (Caur_2212 and Caur_2581) have also been found in the Cfl....”

Dhaf_4382 D-lactate dehydrogenase (cytochrome) from Desulfitobacterium hafniense DCB-2
36% identity, 90% coverage

• Genome sequence of Desulfitobacterium hafniense DCB-2, a Gram-positive anaerobe capable of dehalogenation and metal reduction
  Kim, BMC microbiology 2012
  • “...Dhaf_3294. 3 . pyruvate, phosphate dikinase; Dhaf_1046, Dhaf_4240, Dhaf_4251. 4 . D-lactate dehydrogenase (cytochrome); Dhaf_3228, Dhaf_4382. 5 . L-lactate dehydrogenase; Dhaf_1965. 6 . PEP carboxykinase; Dhaf_1134. 7 . malate dehydrogenase (NADP + ); Dhaf_0902, Dhaf_3085. 8 . pyruvate carboxyltransferase; Dhaf_1012, Dhaf_1059. 9 . pyruvate formate-lyase; Dhaf_0366,...”

Desca_0863 FAD-binding oxidoreductase from Desulfotomaculum nigrificans CO-1-SRB
36% identity, 92% coverage

• Genome analyses of the carboxydotrophic sulfate-reducers Desulfotomaculum nigrificans and Desulfotomaculum carboxydivorans and reclassification of Desulfotomaculum caboxydivorans as a later synonym of Desulfotomaculum nigrificans
  Visser, Standards in genomic sciences 2014
  • “...are predicted to encode L-lactate dehydrogenases (DesniDRAFT_1264, 2906; Desca_0533) and D-lactate dehydrogenase (DesniDRAFT_0054, 1145, 1691; Desca_0863, 2222), which are involved in the oxidation of lactate to pyruvate. For incomplete oxidation of pyruvate to acetate via acetyl-CoA D. nigrificans and D. carboxydivorans have genes encoding a putative...”

GSU1623 glycolate oxidase subunit GlcD, putative from Geobacter sulfurreducens PCA
37% identity, 91% coverage

• Key Enzymes for Anaerobic Lactate Metabolism in Geobacter sulfurreducens
  Ueki, Applied and environmental microbiology 2021
  • “...the succinyl-CoA synthetase in growth on lactate. Genome analysis of Geobacter species identified candidate genes, GSU1623, GSU1624, and GSU1620, for lactate dehydrogenase. Deletion mutants of the identified genes for d-lactate dehydrogenase ( GSU1623 GSU1624 mutant) or l-lactate dehydrogenase ( GSU1620 mutant) could not grow on d-lactate or l-lactate...”

PTH_2230 FAD/FMN-containing dehydrogenases from Pelotomaculum thermopropionicum SI
37% identity, 92% coverage

• Substrate-dependent transcriptomic shifts in Pelotomaculum thermopropionicum grown in syntrophic co-culture with Methanothermobacter thermautotrophicus
  Kato, Microbial biotechnology 2009
  • “...mutase Nterminal domain ( mmcE , PTH_1361); filled square, predicted lactate dehydrogenase ( glcD , PTH_2230); asterisk, malic enzyme ( sfcA , PTH_2899). The approximation curve and correlation coefficient ( r ) are given. Overview of transcriptome data Numbers of differentially expressed CDSs (at least twofold...”
  • “...PTH_14921490); Fht, fumarase (PTH_13561357); Mdh, malate dehydrogenase (PTH_1367); Odc, oxaloacetate decarboxylase (PTH_11891190); Ldh, lactate dehydrogenase (PTH_2230), Pfl, pyruvate formate lyase (PTH_2436); Por, pyruvate:ferredoxin oxidoreductase (PTH_1369); FeH 2 ase, Fehydrogenase (I, PTH_06680670; II, PTH_13771379; III, PTH_20102012); NiFeH 2 ase, NiFehydrogenase (PTH_17011704); Fdh, formate dehydrogenase (I, PTH_17111714; II,...”

Dde_3239 FAD-linked oxidase C-terminal domain-containing protein from Oleidesulfovibrio alaskensis G20
Dde_3239 Glycolate oxidase subunit D from Desulfovibrio desulfuricans G20
36% identity, 91% coverage

• Molecular regulation of conditioning film formation and quorum quenching in sulfate reducing bacteria
  Raya, Frontiers in microbiology 2022
  • “...DVU0700 Chemotaxis * Oleidesulfovibrio alaskensis G20 Dde_0356, Dde_ 2,958 Cell motility Hao et al. (1994) Dde_3239 Lactate oxidation CheD , CheW , CheC , Chez Chemotaxis * feoA , and Dde_2669 Inorganic ion transporter Upregulated Desulfovibrio vulgaris strain Hildenborough DVU2571, DVU2572, and DVU2574 Inorganic ion transporter...”
  • “...DVU1081) in D . vulgaris Hildenborough ( Chen et al., 2019 ) and lactate dehydrogenase (Dde_3239) in D . alaskensis G20 ( Tripathi et al., 2022 ) involved in lactate oxidation were downregulated. Furthermore, the gene encoding for the 30 and 50s ribosomal protein was downregulated...”
• Transcriptomics and Functional Analysis of Copper Stress Response in the Sulfate-Reducing Bacterium Desulfovibrio alaskensis G20
  Tripathi, International journal of molecular sciences 2022
  • “...lactate oxidation was also evident from downregulation (log 2 FC = 3.26) of lactate dehydrogenase (Dde_3239) in 15 M Cu(II). An increase in concentration of some specific amino acids was also observed in 5 M and 15 M Cu(II) as compared to control. For example, in...”
• New model for electron flow for sulfate reduction in Desulfovibrio alaskensis G20
  Keller, Applied and environmental microbiology 2014
  • “...(I2/G20) Ab Dde_0182 Dde_0312 Dde_0750 Dde_1087 Dde_3238 Dde_3239 Dde_3240 GlcD COG-GlcD LdlD COG-GlcD LldP GlcD LdhB (S)-2-Hydroxy acid oxidase...”
• Variation among Desulfovibrio species in electron transfer systems used for syntrophic growth
  Meyer, Journal of bacteriology 2013
  • “...catalytic subunit of the lactate dehydrogenase (LdhA, Dde_3239), two HdrD-like putative iron-sulfur subunits (LdhB-1/2, Dde_3240 and Dde_3245), two phosphate...”

SMUL_2229 FAD-linked oxidase C-terminal domain-containing protein from Sulfurospirillum multivorans DSM 12446
38% identity, 84% coverage

• Hydrogen production by Sulfurospirillum species enables syntrophic interactions of Epsilonproteobacteria
  Kruse, Nature communications 2018
  • “...two candidates of the former class were identified in the genome, encoded by SMUL_1449 and SMUL_2229. Of these, only the latter gene product was detected in the proteome, however, not in altered amounts under fermentative conditions when compared to respiratory cultivation. To detect proteins involved in...”

SMUL_1449 FAD-linked oxidase C-terminal domain-containing protein from Sulfurospirillum multivorans DSM 12446
37% identity, 84% coverage

• Hydrogen production by Sulfurospirillum species enables syntrophic interactions of Epsilonproteobacteria
  Kruse, Nature communications 2018
  • “.... Only two candidates of the former class were identified in the genome, encoded by SMUL_1449 and SMUL_2229. Of these, only the latter gene product was detected in the proteome, however, not in altered amounts under fermentative conditions when compared to respiratory cultivation. To detect proteins...”

Caur_2134 D-lactate dehydrogenase (cytochrome) from Chloroflexus aurantiacus J-10-fl
39% identity, 51% coverage

• Complete genome sequence of the filamentous anoxygenic phototrophic bacterium Chloroflexus aurantiacus
  Tang, BMC genomics 2011
  • “...a putative FAD-dependent oxidase (component K, actK , Caur_2133), D-lactate dehydrogenase (component L, actL , Caur_2134), a Cys-rich protein with Fe-S binding motifs (component M, actM , Caur_2135), components B ( actB , Caur_2136), E ( actE , Caur_2137), A ( actA , Caur_2138), and G...”

Cj1213c putative glycolate oxidase subunit D from Campylobacter jejuni subsp. jejuni NCTC 11168
35% identity, 84% coverage

• In vivo and in silico determination of essential genes of Campylobacter jejuni
  Metris, BMC genomics 2011
  • “...the cell in the case of E. coli [ 16 ]. Since a glyoxylate oxidase (Cj1213c) has been annotated [ 23 ] and since glyoxylate has been shown to be degraded via a malate synthase in H. pylori [ 29 ], we assumed a malate synthase...”
  • “...cj1081c, cj1088c, cj1096c, cj1104, cj1114c, cj1133, cj1149c, cj1150c, cj1151c, cj1152c, cj1177c, cj1183c, cj1196c, cj1198, cj1202, cj1213c, cj1238, cj1243, cj1248, cj1364c, cj1398, cj1400c, cj1401c, cj1402c, cj1404, cj1407c, cj1424c, cj1428c, cj1476c, cj1498c, cj1515c, cj1529c, cj1530, cj1605c, cj1634c, cj1641, cj1645, cj1672c, cj1685c FBA & transposon mutagenesis of this study...”

jhp0459 putative Glycolate oxidase from Helicobacter pylori J99
34% identity, 86% coverage

• Growth phase-dependent response of Helicobacter pylori to iron starvation
  Merrell, Infection and immunity 2003
  • “...0.5 0.5 Energy metabolism HP0509 HP0574 HP1134 JHP0459 JHP0521 JHP1062 Glycolate oxidase subunit, glcD Galactosidase acetyltransferase, lacA ATP synthase F1,...”

HP0509 glycolate oxidase subunit (glcD) from Helicobacter pylori 26695
O25250 Glycolate oxidase subunit (GlcD) from Helicobacter pylori (strain ATCC 700392 / 26695)
34% identity, 86% coverage

• Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single- and double-deletion mutants
  Thiele, Journal of bacteriology 2005
  • “...HP0255 HP0293 HP0329 HP0360 HP0372 HP0380 HP0381 HP0389 HP0476 HP0509 HP0512 HP0588 to HP0591 fucA ppsA frdB, frdA, frdC metK, metX dapE cdsA purA pabB nadE...”
• Comparative analysis of the complete cag pathogenicity island sequence in four Helicobacter pylori isolates
  Blomstergren, Gene 2004 (PubMed)
  • “...and HP0547 (cagA). Sequence similar to that of genes HP0510 and HP0509 was found in the 5 end of this region. The 3 end was similar to the corresponding region...”
  • “...arrows. (A) The 5 end was similar to HP0510 and HP0509. (B) The 3 end showed similarity to the corresponding region of strain ATCC 43504 (bold line) and...”
• Growth phase-dependent response of Helicobacter pylori to iron starvation
  Merrell, Infection and immunity 2003
  • “...methyltransferase, MFOKI 0.5 0.5 Energy metabolism HP0509 HP0574 HP1134 JHP0459 JHP0521 JHP1062 Glycolate oxidase subunit, glcD Galactosidase acetyltransferase,...”
• Genome-scale metabolic model of Helicobacter pylori 26695
  Schilling, Journal of bacteriology 2002
  • “...the experimentally determined essentiality of the glcD gene (HP0509) encoding glycolate oxidase. Table 7 contains a series of 17 deletion results comparing the...”
  • “...Agreement HP0808 HP1038 HP0372 HP1099 HP1100 HP1385 HP0509 HP0735 HP0086 HP1418 HP0740 HP0589, HP0590, HP0591, HP0588 HP1110, HP1111, HP1108, HP1109 HP1257...”
• Systematic identification of selective essential genes in Helicobacter pylori by genome prioritization and allelic replacement mutagenesis
  Chalker, Journal of bacteriology 2001
  • “...(mqo), encoding malate quinone oxidoreductase (EC 1.1.99.16); and HP0509 (glcD), which is thought to encode glycolate oxidase subunit (EC 1.1.3.15). We also...”
  • “...highly in our global genome bioinformatic analysis, but HP0509 (glcD), HP1099 (eda), HP1100 (edd), and HP1385 (fbp) are moderately or highly conserved in other...”
• Outer Membrane Vesicles Secreted by Helicobacter pylori Transmitting Gastric Pathogenic Virulence Factors
  Wei, ACS omega 2022
  • “...P0A0X4 rpsL 252 O25791 Omp27 253 P56417 tyrS 254 O25999 HP_1463 255 P56010 rpsC 256 O25250 GlcD 257 O25572 HP_0914 258 P56006 scoA 259 O25176 HP_0422 260 O24999 mrp 261 P56156 clpP 262 O25360 gltX2 263 O26037 HP_1507 264 O25413 HP_0709 265 O25229 HP_0485 266 O25781...”
  • “...P56061 panC 328 O25281 HP_0555 329 O25748 slyD 330 O25484 ribB 331 P66328 rpsJ 332 O25250 GlcD 333 O25337 CheV 334 O25584 surE 335 P56467 folD 336 O24886 fcl 337 O26075 yajC 338 P56072 sdaA 339 P56011 rpsD 340 O25772 Omp26 341 O24991 lpxD 342 O25166...”

DVU_3027 / Q726S9 quinone-dependent D-lactate dehydrogenase catalytic subunit (EC 1.1.2.5) from Desulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough) (see 3 papers)
DVU3027 glycolate oxidase, subunit GlcD from Desulfovibrio vulgaris Hildenborough
Q726S9 Glycolate oxidase, subunit GlcD from Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)
36% identity, 91% coverage

• Pyridoxal 5'-phosphate synthesis and salvage in Bacteria and Archaea: predicting pathway variant distributions and holes
  Denise, Microbial genomics 2023
  • “...encodes five paralogs, DVU0253 (UniProt ID Q72FG1), DVU0390 (UniProt ID Q72F25), DVU0827 (UniProt ID Q72DV2), DVU3027 (UniProt ID Q72659), and DVU3071 (UniProt ID Q726N5). The genes encoding DVU0827 and DVU3027 are each in an operon with a gene encoding their iron-sulphur subunits, DVU0826, and DVU3028, respectively...”
  • “...dehydrogenase annotation to the DVU0827 subgroup, while tagging the d -lactate oxidase role to the DVU3027 subgroup (Table S9). Fig. 5. Paralogous groups of PF02913, FAD-linked oxidase (glycolate oxidase superfamily). Panel (a). Sequence similarity network (SSN) of members of PF02913 in Desulfovibrionales displayed with an alignment...”
• Key Enzymes for Anaerobic Lactate Metabolism in Geobacter sulfurreducens
  Ueki, Applied and environmental microbiology 2021 (secret)
• Antimicrobial Effects of Free Nitrous Acid on Desulfovibrio vulgaris: Implications for Sulfide-Induced Corrosion of Concrete
  Gao, Applied and environmental microbiology 2016
  • “...includes the genes DVU3026 for lactate permease, DVU3027, DVU3028, DVU3032, and DVU03033 for lactate dehydrogenase subunits, DVU3025 for pyruvate-ferredoxin...”
  • “...DVU1289 DVU1287 DVU1286 DVU1597 Lactate oxidation DVU3030 DVU3027 DVU3031 DVU3032 DVU3028 DVU3033 DVU0600 DVU2110 DVU2285 DVU2451 DVU2683 DVU3026 DVU3029...”
• The primary pathway for lactate oxidation in Desulfovibrio vulgaris
  Vita, Frontiers in microbiology 2015
  • “...domains but without a PTA_PTB protein domain, thus excluding putative Pta activity for this protein. DVU3027 and 3028 were annotated as a glycolate oxidase subunit and iron-sulfur cluster-binding protein encoding gene, respectively. However, their amino acid sequences suggested that they corresponded to two subunits of a...”
  • “...(PF13183) and CCG domain (PF02754), ( Figure 2 ). The C-terminal FAD-linked oxidase domain of DVU3027 contained a sequence close to the motif GEHGD and an essential histidine conserved in enzymes that bind lactate ( Griffin et al., 1992 ). DVU3032 and DVU3033 were annotated as...”
• High-throughput isolation and characterization of untagged membrane protein complexes: outer membrane complexes of Desulfovibrio vulgaris
  Walian, Journal of proteome research 2012
  • “...DVU1065 peptidyl-prolyl cistrans isomerse domain protein DVU2945 conserved domain protein DVU1067 membrane protein, Bmp family DVU3027 glcD, glycolate oxidase, subunit GlcD DVU1133 hypothetical protein DVU3035 methyl-accepting chemotaxis protein, putative DVU1183 HD domain protein DVU3069 conserved hypothetical protein TIGR00247 DVU1260 outer membrane protein P1, putative DVU3082 methyl-accepting...”
• Global transcriptional, physiological, and metabolite analyses of the responses of Desulfovibrio vulgaris hildenborough to salt adaptation
  He, Applied and environmental microbiology 2010
  • “...genes in the operon containing DVU3025, DVU3026, DVU3027, DVU3028, DVU3029, and DVU3030, which encode a putative pyruvate-ferredoxin oxi- Downloaded from...”
• The electron transfer system of syntrophically grown Desulfovibrio vulgaris
  Walker, Journal of bacteriology 2009
  • “...to pyruvate by a putative lactate dehydrogenase (DVU3027 and DVU3028), which likely functions primarily during syntrophic growth. The extracted electrons reduce...”
  • “...glycolate oxidase of E. coli (DVU3027 and DVU3028), a monomeric pyruvate:ferredoxin oxidoreductase (DVU3025), phosphate acetyltransferase (DVU3029),...”
• Response of Desulfovibrio vulgaris to alkaline stress
  Stolyar, Journal of bacteriology 2007
  • “...DVU2370 DVU2526 DVU2571 DVU2572 DVU2816 DVU3025 DVU3026 DVU3027 DVU3028 DVU3029 DVU3030 DVU3035 DVU3081 DVU3108 DVU3110 DVU3298 DVU3299 DVU3300 DVU3301 DVU3303...”
• More
• Combining metabolic flux analysis with proteomics to shed light on the metabolic flexibility: the case of Desulfovibrio vulgaris Hildenborough.
  Marbehan, Frontiers in microbiology 2024
  • “...7 L-lactate permease Ltp Q726T0 DVU_3026 60.8 6 13 6 D-lactate dehydrogenase subunit A D-LdII-A Q726S9 DVU_3027 49.3 85 81 32 D-lactate dehydrogenase subunit B D-LdII-B Q726S8 DVU_3028 45.9 32 45 16 Phosphate acetyl transferase Pta Q726S7 DVU_3029 76.8 121 75 41 Acetate kinase Ack Q726S6...”
• Pyridoxal 5'-phosphate synthesis and salvage in Bacteria and Archaea: predicting pathway variant distributions and holes.
  Denise, Microbial genomics 2023
  • “...separates the paralogous groups. Red node, DVU0827 (UniProt ID Q72DV2); blue node, DVU3027 (UniProt ID Q726S9); green node, DVU0390 (UniProt ID Q72F25); magenta node, DVU0253 (UniProt ID Q72FG1); cyan node, DVU03071 (UniProt ID Q726N5). Panel (b). Genome context () for the paralogs in Desulfovibrio vulgaris str....”

D2S425 D-lactate dehydrogenase (Cytochrome) from Geodermatophilus obscurus (strain ATCC 25078 / DSM 43160 / JCM 3152 / CCUG 61914 / KCC A-0152 / KCTC 9177 / NBRC 13315 / NRRL B-3577 / G-20)
36% identity, 87% coverage

• The sodium leak channel, NALCN, in health and disease.
  Cochet-Bissuel, Frontiers in cellular neuroscience 2014
  • “...susceptibility locus located on chromosome 2, near the UNC-80 gene, linked to alcohol tolerance (markers D2S425, D2S434, D2S424, D2S1323, D2S1333) and the comorbidy of alcoholism and depression (marker DS1371) respectively (Nurnberger et al., 2001 ; Schuckit et al., 2001 ). Restless legs syndrome Restless legs syndrome...”

Q747H0 D-lactate/glycolate dehydrogenase, FAD-binding protein, putative from Geobacter sulfurreducens (strain ATCC 51573 / DSM 12127 / PCA)
GSU3296 glycolate oxidase subunit GlcD, putative from Geobacter sulfurreducens PCA
33% identity, 86% coverage

• Pyridoxal 5'-phosphate synthesis and salvage in Bacteria and Archaea: predicting pathway variant distributions and holes
  Denise, Microbial genomics 2023
  • “...l -lactate catabolism in Geobacter sulfurreducens showed that the glycolate oxidase-like subunits GSU3296/GSU3297 (UniProt ID Q747H0) are not involved in lactate metabolism and must have a housekeeping function [ 84 ]. As pdxB is missing in this organism (Table S5), it is tempting to propose that...”
• Pyridoxal 5'-phosphate synthesis and salvage in Bacteria and Archaea: predicting pathway variant distributions and holes
  Denise, Microbial genomics 2023
  • “...this organism (Table S5), it is tempting to propose that GSU3296/97 fulfils this function. However, GSU3296 is in the same sequence cluster as a SwissProt-curated glycolate oxidase (Fig. S6); hence it is impossible to annotate without further experimental validation steps. In summary, if we can fill...”
• Key Enzymes for Anaerobic Lactate Metabolism in Geobacter sulfurreducens
  Ueki, Applied and environmental microbiology 2021 (secret)

FE46_RS08480 FAD-binding oxidoreductase from Flavobacterium psychrophilum
33% identity, 92% coverage

• Dual RNA-Seq of Flavobacterium psychrophilum and Its Outer Membrane Vesicles Distinguishes Genes Associated with Susceptibility to Bacterial Cold-Water Disease in Rainbow Trout (Oncorhynchus mykiss)
  Chapagain, Pathogens (Basel, Switzerland) 2023
  • “...subunit alpha 24.98 FE46_RS01780 Electron transfer flavo subunit beta family 24.12 FE46_RS05145 Dihydrolipoyl dehydrogenase 23.63 FE46_RS08480 FAD-binding 22.90 FE46_RS05800 Class II fumarate hydratase 22.35 FE46_RS11950 Aldehyde dehydrogenase family 21.72 FE46_RS00480 Succinate dehydrogenase/fumarate reductase iron-sulfur subunit 17.80 pathogens-12-00436-t003_Table 3 Table 3 Differentially expressed F. psychrophilum transcripts, with...”

RHA1_ro03227 probable glycolate oxidase FAD-linked subunit from Rhodococcus sp. RHA1
37% identity, 91% coverage

• A mycofactocin-associated dehydrogenase is essential for ethylene glycol metabolism by Rhodococcus jostii RHA1
  Shimizu, Applied microbiology and biotechnology 2024 (PubMed)
  • “...Deletion of a putative glycolate dehydrogenase gene (RHA1_ro03227) abolished growth with ethylene glycol, indicating that ethylene glycol is assimilated via...”
  • “...Sourceb,c Wild-type strain (WT) Deletion mutant of RHA1_ro03227 Deletion mutant of RHA1_ro06057 Deletion mutant of RHA1_ro06081 Deletion mutant of RHA1_ro06071...”

DVU0827 glycolate oxidase, subunit GlcD, putative from Desulfovibrio vulgaris Hildenborough
Q72DV2 Glycolate oxidase, subunit GlcD, putative from Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)
35% identity, 90% coverage

• Large-scale genetic characterization of the model sulfate-reducing bacterium, Desulfovibrio vulgaris Hildenborough
  Trotter, Frontiers in microbiology 2023
  • “...lacks pyridoxal phosphate (vitamin B 6 ), we identified a putative two-subunit dehydrogenase (DVU0826 and DVU0827) that is required for pyridoxal phosphate biosynthesis ( Figure 4A ). The genes for both subunits have nearly identical fitness patterns (high cofitness) as pdxA (DVU2241), which encodes 4-hydroxythreonine-4-phosphate dehydrogenase....”
  • “...evidence supports a role for the dehydrogenase in pyridoxal phosphate biosynthesis. Figure 4 DVU0826 and DVU0827 are required for vitamin B 6 synthesis. (A) Comparison of gene fitness values across 757 experiments between pdxA (DVU2241) and either DVU0826 (left) or DVU0827 (right). Experiments performed in the...”
• Pyridoxal 5'-phosphate synthesis and salvage in Bacteria and Archaea: predicting pathway variant distributions and holes
  Denise, Microbial genomics 2023
  • “...) and pdxJ ( DVU1908 ) in conditions of B 6 limitation are DVU0826 and DVU0827 (Fig. S5), annotated as encoding the two subunits of the glycolate oxidase complex, the iron-sulphur subunit (GlcF), and the FAD-dependent subunits respectively (GlcD). This co-fitness is conserved in another D....”
  • “...Desulfovibrio vulgaris str. Hildenborough encodes five paralogs, DVU0253 (UniProt ID Q72FG1), DVU0390 (UniProt ID Q72F25), DVU0827 (UniProt ID Q72DV2), DVU3027 (UniProt ID Q72659), and DVU3071 (UniProt ID Q726N5). The genes encoding DVU0827 and DVU3027 are each in an operon with a gene encoding their iron-sulphur subunits,...”
• Large-scale Genetic Characterization of a Model Sulfate-Reducing Bacterium
  Trotter, 2021
• Combining metabolic flux analysis with proteomics to shed light on the metabolic flexibility: the case of Desulfovibrio vulgaris Hildenborough.
  Marbehan, Frontiers in microbiology 2024
  • “...A (Dld-II family) Q72DV3 DVU_0826 47.4 2 4 2 D-lactate dehydrogenase subunit B (Dld-II family) Q72DV2 DVU_0827 50.1 7 22 6 D-lactate dehydrogenase (Dld-II family) Q72F25 DVU_0390 48.2 25 51 17 D-lactate dehydrogenase (Dld-II family) Q72FG1 DVU_0253 103 88 62 52 L-lactate dehydrogenase (LldG family) Q72B57...”
• Pyridoxal 5'-phosphate synthesis and salvage in Bacteria and Archaea: predicting pathway variant distributions and holes.
  Denise, Microbial genomics 2023
  • “...Hildenborough encodes five paralogs, DVU0253 (UniProt ID Q72FG1), DVU0390 (UniProt ID Q72F25), DVU0827 (UniProt ID Q72DV2), DVU3027 (UniProt ID Q72659), and DVU3071 (UniProt ID Q726N5). The genes encoding DVU0827 and DVU3027 are each in an operon with a gene encoding their iron-sulphur subunits, DVU0826, and DVU3028,...”
  • “...140 (nodes are UniProt IDs) that separates the paralogous groups. Red node, DVU0827 (UniProt ID Q72DV2); blue node, DVU3027 (UniProt ID Q726S9); green node, DVU0390 (UniProt ID Q72F25); magenta node, DVU0253 (UniProt ID Q72FG1); cyan node, DVU03071 (UniProt ID Q726N5). Panel (b). Genome context () for...”

Dred_0369 FAD linked oxidase domain protein from Desulfotomaculum reducens MI-1
34% identity, 90% coverage

• Comparative Proteomic Analysis of Desulfotomaculum reducens MI-1: Insights into the Metabolic Versatility of a Gram-Positive Sulfate- and Metal-Reducing Bacterium
  Otwell, Frontiers in microbiology 2016
  • “...beta and alpha subunits of electron transfer flavoproteins (Dred_0367-8) and an FAD-linked oxidase domain-containing protein (Dred_0369). A high number of unique peptides for each of these proteins was detected on all conditions, with the lowest number observed on pyruvate. The average ion intensity of each protein...”

CPE0313 probable glycolate oxidase subunit from Clostridium perfringens str. 13
33% identity, 86% coverage

• Changes in the expression of genes encoding type IV pili-associated proteins are seen when Clostridium perfringens is grown in liquid or on surfaces
  Soncini, BMC genomics 2020
  • “...5.305 0.0405 etfA Electron transfer flavoprotein alpha-subunit CPE0312 5.131 0.0405 glcD Probable glycolate oxidase subunit CPE0313 5.530 0.0405 fucK Rhamnulokinase CPE0317 4.832 0.0405 fucI L-fucose isomerase CPE0318 5.490 0.0405 fucA L-fuculose-phosphate aldolase CPE0319 5.211 0.0405 manX Phosphotransferase system, mannose/fructose-specific component IIA CPE0320 5.914 0.0405 manY Probable...”

Cbei_0312 FAD linked oxidase domain-containing protein from Clostridium beijerincki NCIMB 8052
31% identity, 88% coverage

• Transcriptional analysis of Clostridium beijerinckii NCIMB 8052 to elucidate role of furfural stress during acetone butanol ethanol fermentation
  Zhang, Biotechnology for biofuels 2013
  • “...aldo/keto reductase (Cbei_3974), short-chain dehydrogenase/reductase (SDR) (Cbei_3904), DSBA oxidoreductase (Cbei_2058), FAD linked oxidase domain-containing protein (Cbei_0312), and alcohol dehydrogenase (Cbei_1464) (Figure 1 A and Additional file 1 : Table S4A). The transcriptome of C. beijerinckii 8052 after furfural challenge at the solventogenic phase shows some similarities...”
  • “...in terms of redox enzymes. All the above genes, except FAD linked oxidase domain-containing protein (Cbei_0312), and alcohol dehydrogenase (Cbei_1464), were also induced by furfural challenge at the solventogenic phase (Figure 1 A and Additional file 1 : Table S4C). Figure 1 Comparison of gene expression...”

Adeh_1963 FAD linked oxidase-like from Anaeromyxobacter dehalogenans 2CP-C
35% identity, 92% coverage

• The mosaic genome of Anaeromyxobacter dehalogenans strain 2CP-C suggests an aerobic common ancestor to the delta-proteobacteria
  Thomas, PloS one 2008
  • “...of a query sequence to a hit [94] . Two regions located between Adeh_1913 and Adeh_1963 with 69.5% G+C content contain ribosomal proteins, show no deviation in codon adaptation, and were excluded from further analysis. Motility assays A. dehalogenans was grown as described [6] and cells...”

RHA1_ro02984 probable glycolate oxidase subunit from Rhodococcus sp. RHA1
35% identity, 87% coverage

• Application of Rhodococcus jostii RHA1 glycolate oxidase as an efficient accessory enzyme for lignin conversion by bacterial Dyp peroxidase enzymes
  Alruwaili, Green chemistry : an international journal and green chemistry resource : GC 2023
  • “...been reported. 30 Expression & purification of Rhodococcus jostii RHA1 glycolate oxidase (RjGlOx) from gene RHA1_ro02984 was described by Wei et al. 16 Expression & purification of Agrobacterium sp. DyP peroxidase (AgroDyP) and Comamonas testosteroni DyP (CtDyP) was previously described by Rashid & Bugg. 31 Assay...”

MT1296 oxidoreductase, FAD-binding from Mycobacterium tuberculosis CDC1551
Rv1257c PROBABLE OXIDOREDUCTASE from Mycobacterium tuberculosis H37Rv
38% identity, 91% coverage

• Transcriptional Profiling of Mycobacterium tuberculosis Exposed to In Vitro Lysosomal Stress
  Lin, Infection and immunity 2016
  • “...0.4 MT0456 MT0574 MT0575 MT0618 MT0621 MT0685 MT0693 MT1296 MT1959 MT1961 MT2004 MT2005 MT2018 MT2489 MT2503 MT2504 MT2941 MT3526 MT3527 MT3771 MT3949** Rv0440...”
• Whole-genome sequencing and transcriptome-characterized in vitro evolution of aminoglycoside resistance in Mycobacterium tuberculosis
  Wei, Microbial genomics 2023
  • “...target genes reported as whiB7 -dependent transcripts: Rv2415c, Rv1473, erm (37), cut2, hflX, aspC and Rv1257c. Unsurprisingly, in our study, these genes were upregulated by 4- to 16-fold in the KP4-58 strain. It is of note that although the whiB7 regulon accounted for a small proportion...”
• VapC21 Toxin Contributes to Drug-Tolerance and Interacts With Non-cognate VapB32 Antitoxin in Mycobacterium tuberculosis
  Sharma, Frontiers in microbiology 2020
  • “...overexpression strain ( Figure 6C ). However, the expression levels of other transcripts for Rv0263c, Rv1257c, Rv1473, Rv2301, and Rv2302 belonging to WhiB7 regulon was comparable in the parental and overexpression strain ( Figure 6C ). Previously it has been reported that the expression of whib7...”
• Transcriptional Profiling of Mycobacterium tuberculosis Exposed to In Vitro Lysosomal Stress
  Lin, Infection and immunity 2016
  • “...MT3949** Rv0440 Rv0549c Rv0550c Rv0589 Rv0591 Rv0656c Rv0665 Rv1257c Rv1908c Rv1910c Rv1955 Rv1956 Rv1966 Rv2416c Rv2428 Rv2429 NA Rv3417c Rv3418c Rv3670 Rv3841...”
  • “...not affect the transcription of the downstream gene Rv1257c, 2518 iai.asm.org as assessed by real-time PCR (data not shown). Furthermore, qRT-PCR analysis...”
• Trehalose-6-Phosphate-Mediated Toxicity Determines Essentiality of OtsB2 in Mycobacterium tuberculosis In Vitro and in Mice
  Korte, PLoS pathogens 2016
  • “...change (silenced / induced) Transformed p-value Upregulated Rv1258c Rv1258c 27.12 0.00010 Rv0662c vapB7 23.29 0.00005 Rv1257c Rv1257c 19.22 0.00025 Rv1655 argD 15.99 0.00018 Rv2164c Rv2164c 15.92 0.00041 Rv1652 argC 15.72 0.00006 Rv2165c Rv2165c 15.54 0.00230 Rv1654 argB 14.48 0.00017 Rv1656 argF 13.38 0.00001 Rv1987 Rv1987 12.46...”
• Characterizing the pocketome of Mycobacterium tuberculosis and application in rationalizing polypharmacological target selection
  Anand, Scientific reports 2014
  • “...systemic dermatomyositis, systemic lupus erythematosus, atopic dermatitis, contact dermatitis, exfoliative dermatitis. Erythromycin (DB00199;ERY) 0.53 Rv1181; Rv1257c; Rv1589; Rv2243; Rv3712; Rv3793; Rv3801c; Rv3886c; For use in the treatment of infections caused by susceptible strains of microorganisms in the following diseases: respiratory tract infections (upper and lower) of...”
• Aminoglycoside cross-resistance in Mycobacterium tuberculosis due to mutations in the 5' untranslated region of whiB7
  Reeves, Antimicrobial agents and chemotherapy 2013
  • “...The tap (Rv1258c) (bases 90 to 1230 removed) and Rv1257c deletion (bases 134 to 1188 removed) strains were similarly constructed and confirmed. All plasmids and...”
  • “...in a two-gene operon that includes the cotranscribed gene Rv1257c, which is annotated as coding for a putative oxidoreductase with no known role in antibiotic...”
• Anti-mycobacterial activity of marine fungus-derived 4-deoxybostrycin and nigrosporin
  Wang, Molecules (Basel, Switzerland) 2013
  • “...0.05 Metabolism: Energy production and conversion ctaC Rv2200c 0.37 0.10 Metabolism: Energy production and conversion Rv1257c - 1.74 0.04 Metabolism: Energy production and conversion pks18 Rv1372 0.44 0.04 Metabolism: Lipid metabolism fadD32 Rv3801c 0.47 0.01 Metabolism: Lipid metabolism Rv3815c - 1.77 0.08 Metabolism: Lipid metabolism deoC...”
  • “...Rv1200 1.989 9.219 0.742 0.919 0.937 0.728 0.805 0.807 1 0.817 0.801 0.924 Rv3044 Rv1372 Rv1257c htpX pgk ctaC infB rpsD ogt Rv2264c Rv0907 Rv1335 15.46 0.59 1.023 0.846 0.708 1.069 0.787 0.733 0.826 1.275 0.878 1.26 a The ratio was calculated by dividing the amplified...”
• Functional and genetic characterization of the tap efflux pump in Mycobacterium bovis BCG
  Ramón-García, Antimicrobial agents and chemotherapy 2012
  • “...(4) comprises the region containing the Rv1255c, Rv1256c, and Rv1257c genes, compared to the M. tuberculosis H37Rv genome. The chimeric gene after the fusion of...”
• More

Dtox_0988 D-lactate dehydrogenase (cytochrome) from Desulfotomaculum acetoxidans DSM 771
33% identity, 91% coverage

• Complete genome sequence of Desulfotomaculum acetoxidans type strain (5575)
  Spring, Standards in genomic sciences 2009
  • “...carbon source [ 32 ]. The genome here reported encodes a putative D-lactate dehydrogenase gene (Dtox_0988), which is however only distantly related to genes encoding enzymes known to be involved in the respiration or fermentation of lactate. Hence, it is unclear if this enzyme could be...”

F502_16610 FAD-binding oxidoreductase from Clostridium pasteurianum DSM 525 = ATCC 6013
31% identity, 90% coverage

• Metabolic and proteomic analyses of product selectivity and redox regulation in Clostridium pasteurianum grown on glycerol under varied iron availability
  Groeger, Microbial cell factories 2017
  • “...2.1 2.5 F502_04707 Adenylosuccinate lyase COG0015 303 F502_15080 Rubrerythrin COG1592 YotD 558 2.2 4.5 2.0 F502_16610 Glycolate oxidase COG0277 GlcD 315 1.8 2.3 1.9 F502_18287 Hydrogenase-1 COG1034 NuoG 223 4.5 1.6 2.3 224 5.1 1.9 3.6 F502_18651 NADP-dependent glyceraldehyde-3-phosphate dehydrogenase COG1012 AdhE 736 2.7 1.5 2.1...”
• Fermentation of mixed substrates by Clostridium pasteurianum and its physiological, metabolic and proteomic characterizations
  Sabra, Microbial cell factories 2016
  • “...Stage V sporulation protein T 12.2 F502_15080 Rubrerythrin 2.9 5.5 F502_07198 Single-stranded DNA-binding protein 7.5 F502_16610 Glycolate oxidase 2.7 5.5 F502_16565 Nitrogen regulatory protein P-II 6.2 5.3 F502_03342 Pyruvate phosphate dikinase 4.4, 4.2 4.9, 3,0 F502_04232 Stage IV sporulation protein A 4.1, 3.3 4.6, 2.6 F502_18651...”

MA4631 D-lactate dehydrogenase from Methanosarcina acetivorans C2A
34% identity, 86% coverage

• Transcriptional response of <i>Methanosarcina acetivorans</i> to repression of the energy-conserving methanophenazine: CoM-CoB heterodisulfide reductase enzyme HdrED
  Buan, Microbiology spectrum 2024
  • “...MA0888, NADH dehydrogenase subunit N MA4368, fibrillarin MA0341 (pre-rRNA processing), 6-pyrovoyltetrahydropterin synthase MA4196, D-lactate dehydrogenase MA4631, chemotaxis signaling protein MA3070, and archaeosine tRNA ribosyltransferase MA4632. Another 159 transcripts had strong positive time-dependent abundance ( r 2 > 0.8), and 43 transcripts had strong time-dependent decreasing abundance...”
  • “...exposure to O 2 and was demonstrated to be used in conjunction D-lactate dehydrogenase (LDH, MA4631) to detoxify O 2 ( 30 ). However, when HdrED is depleted, MA4631 is downregulated, indicating that CydAB and LDH can be regulated independently and that CydAB may be induced...”
• Lactate oxidation is linked to energy conservation and to oxygen detoxification via a putative terminal cytochrome oxidase in Methanosarcina acetivorans
  Feregrino-Mondragón, Archives of biochemistry and biophysics 2023 (PubMed)
  • “...Methanosarcina acetivorans contains a putative NAD + -independent d-lactate dehydrogenase (D-iLDH/glycolate oxidase) encoded by the MA4631 gene, belonging to the FAD-oxidase C superfamily. Nucleotide sequences similar to MA4631 gene, were identified in other methanogens and Firmicutes with >90 and 35-40% identity, respectively. Therefore, the lactate metabolism...”
  • “...compared to anaerobic control cells. An E. coli mutant deficient in dld complemented with the MA4631 gene, grew with d-lactate as carbon source and showed membrane-bound d-lactate:quinone oxidoreductase activity. The product of the MA4631 gene is a FAD-containing monomer showing activity of iLDH with preference to...”

CA_C2542, CEA_G2555 FAD-binding oxidoreductase from Clostridium acetobutylicum EA 2018
31% identity, 86% coverage

• Comparative genomic and transcriptomic analysis revealed genetic characteristics related to solvent formation and xylose utilization in Clostridium acetobutylicum EA 2018
  Hu, BMC genomics 2011
  • “...2.509044 1.656072 1.958591 glycosyltransferase CEA_G2025 CA_C2010 3.282342 3.533526 2.84142 3.003615 2.50221 2.005231 Fe-S oxidoreductase CEA_G2555 CA_C2542 8.22595 5.876659 5.423124 5.135223 4.224852 4.280766 FAD/FMN-containing dehydrogenase CEA_G2556 CA_C2543 8.451735 6.100494 5.401602 5.24343 4.426238 3.987954 electron-transferring flavoprotein large subunit CEA_G2557 CA_C2544 7.904188 6.040402 4.848558 4.578106 4.214698 3.969443 electron-transferring flavoprotein...”
  • “...2.812136 2.509044 1.656072 1.958591 glycosyltransferase CEA_G2025 CA_C2010 3.282342 3.533526 2.84142 3.003615 2.50221 2.005231 Fe-S oxidoreductase CEA_G2555 CA_C2542 8.22595 5.876659 5.423124 5.135223 4.224852 4.280766 FAD/FMN-containing dehydrogenase CEA_G2556 CA_C2543 8.451735 6.100494 5.401602 5.24343 4.426238 3.987954 electron-transferring flavoprotein large subunit CEA_G2557 CA_C2544 7.904188 6.040402 4.848558 4.578106 4.214698 3.969443 electron-transferring...”

E6N788 (S)-2-hydroxy-acid oxidase (EC 1.1.3.15); D-lactate dehydrogenase (acceptor) (EC 1.1.99.6) from Candidatus Caldarchaeum subterraneum (see paper)
32% identity, 93% coverage

CLJU_RS10590 FAD-binding oxidoreductase from Clostridium ljungdahlii DSM 13528
31% identity, 86% coverage

• Bioinformatics and metabolic flux analysis highlight a new mechanism involved in lactate oxidation in Clostridium tyrobutyricum
  Munier, International microbiology : the official journal of the Spanish Society for Microbiology 2023
  • “...AWO_RS04430); EtfB (EZN00_RS08615, CLJU_RS10600, and AWO_RS04410); EtfA (EZN00_RS08620, CLJU_RS10595, and AWO_RS04415); LDH, lactate dehydrogenase (EZN00_RS08625, CLJU_RS10590, and AWO_RS04420) According to these results, C.tyrobutyricum would have the same mechanism of lactate oxidation as A. woodii , i.e., involving an EtfAB complex. In order to support our proposal,...”
• Transcriptomic profiles of Clostridium ljungdahlii during lithotrophic growth with syngas or H₂ and CO₂ compared to organotrophic growth with fructose
  Aklujkar, Scientific reports 2017
  • “...The ninth, tenth and thirteenth most upregulated genes ( lutJ CLJU_RS10595, lutI CLJU_RS10600 and lutK CLJU_RS10590, Fig. 1 ) encode an electron transfer flavoprotein and a candidate (R) -lactate dehydrogenase with 28% protein sequence identity to an (R) -lactate-oxidizing enzyme of E . coli 30 ....”

CLP_3877 FAD-binding oxidoreductase from Clostridium butyricum E4 str. BoNT E BL5262
31% identity, 88% coverage

• Type E Botulinum Neurotoxin-Producing Clostridium butyricum Strains Are Aerotolerant during Vegetative Growth
  Camerini, mSystems 2019
  • “...Redox homeostasis 32 489503213 CLP_0082 Oxidoreductase NAD-binding domain protein 2.16 NADNADH Redox homeostasis 33 489505820 CLP_3877 FAD-linked oxidase domain protein 1.58 FADFADH Redox homeostasis 34 489506590 CLP_0595 Thioredoxin-disulfide reductase 3.25 FADFADH, NADNADH Redox homeostasis 35 489506753 CLP_0519 MviM protein NAD(P)-dependent oxidoreductase 3.25 NADPNADPH Redox homeostasis 36...”

ATN24_RS03035 FAD-binding oxidoreductase from Clostridium butyricum
31% identity, 88% coverage

• Cell factories converting lactate and acetate to butyrate: Clostridium butyricum and microbial communities from dark fermentation bioreactors
  Detman, Microbial cell factories 2019
  • “...ATN24_RS03165, 3: ATN24_RS08885) and EtfB (1: ATN24_RS03025, 2: ATN24_RS03160, 3: ATN24_RS08880), and potentially GlcD (1: ATN24_RS03035, 3: ATN24_RS08895, 4: ATN24_RS11095) A similar search was performed for the selected genomes of bacteria Roseburia intestinalis L1-82, Eubacterium rectale ATCC 33656, and Faecalibacterium prausnitzii A2165 recognized as butyrate producers...”

EZN00_RS08625 FAD-binding oxidoreductase from Clostridium tyrobutyricum
30% identity, 86% coverage

• Bioinformatics and metabolic flux analysis highlight a new mechanism involved in lactate oxidation in Clostridium tyrobutyricum
  Munier, International microbiology : the official journal of the Spanish Society for Microbiology 2023
  • “...EZN00_RS10795, 3: EZN00_RS08615), EtfA (1: EZN00_RS10865, 2: EZN00_RS10800, 3: EZN00_RS08620), FAD-binding oxidoreductase (1:: EZN00_RS10870; 3: EZN00_RS08625) In fragment 1, genes encoding the EtfAB complex are next to a FAD-binding oxidoreductase. The EtfAB complex involved in fragment 2 is in a gene cluster involving an enoyl-CoA hydratase...”
  • “...and AWO_RS04430); EtfB (EZN00_RS08615, CLJU_RS10600, and AWO_RS04410); EtfA (EZN00_RS08620, CLJU_RS10595, and AWO_RS04415); LDH, lactate dehydrogenase (EZN00_RS08625, CLJU_RS10590, and AWO_RS04420) According to these results, C.tyrobutyricum would have the same mechanism of lactate oxidation as A. woodii , i.e., involving an EtfAB complex. In order to support our...”

R1AW66 Glycolate dehydrogenase, subunit GlcD from Caldisalinibacter kiritimatiensis
30% identity, 86% coverage

• Looking for the mechanism of arsenate respiration of Fusibacter sp. strain 3D3, independent of ArrAB
  Acosta-Grinok, Frontiers in microbiology 2022
  • “...WP_069871747 Clostridium amylolyticum A0A1M6NXL2 2 10 133 LdhD Lactate/Glycolate dehydrogenase, subunit LdhD/GlcD WP_069871751 Caldisalinibacter kiritimatiensis R1AW66 0 PFOR: pyruvate:ferredoxin oxidoreductase PorA-1 Pyruvate synthase subunit PorA/Pyruvate oxidoreductase chain WP_069871797 Thermotoga maritima O05651 2 10 45 PorA-2 Pyruvate:ferredoxin oxidoreductase, subunit WP_069874428 Acidaminobacter hydrogenoformans A0A1G5RST4 6 10 166 PorB-1...”

Dde_0182 Glycolate oxidase, subunit GlcD (glcD) from Desulfovibrio desulfuricans G20
33% identity, 90% coverage

• New model for electron flow for sulfate reduction in Desulfovibrio alaskensis G20
  Keller, Applied and environmental microbiology 2014
  • “...I2 abundance G20 abundance Log2 R (I2/G20) Ab Dde_0182 Dde_0312 Dde_0750 Dde_1087 Dde_3238 Dde_3239 Dde_3240 GlcD COG-GlcD LdlD COG-GlcD LldP GlcD LdhB...”
• Flexibility of syntrophic enzyme systems in Desulfovibrio species ensures their adaptation capability to environmental changes
  Meyer, Journal of bacteriology 2013
  • “.../ / / / Dde_0750 / / / / Dde_3604 Dde_0182 Dde_1681 / / / / / / / / / Dde_1842-Dde_1844 Dde_3239-Dde_3240 Dde_1085-Dde_1087 Dde_3241 Dde_3242 Dde_1273 /...”

DVU0390 glycolate oxidase, subunit GlcD, putative from Desulfovibrio vulgaris Hildenborough
Q72F25 Glycolate oxidase, subunit GlcD, putative from Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)
34% identity, 87% coverage

• Combining metabolic flux analysis with proteomics to shed light on the metabolic flexibility: the case of Desulfovibrio vulgaris Hildenborough
  Marbehan, Frontiers in microbiology 2024
  • “...al., 2015 ) were detected with confidence ( Table 1 ). In addition, two paralogs (DVU0390 and DVU0253) of the D-LDH located in the luo operon ( Vita et al., 2015 ) and one ortholog of the L-LDH (DVU2789) from Escherichia coli ( Dong et al.,...”
• Pyridoxal 5'-phosphate synthesis and salvage in Bacteria and Archaea: predicting pathway variant distributions and holes
  Denise, Microbial genomics 2023
  • “...5 , panel A). Desulfovibrio vulgaris str. Hildenborough encodes five paralogs, DVU0253 (UniProt ID Q72FG1), DVU0390 (UniProt ID Q72F25), DVU0827 (UniProt ID Q72DV2), DVU3027 (UniProt ID Q72659), and DVU3071 (UniProt ID Q726N5). The genes encoding DVU0827 and DVU3027 are each in an operon with a gene...”
  • “...groups. Red node, DVU0827 (UniProt ID Q72DV2); blue node, DVU3027 (UniProt ID Q726S9); green node, DVU0390 (UniProt ID Q72F25); magenta node, DVU0253 (UniProt ID Q72FG1); cyan node, DVU03071 (UniProt ID Q726N5). Panel (b). Genome context () for the paralogs in Desulfovibrio vulgaris str. Hildenborough (NC_002937.3), colour...”
• The primary pathway for lactate oxidation in Desulfovibrio vulgaris
  Vita, Frontiers in microbiology 2015
  • “...these orthologs into several groups ( Table 4 ). The first group included DVU0826-27, DVU3071, DVU0390, and DVU0253, which are paralogs of DVU3027-28 in the Dld-II family. The second group included DVU1781-82-83, which is a paralog of DVU3032-33 in the LldEFG family. A schematic representation of...”
  • “...the multidomain organization was the equivalent for all of the homologs except for the protein DVU0390, whereas the predicted oligomeric nature of the enzymes was not equivalent ( Figure 2 ). All of the sequences (except for the DVU0390 sequence) contained the structural features for FAD...”
• Combining metabolic flux analysis with proteomics to shed light on the metabolic flexibility: the case of Desulfovibrio vulgaris Hildenborough.
  Marbehan, Frontiers in microbiology 2024
  • “...dehydrogenase subunit B (Dld-II family) Q72DV2 DVU_0827 50.1 7 22 6 D-lactate dehydrogenase (Dld-II family) Q72F25 DVU_0390 48.2 25 51 17 D-lactate dehydrogenase (Dld-II family) Q72FG1 DVU_0253 103 88 62 52 L-lactate dehydrogenase (LldG family) Q72B57 DVU_1781 23.9 L-lactate dehydrogenase (LldH family) Q72B56 DVU_1782 52.6 4...”
• Pyridoxal 5'-phosphate synthesis and salvage in Bacteria and Archaea: predicting pathway variant distributions and holes.
  Denise, Microbial genomics 2023
  • “...A). Desulfovibrio vulgaris str. Hildenborough encodes five paralogs, DVU0253 (UniProt ID Q72FG1), DVU0390 (UniProt ID Q72F25), DVU0827 (UniProt ID Q72DV2), DVU3027 (UniProt ID Q72659), and DVU3071 (UniProt ID Q726N5). The genes encoding DVU0827 and DVU3027 are each in an operon with a gene encoding their iron-sulphur...”
  • “...DVU0827 (UniProt ID Q72DV2); blue node, DVU3027 (UniProt ID Q726S9); green node, DVU0390 (UniProt ID Q72F25); magenta node, DVU0253 (UniProt ID Q72FG1); cyan node, DVU03071 (UniProt ID Q726N5). Panel (b). Genome context () for the paralogs in Desulfovibrio vulgaris str. Hildenborough (NC_002937.3), colour coding for five...”

CD630_11730, CDIF630erm_01321 FAD-binding oxidoreductase from Clostridioides difficile 630
31% identity, 87% coverage

• The WalRK Two-Component System Is Essential for Proper Cell Envelope Biogenesis in Clostridioides difficile
  Müh, Journal of bacteriology 2022
  • “...flavoprotein alpha 3.30 1.40 NC cd630_11720 11720 etfA4 Electron transfer flavoprotein alpha 2.58 1.24 NC cd630_11730 11730 FAD-linked oxidase 2.17 1.08 NC cd630_08320 08320 aksA trans -Homoaconitate synthase 3.11 2.02 NC cd630_08330 08330 acnB Aconitate hydratase 3.06 2.05 NC cd630_08340 08340 icd Isocitrate dehydrogenase 3.07 2.16...”
• Influence of L-lactate and low glucose concentrations on the metabolism and the toxin formation of Clostridioides difficile
  Hofmann, PloS one 2021
  • “...the lactose utilization operon encoding lactate racemase ( larA ), electron confurcating lactate dehydrogenase ( CDIF630erm_01321 ) and the corresponding electron transfer flavoprotein ( etfAB ). Metabolome analyses revealed L-lactate consumption and the formation of pyruvate. The involved electron confurcation process might be responsible for the...”
  • “...These four genes encoding lactate racemase ( larA ), an electron confurcating lactate dehydrogenase ( CDIF630erm_01321 ) and the electron transfer flavoprotein ( etfAB ) are all clustered in one operon ( CDIF630erm_0131801321 , Table 2 ). The lactate dehydrogenase forms a stable complex with the...”
• Iron Regulation in Clostridioides difficile
  Berges, Frontiers in microbiology 2018
  • “...OFF 2.43 OFF CD630_11720 CDIF630erm_01320 etfA Lactate dehydrogenase, electron transfer flavoprotein alpha subunit -0.66 0.63 CD630_11730 CDIF630erm_01321 lactate dehydrogenase (electron bifurcating), catalytic subunit -0.30 -0.57 0.73 OFF CD630_03940 CDIF630erm_00522 ldhA (R)-2-hydroxyisocaproate dehydrogenase -8.37 OFF -8.66 OFF CD630_03950 CDIF630erm_00523 hadA Isocaprenoyl-CoA:2-hydroxyisocaproate CoA-transferase -8.33 OFF -11.10 OFF 00519...”
  • “...2.43 OFF CD630_11720 CDIF630erm_01320 etfA Lactate dehydrogenase, electron transfer flavoprotein alpha subunit -0.66 0.63 CD630_11730 CDIF630erm_01321 lactate dehydrogenase (electron bifurcating), catalytic subunit -0.30 -0.57 0.73 OFF CD630_03940 CDIF630erm_00522 ldhA (R)-2-hydroxyisocaproate dehydrogenase -8.37 OFF -8.66 OFF CD630_03950 CDIF630erm_00523 hadA Isocaprenoyl-CoA:2-hydroxyisocaproate CoA-transferase -8.33 OFF -11.10 OFF 00519 CD630_03960...”
  • “...second (CDIF630erm_01319 01320) in an operon with lactate racemase (LarA, CDIF630erm_01318) and a lactate dehydrogenase (CDIF630erm_01321) and the third downstream of acdB encoding a short chain acyl-CoA dehydrogenase involved in the conversion of 2-enoyl-3-phenylpropionyl-CoA/isocaprenoyl-CoA into 3-phenylpropionyl-CoA/isocaproyl-CoA during phenylalanine/leucine fermentation with formation of 3-phenylpropionate/isocaproate ( Elsden and...”

CPZ25_RS02230 lactate dehydrogenase subunit LctD from Eubacterium maltosivorans
31% identity, 87% coverage

• Comparative genomics and proteomics of Eubacterium maltosivorans: functional identification of trimethylamine methyltransferases and bacterial microcompartments in a human intestinal bacterium with a versatile lifestyle
  Feng, Environmental microbiology 2022
  • “...(over 1000fold compared to homoacetogenic growth and glucose fermentation), including lactate dehydrogenase (Ldh, encoded by CPZ25_RS02230), electron transfer flavoprotein alpha subunit (EtfA, encoded by CPZ25_RS02225), ETF beta subunit (EtfB, encoded by CPZ25_RS02230) and lactate racemase (LctF1, encoded by CPZ25_RS18455) (Fig. 4A ; Table S1 ). The...”

Dde_1087 FAD/FMN-containing dehydrogenases from Desulfovibrio desulfuricans G20
32% identity, 90% coverage

• New model for electron flow for sulfate reduction in Desulfovibrio alaskensis G20
  Keller, Applied and environmental microbiology 2014
  • “...Log2 R (I2/G20) Ab Dde_0182 Dde_0312 Dde_0750 Dde_1087 Dde_3238 Dde_3239 Dde_3240 GlcD COG-GlcD LdlD COG-GlcD LldP GlcD LdhB (S)-2-Hydroxy acid oxidase...”

A9762_26505 FAD-binding oxidoreductase from Pandoraea sp. ISTKB
31% identity, 84% coverage

• Genomic and proteomic analysis of lignin degrading and polyhydroxyalkanoate accumulating β-proteobacterium Pandoraea sp. ISTKB
  Kumar, Biotechnology for biofuels 2018
  • “...58.534 1.25E24 A0A1E3LRG9 A9762_02095 Cytochrome c oxidase assembly protein 1.76256 6 49.8 22.192 2.52E27 A0A1E3LCR8 A9762_26505 2-Hydroxy-acid oxidase 1.92172 13 43.3 51.242 1.38E99 Oxidoreductases A0A1E3L9T7 A9762_09290 NADHquinone oxidoreductase subunit I 1.983 13 54.6 18.63 1.26E66 A0A1E3LC99 A9762_26255 Oxidoreductase 1.46342 9 62.5 26.21 1.99E100 A0A1E3LAC9 A9762_09275 NADH...”

GJQ69_08645 FAD-binding oxidoreductase from Caproicibacterium lactatifermentans
32% identity, 81% coverage

• Revealing the Characteristics of Glucose- and Lactate-Based Chain Elongation for Caproate Production by Caproicibacterium lactatifermentans through Transcriptomic, Bioenergetic, and Regulatory Analyses
  Wang, mSystems 2022
  • “...synthesis of flavin adenine dinucleotide (FAD) which is required for FAD-dependent enzymes, e.g., lactate dehydrogenase (GJQ69_08645), butyryl-CoA dehydrogenase (GJQ69_08630), and electron transfer flavoproteins (GJQ69_08635 and GJQ69_08640). As indicated in Fig.3 , these FAD-dependent enzymes involved in lactate utilization and caproate production were all significantly upregulated under...”
  • “...production 151 TTGCTAAAACTTTAACAA 19.79 cat GJQ69_04210 3,153 7,806 2.02 Butyryl-CoA:acetate CoA-transferase 77 TAGTTACTTTATTAACAA 14.32 ldh-etfB-etfA-bcd GJQ69_08645 6,294 35,189 3.18 Lactate utilization 81 TTTTTTAAGAATTAACAC 9.07 rnfCDGEAB GJQ69_04335 1,032 367 1.04 Electron transport complex 101 TTATTCAATCTTTAACAA 14.29 rpe GJQ69_09515 118 624 3.05 Ribulose-phosphate 3-epimerase 123 TTTTTAACCGCTTAATCA 9.55 hydA...”
• Adaptability of a Caproate-Producing Bacterium Contributes to Its Dominance in an Anaerobic Fermentation System
  Wang, Applied and environmental microbiology 2021 (secret)

AFE_RS00650 FAD-binding oxidoreductase from Acidithiobacillus ferrooxidans ATCC 23270
33% identity, 84% coverage

• Characterize the Growth and Metabolism of <i>Acidithiobacillus ferrooxidans</i> under Electroautotrophic and Chemoautotrophic Conditions
  Wang, Microorganisms 2024
  • “...protease ATPase subunit HslU 1.38 downhill AFE_RS04470 AFE_RS04470 cytochrome ubiquinol oxidase subunit I 1.36 uphill AFE_RS00650 AFE_RS00650 FAD-binding protein 1.34 uphill AFE_RS01260 AFE_RS01260 FAD-dependent oxidoreductase 1.26 uphill AFE_RS12210 apbC NADH:ubiquinone oxidoreductase (complex I) 1.25 uphill AFE_RS04275 clpX ATP-dependent Clp protease ATP-binding subunit ClpX 1.24 downhill AFE_RS14500...”

lctD / H6LBS1 lactate dehydrogenase (EC 1.1.1.436) from Acetobacterium woodii (strain ATCC 29683 / DSM 1030 / JCM 2381 / KCTC 1655 / WB1) (see 2 papers)
LCTD_ACEWD / H6LBS1 Lactate dehydrogenase (NAD(+),ferredoxin) subunit LctD; EC 1.1.1.436 from Acetobacterium woodii (strain ATCC 29683 / DSM 1030 / JCM 2381 / KCTC 1655 / WB1) (see paper)
H6LBS1 lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) from Acetobacterium woodii (see paper)
AWO_RS04420, Awo_c08730, WP_014355267 lactate dehydrogenase subunit LctD from Acetobacterium woodii DSM 1030
28% identity, 90% coverage

• function: The lactate dehydrogenase-Etf complex catalyzes the oxidation of lactate to pyruvate. It uses flavin-based electron confurcation to drive endergonic lactate oxidation with NAD(+) as oxidant at the expense of simultaneous exergonic electron flow from reduced ferredoxin to NAD(+).
  catalytic activity: lactate + 2 reduced [2Fe-2S]-[ferredoxin] + 2 NAD(+) = 2 oxidized [2Fe-2S]-[ferredoxin] + pyruvate + 2 NADH (RHEA:46964)
  cofactor: FAD
  subunit: Part of the stable heterotrimeric lactate dehydrogenase-Etf complex, which is formed by the lactate dehydrogenase LctD and the electron-transferring flavoprotein (Etf) alpha (LctC) and beta (LctB) subunits.
• Redirecting electron flow in Acetobacterium woodii enables growth on CO and improves growth on formate
  Moon, Nature communications 2024
  • “...homologous recombination, each 500bp of upstream and downstream flanking regions (UFR and DFR) of hydA2 (Awo_c08730) were inserted into the multiple cloning sites of the plasmid. As selection marker, the plasmid has a catP gene from Clostridium perfringens for chloramphenicol/thiamphenicol resistance 54 and a pyrE gene...”
• Bioinformatics and metabolic flux analysis highlight a new mechanism involved in lactate oxidation in Clostridium tyrobutyricum
  Munier, International microbiology : the official journal of the Spanish Society for Microbiology 2023
  • “...(EZN00_RS08615, CLJU_RS10600, and AWO_RS04410); EtfA (EZN00_RS08620, CLJU_RS10595, and AWO_RS04415); LDH, lactate dehydrogenase (EZN00_RS08625, CLJU_RS10590, and AWO_RS04420) According to these results, C.tyrobutyricum would have the same mechanism of lactate oxidation as A. woodii , i.e., involving an EtfAB complex. In order to support our proposal, a phylogenetic...”
• Lactate formation from fructose or C1 compounds in the acetogen Acetobacterium woodii by metabolic engineering
  Moon, Applied microbiology and biotechnology 2023
  • “...flanking regions (UFR) of lctB (Awo_c08710) and 1000bp of downstream flanking regions (DFR) of lctD (Awo_c08730) were cloned into the multiple cloning sites to delete the lctBCD genes by homologous recombination. The plasmid also has a catP marker from Clostridium perfringens coding for chloramphenicol/thiamphenicol resistance (Werner...”
  • “...lactate dehydrogenase in A. woodii , the electron bifurcating LDH/ETH complex, encoded by lctBCD (Awo_c08710 Awo_c08730) (Poehlein et al. 2012 ). This enzyme complex is known to be responsible for lactate oxidation during growth of A. woodii on lactate (Weghoff et al. 2015 ). Recently, it...”
• A new metabolic trait in an acetogen: Mixed acid fermentation of fructose in a methylene-tetrahydrofolate reductase mutant of Acetobacterium woodii
  Moon, Environmental microbiology reports 2023
  • “...subunit Lactate metabolism 76,533 548 7.12 Awo_c08720 Electron transfer flavoprotein alpha subunit 123,511 505 7.93 Awo_c08730 Lactate dehydrogenase 226,503 653 8.44 Awo_c08740 Lactate permease 93,321 346 8.08 Awo_c08750 Lactate racemase 71,991 315 7.84 Awo_c12730 CxxC motifcontaining protein Glycerol metabolism 18,012 2346 2.92 Awo_c12740 Thioredoxin reductase 69,136...”
• Cell factories converting lactate and acetate to butyrate: Clostridium butyricum and microbial communities from dark fermentation bioreactors
  Detman, Microbial cell factories 2019
  • “...transfer flavoprotein FAD flavin adenine dinucleotide GlcD domain of FAD-dependent lactate dehydrogenase, FAD/FMN-containing dehydrogenase WP_014355267 (AWO_RS04420) HPLC high performance liquid chromatography LDH lactate dehydrogenase LldP lactate permease OD optical density Authors contributions ASi, MKB, AC, DM, AD planned the work, conceived and designed the experiments. AD,...”
  • “...electron transfer flavoprotein FAD flavin adenine dinucleotide GlcD domain of FAD-dependent lactate dehydrogenase, FAD/FMN-containing dehydrogenase WP_014355267 (AWO_RS04420) HPLC high performance liquid chromatography LDH lactate dehydrogenase LldP lactate permease OD optical density Authors contributions ASi, MKB, AC, DM, AD planned the work, conceived and designed the experiments....”
• Methane-yielding microbial communities processing lactate-rich substrates: a piece of the anaerobic digestion puzzle
  Detman, Biotechnology for biofuels 2018
  • “...racemase WP_014355269 (AWO_RS04430) (LarA), electron transfer flavoprotein subunit alpha WP_014355266 (AWO_RS04415) (EtfA), FAD/FMN-containing dehydrogenase WP_014355267 (AWO_RS04420) (GlcD), electron transporter RnfC WP_014356580 (AWO_RS11370) all from Acetobacterium woodii DSM 1030 genome NC_016894; l -lactate utilization protein LutB containing FeS oxidoreductase WP_028317114 (Q362_RS0100810) from Desulfobulbus elongatus DSM 2908 assembly...”
  • “...lactate racemase WP_014355269 (AWO_RS04430) (LarA), electron transfer flavoprotein subunit alpha WP_014355266 (AWO_RS04415) (EtfA), FAD/FMN-containing dehydrogenase WP_014355267 (AWO_RS04420) (GlcD), electron transporter RnfC WP_014356580 (AWO_RS11370) all from Acetobacterium woodii DSM 1030 genome NC_016894; l -lactate utilization protein LutB containing FeS oxidoreductase WP_028317114 (Q362_RS0100810) from Desulfobulbus elongatus DSM 2908...”
• Comparative Proteomic Analysis of Desulfotomaculum reducens MI-1: Insights into the Metabolic Versatility of a Gram-Positive Sulfate- and Metal-Reducing Bacterium
  Otwell, Frontiers in microbiology 2016
  • “...D. reducens A novel method of lactate metabolism involving a FBEB complex in Acetobacterium woodii (Awo_c08730, 20, and 10) was recently described (Weghoff et al., 2015 ). The researchers suggested that the complex has the same role in many anaerobes, and Dred_0367-9 is the homologous region...”
  • “...a lactate-oxidizing complex recently described in Acetobacterium woodii to operate through flavin-based electron bifurcation (FBEB) (Awo_c08730, 20, and 10; Weghoff et al., 2015 ). Similarity between D. reducens proteins and those from A. woodii is displayed as percent sequence identity across percent query coverage ( http://blast.ncbi.nlm.nih.gov...”

7qh2C / H6LBS1 Cryo-em structure of ldh-etfab complex from acetobacterium woodii (see paper)
28% identity, 90% coverage

• Ligands: flavin-adenine dinucleotide; fe (iii) ion (7qh2C)

ATN24_RS08895 FAD-binding oxidoreductase from Clostridium butyricum
29% identity, 87% coverage

• Cell factories converting lactate and acetate to butyrate: Clostridium butyricum and microbial communities from dark fermentation bioreactors
  Detman, Microbial cell factories 2019
  • “...ATN24_RS08885) and EtfB (1: ATN24_RS03025, 2: ATN24_RS03160, 3: ATN24_RS08880), and potentially GlcD (1: ATN24_RS03035, 3: ATN24_RS08895, 4: ATN24_RS11095) A similar search was performed for the selected genomes of bacteria Roseburia intestinalis L1-82, Eubacterium rectale ATCC 33656, and Faecalibacterium prausnitzii A2165 recognized as butyrate producers but incapable...”

BCAL3287 putative FAD-binding oxidase from Burkholderia cenocepacia J2315
31% identity, 84% coverage

• Whole-Genome Sequencing of Three Clonal Clinical Isolates of B. cenocepacia from a Patient with Cystic Fibrosis
  Miller, PloS one 2015
  • “...-12.9 3319069 BCAL3029 putative alkane monooxygenase T T T C F144L NS Neutral -1.60 3601711 BCAL3287 putative FAD-binding oxidase G G G A S 3605061 BCAL3289 glcE glycolate oxidase FAD binding subunit G G G A G257S NS Neutral 0.10 4114326 BCAM0207 putative tyrosine-protein kinase C...”

BPSL2842 putative FAD-binding oxidase from Burkholderia pseudomallei K96243
30% identity, 84% coverage

• Genomic characterization of Burkholderia pseudomallei isolates selected for medical countermeasures testing: comparative genomics associated with differential virulence
  Sahl, PloS one 2015
  • “...N/A NC_006350.1 3021077 A C N/A N/A intergenic N/A NC_006350.1 3403668 G T T T BPSL2842 FAD-binding oxidase NC_006350.1 3654489 C G N/A N/A intergenic N/A NC_006350.1 3924581 G A H H BPSL3305 cheW; chemotaxis protein NC_006350.1 4073158 T C E G BPSL3430 glutamine amidotransferase NC_006351.1...”

DLD / Q94AX4 D-lactate dehydrogenase (cytochrome c) monomer (EC 1.1.2.4) from Arabidopsis thaliana (see 2 papers)
DLD_ARATH / Q94AX4 D-lactate dehydrogenase [cytochrome], mitochondrial; AtD-LDH; D-lactate ferricytochrome C oxidoreductase; Glycolate dehydrogenase; EC 1.1.2.4 from Arabidopsis thaliana (Mouse-ear cress) (see 2 papers)
AT5G06580 FAD linked oxidase family protein from Arabidopsis thaliana
NP_568170 FAD-linked oxidases family protein from Arabidopsis thaliana
29% identity, 74% coverage

• function: Catalyzes the stereospecific oxidation of D-lactate to pyruvate. Involved in the detoxification of methylglyoxal and D- lactate, but probably not involved in the metabolization of glycolate.
  catalytic activity: (R)-lactate + 2 Fe(III)-[cytochrome c] = 2 Fe(II)-[cytochrome c] + pyruvate + 2 H(+) (RHEA:13521)
  cofactor: FAD (Binds 1 FAD per monomer.)
  subunit: Homodimer.
  disruption phenotype: No visible phenotype when grown under standard conditions, but developmental retardation and lethality when grown in presence of methylglyoxal or D-lactate.
• The branched-chain amino acid-related isoleucic acid: recent research advances
  Mekonnen, Plant biology (Stuttgart, Germany) 2025 (no snippet)
• Glyoxalase I activity affects Arabidopsis sensitivity to ammonium nutrition
  Borysiuk, Plant cell reports 2022
  • “...(AT2G31350) were described by Borysiuk et al. ( 2018 ). New primers designed for D-LDH (AT5G06580), DJ-1A (AT3G14990), DJ-1B (AT1G53280), DJ-1D (AT3G02720), DJ-1E (AT2G38860), and DJ-1F (AT3G54600) used in experiments are listed in Supplementary Table 2. Statistical analysis Values are the meanstandard deviation (SD) of three...”
• Central Metabolism in Mammals and Plants as a Hub for Controlling Cell Fate
  Selinski, Antioxidants & redox signaling 2021
  • “...1.1.1.39) HGNC:6985 (EC 1.1.1.40) YKL029C (EC 1.1.1.38) NAD-ME2 AT4G00570 (EC 1.1.1.39) Lactate dehydrogenase d -LDH AT5G06580 (EC 1.1.2.4) HGNC:19708 (EC 1.1.2.4) YDL174C (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...”
• A D-lactate dehydrogenase from rice is involved in conferring tolerance to multiple abiotic stresses by maintaining cellular homeostasis
  Jain, Scientific reports 2020
  • “...genome at TIGR, was searched with Arabidopsis thaliana D-LDH protein sequence (AtD-LDH encoded by locus At5G06580) with an E value of 1. Since, D-LDH enzyme belong to FAD linked oxidoreductase family of enzymes and require two domains, FAD binding 4 and FAD oxidase c domain, for...”
  • “...of OsD-LDH2 with other known D-LDH enzymes from plants. Parameter OsD-LDH2 (Os07g08950.1) OsD-LDH (Os07g06890) AtD-LDH (At5g06580) Km (M) (with DCIP as co-substrate) 8.0451.7 68.195.38 31731 Kcat (min 1 ) 196.32 156 73 Kcat/Km (min 1 /M 1 ) 24.402 10 6 2.28 10 6 0.231 10...”
• GLYI and D-LDH play key role in methylglyoxal detoxification and abiotic stress tolerance
  Jain, Scientific reports 2018
  • “...The most active and efficient member of each family, AtGLYI (AT1G08110), AtGLYII (AT3G10850) and AtD-LDH (AT5G06580), was selected and a comparative study was undertaken 31 , 41 , 42 . AtGLYI, AtGLYII and AtD-LDH were cloned in pET28a, bacterial expression vector and pYES2, yeast expression vector....”
• Nitric Oxide Regulates Seedling Growth and Mitochondrial Responses in Aged Oat Seeds
  Mao, International journal of molecular sciences 2018
  • “...carrier protein, expressed Oryza sativa subsp. japonic a ns ns 0.68 Misc, oxidase-copper, flavone B4G146 AT5G06580 d -lactate dehydrogenase [cytochrome] mitochondrial Zea mays 0.69 1.58 ns Amino acid metabolism B6SWZ4 AT4G34030 Methylcrotonoyl-CoA carboxylase beta chain mitochondrial Zea mays ns ns 1.21 Co-factor and vitamine metabolism, lipoic...”
• Silencing of D-Lactate Dehydrogenase Impedes Glyoxalase System and Leads to Methylglyoxal Accumulation and Growth Inhibition in Rice
  An, Frontiers in plant science 2017
  • “...The Rice RefSeq RNA Database was searched with the protein sequences of At D -LDH (At5g06580) and ScDLD1 (CAA46852) using the TBLASTN algorithm. The cDNAs of Os D -LDH were isolated from young leaves of rice plants (93-11) by RT-PCR using gene-specific primers encompassing the 5...”
• d-Lactate Dehydrogenase Links Methylglyoxal Degradation and Electron Transport through Cytochrome c
  Welchen, Plant physiology 2016 (PubMed)
  • “...by a single gene in Arabidopsis (Arabidopsis thaliana; At5g06580). It catalyzes in vitro the oxidation of D-lactate to pyruvate using flavin adenine...”
  • “...plants, D-lactate is metabolized by D-lactate dehydrogenase (D-LDH; At5g06580; Engqvist et al., 2009; Wienstroer et al., 2012). In addition to D-lactate, D-LDH...”
• More
• d-Lactate Dehydrogenase Links Methylglyoxal Degradation and Electron Transport through Cytochrome c.
  Welchen, Plant physiology 2016
  • GeneRIF: Overexpression of d-Lactate dehydrogenase (d-LDH) and cytochrome c (CYTc) increased tolerance to d-lactate and methylglyoxal (MGO.
• Mitochondrial glycolate oxidation contributes to photorespiration in higher plants.
  Niessen, Journal of experimental botany 2007 (PubMed)
  • GeneRIF: AtGDH contributes to glycolate metabolism in Arabidopsis, indicating conservation of the chlorophyte pathway in higher plants. [AtGDH] [GDH]
• Two D-2-hydroxy-acid dehydrogenases in Arabidopsis thaliana with catalytic capacities to participate in the last reactions of the methylglyoxal and beta-oxidation pathways
  Engqvist, The Journal of biological chemistry 2009
  • “...following sequences are included: A. thaliana D-LDH (Q94AX4); H. tuberosus (EL444323, EL437620, and EL440912); Zea mays (B4G146); Sorghum bicolor (Sb02g003640);...”

Sb02g003640 No description from Sorghum bicolor
29% identity, 73% coverage

• Two D-2-hydroxy-acid dehydrogenases in Arabidopsis thaliana with catalytic capacities to participate in the last reactions of the methylglyoxal and beta-oxidation pathways
  Engqvist, The Journal of biological chemistry 2009
  • “...and EL440912); Zea mays (B4G146); Sorghum bicolor (Sb02g003640); Oryza sativa (B9FVM4); Ricinus communis (B9SDP2); Vitis vinifera (A7Q036); Medicago truncatula...”

W1QLN6 D-lactate dehydrogenase (cytochrome) (EC 1.1.2.4) from Ogataea angusta (see 2 papers)
31% identity, 74% coverage

B4G146 D-lactate dehydrogenase (cytochrome) from Zea mays
30% identity, 76% coverage

• Nitric Oxide Regulates Seedling Growth and Mitochondrial Responses in Aged Oat Seeds
  Mao, International journal of molecular sciences 2018
  • “...Mitochondrial carrier protein, expressed Oryza sativa subsp. japonic a ns ns 0.68 Misc, oxidase-copper, flavone B4G146 AT5G06580 d -lactate dehydrogenase [cytochrome] mitochondrial Zea mays 0.69 1.58 ns Amino acid metabolism B6SWZ4 AT4G34030 Methylcrotonoyl-CoA carboxylase beta chain mitochondrial Zea mays ns ns 1.21 Co-factor and vitamine metabolism,...”
• Two D-2-hydroxy-acid dehydrogenases in Arabidopsis thaliana with catalytic capacities to participate in the last reactions of the methylglyoxal and beta-oxidation pathways
  Engqvist, The Journal of biological chemistry 2009
  • “...tuberosus (EL444323, EL437620, and EL440912); Zea mays (B4G146); Sorghum bicolor (Sb02g003640); Oryza sativa (B9FVM4); Ricinus communis (B9SDP2); Vitis vinifera...”

H16_A3091 D-Lactate dehydrogenase (Cytochrome) from Ralstonia eutropha H16
H16_A3091 FAD-binding oxidoreductase from Cupriavidus necator H16
31% identity, 84% coverage

• (R/S)-lactate/2-hydroxybutyrate dehydrogenases in and biosynthesis of block copolyesters by Ralstonia eutropha
  Ishihara, Applied microbiology and biotechnology 2023
  • “...del This study pK18ms-B1817ud980 pK18ms derivative; h16 _ B1817 del This study pK18ms-A3091ud980 pK18ms derivative; h16_A3091 del This study pK18ms-B0093-B0092-B0091ud980 pK18ms derivative; h16_B0093 - B0092 - B0091 del This study pK18ms-A1681-A1682ud900 pK18ms derivative; h16_A1681 - A1682 del This study pBBR1MCS-2 Broad host range plasmid; Km r...”
  • “...-LDHs H16_A1681 LdhA1 d -Lactate dehydrogenase NAD(P)H 331 H16_A1682 LdhA2 d -Lactate dehydrogenase NAD(P)H 331 H16_A3091 Dld d -Lactate dehydrogenase Cytochrome 476 l -LDHs H16_A0666 Ldh l -Lactate dehydrogenase NAD(P)H 349 H16_B0460 LldA l -Lactate cytochrome reductase Cytochrome 381 H16_B1817 LldD l -Lactate cytochrome c reductase...”

lp_0291 oxidoreductase from Lactobacillus plantarum WCFS1
31% identity, 81% coverage

• Impact of 4 Lactobacillus plantarum capsular polysaccharide clusters on surface glycan composition and host cell signaling
  Remus, Microbial cell factories 2012
  • “...( lp _ 3563 ). In addition, expression of a FAD/FMN-containing dehydrogenase encoding gene ( lp_0291 ) appeared to be differentially affected in the 4 cps deletion strains, i.e., downregulated upon deletion of cps cluster 1 or 2, but upregulated when cps cluster 3 or 4...”
• Involvement of the mannose phosphotransferase system of Lactobacillus plantarum WCFS1 in peroxide stress tolerance
  Stevens, Applied and environmental microbiology 2010
  • “...1.43E-02 3.45 2.49 2.16 Hypothetical protein lp_0199 lp_0291 lp_1098 lp_1684 lp_3256 lp_3353 lp_0199 lp_0291 lp_1098 lp_1684 lp_3256 lp_3353 Unknown...”
• Major role of NAD-dependent lactate dehydrogenases in aerobic lactate utilization in Lactobacillus plantarum during early stationary phase
  Goffin, Journal of bacteriology 2004
  • “...glucose exhaustion. The L. plantarum gene coding for LoxD (lp_0291) is annotated as an oxidoreductase in the WCFS1 genome (14) and was identified by homology...”

EZN00_RS10870 FAD-binding oxidoreductase from Clostridium tyrobutyricum
31% identity, 87% coverage

• Bioinformatics and metabolic flux analysis highlight a new mechanism involved in lactate oxidation in Clostridium tyrobutyricum
  Munier, International microbiology : the official journal of the Spanish Society for Microbiology 2023
  • “...EZN00_RS10860, 2: EZN00_RS10795, 3: EZN00_RS08615), EtfA (1: EZN00_RS10865, 2: EZN00_RS10800, 3: EZN00_RS08620), FAD-binding oxidoreductase (1:: EZN00_RS10870; 3: EZN00_RS08625) In fragment 1, genes encoding the EtfAB complex are next to a FAD-binding oxidoreductase. The EtfAB complex involved in fragment 2 is in a gene cluster involving an...”

DLD_ANAHA / D4MUV9 D-lactate dehydrogenase; EC 1.1.99.6 from Anaerostipes hadrus (see paper)
29% identity, 86% coverage

• function: Catalyzes the dehydrogenation of (R)-lactate (D-lactate) to pyruvate. Active in vitro with the artificial electron acceptor 2,6- dichlorophenolindophenol (DCPIP), but not with NAD, NADP, or cytochrome c. Also displays a very low oxidase activity in vitro on D-lactate and L-lactate with O2 as the electron acceptor, but this activity is most likely not physiological.
  catalytic activity: (R)-lactate + A = pyruvate + AH2 (RHEA:15089)
  cofactor: FAD (Binds 1 FAD non-covalently per subunit.)
  cofactor: Zn(2+) (Binds 1 Zn(2+) ion per subunit.)
• Experimental and computational investigation of enzyme functional annotations uncovers misannotation in the EC 1.1.3.15 enzyme class
  Rembeza, PLoS computational biology 2021
  • “...be active with glycerol-3-phosphate as a substrate (A0A0R3K2G2 from Caloramator mitchellensis ), one with D-lactate (D4MUV9 from Anaerostipes hadrus ) and one with D-2-hydroxyglutarate (A0A077SBA9 from Xanthomonas campestris ). Additionally, three proteins (A0A0U5JSS4 from a Clostridium species, D4XIR1 from Achromobacter piechaudii , Q5WIP4 from Bacillus clausii...”
  • “...kinetic parameters calculated ( Table 1 and S10B Fig ). Three of the four enzymes (D4MUV9, A0A077SBA9, S2DJ52) showed good catalytic efficiency with substrate affinities in the low micromolar range and k cat / K M values above 1 x 10 4 M -1 s -1...”

B9SDP2 D-lactate dehydrogenase (cytochrome) from Ricinus communis
29% identity, 76% coverage

• Two D-2-hydroxy-acid dehydrogenases in Arabidopsis thaliana with catalytic capacities to participate in the last reactions of the methylglyoxal and beta-oxidation pathways
  Engqvist, The Journal of biological chemistry 2009
  • “...(Sb02g003640); Oryza sativa (B9FVM4); Ricinus communis (B9SDP2); Vitis vinifera (A7Q036); Medicago truncatula (BF636550, BF636365, BF636697, BQ123259, CA858805,...”

VPARA_21730 FAD-binding oxidoreductase from Variovorax paradoxus
30% identity, 84% coverage

• The catabolism of 3,3'-thiodipropionic acid in Variovorax paradoxus strain TBEA6: A proteomic analysis
  Heine, PloS one 2019
  • “...an altered phenotype with TDP as the only carbon source. Deletion mutants lacking VPARA_05540, VPARA_05550, VPARA_21730, VPARA_24900, or VPARA_27740 showed no change in growth with TDP (not shown). Still, they might be involved in the general sulfur metabolism (e. g. amino acid biosynthesis, detoxification) due the...”
  • “...( Fig 3 ) to important genes of the TDP metabolism. For the other genes (VPARA_21730, VPARA_27740, VPARA_27760), no connections to the TDP catabolism were identified. Enoyl-CoA hydratases (VPARA_05520, VPARA_05530) and a crotonase family protein (VPARA_05510) Ech-20 and Ech-30 were of special interest, as they seemed...”

AFUA_7G02560 D-lactate dehydrogenase (cytochrome) from Aspergillus fumigatus Af293
30% identity, 70% coverage

• The Transcription Factor ZafA Regulates the Homeostatic and Adaptive Response to Zinc Starvation in Aspergillus fumigatus
  Vicentefranqueira, Genes 2018
  • “...AFUA_6G09740 DZR gliT 53.6 3.9 477.3 59.7 Induction AFUA_7G00250 IZR tubB2 7.0 0.5 10.0 1.2 AFUA_7G02560 Control dld1 1.1 0.1 1.0 0.1 AFUA_7G04730 IZR enb1 48.3 5.8 2.4 0.2 AFUA_7G05070 NZR frdA 56.5 7.4 1.9 0.1 Repression DZR AFUA_7G06570 DZR zrcA 5.9 0.7 16.6 1.5 Repression...”
• Conservation of nucleosome positions in duplicated and orthologous gene pairs
  Nishida, TheScientificWorldJournal 2012
  • “...AFUA_3G07540 0.201465401 YOL077C AFUA_1G02210 0.196710807 YLR426W AFUA_1G06280 0.196041865 YMR060C AFUA_2G03840 0.194299595 YOR048C AFUA_1G13730 0.193994391 YDL174C AFUA_7G02560 0.193117882 YJL221C AFUA_8G07070 0.187015236 YGR054W AFUA_3G05970 0.181434929 YPR176C AFUA_7G04460 0.180215936 YML003W AFUA_1G09870 0.173517378 YKR084C AFUA_2G04630 0.171646807 YDR270W AFUA_4G12620 0.171601357 YOR336W AFUA_2G02360 0.164107564 YFL058W AFUA_5G02470 0.160695353 YNL301C AFUA_2G07380 0.151927636 YJL221C AFUA_7G06380...”

AF_0808 glycolate oxidase subunit GlcD from Archaeoglobus fulgidus DSM 4304
AF0808 glycolate oxidase subunit (glcD) from Archaeoglobus fulgidus DSM 4304
29% identity, 84% coverage

• A novel methoxydotrophic metabolism discovered in the hyperthermophilic archaeon Archaeoglobus fulgidus
  Welte, Environmental microbiology 2021
  • “...PflCD (AF_1449/50), PflX (AF_1961) and Act14 (AF_0117, AF_0918, AF_1330, AF_2278), Dlactate dehydrogenase Dld (AF_0394 & AF_0808), Llactate dehydrogenase LldD (AF_0807) and LldEFG (AF_0809AF_0811), lactate permease lctP (AF_0806), pyruvate carboxylase PycA (AF_0220) and oxaloacetate decarboxylase Oad (AF_1252), malate dehydrogenase MdhA (AF_0855) and malate oxidoreductase Mae (AF_1727), fumarate...”
• Physiological and Genomic Characterization of a Hyperthermophilic Archaeon Archaeoglobus neptunius sp. nov. Isolated From a Deep-Sea Hydrothermal Vent Warrants the Reclassification of the Genus Archaeoglobus
  Slobodkina, Frontiers in microbiology 2021
  • “...(AF0807) is part of a cluster and operates along with L-lactate permease (AF0806), monomeric dld (AF0808), and oligomeric LldEFG (AF0809AF0811) lactate dehydrogenases ( Hocking et al., 2014 ). This study also suggested to consider two more oxidoreductases (AF0507 and AF0867) as putative lactate dehydrogenases. In the...”
• Identification of key components in the energy metabolism of the hyperthermophilic sulfate-reducing archaeon Archaeoglobus fulgidus by transcriptome analyses
  Hocking, Frontiers in microbiology 2014
  • “...5 putative lactate dehydrogenase (LDH) genes ( lctp ; AF0806, lldD ; AF0807, dld ; AF0808 and lldEFG ; AF0809-AF0811, Table 1E , Figures 3 , 5 ). The genes AF0809-AF0811 may encode an oligomeric LDH ( lldEFG ) based on the presence of conserved domains...”
  • “...The conserved modular domain composition of the proteins encoded by the genes dld, the ORF AF0808 and AF0809, may facilitate a multimeric complex that functions as monomeric homologs encoded in other species (Dvu3071, Figures 3 , 5 ). The presence of a gene cluster with identical...”
• The Archaeoglobus fulgidus D-lactate dehydrogenase is a Zn(2+) flavoprotein
  Reed, Journal of bacteriology 1999
  • “...A. fulgidus (18) genome has three ORFs, AF0394, AF0808, and AF0868, predicted to encode proteins related to D-lactate dehydrogenases. A BLAST (Blosum62)...”
  • “...has 30% identity and 48% similarity with KIDLD, whereas AF0808 has 29% identity and 46% similarity, and AF0868 has 25% identity and 42% similarity. All three...”

APA386B_1053 FAD-binding oxidoreductase from Acetobacter pasteurianus 386B
30% identity, 85% coverage

• Complete genome sequence and comparative analysis of Acetobacter pasteurianus 386B, a strain well-adapted to the cocoa bean fermentation ecosystem
  Illeghems, BMC genomics 2013
  • “...(27) lactoylgluthathione lyase (APA386B_2164 and APA386B_1276); (28) hydroxyacylglutathione hydrolase (APA386B_2280); (29) lactate dehydrogenase (APA386B_910 and APA386B_1053); (30) pyruvate dehydrogenase E1 (APA386B_2083 - APA386B_2084 and APA386B_2737 - APA386B_2738); (31) pyruvate dehydrogenase E2 (APA386B_2085 and APA386B_2736); (32) dihydrolipoamide dehydrogenase (APA386B_2735 and APA386B_2271); (33) pyruvate decarboxylase (APA386B_1186); (34) alcohol...”

ATN24_RS11095 FAD-binding oxidoreductase from Clostridium butyricum
30% identity, 86% coverage

• Cell factories converting lactate and acetate to butyrate: Clostridium butyricum and microbial communities from dark fermentation bioreactors
  Detman, Microbial cell factories 2019
  • “...EtfB (1: ATN24_RS03025, 2: ATN24_RS03160, 3: ATN24_RS08880), and potentially GlcD (1: ATN24_RS03035, 3: ATN24_RS08895, 4: ATN24_RS11095) A similar search was performed for the selected genomes of bacteria Roseburia intestinalis L1-82, Eubacterium rectale ATCC 33656, and Faecalibacterium prausnitzii A2165 recognized as butyrate producers but incapable of lactate...”

Rv2280 Probable dehydrogenase from Mycobacterium tuberculosis H37Rv
32% identity, 91% coverage

• Large genomic deletions delineate Mycobacterium tuberculosis L4 sublineages in South American countries
  Baena, PloS one 2023
  • “...rv2272 , rv2273 , mazF8 , mazE8 , rv2275 , cyp121 , rv2277c , and rv2280 ( Fig 7 , panel A). Additionally, several strains of the sister clades 4.1.2.1Col1, 4.1.2.1Peru1, and 4.1.2.1cpb share a specific large deletion that spans 4,752 bases and that affects genes...”
  • “...rv2272 , rv2273 , mazF8 , mazE8 , rv2275 , cyp121 , rv2277c , and rv2280 . Panel B . Genomic deletion of 4,752 bp. that is common in the Latin American lineages 4.1.2.1Col1, 4.1.2.1Peru1, and 4.1.2.1cpb, and is present in 30 genomes. This deletion affects...”
• Aptamer-Based Diagnostic Systems for the Rapid Screening of TB at the Point-of-Care
  Martin, Diagnostics (Basel, Switzerland) 2021
  • “...stages of M. tb [ 200 ]. The probable dehydrogenase protein is encoded by the RV2280 gene which was shown to be linked with PE-PGRS genes. The RV2280 gene was reported to be upregulated by the IS6110 and IS110 genes. The IS110 gene may directly influence...”
  • “...system through insertional inactivation and upregulation of PE-PGRS genes [ 201 , 202 ]. The RV2280 gene was also predicted to encode for a 459 amino acid protein [ 192 ] which was closely related to a family of FAD/FMN-containing dehydrogenases and FAD-linked glycolate oxidases [...”
• Distinct Persistence Fate of Mycobacterium tuberculosis in Various Types of Cells
  Chen, mSystems 2021
  • “...ACTB, which is an interaction partner of ITGB3 ( 20 ). Meanwhile, we observed that Rv2280 interacted with CD14, which is also an interaction partner of ITGB3. It could be possible that these ITGB3-ACTB-Rv1477 and ITGB3-CD14-Rv2280 axes were involved in regulating the survival of M. tuberculosis...”
• A snapshot of translation in Mycobacterium tuberculosis during exponential growth and nutrient starvation revealed by ribosome profiling
  Sawyer, Cell reports 2021
  • “...phosphate starvation-inducible protein (Rv2368c), the 6-kDa early secretory antigenic target EsxA (Rv3875), a probable dehydrogenase (Rv2280), and three conserved hypothetical or unknown proteins (Rv0060, Rv1813c, and Rv0272c). As RO is a measure of RPF/mRNA and cannot account for protein degradation, the proteins with high ROs are...”
• One-Year Old Dormant, "Non-culturable" Mycobacterium tuberculosis Preserves Significantly Diverse Protein Profile
  Trutneva, Frontiers in cellular and infection microbiology 2020
  • “...Rv1017c Probable ribose-phosphate pyrophosphokinase PrsA (phosphoribosyl pyrophosphate synthetase) Rv1310 Probable ATP synthase beta chain AtpD Rv2280 Probable dehydrogenase Rv2145c Diviva family protein Wag31 Rv3028c Probable electron transfer flavoprotein (alpha-subunit) FixB (alpha-ETF) (electron transfer flavoprotein large subunit) (ETFLS) Rv1886c Secreted antigen 85-B FbpB (85B) (antigen 85 complex...”
• Role of VapBC12 Toxin-Antitoxin Locus in Cholesterol-Induced Mycobacterial Persistence
  Talwar, mSystems 2020
  • “...Rv3540c ( ltp2 ) Up 4.699170107 Lipid metabolism Rv2944 Up 7.224902316 Insertion sequences and phages Rv2280 Down 1.619272741 Intermediary metabolism and respiration Rv1499 Up 6.653957073 Conserved hypotheticals Rv2857c Up 4.523021237 Intermediary metabolism and respiration Rv2549c ( vapC20 ) Down 6.254071649 Virulence, detoxification, adaptation Rv1309 ( atpG...”
• Identification of Novel Antigens Recognized by Serum Antibodies in Bovine Tuberculosis
  Lyashchenko, Clinical and vaccine immunology : CVI 2017
  • “...excluded from the data analyses): Rv0483, Rv0509, Rv1193, Rv2280, Rv3029c, and Rv3340, which were produced at APHA as described previously (30), and Rv3614 and...”
• Analysis of IS6110 insertion sites provide a glimpse into genome evolution of Mycobacterium tuberculosis
  Roychowdhury, Scientific reports 2015
  • “...regions detected by us have already been reported such as, the promoter regions of Rv2353, Rv2280, Rv3427 (38bp upstream in 300 L2, 2 L3 and 3 L4 isolates) and Rv3018 (308bp upstream of 232 L2 isolates) 34 46 validating the method used here. ESAT-6 related proteins...”
• More

Q148K4 D-lactate dehydrogenase (cytochrome) from Bos taurus
28% identity, 86% coverage

• D- and L-lactate dehydrogenases during invertebrate evolution
  Cristescu, BMC evolutionary biology 2008
  • “...D-LDH EC 1.1.2.4 Arabidopsis thaliana mouse-ear cress [GeneBank: NM_120741 ] unpublished Bos taurus cattle [Swiss-Prot: Q148K4 ] Moore et al. 2006 unpublished Caenorhabditis elegans nematode [GeneBank: NP_001023872 ] unpublished DLD1 Candida sphaerica yeast [Swiss-Prot: Q12627 ] [ 62 ] Canis familiaris dog [GeneBank: XP_852976 ] unpublished...”

BMEI0599 D-LACTATE DEHYDROGENASE (CYTOCHROME) from Brucella melitensis 16M
31% identity, 84% coverage

• RNA-seq reveals the critical role of OtpR in regulating Brucella melitensis metabolism and virulence under acidic stress
  Liu, Scientific reports 2015
  • “...relating the pyruvate metabolism were down-regulated in the otpR mutant, including mdh (BMEI0137), FAD-linked oxidase (BMEI0599), pdhB (BMEI0855), and aceF (BMEI0856). Furthermore, the entire NADH dehydrogenase operon was down-regulated in 16M otpR . The genes encoding the cytochrome D ubiquinol oxidase subunits I, II, and III...”

GOX2071 D-Lactate dehydrogenase from Gluconobacter oxydans 621H
29% identity, 85% coverage

• Utilization of D-Lactate as an Energy Source Supports the Growth of Gluconobacter oxydans
  Sheng, Applied and environmental microbiology 2015
  • “...two putative NAD-independent D-lactate dehydrogenases, GOX1253 and GOX2071, were capable of oxidizing D-lactate, GOX1253 was the only enzyme able to support...”
  • “...dehydrogenase with high activity toward D-lactate, while GOX2071 was characterized as a soluble oxidase with broad substrate specificity toward D-2-hydroxy...”

Q9YEU4 D-lactate dehydrogenase (EC 1.1.1.28); D-lactate dehydrogenase (acceptor) (EC 1.1.99.6) from Aeropyrum pernix (see 2 papers)
29% identity, 84% coverage

G4MWZ3 D-lactate dehydrogenase (EC 1.1.1.28) from Pyricularia oryzae (see paper)
28% identity, 69% coverage

NP_919417 probable D-lactate dehydrogenase, mitochondrial isoform 2 precursor from Homo sapiens
27% identity, 84% coverage

• Systematic analysis of the role of LDHs subtype in pan-cancer demonstrates the importance of LDHD in the prognosis of hepatocellular carcinoma patients.
  Wang, BMC cancer 2024
  • GeneRIF: Systematic analysis of the role of LDHs subtype in pan-cancer demonstrates the importance of LDHD in the prognosis of hepatocellular carcinoma patients.
• Early-onset gout and rare deficient variants of the lactate dehydrogenase D gene.
  Bardin, Rheumatology (Oxford, England) 2023 (PubMed)
  • GeneRIF: Early-onset gout and rare deficient variants of the lactate dehydrogenase D gene.
• Cancer/testis antigen LDHC promotes proliferation and metastasis by activating the PI3K/Akt/GSK-3β-signaling pathway and the in lung adenocarcinoma.
  Chen, Experimental cell research 2021 (PubMed)
  • GeneRIF: Cancer/testis antigen LDHC promotes proliferation and metastasis by activating the PI3K/Akt/GSK-3beta-signaling pathway and the in lung adenocarcinoma.
• Hyperuricemia and gout caused by missense mutation in d-lactate dehydrogenase.
  Drabkin, The Journal of clinical investigation 2019
  • GeneRIF: gout can be caused by a mutation in LDHD within the putative catalytic site of the encoded d-lactate dehydrogenase, resulting in augmented blood levels of d-lactate, a stereoisomer of l-lactate
• Prostate cancer cells metabolize d-lactate inside mitochondria via a D-lactate dehydrogenase which is more active and highly expressed than in normal cells.
  de, FEBS letters 2013 (PubMed)
  • GeneRIF: The activity and expression of the mitochondrial D-lactate dehydrogenase, is higher in prostate cancer versus normal prostate cells.
• Fine mapping and association studies of a high-density lipoprotein cholesterol linkage region on chromosome 16 in French-Canadian subjects.
  Dastani, European journal of human genetics : EJHG 2010
  • GeneRIF: Observational study of gene-disease association. (HuGE Navigator)
• Elevated serum lactate dehydrogenase isoenzymes and aspartate transaminase distinguish Albers-Schönberg disease (Chloride Channel 7 Deficiency Osteopetrosis) among the sclerosing bone disorders.
  Whyte, Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research 2010 (PubMed)
  • GeneRIF: Elevated serum LDH isoenzymes and AST indicate a disturbance (of uncertain clinical significance) within multiple extraosseous tissues when there is CLCN7 deficiency.
• Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
  Hendrickson, PloS one 2010
  • GeneRIF: Observational study of gene-disease association. (HuGE Navigator)
• More

B9FVM4 D-lactate dehydrogenase (cytochrome) from Oryza sativa subsp. japonica
30% identity, 77% coverage

• Two D-2-hydroxy-acid dehydrogenases in Arabidopsis thaliana with catalytic capacities to participate in the last reactions of the methylglyoxal and beta-oxidation pathways
  Engqvist, The Journal of biological chemistry 2009
  • “...(B4G146); Sorghum bicolor (Sb02g003640); Oryza sativa (B9FVM4); Ricinus communis (B9SDP2); Vitis vinifera (A7Q036); Medicago truncatula (BF636550, BF636365,...”

LDHD_DANRE / F1QXM5 Probable D-lactate dehydrogenase, mitochondrial; DLD; Lactate dehydrogenase D; EC 1.1.2.4 from Danio rerio (Zebrafish) (Brachydanio rerio) (see paper)
27% identity, 84% coverage

• function: Involved in D-lactate, but not L-lactate catabolic process.
  catalytic activity: (R)-lactate + 2 Fe(III)-[cytochrome c] = 2 Fe(II)-[cytochrome c] + pyruvate + 2 H(+) (RHEA:13521)
  cofactor: FAD
  disruption phenotype: At 3 dpf, mutant embryos show no visible abnormalities compared to wild-type embryos. They do not display any ocular abnormalities at 5 dpf. They nevertheless exhibit elevated levels of D-lactate, but not L-lactate compared to wild-type larvae.

NP_956167 probable D-lactate dehydrogenase, mitochondrial from Danio rerio
27% identity, 84% coverage

• Identification of human D lactate dehydrogenase deficiency.
  Monroe, Nature communications 2019
  • GeneRIF: LDHD loss-of-function in zebrafish results in increased concentrations of D-lactate.

BOV_RS06750 FAD-binding oxidoreductase from Brucella ovis ATCC 25840
31% identity, 84% coverage

• Mining the Flavoproteome of Brucella ovis, the Brucellosis Causing Agent in Ovis aries
  Minjárez-Sáenz, Microbiology spectrum 2022
  • “...GMC_oxred_C (PF05199) 388-524 4 1.1.-.- b Potential FAD-binding oxygen oxidoreductase (glcE?) c FAD_binding_4 (PF01565) 54-187 BOV_RS06750 ABQ60928.1 FAD 3PM9 (29) FAD-oxidase_C (PF02913) 223-463 5 1.1.-.- b Potential FAD-binding oxygen oxidoreductase (glcE?) FAD_binding_4 (PF01565) 43-180 BOV_RS02095 ABQ61939.1 FAD 3PM9 (60) FAD-oxidase_C (PF02913) 219-469 6 1.3.1.1 NADH dependent...”

EHLA_0974 FAD-binding oxidoreductase from Anaerobutyricum hallii
29% identity, 86% coverage

• Unravelling lactate-acetate and sugar conversion into butyrate by intestinal Anaerobutyricum and Anaerostipes species by comparative proteogenomics
  Shetty, Environmental microbiology 2020
  • “...and Microbiome System webserver (Markowitz et al ., 2012 ). The amino acid sequences for EHLA_0974 and EHLA_0978 were searched against the IMG database (Markowitz et al ., 2012 ). The BLASTp hits were limited to only those with an E value cutoff of 1e10 and...”
  • “...were shared between the two comparisons (including those encoded by genes with locus tags EHLA_0973, EHLA_0974, EHLA_0976, EHLA_0977, EHLA_0978, EHLA_0979) that were induced by growth on d , l lactate. Proteins with significantly higher abundance during growth on d , l lactate included lactate permease, lactate...”

AO090003001006 No description from Aspergillus oryzae RIB40
28% identity, 77% coverage

• RNA-Seq Based Transcriptome Analysis of Aspergillus oryzae DSM 1863 Grown on Glucose, Acetate and an Aqueous Condensate from the Fast Pyrolysis of Wheat Straw
  Kubisch, Journal of fungi (Basel, Switzerland) 2022
  • “...we found a gene encoding cytochrome c-linked D-LDH to be upregulated compared to pure acetate (AO090003001006; log 2 FC = 1.75), whereas a NADH-dependent D-LDH gene showed decreased expression (AO090023000577; log 2 FC = 1.11) ( Supplementary Table S2 ). However, an even more significant differential...”

AFUA_1G00510, Afu1g00510 D-lactate dehydrogenase (cytochrome), putative from Aspergillus fumigatus Af293
28% identity, 77% coverage

• Transcriptomic and proteomic analyses of the Aspergillus fumigatus hypoxia response using an oxygen-controlled fermenter
  Barker, BMC genomics 2012
  • “...observed in A. nidulans . In support of this hypothesis, a mitochondrial lactate dehydrogenase transcript (Afu1g00510) was transcriptionally increased in response to hypoxia. However, the determined lactate concentration in the culture supernatant was only in the micromolar range (see Figure 1B ). Thus, the role of...”
• Conservation of nucleosome positions in duplicated and orthologous gene pairs
  Nishida, TheScientificWorldJournal 2012
  • “...AFUA_5G01430 0.331554435 YHR091C AFUA_2G14030 0.337931682 YIL030C AFUA_2G08650 0.350942099 YFR037C AFUA_7G05510 0.356342064 YOR391C AFUA_5G01430 0.356843862 YDL174C AFUA_1G00510 0.402217656 YML121W AFUA_5G09650 0.410825283 YFL060C AFUA_2G08580 0.411505108 YDR301W AFUA_8G04040 0.413112754 YJL221C AFUA_3G07380 0.413321446 YLR326W AFUA_5G12410 0.458648708 YBL108C-A AFUA_4G03360 0.487139446 YGR165W AFUA_5G08380 0.519339895 YKL157W AFUA_4G09030 0.604021491 YNL334C AFUA_2G08580 0.720610634...”

LDHD / Q86WU2 mitochondrial D-lactate dehydrogenase (EC 1.1.2.4) from Homo sapiens (see 3 papers)
LDHD_HUMAN / Q86WU2 Probable D-lactate dehydrogenase, mitochondrial; DLD; Lactate dehydrogenase D; EC 1.1.2.4 from Homo sapiens (Human) (see 3 papers)
Q86WU2 D-lactate dehydrogenase (cytochrome) (EC 1.1.2.4) from Homo sapiens (see paper)
27% identity, 82% coverage

• function: Involved in D-lactate, but not L-lactate catabolic process.
  catalytic activity: (R)-lactate + 2 Fe(III)-[cytochrome c] = 2 Fe(II)-[cytochrome c] + pyruvate + 2 H(+) (RHEA:13521)
  cofactor: FAD
  subunit: Interacts with CSRP3.
• Distinct or Overlapping Areas of Mitochondrial Thioredoxin 2 May Be Used for Its Covalent and Strong Non-Covalent Interactions with Protein Ligands.
  Ntallis, Antioxidants (Basel, Switzerland) 2023
  • “...BioGRID 37 P60174 Triosephosphate isomerase 6upf (chain A) 1.04 1zvnAB 9.7 75 NC, C 38 Q86WU2 Probable D-lactate dehydrogenase, mitochondrial AF 2.67 2j0fAC 8.4 710 C a Fiberdock scoring, b at 25.0 , c Abbreviations used: C, covalent interaction confirmed by DTT; NC, non-covalent interaction (confirmed...”
• Comparative Proteomic Analysis of Visceral Adipose Tissue in Morbidly Obese and Normal Weight Chinese Women.
  Shang, International journal of endocrinology 2019
  • “...Swiss-prot accession number Gene symbol Name Ratio (O/N) Style P04271 S100B Protein S100-B 0.147332273 Down Q86WU2 LDHD Probable D-lactate dehydrogenase, mitochondrial 0.168476843 Down Q13085 ACACA Acetyl-CoA carboxylase 1 0.178573909 Down P61960 UFM1 Ubiquitin-fold modifier 1 0.181188644 Down P49327 FASN Fatty acid synthase 0.18307047 Down P24298 GPT...”
• Two D-2-hydroxy-acid dehydrogenases in Arabidopsis thaliana with catalytic capacities to participate in the last reactions of the methylglyoxal and beta-oxidation pathways
  Engqvist, The Journal of biological chemistry 2009
  • “...BQ123259, CA858805, CA858793, and DY617162); H. sapiens (Q86WU2); Danio rerio (Q803V9); M. musculus (Q7TNG8); S. cerevisiae DLD1 (P32891); K. lactis (Q12627);...”
• D- and L-lactate dehydrogenases during invertebrate evolution
  Cristescu, BMC evolutionary biology 2008
  • “...gastropod gi: 229861 unpublished Helobdella robusta segmented worm gi: 185793 unpublished Homo sapiens human [Swiss-Prot: Q86WU2 ] [ 5 ] Monodelphis domestica gray short-tailed opossum [GeneBank: XP_001375142 ] unpublished Mus musculus house mouse [Swiss-Prot: Q7TNG8 ] [ 5 ] Nematostella vectensis starlet sea anemone [GeneBank: XP_001626025...”

AFUA_3G06820 oxidoreductase, FAD-binding from Aspergillus fumigatus Af293
26% identity, 72% coverage

• Genome-Wide Association Analysis for Triazole Resistance in Aspergillus fumigatus
  Fan, Pathogens (Basel, Switzerland) 2021
  • “...Missense Variant (Gln77Pro) Uncharacterized protein 3 1,693,467 AFUA_3G06800 Missense Variant (Arg615Thr) Uncharacterized protein 3 1,700,605 AFUA_3G06820 Missense Variant (Lys540Arg) Oxidoreductase, FAD-binding 3 2,132,951 AFUA_3G08280 Missense Variant (Glu28Lys) Cell cycle regulatory protein (Srw1), putative 3 2,155,356 AFUA_3G08400 Missense Variant (Glu393Lys) SNF2 family helicase/ATPase, putative 3 2,304,691 AFUA_3G09040...”
• Conservation of nucleosome positions in duplicated and orthologous gene pairs
  Nishida, TheScientificWorldJournal 2012
  • “...AFUA_2G16210 0.269616243 YJR141W AFUA_3G07970 0.2738444 YOR365C AFUA_2G17650 0.274036262 YDL116W AFUA_1G10860 0.278315121 YKL020C AFUA_1G12550 0.278379939 YDL174C AFUA_3G06820 0.286419799 YBR029C AFUA_1G07010 0.296926336 YLR096W AFUA_1G11080 0.297540349 YFL028C AFUA_6G05080 0.303502181 YOR089C AFUA_3G10740 0.30892361 YPR010C AFUA_2G13000 0.309890067 YJL219W AFUA_5G01160 0.321415181 YNL097C AFUA_4G11660 0.329160424 YMR116C AFUA_4G13170 0.329415498 YPL280W AFUA_5G01430 0.331554435 YHR091C AFUA_2G14030...”

Q974L0 D-lactate dehydrogenase (acceptor) (EC 1.1.99.6) from Sulfurisphaera tokodaii (see paper)
ST0649 440aa long hypothetical glycolate oxidase subunit glcD from Sulfolobus tokodaii str. 7
27% identity, 88% coverage

• Polysaccharide-degrading thermophiles generated by heterologous gene expression in Geobacillus kaustophilus HTA426
  Suzuki, Applied and environmental microbiology 2013
  • “...OT3 (JCM 9974) chromosome and the PCAL1307 and ST0649 genes were derived from Pyrobaculum calidifontis JCM 11548 and Sulfolobus tokodaii strain 7 (JCM 10545)...”
  • “...YP_149281 53 55 PH0380 PH1171c PH1171sc PCAL1307 ST0649 GK3428 5152 aem.asm.org Applied and Environmental Microbiology Downloaded from http://aem.asm.org/ on...”
• A novel flavin adenine dinucleotide (FAD) containing d-lactate dehydrogenase from the thermoacidophilic crenarchaeota Sulfolobus tokodaii strain 7: purification, characterization and expression in Escherichia coli
  Satomura, Journal of bioscience and bioengineering 2008 (PubMed)
  • “...reported genome information, the gene encoding the enzyme (ST0649) was identified. It was subsequently cloned and expressed in Escherichia coli and found to...”

An11g09520 uncharacterized protein from Aspergillus niger
26% identity, 73% coverage

• The effect of natamycin on the transcriptome of conidia of Aspergillus niger
  van, Studies in mycology 2013
  • “...of natamycin ( Table 7 ). This included an alcohol dehydrogenase (An13g00950, 39-fold), D-lactate dehydrogenase (An11g09520, 12.4-fold); pyruvate decarboxylate (An 09g01030, 11.3-fold); isocitrate lyase (An01g09270, 81-fold) and a malate synthase gene (An15g01860, 52-fold). A gene with similarity to 2-methylisocitrate lyase (An12g07630) that could have a role...”
• Transcriptome analysis of Aspergillus niger grown on sugarcane bagasse
  de, Biotechnology for biofuels 2011
  • “...fermentation, such as alcohol dehydrogenase ( AlcB ; An01g12170) and lactate dehydrogenase ( Ldh ; An11g09520), raising the possibility that lactate and alcohol fermentation occurs concomitantly with biomass saccharification. As expected, there is an intense modulation of several genes involved in C compound and carbohydrate metabolism...”

DLD_ARCFU / O29853 D-lactate dehydrogenase; EC 1.1.99.6 from Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16) (see 2 papers)
O29853 D-lactate dehydrogenase (acceptor) (EC 1.1.99.6) from Archaeoglobus fulgidus (see 2 papers)
AF_0394 D-lactate dehydrogenase from Archaeoglobus fulgidus DSM 4304
AF0394 D-lactate dehydrogenase, cytochrome-type (dld) from Archaeoglobus fulgidus DSM 4304
31% identity, 84% coverage

• function: Catalyzes the dehydrogenation of (R)-lactate (D-lactate) to pyruvate. Is likely involved in the utilization of D-lactate as a sole source for both carbon and electrons for dissimilatory sulfate reduction. Cannot use L-lactate as substrate, and NAD(+), horse cytochrome c, methylene blue or dimethylnaphthoquinone as acceptors. Active in vitro with artificial electron acceptors such as 2,6- dichlorophenolindophenol (DCPIP); the physiological acceptor is not known, but potential acceptors include cytochromes or quinones.
  catalytic activity: (R)-lactate + A = pyruvate + AH2 (RHEA:15089)
  cofactor: FAD (Binds 1 FAD non-covalently per subunit.)
  cofactor: Zn(2+) (Binds 1 Zn(2+) ion per subunit.)
• A novel methoxydotrophic metabolism discovered in the hyperthermophilic archaeon Archaeoglobus fulgidus
  Welte, Environmental microbiology 2021
  • “...formate lyase PflCD (AF_1449/50), PflX (AF_1961) and Act14 (AF_0117, AF_0918, AF_1330, AF_2278), Dlactate dehydrogenase Dld (AF_0394 & AF_0808), Llactate dehydrogenase LldD (AF_0807) and LldEFG (AF_0809AF_0811), lactate permease lctP (AF_0806), pyruvate carboxylase PycA (AF_0220) and oxaloacetate decarboxylase Oad (AF_1252), malate dehydrogenase MdhA (AF_0855) and malate oxidoreductase Mae...”
• Physiological and Genomic Characterization of a Hyperthermophilic Archaeon Archaeoglobus neptunius sp. nov. Isolated From a Deep-Sea Hydrothermal Vent Warrants the Reclassification of the Genus Archaeoglobus
  Slobodkina, Frontiers in microbiology 2021
  • “...of oxidizing lactate with sulfate. The genes for D-lactate and L-lactate dehydrogenases ( dld , AF0394 and lldD , AF0807) were annotated in the genome of the type strain A. fulgidus ( Klenk et al., 1997 ). The transcriptomic study proposed that lldD (AF0807) is part...”
  • “...of strain SE56 T , we have found close homologs (6278%) of proteins encoded by AF0394, AF0507, and AF0867 and the homologs of the subunits of LldEFG lactate dehydrogenase. Yet, the homologs of L-lactate permease and lactate dehydrogenases lldD and dld, encoded by the genes AF0806AF0808...”
• Assessment of the Carbon Monoxide Metabolism of the Hyperthermophilic Sulfate-Reducing Archaeon Archaeoglobus fulgidus VC-16 by Comparative Transcriptome Analyses
  Hocking, Archaea (Vancouver, B.C.) 2015
  • “...by more than 1.5-fold encode ferredoxin ( fdx-3 , AF0355) and a d -lactate dehydrogenase (AF0394) ( Figure 4 , Table S2). Minor downregulation was observed for genes encoding enzymes catalyzing the acetyl-CoA pathway: the methylenetetrahydromethanopterin reductase ( mer-1 ) and tungsten formylmethanofuran dehydrogenase, subunit B...”
• Identification of key components in the energy metabolism of the hyperthermophilic sulfate-reducing archaeon Archaeoglobus fulgidus by transcriptome analyses
  Hocking, Frontiers in microbiology 2014
  • “...) . i Inferred locus annotation . Surprisingly, the genes corresponding to d -lactate dehydrogenase (AF0394) and a putative d-lactate dehydrogenase gene (AF0868) (Reed and Hartzell, 1999 ; Pagala et al., 2002 ) were induced during growth with T-H 2 /CO 2 . The gene AF0394...”
• H(2)O(2)-forming NADH oxidase with diaphorase (cytochrome) activity from Archaeoglobus fulgidus
  Reed, Journal of bacteriology 2001
  • “...studied. The D-lactate dehydrogenase (Dld) coded for by AF0394 (dld) is the enzyme responsible for D-lactate catabolism leading to the eventual transfer of...”
• The Archaeoglobus fulgidus D-lactate dehydrogenase is a Zn(2+) flavoprotein
  Reed, Journal of bacteriology 1999
  • “...and electrons. The A. fulgidus open reading frame, AF0394, which is predicted to encode a D-()-lactate dehydrogenase (Dld), was cloned, and its product was...”
  • “...in A. fulgidus, an open reading frame (ORF) (AF0394) (18) whose predicted product resembles the S. cerevisiae and K. lactis D-lactate dehydrogenases was cloned....”

A1D828 D-lactate dehydrogenase (cytochrome) from Neosartorya fischeri (strain ATCC 1020 / DSM 3700 / CBS 544.65 / FGSC A1164 / JCM 1740 / NRRL 181 / WB 181)
25% identity, 72% coverage

• Two D-2-hydroxy-acid dehydrogenases in Arabidopsis thaliana with catalytic capacities to participate in the last reactions of the methylglyoxal and beta-oxidation pathways
  Engqvist, The Journal of biological chemistry 2009
  • “...(B2WBK4); Aspergillus fulmigatus (Q4WE96); and Neosartorya fischeri (A1D828). B, phylogenetic tree of AtD-2HGDH homologous proteins. The following sequences are...”

A1L2R0 D-lactate dehydrogenase (cytochrome) (Fragment) from Xenopus laevis
26% identity, 84% coverage

• D- and L-lactate dehydrogenases during invertebrate evolution
  Cristescu, BMC evolutionary biology 2008
  • “...nigroviridis Green puffer [Swiss-Prot: Q4T6R2 ] [ 65 ] Xenopus laevis African clawed frog [Swiss-Prot: A1L2R0 ] [ 66 ] Authors' contributions The data were collected and analyzed by MEC and TJC. The manuscript was drafted by MEC and TJC with contributions by DJI and JHS....”

MAA_00771 D-lactate dehydrogenase from Metarhizium robertsii ARSEF 23
26% identity, 71% coverage

• Metarhizium robertsii ammonium permeases (MepC and Mep2) contribute to rhizoplane colonization and modulates the transfer of insect derived nitrogen to plants
  Moonjely, PloS one 2019
  • “...( MAA_05675 ) and two other genes that encode putative uncharacterized proteins ( MAA_08959 and MAA_00771 ). The protein sequence of MAA_08959 (hypothetical protein) was surveyed in GenBank, and similar sequences were reported in other Metarhizium species, however these were also categorized as putative uncharacterized or...”

CBG09729 Protein CBG09729 from Caenorhabditis briggsae
27% identity, 46% coverage

• RNA-seq analysis of the C. briggsae transcriptome
  Uyar, Genome research 2012
  • “...). ( C ) Split: Based on homology, a single WormBase C. briggsae gene model CBG09729 is split into three separate gene models JNC_CBG16717, JNC_CBG16718, and JNC_CBG16719, which are homologous with three fully confirmed C. elegans gene models F32D8.14 (PID = 91.63%), F32D8.4 (PID = 70.55%),...”

B2WBK4 D-lactate dehydrogenase (cytochrome) from Pyrenophora tritici-repentis (strain Pt-1C-BFP)
25% identity, 76% coverage

• Two D-2-hydroxy-acid dehydrogenases in Arabidopsis thaliana with catalytic capacities to participate in the last reactions of the methylglyoxal and beta-oxidation pathways
  Engqvist, The Journal of biological chemistry 2009
  • “...Neurospora crassa (Q7SE05); Pyrenophora tritici-repentis (B2WBK4); Aspergillus fulmigatus (Q4WE96); and Neosartorya fischeri (A1D828). B, phylogenetic tree...”

Q5WIP4 D-lactate dehydrogenase (cytochrome) from Shouchella clausii (strain KSM-K16)
28% identity, 84% coverage

• Experimental and computational investigation of enzyme functional annotations uncovers misannotation in the EC 1.1.3.15 enzyme class.
  Rembeza, PLoS computational biology 2021
  • “...campestris ). Additionally, three proteins (A0A0U5JSS4 from a Clostridium species, D4XIR1 from Achromobacter piechaudii , Q5WIP4 from Bacillus clausii ) were active with each of the three substrates only in the AR screen ( S8 Fig ). None of the proteins were active with the electron...”

W5P8U2 D-lactate dehydrogenase (cytochrome) from Ovis aries
28% identity, 85% coverage

• Quantification of cytosol and membrane proteins in rumen epithelium of sheep with low or high CH4 emission phenotype
  Bond, PloS one 2022
  • “...No. Peptides matched FC A) L CH 4 > H CH 4 protein FC ENSOARP00000006849.1 W5P8U2 Lactate dehydrogenase D LDHD mitochondria 1 2.20 ENSOARP00000008043.1 W5PC82 Malic enzyme ME1 cytosol 5 1.57 ENSOARP00000002425.1 W5NW78 Resistin RETN extracellular 2 2.37 ENSOARP00000004349.1 W5P1Q0 AP complex subunit beta AP1B1 cytosol...”

RPA3503 putative D-lactate dehydrogenase, oxidoreductase from Rhodopseudomonas palustris CGA009
27% identity, 85% coverage

• Characteristics and Application of Rhodopseudomonas palustris as a Microbial Cell Factory
  Li, Frontiers in bioengineering and biotechnology 2022
  • “...assimilation pathway of lactate in R. palustris has not been reported; however, a gene ( RPA3503 ) encoding D-lactate dehydrogenase and a gene ( RPA1136 ) encoding lactate permease were predicated in the genome of R. palustris CGA009 ( Larimer et al., 2003 ). Under different...”
• Essential Genome of the Metabolically Versatile Alphaproteobacterium Rhodopseudomonas palustris
  Pechter, Journal of bacteriology 2015
  • “...shock proteins with DNA-binding domains (RPA2525 and RPA3503), and the pucAd light-harvesting complex subunit (RPA3012). We hypothesize that these gene products...”

XP_002500277 acetyltransferase-like/FAD linked oxidase from Micromonas commoda
29% identity, 47% coverage

• Analysis of EST data of the marine protist Oxyrrhis marina, an emerging model for alveolate biology and evolution
  Lee, BMC genomics 2014
  • “...12 132 Cysteine protease 1 Noctiluca scintillans XP_002506839 12 61 Acetate-coa ligase Micromonas sp. RCC299 XP_002500277 11 27 Acetyltransferase-like/FAD linked oxidase Micromonas sp. RCC299 AAM02973 10 90 Heat shock protein 70 Crypthecodinium cohnii XP_002775922 10 27 Succinate dehydrogenase, putative Perkinsus marinus XP_002780969 10 25 Heterogeneous nuclear...”
  • “...14-3-3 protein, putative Perkinsus marinus XP_002766754 2 30 40S ribosomal protein S11, putative Perkinsus marinus XP_002500277 11 27 Acetyltransferase-like/FAD linked oxidase Micromonas sp. RCC299 XP_002775922 10 27 Succinate dehydrogenase, putative Perkinsus marinus ABD46571 4 27 Alcohol dehydrogenase-like protein Euglena gracilis XP_002786429 4 27 Osmotic growth protein,...”

LDHD_MOUSE / Q7TNG8 Probable D-lactate dehydrogenase, mitochondrial; DLD; Lactate dehydrogenase D; EC 1.1.2.4 from Mus musculus (Mouse) (see paper)
NP_081846 probable D-lactate dehydrogenase, mitochondrial from Mus musculus
27% identity, 84% coverage

• function: Involved in D-lactate, but not L-lactate catabolic process.
  catalytic activity: (R)-lactate + 2 Fe(III)-[cytochrome c] = 2 Fe(II)-[cytochrome c] + pyruvate + 2 H(+) (RHEA:13521)
  cofactor: FAD
  subunit: Interacts with CSRP3.
• Hyperuricemia and gout caused by missense mutation in d-lactate dehydrogenase.
  Drabkin, The Journal of clinical investigation 2019
  • GeneRIF: gout can be caused by a mutation in LDHD within the putative catalytic site of the encoded d-lactate dehydrogenase, resulting in augmented blood levels of d-lactate, a stereoisomer of l-lactate
• Identification of putative mammalian D-lactate dehydrogenase enzymes.
  Flick, Biochemical and biophysical research communications 2002 (PubMed)
  • GeneRIF: identification and characterization of human and mouse D-lactate dehydrogenase (NAD) [D-LDH]
• The central nervous system can directly regulate breast cancer progression and blockage by quercetin.
  Luo, Annals of translational medicine 2021
  • “...Krt75 0.4537 0.0265 Q03311 Bche 0.4468 0.0000 Q99LC9 Pex6 0.3942 0.0334 Q8BQM8 Eml5 0.3845 0.0320 Q7TNG8 Ldhd 0.7991 0.0159 Q8N7N5 Dcaf8 0.7974 0.0002 Q8BKH7 Mapkap1 0.7955 0.0215 Q91WR3 Ascc2 0.7802 0.0074 Q3UZA1 Rcsd1 0.7801 0.0440 Q9JJ26 Mefv 0.7797 0.0034 Q8VE96 Slc35f6 0.7783 0.0102 Q9R0X0 Med20 0.7679...”
• The Effect of Environmental Enrichment on Glutathione-Mediated Xenobiotic Metabolism and Antioxidation in Normal Adult Mice
  Seo, Frontiers in neurology 2018
  • “...Q5SGK3 AOXB_MOUSE Aldehyde oxidase 3 Aox3l1 1.8 0.0001 O70475 UGDH_MOUSE UDP-glucose 6-dehydrogenase Ugdh 1.7 0.0001 Q7TNG8 LDHD_MOUSE Probable D-lactate dehydrogenase, mitochondrial Ldhd 1.7 0.0001 B2RX12 MRP3_MOUSE Isoform 2 of Canalicular multispecific organic anion transporter 2 Abcc3 1.7 0.0011 O35945 AL1A7_MOUSE Aldehyde dehydrogenase, cytosolic 1 Aldh1a7 1.7...”
• Renal proteome in mice with different susceptibilities to fluorosis
  Carvalho, PloS one 2013
  • “...synthase, cytoplasmic 56/5.7 57.6/5.65 2/62 Q8JZK9 Metabolism 586 Probable D-lactate dehydrogenase, mitochondrial 37.5/8.23 19.1/6.2 2/84 Q7TNG8 Metabolism 562 Thiomorpholine-carboxylate dehydrogenase 37.5/5.09 33.5/5.44 8/395 O54983 Metabolism 560 Phenazine biosynthesis-like domain-containing protein 2 34/4.795 32/5.2 4/130 Q9CXN7 Process 561 Biliverdin reductase A 37.5/6.755 33.3/6.5 3/86 Q9CY64 Process 576...”
• Biological and tumor-promoting effects of dioxin-like and non-dioxin-like polychlorinated biphenyls in mouse liver after single or combined treatment.
  Rignall, Toxicological sciences : an official journal of the Society of Toxicology 2013
• Mitochondrial proteomic analysis reveals deficiencies in oxygen utilization in medullary thick ascending limb of Henle in the Dahl salt-sensitive rat.
  Zheleznova, Physiological genomics 2012
• Two D-2-hydroxy-acid dehydrogenases in Arabidopsis thaliana with catalytic capacities to participate in the last reactions of the methylglyoxal and beta-oxidation pathways
  Engqvist, The Journal of biological chemistry 2009
  • “...sapiens (Q86WU2); Danio rerio (Q803V9); M. musculus (Q7TNG8); S. cerevisiae DLD1 (P32891); K. lactis (Q12627); Neurospora crassa (Q7SE05); Pyrenophora...”
• D- and L-lactate dehydrogenases during invertebrate evolution
  Cristescu, BMC evolutionary biology 2008
  • “...] Monodelphis domestica gray short-tailed opossum [GeneBank: XP_001375142 ] unpublished Mus musculus house mouse [Swiss-Prot: Q7TNG8 ] [ 5 ] Nematostella vectensis starlet sea anemone [GeneBank: XP_001626025 ] unpublished Pan troglodytes chimpanzee [GeneBank: XP_001139010 ] unpublished Rattus norvegicus Norway rat [Swiss-Prot: Q7TPJ4 ] Xu et al....”

A4I309 D-lactate dehydrogenase (cytochrome) from Leishmania infantum
28% identity, 93% coverage

• A Computational Approach Using Bioinformatics to Screening Drug Targets for Leishmania infantum Species
  Chávez-Fumagalli, Evidence-based complementary and alternative medicine : eCAM 2018
  • “...+ 00 52 Q2PYN0 Glyoxalase II N.C. 1 E 39 36 3 E 42 37 A4I309 D-lactate dehydrogenase-like protein 0,949 1 E 79 36 1 E 72 35 A4I1U1 Methylmalonyl-CoA epimerase-like protein 0,892 2 E 50 61 1 E 50 60 A4HSD8 NUDIX hydrolase dihydroneopterin triphosphate...”

KLMA_40583 D-lactate dehydrogenase [cytochrome] 1 from Kluyveromyces marxianus DMKU3-1042
28% identity, 74% coverage

• Genetic basis of the highly efficient yeast Kluyveromyces marxianus: complete genome sequence and transcriptome analyses
  Lertwattanasakul, Biotechnology for biofuels 2015
  • “...PRS5 KLMA_10783 Sorbose reductase SOU1 Mannitol, glucitol, L-sorbose KLMA_10649 D-Lactate dehydrogenase [cytochrome], mitochondrial DLD1 Lactate KLMA_40583 D-Lactate dehydrogenase [cytochrome] 1, mitochondrial DLD1 KLMA_50301 D-Lactate dehydrogenase [cytochrome], mitochondrial DLD1 KLMA_60482 D-Lactate dehydrogenase [cytochrome] 2, mitochondrial DLD2 KLMA_10179 Glycerol-3-phosphate dehydrogenase [NAD(+)] 1 GPD1 Glycerol KLMA_30722 Glycerol-3-phosphate dehydrogenase, mitochondrial...”

Q12627 D-lactate dehydrogenase [cytochrome], mitochondrial from Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
27% identity, 73% coverage

• Two D-2-hydroxy-acid dehydrogenases in Arabidopsis thaliana with catalytic capacities to participate in the last reactions of the methylglyoxal and beta-oxidation pathways
  Engqvist, The Journal of biological chemistry 2009
  • “...S. cerevisiae DLD1 (P32891); K. lactis (Q12627); Neurospora crassa (Q7SE05); Pyrenophora tritici-repentis (B2WBK4); Aspergillus fulmigatus (Q4WE96); and...”
• D- and L-lactate dehydrogenases during invertebrate evolution.
  Cristescu, BMC evolutionary biology 2008
  • “...al. 2006 unpublished Caenorhabditis elegans nematode [GeneBank: NP_001023872 ] unpublished DLD1 Candida sphaerica yeast [Swiss-Prot: Q12627 ] [ 62 ] Canis familiaris dog [GeneBank: XP_852976 ] unpublished Ciona intestinalis tunicate gi: 289925 unpublished Capitella capitata segmented worm gi: 177524 unpublished Danio rerio zebrafish [GeneBank: NP_956157 ]...”

D2HDH_STUS1 / A4VGK4 D-2-hydroxyglutarate dehydrogenase; D-2-HG dehydrogenase; D2HGDH; D-malate dehydrogenase; EC 1.1.99.39; EC 1.1.99.- from Stutzerimonas stutzeri (strain A1501) (Pseudomonas stutzeri) (see 2 papers)
29% identity, 91% coverage

• function: Catalyzes the dehydrogenation of (R)-2-hydroxyglutarate (D-2- hydroxyglutarate or D-2-HG) to 2-oxoglutarate and of (R)-malate (D- malate) to oxaloacetate. Is functionally tied to L-serine biosynthesis, via its coupling with the D-3-phosphoglycerate dehydrogenase SerA, encoded by the adjacent gene in the locus. Is required for the utilization of D-2-hydroxyglutarate as well as D-malate as the sole carbon source for growth of P.stutzeri. Active in vitro with artificial electron acceptors such as 2,6-dichlorophenolindophenol (DCPIP) and appears to couple with electron transfer flavoprotein (ETF) for efficient oxidation of both D-2-hydroxyglutarate and D-malate in vivo. Cannot catalyze the oxidation of L-2-hydroxyglutarate, D-lactate, D- tartrate, D-2-hydroxybutanoate, D-mandelate, D-glycerate and D- phenyllactate.
  catalytic activity: (R)-2-hydroxyglutarate + A = AH2 + 2-oxoglutarate (RHEA:38295)
  catalytic activity: (R)-malate + A = oxaloacetate + AH2 (RHEA:67460)
  cofactor: FAD (Binds 1 FAD per subunit.)
  subunit: Homodimer.
  disruption phenotype: The deletion mutant is barely able to use D-2-HG for growth and displays a relatively slower growth in a medium containing glucose. Cells lacking this gene also show high accumulation of extracellular and intracellular D-2-HG (PubMed:28827360). Moreover, the mutant strain loses the ability to utilize D-malate for growth (PubMed:30131334).

KLMA_10649 D-lactate dehydrogenase [cytochrome] from Kluyveromyces marxianus DMKU3-1042
25% identity, 80% coverage

• Genetic basis of the highly efficient yeast Kluyveromyces marxianus: complete genome sequence and transcriptome analyses
  Lertwattanasakul, Biotechnology for biofuels 2015
  • “...ribokinase RBK1 D-Ribose KLMA_10176 Ribose-phosphate pyrophosphokinase 5 PRS5 KLMA_10783 Sorbose reductase SOU1 Mannitol, glucitol, L-sorbose KLMA_10649 D-Lactate dehydrogenase [cytochrome], mitochondrial DLD1 Lactate KLMA_40583 D-Lactate dehydrogenase [cytochrome] 1, mitochondrial DLD1 KLMA_50301 D-Lactate dehydrogenase [cytochrome], mitochondrial DLD1 KLMA_60482 D-Lactate dehydrogenase [cytochrome] 2, mitochondrial DLD2 KLMA_10179 Glycerol-3-phosphate dehydrogenase [NAD(+)]...”

KLMA_50301 D-lactate dehydrogenase from Kluyveromyces marxianus DMKU3-1042
26% identity, 71% coverage

• Genetic basis of the highly efficient yeast Kluyveromyces marxianus: complete genome sequence and transcriptome analyses
  Lertwattanasakul, Biotechnology for biofuels 2015
  • “...L-sorbose KLMA_10649 D-Lactate dehydrogenase [cytochrome], mitochondrial DLD1 Lactate KLMA_40583 D-Lactate dehydrogenase [cytochrome] 1, mitochondrial DLD1 KLMA_50301 D-Lactate dehydrogenase [cytochrome], mitochondrial DLD1 KLMA_60482 D-Lactate dehydrogenase [cytochrome] 2, mitochondrial DLD2 KLMA_10179 Glycerol-3-phosphate dehydrogenase [NAD(+)] 1 GPD1 Glycerol KLMA_30722 Glycerol-3-phosphate dehydrogenase, mitochondrial GUT2 KLMA_60361 Glycerol uptake protein 1 GUP1...”

A0A0G2K1W9 D-lactate dehydrogenase (EC 1.1.1.28) from Rattus norvegicus (see paper)
26% identity, 84% coverage

8jdbA / Q7TNG8 Crystal structure of h405a mldhd in complex with d-2-hydroxyoctanoic acid (see paper)
27% identity, 84% coverage

• Ligands: flavin-adenine dinucleotide; (2r)-2-oxidanyloctanoic acid (8jdbA)

Q9I6H4 D-2-hydroxyglutarate dehydrogenase (EC 1.1.99.39) from Pseudomonas aeruginosa (see paper)
PA0317 hypothetical protein from Pseudomonas aeruginosa PAO1
29% identity, 91% coverage

• Metal-Triggered FAD Reduction in d-2-Hydroxyglutarate Dehydrogenase from Pseudomonas aeruginosa PAO1
  Quaye, ACS bio & med chem Au 2024
• The Pseudomonas aeruginosa PAO1 metallo flavoprotein d-2-hydroxyglutarate dehydrogenase requires Zn²⁺ for substrate orientation and activation
  Quaye, The Journal of biological chemistry 2023
  • “...catalytic mechanisms of metallo flavoproteins. Experimental procedures Materials The Pa D2HGDH pET20b(+) plasmid harboring the PA0317 gene was designed in-lab and purchased from GenScript. The plasmid was sequenced to verify the presence of the wildtype gene. Escherichia coli strain Rosetta(DE3)pLysS was from Novagen. Bovine serum albumin...”
• Uncovering Zn²⁺ as a cofactor of FAD-dependent Pseudomonas aeruginosa PAO1 d-2-hydroxyglutarate dehydrogenase
  Quaye, The Journal of biological chemistry 2023
  • “...therapeutic targets against P.aeruginosa infections. Experimental procedures Materials The Pa D2HGDH pET20b(+) plasmid harboring the PA0317 gene was designed in-lab and purchased from GenScript. The plasmid was sequenced to verify the presence of the wildtype gene. E.coli strain Rosetta(DE3)pLysS was from Novagen. Bovine serum albumin was...”
• A D-2-hydroxyglutarate biosensor based on specific transcriptional regulator DhdR
  Xiao, Nature communications 2021
  • “...6a and Supplementary Figs. 16 and 17 ). In P. aeruginosa PAO1, SerA and D2HGDH (PA0317) are considered the key enzymes responsible for d -2-HG anabolism and catabolism, respectively. Deletion of PA0317 causes extracellular d -2-HG accumulation in P. aeruginosa PAO1 ( PA0317 ) 7 ....”
  • “...3-dehydrogenase, WbpB (Fig. 6b ). As shown in Fig. 6a , P. aeruginosa PAO1 ( PA0317 serA wbpB ) no longer accumulated d -2-HG, suggesting that WbpB may also be involved in d -2-HG anabolism in P. aeruginosa PAO1. Thus, WbpB of P. aeruginosa PAO1 was...”
• The Breadth and Molecular Basis of Hcp-Driven Type VI Secretion System Effector Delivery
  Howard, mBio 2021
  • “...2.41 NAD-dependent malic enzyme 62.4 PA1588 SucC 4.8 2.73 Succinate-CoA ligase (ADP-forming) subunit beta 41.5 PA0317 4.8 2.02 d -2-Hydroxyglutarate dehydrogenase 51.3 PA1589 SucD 4.5 1.78 Succinate-CoA ligase (ADP-forming) subunit alpha 30.3 PA5427 AdhA 4.5 1.90 Alcohol dehydrogenase 35.9 PA2553 4.5 2.42 Probable acyl-CoA thiolase 41.4...”
• Kinetic and Bioinformatic Characterization of d-2-Hydroxyglutarate Dehydrogenase from Pseudomonas aeruginosa PAO1
  Quaye, Biochemistry 2020 (PubMed)
  • “...In this study, recombinant His-tagged PaD2HGDH was expressed and purified to high levels from gene PA0317, which was previously annotated as an FAD-binding PCMH-type domain-containing protein. The enzyme cofactor was identified as FAD with fluorescence emission after phosphodiesterase treatment and with mass spectrometry analysis. PaD2HGDH had...”
• Coupling between d-3-phosphoglycerate dehydrogenase and d-2-hydroxyglutarate dehydrogenase drives bacterial l-serine synthesis
  Zhang, Proceedings of the National Academy of Sciences of the United States of America 2017
  • “...mM) (Fig. 6A). The deletion of the D2HGDH-encoding gene (PA0317; Gene ID: 878323) in P. aeruginosa PAO1 (PA0317) also yielded a slower growth (Fig. 6A) and...”
• Anabolic ornithine carbamoyltransferase of Pseudomonas aeruginosa: nucleotide sequence and transcriptional control of the argF structural gene
  Itoh, Journal of bacteriology 1988
  • “...15, 2017 by University of California, Berkeley PAO1 PA025 PA0317 PA0990 E. coli K-12 CM236 JM1o1 VOL. 170, 1988 2727 cross-linked enzyme was boiled 5 min in...”
• More
• Proteome-wide identification of druggable targets and inhibitors for multidrug-resistant <i>Pseudomonas aeruginosa</i> using an integrative subtractive proteomics and virtual screening approach
  Vemula, Heliyon 2025
• The Pseudomonas aeruginosa PAO1 metallo flavoprotein d-2-hydroxyglutarate dehydrogenase requires Zn²⁺ for substrate orientation and activation
  Quaye, The Journal of biological chemistry 2023
  • “...graphics and analyses performed with UCSF Chimera. Protein Data Bank accession codes for Pa D2HGDH: Q9I6H4 and h D2HGDH: 6LPP. Author contributions J. A. Q. and G. G. methodology; J. A. Q. investigation; J. A. Q. and G. G. data curation; J. A. Q. and G....”
• Uncovering Zn²⁺ as a cofactor of FAD-dependent Pseudomonas aeruginosa PAO1 d-2-hydroxyglutarate dehydrogenase
  Quaye, The Journal of biological chemistry 2023
  • “...graphics and analyses performed with UCSF Chimera. Protein Data Bank accession codes for Pa D2HGDH (Q9I6H4) and h D2HGDH (6LPP). Author contributions J. A. Q. and G. G. methodology; J. A. Q. investigation; J. A. Q. and G. G. data curation; J. A. Q. and G....”

DLD1 / P32891 D-lactate dehydrogenase (EC 1.1.2.4) from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (see 11 papers)
DLD1_YEAST / P32891 D-lactate dehydrogenase [cytochrome] 1, mitochondrial; D-lactate ferricytochrome C oxidoreductase; D-LCR; EC 1.1.2.4 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 3 papers)
NP_010107 D-lactate dehydrogenase from Saccharomyces cerevisiae S288C
YDL174C D-lactate dehydrogenase, oxidizes D-lactate to pyruvate, transcription is heme-dependent, repressed by glucose, and derepressed in ethanol or lactate; located in the mitochondrial inner membrane from Saccharomyces cerevisiae
26% identity, 72% coverage

• function: Catalyzes the stereospecific oxidation of D-lactate to pyruvate.
  catalytic activity: (R)-lactate + 2 Fe(III)-[cytochrome c] = 2 Fe(II)-[cytochrome c] + pyruvate + 2 H(+) (RHEA:13521)
  cofactor: FAD (Binds 2 FAD.)
• Redirection of pyruvate flux toward desired metabolic pathways through substrate channeling between pyruvate kinase and pyruvate-converting enzymes in Saccharomyces cerevisiae.
  Kim, Scientific reports 2016
  • GeneRIF: Data show that the pyruvate-forming enzyme Pyk1 was tethered to heterologous pyruvate-converting enzymes, lactate dehydrogenase and alpha-acetolactate synthase, to producelactic acid and 2,3-butanediol, respectively.
• Kinetic activation of yeast mitochondrial D-lactate dehydrogenase by carboxylic acids.
  Mourier, Biochimica et biophysica acta 2008 (PubMed)
  • GeneRIF: Data show that mitochondrial respiratory rate in phosphorylating or non-phosphorylating conditions with D-lactate as substrate is stimulated by carboxylic acids at the level of D-lactate dehydrogenase.
• Altered proteome in translation initiation fidelity defective eIF5^G31R mutant causes oxidative stress and DNA damage
  Ram, Scientific reports 2022
  • “...P08456 CHO1 0.6500 0.0246 5 P32916 SRP101 0.6570 0.0304 6 P38779 CIC1 0.6613 0.0200 7 P32891 DLD1 0.6661 0.0050 8 P50861 RIB4 1.5247 0.0261 9 P31382 PMT2 1.5368 0.0344 10 P07807 DFR1 1.5977 0.0424 11 Q07825 FRA1 1.6199 0.0396 12 P40043 RGI1 1.6674 0.0044 13 Q01454...”
• Two D-2-hydroxy-acid dehydrogenases in Arabidopsis thaliana with catalytic capacities to participate in the last reactions of the methylglyoxal and beta-oxidation pathways
  Engqvist, The Journal of biological chemistry 2009
  • “...D-LDH (ScD-LDH or DLD1, UniProtKB/Swiss-Prot accession number P32891) protein sequence, using the BLAST search algorithm. The top hit was a polypeptide...”
  • “...M. musculus (Q7TNG8); S. cerevisiae DLD1 (P32891); K. lactis (Q12627); Neurospora crassa (Q7SE05); Pyrenophora tritici-repentis (B2WBK4); Aspergillus fulmigatus...”
• Transcriptional response of Saccharomyces cerevisiae to lactic acid enantiomers
  Drozdova, Applied microbiology and biotechnology 2024
  • “...terms lactate metabolic process (GO:0006089) and lactate biosynthetic process (GO:0019249) largely overlapped and contained DLD1 (YDL174C), DLD3 (YEL071W), SNO4 (YMR322C), and HSP32 (YPL280W). The former two genes indeed encode D-lactate dehydrogenases, mitochondrial Dld1 and cytoplasmic Dld3 (Pallotta 2012 ); according to the literature, Dld3 can also...”
• Central Metabolism in Mammals and Plants as a Hub for Controlling Cell Fate
  Selinski, Antioxidants & redox signaling 2021
  • “...1.1.1.38) NAD-ME2 AT4G00570 (EC 1.1.1.39) Lactate dehydrogenase d -LDH AT5G06580 (EC 1.1.2.4) HGNC:19708 (EC 1.1.2.4) YDL174C (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...”
• Transcriptional profiling reveals molecular basis and novel genetic targets for improved resistance to multiple fermentation inhibitors in Saccharomyces cerevisiae
  Chen, Biotechnology for biofuels 2016
  • “...Genes Annotated to the GO term Carbohydrate metabolic process (GO:0005975) YBR001C, YBR105C, YCL018W, YCL040W, YCR005C, YDL174C, YDL193W, YER062C, YFL053W, YGL134W, YGR254W, YHR046C, YHR174W, YJR096W, YKL201C, YLL026W, YML100W, YMR135C, YMR145C, YNR001C, YOL032W, YOL059W, YOL086C, YOL136C, YOR299W Response to chemical (GO:0042221) YBR006W, YBR101C, YCR021C, YDL124W, YDR135C, YFL053W, YFR022W,...”
• A Tool for Multiple Targeted Genome Deletions that Is Precise, Scar-Free, and Suitable for Automation
  Aubrey, PloS one 2015
  • “...R TATCTATGTGGCGTAGTATGTGCTTATAATAGTGAGTAG YBR052C PCR2 F TGTTTCGAACCGTGGTCCAGCAATC ATTAAGATCATCGTAGTAAGTACATAAG TAAAAAACAAGA AGCGACAAGAAGAGATAG YBR052C PCR2 R TTACAAATCTTTGATACGGTCGTAAAAGGCCTTCCCTTGAAGTTG GATCCC AATACAACAGAT YDL174C PCR1 F AGTACGGGAGACGGCTTGGACATAGATTTA YDL174C PCR1 R TGTTCTTGCTTTTGTTTCCAGCTGGATCGG YDL174C PCR2 F CCAGCTGGAAACAAAAGCAAGAACA GTATCTGATTTTCCTTTTTCACCCTTCAC GTAAACCTGAA CACACATTACTTGCCTC YDL174C PCR2 R TCACCTGTAATCATTAGCGGGCTCGTTTGGATCAGTTTTAAAGAT GATCCC AATACAACAGAT YIR013C PCR1 F GTTTCTAACCCTCTGATGGCAAGACTTTCATCATCTTCCTGAT YIR013C PCR1 R AGCGACCCTGTAATGTTATGTTTCTAGCTAGGAACAGAAAGTG YIR013C PCR2...”
• Lipid droplet dynamics in budding yeast
  Wang, Cellular and molecular life sciences : CMLS 2015
  • “...DFM1 YDR411C V ER DGA1 YOR245C V V V ER/LP DLD1 YDL174C DPL1 YDR294C V DPM1 YPR183W V V ECM29 YHL030W EFT1/2 YOR133W/ YDR385W EHT1 YBR177C ENO2 YHR174W V PM/M/V...”
• The flavoproteome of the yeast Saccharomyces cerevisiae
  Gudipati, Biochimica et biophysica acta 2014
  • “...Mito. intermembr. sp. cyb2 YML054C 2 1.1.2.4 d -Lactate dehydrogenase FAD/heme I. mito. membr. dld1 YDL174C Mito. matrix dld2 YDL178W Cytoplasm dld3 YEL071W 3 1.1.3.37 d -Arabino-1,4-lactone oxidase 8-(N3-His) -FAD FAD_PCMH O. mito. membr. alo1 YML086C 4 1.1.5.3 Glycerol-3-phosphate dehydrogenase FAD NADP_Rossmann (DAO) I. mito. membr....”
• Dissecting stop transfer versus conservative sorting pathways for mitochondrial inner membrane proteins in vivo
  Park, The Journal of biological chemistry 2013
  • “...study Gene name YBR024w YBR037c YBR044c YBR185c YDL174c YDR316w YDR393w YEL024w YER017c YER154w YGR062c YIL111w YMR302c YNL052w YOR065w YOR334w YPL063w YPR024w...”
  • “...Length (aa) Predicted TM domains YBR024w YBR037c YBR044c YBR185c YDL174c YDR178w YDR178w Sco2 MFP Sco1 MFP Tcm62 MFP Mba1 MFP Dld1 MFP Sdh4 (1TM) MFP Sdh4...”
• A Whole Genome Screen for Minisatellite Stability Genes in Stationary-Phase Yeast Cells
  Alver, G3 (Bethesda, Md.) 2013
  • “...PIR3 YKL163w UTR2 YEL040w YMR010W YMR010w DGR2 YKL121w PLB1 YMR008c VBA4 YDR119w YMR085W YMR085w DLD1 YDL174c PMP2 YEL017c-a VMA21 YGR105w YMR090W YMR090w EAP1 YKL204w PMS1 YNL082w VMS1 YDR049w YMR258C YMR258c EDC3 YEL015w PRM4 YPL156c VPS61 YDR136c YMR304C-A YMR304c-a EFT2 YDR385w PSD2 YGR170w VTC1 YER072w YOL024W YOL024w...”
• More

AFUA_1G17520 D-lactate dehydrogenase (cytochrome), putative from Aspergillus fumigatus Af293
26% identity, 65% coverage

• Conservation of nucleosome positions in duplicated and orthologous gene pairs
  Nishida, TheScientificWorldJournal 2012
  • “...AFUA_4G00960 0.304340045 YBR279W AFUA_2G11000 0.303224 YPL078C AFUA_8G05440 0.300712891 YLR059C AFUA_3G11820 0.296403753 YLR380W AFUA_6G12690 0.295562758 YDL174C AFUA_1G17520 0.29517154 YCL057W AFUA_7G05930 0.293762978 YDR234W AFUA_5G08890 0.293096856 YDR438W AFUA_5G12140 0.287954196 YGL028C AFUA_8G05610 0.287899385 YML004C AFUA_6G07940 0.285261452 YOL045W AFUA_2G02850 0.284622252 YLR429W AFUA_2G14270 0.283845667 YDR397C AFUA_3G02340 0.283499213 YBR260C AFUA_3G06280 0.282196097 YCR087C-A AFUA_7G04700...”

Q7SE05 D-lactate dehydrogenase (cytochrome) from Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
26% identity, 72% coverage

• Two D-2-hydroxy-acid dehydrogenases in Arabidopsis thaliana with catalytic capacities to participate in the last reactions of the methylglyoxal and beta-oxidation pathways
  Engqvist, The Journal of biological chemistry 2009
  • “...K. lactis (Q12627); Neurospora crassa (Q7SE05); Pyrenophora tritici-repentis (B2WBK4); Aspergillus fulmigatus (Q4WE96); and Neosartorya fischeri (A1D828)....”

cg2543 glycolate oxidase FAD-linked subunit oxidoreductase from Corynebacterium glutamicum ATCC 13032
28% identity, 44% coverage

• Physiology and Transcriptional Analysis of (p)ppGpp-Related Regulatory Effects in Corynebacterium glutamicum
  Ruwe, Frontiers in microbiology 2019
  • “...1.25 1.64564E61 cg1665 putative secreted protein 1.09 6.95957E12 cg1784 ocd putative ornithine cyclodeaminase 1.44 5.2046E16 cg2543 glcD putative (S)-2-hydroxy-acid oxidase 1.66 1.09228E47 cg2545 putative secreted or membrane protein 1.34 1.85048E09 cg2546 putative secondary C4-dicarboxylate transporter, tripartite ATP-independent transporter (TRAP-T) family 1.46 1.04406E29 cg3113 cysY sirohydrochlorin ferrochelatase...”

PHYSODRAFT_353864 hypothetical protein from Phytophthora sojae
28% identity, 73% coverage

• Insights into the adaptive response of the plant-pathogenic oomycete Phytophthora capsici to the fungicide flumorph
  Pang, Scientific reports 2016
  • “...compound metabolism 348684155 hypothetical protein PHYSODRAFT_478148 Others 348684075 hypothetical protein PHYSODRAFT_349787 Others 348683892 hypothetical protein PHYSODRAFT_353864 Others 348683825 putative dehydratase Others 348681277 hypothetical protein PHYSODRAFT_557322 Others 348673004 hypothetical protein PHYSODRAFT_354913 Others 348673003 hypothetical protein PHYSODRAFT_354912 Others 262105863 aldo/keto reductase family Others 262103226 succinate semialdehyde dehydrogenase Others...”

F1S451 D-lactate dehydrogenase (cytochrome) from Sus scrofa
27% identity, 84% coverage

• Mammary tissue proteomics in a pig model indicates that dietary valine supplementation increases milk fat content via increased de novo synthesis of fatty acid.
  Che, Food science & nutrition 2021
  • “...ion transport and metabolism F1S5A6 Uncharacterized protein SLC34A2 2.04 .008 Inorganic ion transport and metabolism F1S451 Uncharacterized protein LDHD 5.49 .025 Energy production and conversion A0A287AKR7 Uncharacterized protein HSPA14 5.20 .035 Energy production and conversion F1RM08 Amino acid transporter SLC1A5 2.77 .009 Energy production and conversion...”

D2HDH_XANCL / P0DV35 D-2-hydroxyglutarate dehydrogenase; D2HGDH; EC 1.1.99.39 from Xanthomonas citri pv. viticola (strain LMG 965 / NCPPB 2475 / ICMP 3867 / CFBP 7660) (Xanthomonas campestris pv. viticola) (see paper)
28% identity, 91% coverage

• function: Catalyzes the dehydrogenation of (R)-2-hydroxyglutarate (D-2- hydroxyglutarate) to 2-oxoglutarate. Has also a low activity on D- malate in vitro (PubMed:34555022). Is functionally tied to L-serine biosynthesis, via its coupling with the D-3-phosphoglycerate dehydrogenase SerA, encoded by the adjacent gene in the locus (By similarity). Active in vitro with the artificial electron acceptor 2,6- dichlorophenolindophenol (DCPIP), but not with NAD, NADP, or cytochrome c. Also displays a very low oxidase activity in vitro on D-2- hydroxyglutarate and L-2-hydroxyglutarate with O2 as the electron acceptor, but this activity is most likely not physiological (PubMed:34555022).
  catalytic activity: (R)-2-hydroxyglutarate + A = AH2 + 2-oxoglutarate (RHEA:38295)
  catalytic activity: (R)-malate + A = oxaloacetate + AH2 (RHEA:67460)
  cofactor: FAD (Binds 1 FAD per subunit.)
  subunit: Homodimer.

DLD2_YEAST / P46681 D-2-hydroxyglutarate--pyruvate transhydrogenase DLD2; D-2HG--pyruvate transhydrogenase DLD2; Actin-interacting protein 2; D-lactate dehydrogenase [cytochrome] 2, mitochondrial; D-lactate ferricytochrome C oxidoreductase; D-LCR; EC 1.1.99.40; EC 1.1.2.4 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 4 papers)
NP_010103 D-lactate dehydrogenase from Saccharomyces cerevisiae S288C
YDL178W D-lactate dehydrogenase, located in the mitochondrial matrix from Saccharomyces cerevisiae
28% identity, 88% coverage

• function: Catalyzes the reversible oxidation of (R)-2-hydroxyglutarate to 2-oxoglutarate coupled to reduction of pyruvate to (R)-lactate. Can also use oxaloacetate as electron acceptor instead of pyruvate producing (R)-malate (PubMed:26774271). In addition to its enzymatic role it could play an important role in the yeast cell morphology (PubMed:10509019).
  catalytic activity: (R)-lactate + 2 Fe(III)-[cytochrome c] = 2 Fe(II)-[cytochrome c] + pyruvate + 2 H(+) (RHEA:13521)
  catalytic activity: (R)-2-hydroxyglutarate + pyruvate = (R)-lactate + 2- oxoglutarate (RHEA:51608)
  cofactor: FAD
  subunit: Interacts with F-actin.
• Protein domain embeddings for fast and accurate similarity search.
  Iovino, Genome research 2024
  • “...3.40.50.300] supfam-nomax50 49,365 (24,708) Same as pfam-nomax50 but based on SCOP domains Q9T0N8 [56,176, 55,103] P46681 [56,176, 55,103] a The benchmarks are denoted as pfam-max50, gene3d-nomax50, and so on to indicate the domain database used for defining the homologs, with the number of pairs (total/homologs) in...”
• Two D-2-hydroxy-acid dehydrogenases in Arabidopsis thaliana with catalytic capacities to participate in the last reactions of the methylglyoxal and beta-oxidation pathways
  Engqvist, The Journal of biological chemistry 2009
  • “...(A1L258); M. musculus (Q8CIM3); S. cerevisiae DLD2 (P46681); S. cerevisiae DLD3 (P39976); K. lactis (Q6CL48); N. crassa (Q7RYX6); P. tritici-repentis (B2WHR3);...”
• Mutations in the D-2-hydroxyglutarate dehydrogenase gene cause D-2-hydroxyglutaric aciduria
  Struys, American journal of human genetics 2005
  • “...the actin-interacting protein 2 (NCBI accession number P46681) of Saccharomyces cerevisiae (Achouri et al. 2004 ). Overexpression of the mutant...”
• Identification of a dehydrogenase acting on D-2-hydroxyglutarate
  Achouri, The Biochemical journal 2004
  • “...as with Saccharomyces cerevisiae `actin-interacting protein 2' (P46681). These sequences are more distantly related to D-lactate dehydrogenases, including the...”
• Closing the gap: yeast electron-transferring flavoprotein links the oxidation of d-lactate and d-α-hydroxyglutarate to energy production via the respiratory chain.
  Toplak, The FEBS journal 2019
  • GeneRIF: we conclude that the formation of a product-reduced Dld2 complex suppresses electron transfer to dioxygen but favors the rapid reduction in yETF, thus preventing the loss of electrons and the generation of reactive oxygen species.
• Saccharomyces cerevisiae Forms D-2-Hydroxyglutarate and Couples Its Degradation to D-Lactate Formation via a Cytosolic Transhydrogenase.
  Becker-Kettern, The Journal of biological chemistry 2016
  • GeneRIF: Dld2 and Dld3, both currently annotated as D-lactate dehydrogenases, efficiently oxidized d-2-hydroxyglutarate to alpha-ketoglutarate.
• Comparative genome-scale reconstruction of gapless metabolic networks for present and ancestral species
  Pitkänen, PLoS computational biology 2014
  • “...deleted. For the four complexes shown, YEL039C knockout will result also in the deletion of YDL178W and reactions associated with it because no other YDL178W containing complex remains. In contrast, YEL071W is not deleted, because it participates in a still functional complex with YJR048W. Identically to...”
• The flavoproteome of the yeast Saccharomyces cerevisiae
  Gudipati, Biochimica et biophysica acta 2014
  • “...YML054C 2 1.1.2.4 d -Lactate dehydrogenase FAD/heme I. mito. membr. dld1 YDL174C Mito. matrix dld2 YDL178W Cytoplasm dld3 YEL071W 3 1.1.3.37 d -Arabino-1,4-lactone oxidase 8-(N3-His) -FAD FAD_PCMH O. mito. membr. alo1 YML086C 4 1.1.5.3 Glycerol-3-phosphate dehydrogenase FAD NADP_Rossmann (DAO) I. mito. membr. gut2 YIL155C 5 1.3.1.90...”
• Gene expression and biochemical analysis of cheese-ripening yeasts: focus on catabolism of L-methionine, lactate, and lactose
  Cholet, Applied and environmental microbiology 2007
  • “...DEHA0D09658g* DLD2 ILV2 ILV6 PDA1 PDB1 YDL178w YMR108w YCL009c YER178w YBR221c DEHA0F07612g* DEHA0G02574g* DEHA0E22869g* DEHA0G13728g* DEHA0C10065g PDC1 YLR044c...”
• Metabolic functions of duplicate genes in Saccharomyces cerevisiae
  Kuepfer, Genome research 2005
  • “...YDR111C YHR208W YJR148W YNR001C YCR005C YPR001W YDL174C YDL178W YEL071W YDR272W YOR040W YDL022W YOL059W YDL066W YLR174W YNL009W YNL104 YOR108W YKL085W YDL078C...”
• The complete set of predicted genes from Saccharomyces cerevisiae in a readily usable form
  Hudson, Genome research 1997
  • “...YDL207w (1617 bp), YDL197c (1578 bp), YDL189w (1612 bp), YDL178w (1593 bp), YDL170w (1587 bp), YDL160c (1521 bp), YDL159w (1548 bp), YDL156w (1569 bp), YDL146w...”

A1D092 Actin interacting protein 2 from Neosartorya fischeri (strain ATCC 1020 / DSM 3700 / CBS 544.65 / FGSC A1164 / JCM 1740 / NRRL 181 / WB 181)
26% identity, 86% coverage

• Two D-2-hydroxy-acid dehydrogenases in Arabidopsis thaliana with catalytic capacities to participate in the last reactions of the methylglyoxal and beta-oxidation pathways
  Engqvist, The Journal of biological chemistry 2009
  • “...tritici-repentis (B2WHR3); A. fulmigatus (Q4WE96); and N. fischeri (A1D092). SEPTEMBER 11, 2009 * VOLUME 284 * NUMBER 37 JOURNAL OF BIOLOGICAL CHEMISTRY 25031...”

Q6CCU5 YALI0C06446p from Yarrowia lipolytica (strain CLIB 122 / E 150)
27% identity, 85% coverage

• Proteomes reveal metabolic capabilities of <i>Yarrowia lipolytica</i> for biological upcycling of polyethylene into high-value chemicals
  Walker, mSystems 2023
  • “...P = 0.0041), YarlipO1F2_208678 (Q6C4G4, YALI0E27005p, pyruvate dehydrogenase) by 60-fold ( P = 0.0183), YarlipO1F2_233609 (Q6CCU5, YALI0C06446p, proteins containing the FAD binding domain) by 55-fold ( P = 0.0129), YarlipO1F2_238445 (Q6CGH0, YALI0A19448p, aldehyde dehydrogenase) by 48-fold ( P = 0.0044), and YarlipO1F2_86039 (Q6C7X2, YALI0D24629p, and acyl...”

G4RPF4 D-lactate dehydrogenase (acceptor) (EC 1.1.99.6) from Thermoproteus tenax (see paper)
29% identity, 84% coverage

NMB1524 putative oxidoreductase from Neisseria meningitidis MC58
25% identity, 85% coverage

• Characterization and Distribution of the autB Gene in Neisseria meningitidis
  Zhang, Frontiers in cellular and infection microbiology 2017
  • “...and the primers were redesigned according to the sequences of the smpB (NMB1526) and glcD (NMB1524) from the whole genome of N. meningitidis MC58 (Accession number NC_003112 ) (Tettelin et al., 2000 ; Shao and Zhu, 2016 ). The primer sequences are listed as follows: autB-F:...”
• Regulation of Neisseria meningitidis cytochrome bc₁ components by NrrF, a Fur-controlled small noncoding RNA
  Pannekoek, FEBS open bio 2017
  • “...transporter 8.6 NMB1839 fhs Formatetetrahydrofolate ligase Carbon metabolism 7.2 NMB0477 GTPbinding protein Unknown 5.1 Yes NMB1524 FADbinding oxidoreductase Unknown 3.4 NMB1383 hscB Cochaperone protein Protein folding 3.2 NMB1428 Putative metalloaminopeptidase Aminopeptidase 2.6 NMB1729 exbB Biopolymer transport protein Iron transporter 2.0 Yes NMB1445 recA Protein RecA DNA...”
• The majority of genes in the pathogenic Neisseria species are present in non-pathogenic Neisseria lactamica, including those designated as 'virulence genes'
  Snyder, BMC genomics 2006
  • “...in this location in all the assessed strains. Panel C: the region between smpB and NMB1524 contains virG in the pathogen genome sequences and a hypothetical gene in the N. lactamica genome sequence. Panel D: the region between trpB and comA contains iga , flanked by...”

NMY220_1433, NMY233_1412 FAD-binding oxidoreductase from Neisseria meningitidis NM233
25% identity, 85% coverage

• Whole genome sequencing to investigate the emergence of clonal complex 23 Neisseria meningitidis serogroup Y disease in the United States
  Krauland, PloS one 2012
  • “...0.0936 0.3545 NMY220_0390 NMY233_0372 shikimate 5-dehydrogenase (AroE) 0.0951 0.2212 NMY220_1068 NMY233_1071 putative lipoprotein 0.0299 0.3518 NMY220_1433 NMY233_1411 ornithine carbamoyltransferase 0.0936 0.3545 NMY220_0390 NMY233_0372 shikimate 5-dehydrogenase (AroE) 0.0266 0.3293 NMY220_0388 NMY233_0370 lipopolysaccharide ABC transporter,ATP-binding protein 0.0921 0.3260 NMY220_0548 NMY233_0521 PilV 0.0921 0.3260 NMY220_0548 NMY233_0521 PilV 0.0786 0.5293...”
  • “...NMY233_0947 phosphoribosyl aminoimidazolecarboxylase, ATPase subunit 0.0754 0.2449 NMY220_0822 NMY233_0800 conserved hypothetical protein 0.0334 0.3023 NMY220_1434 NMY233_1412 ketol-acid reductoisomerase 0.0628 0.1951 NMY220_1465 NMY233_1442 two component sensor kinase 0.0239 0.3011 NMY220_1869 NMY233_1848 cysteinyl-tRNA synthetase 0.0613 0.2013 NMY220_0445 NMY233_0426 sel1 repeat protein 0.0959 0.2951 NMY220_1241 NMY233_1228 conserved hypothetical protein...”

3pm9A / Q6NAV4 Crystal structure of a putative dehydrogenase (rpa1076) from rhodopseudomonas palustris cga009 at 2.57 a resolution
28% identity, 91% coverage

• Ligand: flavin-adenine dinucleotide (3pm9A)

PP_5154 oxidoreductase, FAD-binding, putative from Pseudomonas putida KT2440
27% identity, 86% coverage

• Production of selenium nanoparticles occurs through an interconnected pathway of sulphur metabolism and oxidative stress response in Pseudomonas putida KT2440
  Avendaño, Microbial biotechnology 2023
  • “...JJ14 PP_0053 sqr Sulphidequinone oxidoreductase RF16 PP_4189 sucA 2oxoglutarate dehydrogenase Central metabolism/Glutathione biosynthesis Delayed RF18 PP_5154 D2HGDH D2hydroxyglutarate dehydrogenase RF20 PP_5154 D2HGDH D2hydroxyglutarate dehydrogenase RF4 PP_3998 gqr Glutathionylhydroquinone reductase Glutathione biosynthesis JJ24 PP_4322 ccmF Holocytochrome C synthetase Cytochrome c biosynthesis Delayed RF24 PP_4799 Muranoyltetrapeptide carboxypeptidase Membrane...”
• Understanding of bacterial lignin extracellular degradation mechanisms by Pseudomonas putida KT2440 via secretomic analysis
  Xu, Biotechnology for biofuels and bioproducts 2022
  • “...(PP_3248); CopA, multicopper oxidase (copA-II); GST, glutathione S-transferase (PP_1644); gor, glutathione reductase; betA, choline dehydrogenase; PP_5154, FAD-binding oxidoreductase; aldA/aldB-I, aldehyde dehydrogenase. Detailed enzyme information can be found in Additional file 2 : Table S4 Limited -O-4 bond cleavage (Table 1 ) was observed when lignin was...”
  • “...on the homologous alignment of the amino acid sequence in NCBI database (blastp), FAD-binding oxidoreductase (PP_5154) exhibited the 62.8% similarity to pinoresinol -hydroxylase in Pseudomonas sp. SG-MS2 [ 48 ]. Therefore, resinol linkage might be converted to vanillin and vanillic acid by FAD-binding oxidoreductase (Fig. 5...”

RPA1076 putative oxidoreductase from Rhodopseudomonas palustris CGA009
28% identity, 91% coverage

• Structure, substrate specificity, and catalytic mechanism of human D-2-HGDH and insights into pathogenicity of disease-associated mutations
  Yang, Cell discovery 2021
  • “...molecular replacement (MR) method implemented in Phenix 50 using the structure of a putative dehydrogenase RPA1076 from Rhodopseudomonas palustris (PDB code: 3PM9) as the search model. The structures of D-2-HGDH in complexes with D-2-HG, D-MAL, D-LAC, L-2-HG, and 2-OG were solved by the MR method using...”
• Crystallization and preliminary X-ray analysis of a dye-linked D-lactate dehydrogenase from the aerobic hyperthermophilic archaeon Aeropyrum pernix
  Shibahara, Acta crystallographica. Section F, Structural biology and crystallization communications 2011
  • “...highest identity (31.3%) to a putative dehydrogenase (RPA1076) from Rhodopseudomonas palustris CGA009 (PDB entry 3pm9; Joint Center for Structural Genomics,...”

Q7TPJ4 D-lactate dehydrogenase (cytochrome) from Rattus norvegicus
25% identity, 76% coverage

• D- and L-lactate dehydrogenases during invertebrate evolution
  Cristescu, BMC evolutionary biology 2008
  • “...XP_001626025 ] unpublished Pan troglodytes chimpanzee [GeneBank: XP_001139010 ] unpublished Rattus norvegicus Norway rat [Swiss-Prot: Q7TPJ4 ] Xu et al. 2003 unpublished DLD1 Saccharomyces cerevisiae baker's yeast [Swiss-Prot: YDL174C ] [ 64 ] Strongylocentrotus purpuratus purple urchin [GeneBank: XP_796456 ] unpublished Tetraodon nigroviridis Green puffer [Swiss-Prot:...”

Q4T6R2 D-lactate dehydrogenase (cytochrome) (Fragment) from Tetraodon nigroviridis
24% identity, 70% coverage

• D- and L-lactate dehydrogenases during invertebrate evolution
  Cristescu, BMC evolutionary biology 2008
  • “...64 ] Strongylocentrotus purpuratus purple urchin [GeneBank: XP_796456 ] unpublished Tetraodon nigroviridis Green puffer [Swiss-Prot: Q4T6R2 ] [ 65 ] Xenopus laevis African clawed frog [Swiss-Prot: A1L2R0 ] [ 66 ] Authors' contributions The data were collected and analyzed by MEC and TJC. The manuscript was...”

DLD3_YEAST / P39976 D-2-hydroxyglutarate--pyruvate transhydrogenase DLD3; D-2HG--pyruvate transhydrogenase DLD3; (R)-2-hydroxyglutarate--pyruvate transhydrogenase; D-lactate dehydrogenase [cytochrome] 3; D-lactate ferricytochrome C oxidoreductase; D-LCR; EC 1.1.99.40; EC 1.1.2.4 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 3 papers)
P39976 (R)-2-hydroxyglutarate-pyruvate transhydrogenase (EC 1.1.99.40) from Saccharomyces cerevisiae (see paper)
NP_010843 D-lactate dehydrogenase from Saccharomyces cerevisiae S288C
YEL071W D-lactate dehydrogenase, part of the retrograde regulon which consists of genes whose expression is stimulated by damage to mitochondria and reduced in cells grown with glutamate as the sole nitrogen source, located in the cytoplasm from Saccharomyces cerevisiae
25% identity, 91% coverage

• function: Catalyzes the reversible oxidation of (R)-2-hydroxyglutarate to 2-oxoglutarate coupled to reduction of pyruvate to (R)-lactate. Can also use oxaloacetate as electron acceptor instead of pyruvate producing (R)-malate.
  catalytic activity: (R)-lactate + 2 Fe(III)-[cytochrome c] = 2 Fe(II)-[cytochrome c] + pyruvate + 2 H(+) (RHEA:13521)
  catalytic activity: (R)-2-hydroxyglutarate + pyruvate = (R)-lactate + 2- oxoglutarate (RHEA:51608)
  cofactor: FAD
• No Chance to Survive: Mo-CBP₃-PepII Synthetic Peptide Acts on Cryptococcus neoformans by Multiple Mechanisms of Action
  Aguiar, Antibiotics (Basel, Switzerland) 2023
  • “...enzyme Nonribosomal peptide synthase agiA B8NY88 Aspergillus flavus Endoplasmic reticulum 0.609201703 Oxidoreductase D-2-hydroxyglutarate--pyruvate transhydrogenase DLD3 P39976 Saccharomyces cerevisiae Cytoplasm 1.992460047 3-isopropylmalate dehydrogenase A P87256 Aspergillus niger Cytoplasm 1.782962796 Acyl-coenzyme A oxidase Q6FY63 Candida glabrata Peroxisome 1.03315885 Alcohol dehydrogenase 2 P54202 Emericella nidulans Cytoplasm 0.609201703 Protein Binding...”
• The proteome response to amyloid protein expression in vivo
  Gomes, PloS one 2012
  • “...3.17E-06 EM P07262 837 977 771 9 DLD3 D-lactate dehydrogenase [cytochrome] 3 1.4 1.29E-03 CRH P39976 780 1020 797 8 DTD D-tyrosyl-tRNA(Tyr) deacylase +1.4 2.59E-02 T Q07648 1642 84 63 2 DUG1 Cys-Glymetallodipeptidase DUG1 +1.6 3.17E-06 PFD P43616 837 343 303 4 EF1A Elongation factor 1-alpha...”
• Two D-2-hydroxy-acid dehydrogenases in Arabidopsis thaliana with catalytic capacities to participate in the last reactions of the methylglyoxal and beta-oxidation pathways
  Engqvist, The Journal of biological chemistry 2009
  • “...S. cerevisiae DLD2 (P46681); S. cerevisiae DLD3 (P39976); K. lactis (Q6CL48); N. crassa (Q7RYX6); P. tritici-repentis (B2WHR3); A. fulmigatus (Q4WE96); and...”
• Regulation of xylose metabolism in recombinant Saccharomyces cerevisiae
  Salusjärvi, Microbial cell factories 2008
  • “...0.5 -2.7 0.2 P14306 Dka1p YLR178C carboxypeptidase Y inhibitor -1.2 -0.6 1.7 0.8 2.9 1.4 P39976 Dld3p YEL071W D-lactate dehydrogenase (cytochrome) -2.0 -0.2 -2.4 -0.6 -0.3 -0.4 P00924 Eno1p_a YGR254W phosphopyruvate hydratase 1.5 0.6 5.2 0.5 3.7 -0.1 P00924 Eno1p_b YGR254W phosphopyruvate hydratase 3.5 0.6 5.7...”
• Computational identification of ubiquitylation sites from protein sequences.
  Tung, BMC bioinformatics 2008
  • “...Accession number Position Score Accession number Position Score Accession number Position Score P19358 114 0.99 P39976 323 0.90 P38080 809 0.87 Q9Y6K9 35 0.96 P38261 147 0.89 P10592 54 0.87 P25694 6 0.96 P25360 846 0.89 P38080 792 0.87 P40087 325 0.95 P09936 195 0.88 P12866...”
• Saccharomyces cerevisiae Forms D-2-Hydroxyglutarate and Couples Its Degradation to D-Lactate Formation via a Cytosolic Transhydrogenase.
  Becker-Kettern, The Journal of biological chemistry 2016
  • GeneRIF: Dld2 and Dld3, both currently annotated as D-lactate dehydrogenases, efficiently oxidized d-2-hydroxyglutarate to alpha-ketoglutarate.
• Transcriptional response of Saccharomyces cerevisiae to lactic acid enantiomers
  Drozdova, Applied microbiology and biotechnology 2024
  • “...metabolic process (GO:0006089) and lactate biosynthetic process (GO:0019249) largely overlapped and contained DLD1 (YDL174C), DLD3 (YEL071W), SNO4 (YMR322C), and HSP32 (YPL280W). The former two genes indeed encode D-lactate dehydrogenases, mitochondrial Dld1 and cytoplasmic Dld3 (Pallotta 2012 ); according to the literature, Dld3 can also oxidize D-2-hydroxyglutarate...”
  • “...as a representative of a larger group of iron uptake-related proteins (Table 1 ). DLD3 (YEL071W) codes for a protein with D-lactate dehydrogenase activity in vitro, but there is evidence that in vivo it contributes to D-lactate synthesis (Chelstowska et al. 1999 ; Becker-Kettern et al....”
• High-throughput metabolomics for the design and validation of a diauxic shift model
  Brunnsåker, NPJ systems biology and applications 2023
  • “...YOL051W Transcription factor Galactose metabolism 0.000428 OCA1 YNL099C Putative, phosphatase Cell cycle arrest 0.000427 DLD3 YEL071W Dehydrogenase D-Lactate dehydrogenase 0.000427 Details and simulated growth rate differences of deletion mutants using model paradigm and model structures proposed by Coutant et al. In descending order of absolute growth...”
• Heme, A Metabolic Sensor, Directly Regulates the Activity of the KDM4 Histone Demethylase Family and Their Interactions with Partner Proteins
  Konduri, Cells 2020
  • “...DBP5 YOR046C 6324620 Cytoplasmic ATP-dependent RNA helicase of the DEAD-box family DDX19B, DDX25 + DLD3 YEL071W 6320764 D-2-hydroxyglutarate--pyruvate transhydrogenase AGPS, D2HGDH, LDHD + + + DUF1 YOL087C 6324485 Uncharacterized WD repeat-containing protein WDR48 ERG11 YHR007C 6321795 Lanosterol 14-alpha-demethylase CYP51A1 + + + GAL83 YER027C 6320865 One...”
• Precise control of SCRaMbLE in synthetic haploid and diploid yeast
  Jia, Nature communications 2018
  • “...diploid (yJBD001), we used qPCR to analyze the DNA copy numbers of four genes ( YEL071W , CrtE , YEL022W , and YER043C ) that were representative of the duplicated segments (Fig. 4e ). For yJBS001, the fold change in the copy numbers of the YEL072W-YEL071W...”
  • “...of duplications, yeast genomic DNA was used for qPCR analysis. The ALG9 gene and the YEL071W , CrtE , YEL022W , YER043C , and YER036C genes were chosen as the reference gene and target genes, respectively. The copy numbers were quantified by comparing the Cq values...”
• Comparative genome-scale reconstruction of gapless metabolic networks for present and ancestral species
  Pitkänen, PLoS computational biology 2014
  • “...YDL178W and reactions associated with it because no other YDL178W containing complex remains. In contrast, YEL071W is not deleted, because it participates in a still functional complex with YJR048W. Identically to [34] , growth was considered to be successfully predicted if the absolute difference between the...”
• The flavoproteome of the yeast Saccharomyces cerevisiae
  Gudipati, Biochimica et biophysica acta 2014
  • “...d -Lactate dehydrogenase FAD/heme I. mito. membr. dld1 YDL174C Mito. matrix dld2 YDL178W Cytoplasm dld3 YEL071W 3 1.1.3.37 d -Arabino-1,4-lactone oxidase 8-(N3-His) -FAD FAD_PCMH O. mito. membr. alo1 YML086C 4 1.1.5.3 Glycerol-3-phosphate dehydrogenase FAD NADP_Rossmann (DAO) I. mito. membr. gut2 YIL155C 5 1.3.1.90 tRNA dihydrouridine synthase...”
• Comparative proteome analysis of Saccharomyces cerevisiae: a global overview of in vivo targets of the yeast activator protein 1
  Jun, BMC genomics 2012
  • “...Ald6p Aldehyde dehydrogenase YPL061W 161 33 329 40 2.04 0.005 + Dld3p D-lactate dehydrogenase 3 YEL071W 290 20 501 79 1.73 0.011 - Pentose phosphate pathway Tkl1p # Transketolase 1 YPR074C 284 10 619 165 2.18 0.025 + Gnd1p 6-phosphogluconate dehydrogenase 1 YHR183W 633 124 876...”
• Construction and application of a protein and genetic interaction network (yeast interactome)
  Stuart, Nucleic acids research 2009
  • “...YML026C RPS18B 6.03 Protein component of the small (40S) ribosomal subunit; nearly identical to Rps18Ap YEL071W DLD3 6.48 D-lactate dehydrogenase; retrograde regulon (genes stimulated by damage to mitochondria) YAR073W IMD1 6.60 Nonfunctional protein with homology to IMP dehydrogenase; probable pseudogene, located close to the telomere YFL057C...”
• More

Q4WE96 Actin interacting protein 2 from Aspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293)
25% identity, 81% coverage

• Two D-2-hydroxy-acid dehydrogenases in Arabidopsis thaliana with catalytic capacities to participate in the last reactions of the methylglyoxal and beta-oxidation pathways
  Engqvist, The Journal of biological chemistry 2009
  • “...Pyrenophora tritici-repentis (B2WBK4); Aspergillus fulmigatus (Q4WE96); and Neosartorya fischeri (A1D828). B, phylogenetic tree of AtD-2HGDH homologous...”
  • “...N. crassa (Q7RYX6); P. tritici-repentis (B2WHR3); A. fulmigatus (Q4WE96); and N. fischeri (A1D092). SEPTEMBER 11, 2009 * VOLUME 284 * NUMBER 37 JOURNAL OF...”

trd_1165 glycolate oxidase subunit from Thermomicrobium roseum DSM 5159
25% identity, 46% coverage

• Complete genome sequence of the aerobic CO-oxidizing thermophile Thermomicrobium roseum
  Wu, PloS one 2009
  • “...gene cluster encodes two conserved hypothetical proteins (trd-1160, trd_1167) and a paralog of glycolate oxidase (trd_1165). One or more of these genes might be responsible for the proposed introduction of the 2,2 hydroxyl groups ( Figure 4C, Step 1 ). No homologs were found to any...”

NP_384973 putative oxidoreductase protein from Sinorhizobium meliloti 1021
SMc00985 FAD-binding oxidoreductase from Sinorhizobium meliloti 1021
28% identity, 91% coverage

• 'Ca. Liberibacter asiaticus' proteins orthologous with pSymA-encoded proteins of Sinorhizobium meliloti: hypothetical roles in plant host interaction
  Kuykendall, PloS one 2012
  • “...quinone oxidoreductase NP_435950.1 YP_003064703 4E-12 269 40 NP_386798 5E-42 quinoneoxidoreductase NP_435375.1 YP_003065174 3E-76 425 56 NP_384973 7E-99 prob FAD-dependent oxidoreductase NP_435937.1 YP_003065041 9E-20 187 51 NP_384479 3E-19 coproporphyrinogen III oxidase NP_436285.1 YP_003064696 1E-22 134 61 NP_385673 1E-31 thioredoxin reductase (NADPH) Genbank numbers, E-values, number of amino...”
• Pyridoxal 5'-phosphate synthesis and salvage in Bacteria and Archaea: predicting pathway variant distributions and holes
  Denise, Microbial genomics 2023
  • “...possibilities rely on non-orthologous displacement, as seen in R. meliloti where the FAD-dependent oxidase PdxR (SMc00985) replaces the NAD-dependent PdxB. Analysis of TnSeq data available for Desulfovibrio vulgaris str. Hildenborough shows that the two genes that have the highest co-fitness scores with pdxA ( DVU2241 )...”
  • “...D. vulgaris strain (Fig. S5). DVU0827 is 33% identical in sequence to S. meliloti PdxR (SMc00985). The proposal that DVU0826/DVU0827 replaces PdxB has independently been made by Trotter et al . [ 82 ]. The glycolate oxidase family is complex with many paralogs and redundant systems...”
• Flavin adenine dinucleotide-dependent 4-phospho-D-erythronate dehydrogenase is responsible for the 4-phosphohydroxy-L-threonine pathway in vitamin B6 biosynthesis in Sinorhizobium meliloti
  Tazoe, Journal of bacteriology 2006
  • “...to that of the coding sequence region of SMc00985 (positions 951316 to 952806, complement; accession number NC_003047). The DNA fragment containing pdxR and a...”

A1L258 D-2-hydroxyglutarate dehydrogenase, mitochondrial from Danio rerio
27% identity, 77% coverage

• Two D-2-hydroxy-acid dehydrogenases in Arabidopsis thaliana with catalytic capacities to participate in the last reactions of the methylglyoxal and beta-oxidation pathways
  Engqvist, The Journal of biological chemistry 2009
  • “...truncatula (MtAC136451_19.4); H. sapiens (Q8N465); D. rerio (A1L258); M. musculus (Q8CIM3); S. cerevisiae DLD2 (P46681); S. cerevisiae DLD3 (P39976); K. lactis...”

B9S687 D-lactate dehydrognease 2, putative from Ricinus communis
26% identity, 76% coverage

• Two D-2-hydroxy-acid dehydrogenases in Arabidopsis thaliana with catalytic capacities to participate in the last reactions of the methylglyoxal and beta-oxidation pathways
  Engqvist, The Journal of biological chemistry 2009
  • “...bicolor (e_gw1.2.1014.1); O. sativa (Q7XI14); R. communis (B9S687); V. vinifera (A7QE54); M. truncatula (MtAC136451_19.4); H. sapiens (Q8N465); D. rerio...”

O46096 D-2-hydroxyglutarate dehydrogenase, mitochondrial from Drosophila melanogaster
28% identity, 81% coverage

• Proteomic characterization of inbreeding-related cold sensitivity in Drosophila melanogaster
  Vermeulen, PloS one 2013
  • “...86B486B4 4108 cuticular protein 49Ab See SN2101 See SN2101 4108 Tal Q9W1G0 60A1260A12 4301 EG:87B1.3 O46096 2D42D4 4303 CG1440, isoform A Q9W3F6 7E97E9 4311 RE37426p Q5U189 29F529F5 4703 CG1516, isoform E Q7KN97 46B446B4 5302 HMG coenzyme A synthase, isoform A Q7K4Q9 53C153C1 5401 CG5384 Q9VKZ8 31D431D5...”

NP_726795 D-2-hydroxyglutaric acid dehydrogenase, isoform C from Drosophila melanogaster
28% identity, 81% coverage

• Genetic dissection of leukemia-associated IDH1 and IDH2 mutants and D-2-hydroxyglutarate in Drosophila.
  Reitman, Blood 2015
  • GeneRIF: We identified the fly homolog of D-2-hydroxyglutaric acid dehydrogenase (CG3835), which metabolizes D-2HG, and showed that coexpression of this enzyme with mutant Idh abolishes mutant Idh-associated phenotype

F7XD40 4-phospho-D-erythronate dehydrogenase from Sinorhizobium meliloti (strain SM11)
29% identity, 92% coverage

• Pyridoxal 5'-phosphate synthesis and salvage in Bacteria and Archaea: predicting pathway variant distributions and holes
  Denise, Microbial genomics 2023
  • “...replaced in some organisms, such as Sinorhizobium meliloti, by a non-orthologous enzyme PdxR (Uniprot Id F7XD40) [ 20 ]. This last enzyme should not be confused with the transcriptional regulator of the same name but of a different family that regulates PLP synthesis genes in several...”
  • “...propagated to other subgroups without additional experiments. For example, the R. meliloti PdxR (UniProt ID F7XD40) is in another cluster in the SSN generated for Bacteria superkingdom (Fig. S6). In addition, analysis of d / l -lactate catabolism in Geobacter sulfurreducens showed that the glycolate oxidase-like...”

KLMA_60482 D-lactate dehydrogenase from Kluyveromyces marxianus DMKU3-1042
28% identity, 79% coverage

• Genetic basis of the highly efficient yeast Kluyveromyces marxianus: complete genome sequence and transcriptome analyses
  Lertwattanasakul, Biotechnology for biofuels 2015
  • “...DLD1 Lactate KLMA_40583 D-Lactate dehydrogenase [cytochrome] 1, mitochondrial DLD1 KLMA_50301 D-Lactate dehydrogenase [cytochrome], mitochondrial DLD1 KLMA_60482 D-Lactate dehydrogenase [cytochrome] 2, mitochondrial DLD2 KLMA_10179 Glycerol-3-phosphate dehydrogenase [NAD(+)] 1 GPD1 Glycerol KLMA_30722 Glycerol-3-phosphate dehydrogenase, mitochondrial GUT2 KLMA_60361 Glycerol uptake protein 1 GUP1 KLMA_80411 Glycerol uptake/efflux facilitator protein FPS1...”

B4FWJ7 D-2-hydroxyglutarate dehydrogenase mitochondrial from Zea mays
26% identity, 80% coverage

• Two D-2-hydroxy-acid dehydrogenases in Arabidopsis thaliana with catalytic capacities to participate in the last reactions of the methylglyoxal and beta-oxidation pathways
  Engqvist, The Journal of biological chemistry 2009
  • “...D-2HGDH (O23240); H. tuberosus (EL452354); Z. mays (B4FWJ7); S. bicolor (e_gw1.2.1014.1); O. sativa (Q7XI14); R. communis (B9S687); V. vinifera (A7QE54); M....”

D2HDH_ARATH / O23240 D-2-hydroxyglutarate dehydrogenase, mitochondrial; AtD-2HGDH; EC 1.1.99.39 from Arabidopsis thaliana (Mouse-ear cress) (see 3 papers)
NP_974692 FAD-linked oxidases family protein from Arabidopsis thaliana
AT4G36400 FAD linked oxidase family protein from Arabidopsis thaliana
27% identity, 80% coverage

• function: Catalyzes the oxidation of (R)-2-hydroxyglutarate to 2- oxoglutarate. May be involved in the catabolism of propionyl-CoA derived from beta-oxidation. Involved in degradation of lysine for the supply of carbon and electrons to the ETF/ETFQO complex during dark- induced sugar starvation.
  catalytic activity: (R)-2-hydroxyglutarate + A = AH2 + 2-oxoglutarate (RHEA:38295)
  cofactor: FAD (Binds 1 FAD per monomer.)
  subunit: Homodimer.
  disruption phenotype: No visible phenotype when grown under standard conditions.
• Plants Possess a Cyclic Mitochondrial Metabolic Pathway similar to the Mammalian Metabolic Repair Mechanism Involving Malate Dehydrogenase and l-2-Hydroxyglutarate Dehydrogenase.
  Hüdig, Plant & cell physiology 2015 (PubMed)
  • GeneRIF: a mitochondrial metabolic repair mechanism in Arabidopsis thaliana involving malate dehydrogenase (mMDH) and l-2-hydroxyglutarate dehydrogenase (l-2HGDH), was characterized.
• Identification of the 2-hydroxyglutarate and isovaleryl-CoA dehydrogenases as alternative electron donors linking lysine catabolism to the electron transport chain of Arabidopsis mitochondria.
  Araújo, The Plant cell 2010
  • GeneRIF: Data elucidates the pathway of plant Lys catabolism and demonstrate that both isovaleryl-CoA dehydrogenase and 2-hydroxyglutarate dehydrogenase act as electron donors to the ubiquinol pool via an ETF/ETFQO-mediated route. [D2HGDH]
• Two D-2-hydroxy-acid dehydrogenases in Arabidopsis thaliana with catalytic capacities to participate in the last reactions of the methylglyoxal and beta-oxidation pathways
  Engqvist, The Journal of biological chemistry 2009
  • “...following sequences are included: A. thaliana D-2HGDH (O23240); H. tuberosus (EL452354); Z. mays (B4FWJ7); S. bicolor (e_gw1.2.1014.1); O. sativa (Q7XI14); R....”
• DAip1, a Dictyostelium homologue of the yeast actin-interacting protein 1, is involved in endocytosis, cytokinesis, and motility
  Konzok, The Journal of cell biology 1999
  • “...and P. polycephalum ( Fig. 1 A), and recently in Arabidopsis thaliana (GenBank accession number O23240), Xenopus laevis ( Okada et al. 1999 ), and chickens, mice, and humans ( Adler et al. 1999 ). Sequence identities of these proteins with DAip1 vary between 37 and...”
• Using UAV-Based Temporal Spectral Indices to Dissect Changes in the Stay-Green Trait in Wheat
  Yu, Plant phenomics (Washington, D.C.) 2024
  • “...and SG OSAVI in the 2020 to 2021 season and showed 72.43% homology with Arabidopsis AT4G36400 ( D2HGDH ) at the protein level. AT4G36400 belongs to the same network as several genes involved in -oxidation and degradation of branched-chain amino acids in chlorophyll. This network plays...”
• Identification of cleavage sites and substrate proteins for two mitochondrial intermediate peptidases in Arabidopsis thaliana
  Carrie, Journal of experimental botany 2015
  • “...AT4G08900 Arginase FT FTSVSASSIEKGQNR SVSASSIEKGQNR 15 AT4G35460 NADPH-dependent thioredoxin reductase B F FSSSAVMNGLETHNTR SSSAVMNGLETHNTR 16 AT4G36400 FAD-linked oxidases family protein F FGSSAASLIQR GSSAASLIQR 17 AT4G37910 Hsp70-1 FC FCSRPVGNDVIGIDLGTTNSCVSVMEGKTAR SRPVGNDVIGIDLGTTNSCVSVMEGKTAR 18 AT5G09450 Pentatricopeptide repeat (PPR) protein YN YNADAAIGNSLVEESEEKDDLKSR ADAAIGNSLVEESEEKDDLKSR 19 AT5G47630 Mitochondrial acyl carrier protein 3 FT...”
• 2-Hydroxy Acids in Plant Metabolism
  Maurino, The arabidopsis book 2015
  • “...III, cyt c: cytochrome c, C IV: complex IV. (At4g36400) (Engqvist et al., 2009; Engqvist et al., 2011). At the time of characterization, this enzyme was added...”
• Respiratory electron transfer pathways in plant mitochondria
  Schertl, Frontiers in plant science 2014
  • “...2001 Dschner et al., 2001 Goetzman et al., 2005 Arajo et al., 2010 D-2-Hydroxyglutarate dehydrogenase At4g36400 D-2-hydroxyglutarate + acceptor (ETF) 2-oxoglutarate + reduced acceptor (ETF) (homodimeric complex) Engqvist et al., 2009 Arajo et al., 2010 Engqvist et al., 2011 Saccharopine dehydrogenase At5g39410 Saccharopine + NAD +...”
• Fusarium oxysporum f.sp. ciceri race 1 induced redox state alterations are coupled to downstream defense signaling in root tissues of chickpea (Cicer arietinum L.)
  Gupta, PloS one 2013
  • “...b561 Fe reductase FRO FRO7 TC15027 AT5G49740 FAD linked oxidase family protein - - TC16285 AT4G36400 NADH cytochrome b5 reductase CBR ATCBR TC14723 AT5G17770 C. INTRACELLULAR ROS SIGNAL TRANSDUCERS NADP dependent oxidoreductase - - TC15458 AT5G16990 Quinone oxidoreductase FQR FQR1 TC18358 AT5G54500 Fe (II) oxidoreductase -...”
• Synergistic use of plant-prokaryote comparative genomics for functional annotations
  Gerdes, BMC genomics 2011
  • “...in thiamine salvage Cannot replace 5-FCL and lacks detectable 5-FCL activity 41 Manuscript submitted 10 At4g36400 0277 bll2569 COG0277 D-2-hydroxyglutarate dehydrogenase D-2-hydroxyglutarate dehydrogenase 158 [ 83 ] (2009) 11 At5g10910 0275 mraW 16S rRNA modification within P site of ribosome SAM-dependent methyltransferase involved in a process...”
  • “...n/a Tetrahydrofolate metabolic process (4.56), negative regulation of transcription, response to abscisic acid stimulus (0.89) At4g36400 none D-2-hydroxyglutarate dehydrogenase n/a Cytoskeleton organization and biogenesis (2.39), actin cytoskeleton organization and biogenesis, ubiquitin-dependent protein catabolic process, response to light stimulus, response to wounding, seed germination (1.24) At1g45110 yraL...”
• Plant D-2-hydroxyglutarate dehydrogenase participates in the catabolism of lysine especially during senescence
  Engqvist, The Journal of biological chemistry 2011
  • “...studies using mass spectrometry (31). In this study, At4g36400 was described as a glycolate dehydrogenase because of its close relatedness to At5g06580, which...”
• Two D-2-hydroxy-acid dehydrogenases in Arabidopsis thaliana with catalytic capacities to participate in the last reactions of the methylglyoxal and beta-oxidation pathways
  Engqvist, The Journal of biological chemistry 2009
  • “...the existence of a paralogous protein encoded by locus At4g36400. The recombinant protein is a homodimer of 61-kDa subunits with one FAD per monomer. A...”
  • “...Network Analysis--Genes that are coexpressed with At5g06580 and At4g36400 were identified using the ATTED-II data base (25) and summarized in supplemental Table...”

Q7XI14 Probable D-2-hydroxyglutarate dehydrogenase, mitochondrial from Oryza sativa subsp. japonica
25% identity, 80% coverage

• iTRAQ-based proteome profile analysis of superior and inferior Spikelets at early grain filling stage in japonica Rice
  You, BMC plant biology 2017
  • “...2.721.11 ns 125 Os06g0326400 Q69T78 Pyrophosphate-fructose 6-phosphate 1-phosphotransferase subunit alpha 2.050.21 ns 2.270.28 127 Os07g0187200 Q7XI14 Probable D-2-hydroxyglutarate dehydrogenase, mitochondrial 4.600.81 ns ns 173 Os04g0486950 Q7XUG1 Malate synthase 5.851.70 4.640.51 ns Photosynthesis 1 Os01g0711000 Q8S7T5 ATP synthase subunit alpha ns 4.231.46 ns 3 Os10g0356000 P0C512 Ribulose...”
• Differential Proteomic Analysis Using iTRAQ Reveals Alterations in Hull Development in Rice (Oryza sativa L.)
  Wang, PloS one 2015
  • “...B7E6V7; Q0DWI9; thioredoxin reductase (B8B5I4); Q0D8R4; putative ferredoxin-NADP(H) oxidoreductase (Q6ZFJ3); probable D-2-hydroxyglutarate dehydrogenase, mitochondrial (D2HGDH; Q7XI14); acetolactate synthase (ALS; A5X300); and putative CPRD2 (Q5Z952) were annotated with GO:0050660. 10.1371/journal.pone.0133696.g004 Fig 4 Molecular function analysis of differentially expressed proteins in three growth stages of rice hull. P1,...”
• Two D-2-hydroxy-acid dehydrogenases in Arabidopsis thaliana with catalytic capacities to participate in the last reactions of the methylglyoxal and beta-oxidation pathways
  Engqvist, The Journal of biological chemistry 2009
  • “...mays (B4FWJ7); S. bicolor (e_gw1.2.1014.1); O. sativa (Q7XI14); R. communis (B9S687); V. vinifera (A7QE54); M. truncatula (MtAC136451_19.4); H. sapiens...”

Q7RYX6 D-lactate dehydrogenase 2 from Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
25% identity, 79% coverage

• Two D-2-hydroxy-acid dehydrogenases in Arabidopsis thaliana with catalytic capacities to participate in the last reactions of the methylglyoxal and beta-oxidation pathways
  Engqvist, The Journal of biological chemistry 2009
  • “...DLD3 (P39976); K. lactis (Q6CL48); N. crassa (Q7RYX6); P. tritici-repentis (B2WHR3); A. fulmigatus (Q4WE96); and N. fischeri (A1D092). SEPTEMBER 11, 2009...”

D4XIR1 FAD linked oxidase, C-terminal domain protein from Achromobacter piechaudii ATCC 43553
27% identity, 91% coverage

• Experimental and computational investigation of enzyme functional annotations uncovers misannotation in the EC 1.1.3.15 enzyme class
  Rembeza, PLoS computational biology 2021
  • “...with D-2-hydroxyglutarate (A0A077SBA9 from Xanthomonas campestris ). Additionally, three proteins (A0A0U5JSS4 from a Clostridium species, D4XIR1 from Achromobacter piechaudii , Q5WIP4 from Bacillus clausii ) were active with each of the three substrates only in the AR screen ( S8 Fig ). None of the proteins...”

BMEI1527 GLYCOLATE OXIDASE SUBUNIT GLCD from Brucella melitensis 16M
26% identity, 91% coverage

• Immuno-profiling of Brucella proteins for developing improved vaccines and DIVA capable serodiagnostic assays for brucellosis
  Nandini, Frontiers in microbiology 2023
  • “...starvation/stationary phase protection protein Dps BMEI1980 Ferric uptake regulation protein BMEI0375 Glycolate oxidase subunit GLCD BMEI1527 High-affinity zinc uptake system protein ZNUA BMEII0178 Hypothetical protein BMEI1724 Leucine- isoleucine- valine- threonine- and alanine-binding protein precursor BMEI1930 CobT protein BMEI0050 AsnC family transcriptional regulator BMEI0357 Outer membrane lipoprotein...”

D2HGDH / Q8N465 D-2-hydroxyglutarate dehydrogenase, mitochondrial (EC 1.1.99.39) from Homo sapiens (see paper)
D2HDH_HUMAN / Q8N465 D-2-hydroxyglutarate dehydrogenase, mitochondrial; EC 1.1.99.39 from Homo sapiens (Human) (see 7 papers)
Q8N465 D-2-hydroxyglutarate dehydrogenase (EC 1.1.99.39) from Homo sapiens (see 3 papers)
NP_689996 D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform 1 precursor from Homo sapiens
26% identity, 87% coverage

• function: Catalyzes the oxidation of D-2-hydroxyglutarate (D-2-HG) to alpha-ketoglutarate (PubMed:15070399, PubMed:15609246, PubMed:16037974, PubMed:20020533, PubMed:33431826). Also catalyzes the oxidation of other D-2-hydroxyacids, such as D-malate (D-MAL) and D-lactate (D-LAC) (PubMed:33431826). Exhibits high activities towards D-2-HG and D-MAL but a very weak activity towards D-LAC (PubMed:33431826).
  catalytic activity: (R)-2-hydroxyglutarate + A = AH2 + 2-oxoglutarate (RHEA:38295)
  catalytic activity: (R)-malate + A = oxaloacetate + AH2 (RHEA:67460)
  cofactor: FAD
• Quantitative proteomics analysis in small cell carcinoma of cervix reveals novel therapeutic targets.
  Qiu, Clinical proteomics 2023
  • “...Tumor suppressor candidate 2 TUSC2_HUMAN 2.959401424 0.016305413 Q02338 BDH1 D-beta-hydroxybutyrate dehydrogenase, mitochondrial BDH_HUMAN 4.07081439 0.042339021 Q8N465 D2HGDH D-2-hydroxyglutarate dehydrogenase, mitochondrial D2HDH_HUMAN 7.083717569 0.0431335 Discussion For SCCC, the significant aggressiveness and poor prognosis (even after extensive treatments) have been well documented in previous studies [ 22 ]....”
• D2HGDH-mediated D2HG catabolism enhances the anti-tumor activities of CAR-T cells in an immunosuppressive microenvironment.
  Yang, Molecular therapy : the journal of the American Society of Gene Therapy 2022
  • “...of the EF-1 promoter. The human D2HGDH domain sequence was obtained from the UniProt database (Q8N465), and the cDNA template (CCDS33426.1) was procured by PCR amplification. The T2A linker was used for co-expression of the CAR and D2HGDH. Cells and culture conditions Low-passage HEK293T cells were...”
• Electron transfer flavoprotein and its role in mitochondrial energy metabolism in health and disease.
  Henriques, Gene 2021
  • “...Choline metabolism sarcosine DMGDH Dimethylglycine dehydrogenase DMGDH Q9UI17 Choline metabolism N,N-dimethylglycine D2HGDH D-2-hydroxyglutarate dehydrogenase D2HGDH Q8N465 n.d. D-2-hydroxyglutarate n.d. - not determined. Table 2 Characteristics of the human genes and transcripts encoding ETF subunits a . Gene Chro. CCDS code RefSeq Trascript ID Ensemble Transcript ID...”
• A Combined N-terminomics and Shotgun Proteomics Approach to Investigate the Responses of Human Cells to Rapamycin and Zinc at the Mitochondrial Level
  Bons, Molecular & cellular proteomics : MCP 2019 (secret)
• Two D-2-hydroxy-acid dehydrogenases in Arabidopsis thaliana with catalytic capacities to participate in the last reactions of the methylglyoxal and beta-oxidation pathways
  Engqvist, The Journal of biological chemistry 2009
  • “...vinifera (A7QE54); M. truncatula (MtAC136451_19.4); H. sapiens (Q8N465); D. rerio (A1L258); M. musculus (Q8CIM3); S. cerevisiae DLD2 (P46681); S. cerevisiae...”
• D-2-hydroxyglutarate dehydrogenase in breast carcinoma as a potent prognostic marker associated with proliferation.
  Hayashi, Histology and histopathology 2021 (PubMed)
  • GeneRIF: D-2-hydroxyglutarate dehydrogenase in breast carcinoma as a potent prognostic marker associated with proliferation.
• MYC Regulation of D2HGDH and L2HGDH Influences the Epigenome and Epitranscriptome.
  Qiu, Cell chemical biology 2020
  • GeneRIF: MYC Regulation of D2HGDH and L2HGDH Influences the Epigenome and Epitranscriptome.
• Adult diffuse glioma GWAS by molecular subtype identifies variants in D2HGDH and FAM20C.
  Eckel-Passow, Neuro-oncology 2020
  • GeneRIF: Adult diffuse glioma GWAS by molecular subtype identifies variants in D2HGDH and FAM20C.
• D-2-hydroxyglutaric aciduria Type I: Functional analysis of D2HGDH missense variants.
  Pop, Human mutation 2019
  • GeneRIF: Study presents the functional characterization of 31 D2HGDH missense variants, and the identification of 10 novel variants in a large cohort of patients with D-2-hydroxyglutaric aciduria Type I. The functional tests proved effective in classifying missense variants associated with severely impaired D-2-HGDH activity.
• Biochemical characterization of human D-2-hydroxyglutarate dehydrogenase and two disease related variants reveals the molecular cause of D-2-hydroxyglutaric aciduria.
  Toplak, Biochimica et biophysica acta. Proteins and proteomics 2019 (PubMed)
  • GeneRIF: hD2HGDH directly reduces recombinant human ETF, thus establishing a metabolic link between the oxidation of D-2-hydroxyglutarate and the mitochondrial electron transport chain.
• Recurrent cis-SAGe chimeric RNA, D2HGDH-GAL3ST2, in prostate cancer.
  Qin, Cancer letters 2016
  • GeneRIF: D2HGDH-GAL3ST2 is more frequently seen in prostate cancer samples, and seems to be enriched in African Americans.
• D2HGDH regulates alpha-ketoglutarate levels and dioxygenase function by modulating IDH2.
  Lin, Nature communications 2015
  • GeneRIF: D2HGDH elevates alpha-KG levels via IDH2 expression modulation, influencing histone and DNA methylation, and HIF1alpha hydroxylation. D2HGDH mutants found in diffuse large B-cell lymphoma are enzymatically inert.
• Mutational analysis of D2HGDH and L2HGDH in brain tumours without IDH1 or IDH2 mutations.
  Brehmer, Neuropathology and applied neurobiology 2011 (PubMed)
  • GeneRIF: We did not find evidence for mutations in the genes D2HGDH and L2HGDH as an alternative mechanism for raised 2-hydroxyglutarate levels in brain tumours
  • GeneRIF: Observational study of gene-disease association. (HuGE Navigator)
• More

BOV_RS02095 FAD-binding oxidoreductase from Brucella ovis ATCC 25840
26% identity, 91% coverage

• Mining the Flavoproteome of Brucella ovis, the Brucellosis Causing Agent in Ovis aries
  Minjárez-Sáenz, Microbiology spectrum 2022
  • “...(29) FAD-oxidase_C (PF02913) 223-463 5 1.1.-.- b Potential FAD-binding oxygen oxidoreductase (glcE?) FAD_binding_4 (PF01565) 43-180 BOV_RS02095 ABQ61939.1 FAD 3PM9 (60) FAD-oxidase_C (PF02913) 219-469 6 1.3.1.1 NADH dependent Dihydropyrimidine dehydrogenase subunit PreA DHO_dh (PF01180) 4-307 BOV_RS01510 (preA) ABQ60560.1 FMN 2B4G (24) 1GTE (37) Fer4_21 (PF14697) 340-400 2x(4Fe-4S)...”

CNAG_02664 D-lactate dehydrogenase from Cryptococcus neoformans var. grubii H99
26% identity, 84% coverage

• Identification of Multiple Cryptococcal Fungicidal Drug Targets by Combined Gene Dosing and Drug Affinity Responsive Target Stability Screening
  Park, mBio 2016
  • “...and VAL-441. (B) d -Lactate dehydrogenase (DLD) showed major interactions of bithionol with the DLD (CNAG_02664) binding pocket. There are two very strong hydrogen bonding interactions between bithionol and ASP-146 and ASP-342 on DLD. (C) Dihydrolipoyl dehydrogenase catalyzes major interactions of bithionol with the dihydrolipoyl dehydrogenase...”

VPARA_05580 FAD-binding oxidoreductase from Variovorax paradoxus
26% identity, 87% coverage

• The catabolism of 3,3'-thiodipropionic acid in Variovorax paradoxus strain TBEA6: A proteomic analysis
  Heine, PloS one 2019
  • “...been identified until now as indicated in Fig 1 . Initially, a FAD-dependent oxidoreductase Fox (VPARA_05580) was assumed to catalyze this reaction. Insertions of Tn 5 :: mob in the corresponding gene led to impaired growth of the mutants with TDP [ 2 ]. However, a...”
• The unexpected function of a Flavin-dependent oxidoreductase from Variovorax paradoxus TBEA6
  Meinert, FEMS microbiology letters 2018 (PubMed)
  • “...was assumed that the initial cleavage of TDP is catalyzed by an FAD-dependent oxidoreductase (Fox, VPARA_05580). Accordingly, fox was heterologously expressed as a thioredoxin fusion protein. Analytical size exclusion chromatography revealed a homodimeric structure and the presence of the cofactor FAD. In vitro experiments showed that...”

6lpnB / Q8N465 Crystal structure of human d-2-hydroxyglutarate dehydrogenase in apo form (see paper)
26% identity, 91% coverage

• Ligand: flavin-adenine dinucleotide (6lpnB)

D2HDH_RAT / P84850 D-2-hydroxyglutarate dehydrogenase, mitochondrial; EC 1.1.99.39 from Rattus norvegicus (Rat) (see paper)
26% identity, 85% coverage

• function: Catalyzes the oxidation of D-2-hydroxyglutarate (D-2-HG) to alpha-ketoglutarate (PubMed:15070399). Also catalyzes the oxidation of other D-2-hydroxyacids, such as D-malate (D-MAL) and D-lactate (D-LAC) (PubMed:15070399). Exhibits high activities towards D-2-HG and D-MAL but a very weak activity towards D-LAC (By similarity).
  catalytic activity: (R)-2-hydroxyglutarate + A = AH2 + 2-oxoglutarate (RHEA:38295)
  catalytic activity: (R)-malate + A = oxaloacetate + AH2 (RHEA:67460)
  cofactor: FAD

e_gw1.2.1014.1 No description from Sorghum bicolor
27% identity, 79% coverage

• Two D-2-hydroxy-acid dehydrogenases in Arabidopsis thaliana with catalytic capacities to participate in the last reactions of the methylglyoxal and beta-oxidation pathways
  Engqvist, The Journal of biological chemistry 2009
  • “...tuberosus (EL452354); Z. mays (B4FWJ7); S. bicolor (e_gw1.2.1014.1); O. sativa (Q7XI14); R. communis (B9S687); V. vinifera (A7QE54); M. truncatula...”

ZMO1008 FAD linked oxidase domain protein from Zymomonas mobilis subsp. mobilis ZM4
26% identity, 87% coverage

• Model-driven analysis of mutant fitness experiments improves genome-scale metabolic models of Zymomonas mobilis ZM4
  Ong, PLoS computational biology 2020
  • “...(isozyme) MEGS pabA Glutamine amidotransferase of anthranilate synthase ZMO0563 Chorismate-pyruvate lyase MEGS ubiC Chorismate mutase ZMO1008 Erythronate-4-phosphate dehydrogenase MEGS pdxB FAD linked oxidase domain protein ZMO1518 Histidinol phosphatase Bar-Seq Correlation N/A Inositol-monophosphatase ZMO1916 Pimeloyl-ACP methyl ester esterase MEGS bioH Conserved Hypothetical Protein E . coli knockout...”
  • “...or M9 minimal medium with 20 mM glucose ( bioH ), respectively. Plasmids that contained ZMO1008 or ZMO1916 complemented growth of the pdxB and bioH E . coli mutants, respectively. Therefore, ZMO1008 (annotated as a FAD linked oxidase domain protein) likely encodes an erythronate-4-phosphate dehydrogenase and...”

SMa0244 hypothetical protein from Sinorhizobium meliloti 1021
27% identity, 92% coverage

• Control of gluconate utilization in Sinorhizobium meliloti
  Steele, Journal of bacteriology 2009
  • “...gntR6::Tn5-110 gntR8::Tn5-110 gntR (deletion created using pJG230) SMa0244 (deletion created using pJG252) SMa0244 gntR4 SMa0247 (deletion created using pJG268)...”
  • “...gntR (primers oJG608, -609, -610, and -611) pJQ200sk, SMa0244 (primers oJG650, -651, -652, and -653) pJQ200sk, SMa0247 (primers oJG672, -673, -674, and -675)...”

Q6CL48 KLLA0F05753p from Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
27% identity, 80% coverage

• Two D-2-hydroxy-acid dehydrogenases in Arabidopsis thaliana with catalytic capacities to participate in the last reactions of the methylglyoxal and beta-oxidation pathways
  Engqvist, The Journal of biological chemistry 2009
  • “...(P46681); S. cerevisiae DLD3 (P39976); K. lactis (Q6CL48); N. crassa (Q7RYX6); P. tritici-repentis (B2WHR3); A. fulmigatus (Q4WE96); and N. fischeri (A1D092)....”

B7FZP8 D-lactate dehydrogenase from Phaeodactylum tricornutum (strain CCAP 1055/1)
28% identity, 88% coverage

• Metabolomic, proteomic and lactylated proteomic analyses indicate lactate plays important roles in maintaining energy and C:N homeostasis in Phaeodactylum tricornutum
  Huang, Biotechnology for biofuels and bioproducts 2022
  • “...0.08 28 B7GDA9 Pyruvate dehydrogenase E2 component (dihydrolipoamide acetyltransferase) 1.44 0.05 1.16 0.22 Lactate metabolism B7FZP8 D-2-hydroxyglutarate dehydrogenase 0.83 0.36 0.97 0.95 B7G085 Lactoylglutathione lyase 0.97 0.98 0.73 0.27 B7GDI1 Hydroxyacylglutathione hydrolase 1.28 0.19 1.31 0.10 B7GDI2 Sulphur dioxygenase 1.51 0.21 1.51 0.11 Light-harvesting complex 62...”

Q8CIM3 D-2-hydroxyglutarate dehydrogenase, mitochondrial from Mus musculus
26% identity, 85% coverage

• Quantitative Proteomics Reveal an Altered Pattern of Protein Expression in Brain Tissue from Mice Lacking GPR37 and GPR37L1.
  Nguyen, Journal of proteome research 2020
  • “...(Benjamini-Hochberg) Max single-sample Razor+Unique Peptide Counts DKO WT P09813 Apoa2 581% 2.73E-05 5.3% 2 3 Q8CIM3 D2hgdh 501% 5.85E-05 5.4% 5 0 Q91XF0 Pnpo 56% 1.05E-04 6.6% 4 3 Q91V76 4931406C07Rik 40% 1.53E-04 6.6% 8 8 P28665 Mug1 279% 2.42E-04 9.2% 16 7 Q00623 Apoa1 77%...”
• ITRAQ-based quantitative proteomic analysis of processed Euphorbia lathyris L. for reducing the intestinal toxicity.
  Zhang, Proteome science 2018
  • “...Ang4 1 0.5795 0.549 0.6082 Q08189 Protein-glutamine gamma-glutamyltransferase E Tgm3 Tgase3 1 0.6085 0.728 0.528 Q8CIM3 D-2-hydroxyglutarate dehydrogenase, mitochondrial D2hgdh 1 0.61 0.704 1.0195 Q9D7Z6 Calcium-activated chloride channel regulator 1 Clca1 1 0.649 0.709 0.637 O88273 Gremlin-2 (Protein related to DAN and cerberus) Prdc 1 0.6542...”
• 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
  • “...Enoyl-CoA hydratase domain-containing protein 2, mitochondrial ECHD2_MOUSE 12.84 5 0.858 0.053 0.565 0.019 0.002 34 (Q8CIM3) D-2-hydroxyglutarate dehydrogenase, mitochondrial D2HDH_MOUSE 12.15 6 0.964 0.038 0.674 0.057 0.005 30 (Q8BH86) UPF0317 protein C14orf159 homolog, mitochondrial CN159_MOUSE 3.57 3 0.975 0.069 0.702 0.064 0.027 28 (Q9CZB0) Succinate dehydrogenase...”
• Two D-2-hydroxy-acid dehydrogenases in Arabidopsis thaliana with catalytic capacities to participate in the last reactions of the methylglyoxal and beta-oxidation pathways
  Engqvist, The Journal of biological chemistry 2009
  • “...H. sapiens (Q8N465); D. rerio (A1L258); M. musculus (Q8CIM3); S. cerevisiae DLD2 (P46681); S. cerevisiae DLD3 (P39976); K. lactis (Q6CL48); N. crassa (Q7RYX6);...”

BAB1_0435 RNA-binding region RNP-1 (RNA recognition motif):FAD linked oxidase, C-terminal:FAD linked oxidase, N-terminal from Brucella melitensis biovar Abortus 2308
26% identity, 91% coverage

• Transposon Sequencing of Brucella abortus Uncovers Essential Genes for Growth In Vitro and Inside Macrophages
  Sternon, Infection and immunity 2018
  • “...BAB2_0703 BAB1_2145 BAB1_1345 Metabolism BAB2_1010 BAB1_0435 BAB1_1918 BAB1_0898 BAB1_1476 BAB1_0113 BAB1_0318 Unknown functions BAB1_1485 BAB1_1766 BAB1_0478...”
• Iron-dependent reconfiguration of the proteome underlies the intracellular lifestyle of Brucella abortus
  Roset, Scientific reports 2017
  • “...82698965 BAB1_0036 cytochrome c heme-binding site:cytochrome c, class IA/ IB CM NO 0.51 0.08 GI:82615422 BAB1_0435 FAD linked oxidase C C NO 1.37 0.03 GI:82700730 BAB1_1971 etfA electron transfer flavoprotein alpha subunit U NO 1.47 0.11 GI:82700731 BAB1_1972 etfB electron transfer flavoprotein subunit beta C NO...”

V8V93_06090 FAD-binding and (Fe-S)-binding domain-containing protein from Pseudodesulfovibrio methanolicus
26% identity, 47% coverage

• Phenotypic and Genomic Characterization of a Sulfate-Reducing Bacterium Pseudodesulfovibrio methanolicus sp. nov. Isolated from a Petroleum Reservoir in Russia
  Bidzhieva, Biology 2024
  • “...fumarate, and succinate during sulfate reduction. In the genome of the strain, the gene dld (V8V93_06090) was annotated, encoding predicted enzyme D-lactate dehydrogenase (Fe-S protein, FAD/FMN-containing dehydrogenase, EC:1.1.99.6), which catalyzes the oxidation reaction of D-lactate to pyruvate ( Figure S6 ). Pyruvate ferredoxin oxidoreductase (EC: 1.2.7.1)...”

BCAL0052 putative oxidoreductase from Burkholderia cenocepacia J2315
28% identity, 84% coverage

• Response of Burkholderia cenocepacia H111 to micro-oxia
  Pessi, PloS one 2013
  • “...of the metabolite transporter (DMT) superfamily TM nd M only Energy production and conversion CCE49315 BCAL0052 D-2-hydroxyglutarate dehydrogenase nd 15.0 CCE48192 BCAL0522 Flagellum-specific ATP synthase FliI nd A only CCE48177 BCAL0536 FerredoxinNADP(+) reductase 3.1 1.4 CCE53334 BCAL0785 Cytochrome d ubiquinol oxidase subunit I TM 3.1 6.7...”
• Reciprocal regulation by the CepIR and CciIR quorum sensing systems in Burkholderia cenocepacia
  O'Grady, BMC genomics 2009
  • “...(fold) for K56- 2cepRcciIR vs K56-2 c BCAL0051 periplasmic solute-binding protein MST2001 -2.1 2.5 NC BCAL0052 putative oxidoreductase downstream from MST2001 -2.2 2.7 NC BCAL0232 elongation factor Tu MST2002 -2.1 NC NC BCAL0340 putative lipoprotein of T6SS MST005 & MST2004 -2.8 NC NC BCAL0341 putative type...”

SCO5966 oxidase from Streptomyces coelicolor A3(2)
25% identity, 40% coverage

• Deciphering the regulon of Streptomyces coelicolor AbrC3, a positive response regulator of antibiotic production
  Rico, Applied and environmental microbiology 2014
  • “...SCO5236 SCO5330 SCO5332 SCO5632 SCO5638 SCO5691 SCO5729 SCO5912 SCO5966 SCO6273 SCO6732 SCO6820 SCO6941 SCO6951 SCO6992 SCO7077 SCO7545 2.45 2.22 5.44 4.22 2.60...”

PfGW456L13_5118 D-lactate dehydrogenase (quinone), FeS subunit (EC 1.1.5.12) from Pseudomonas fluorescens GW456-L13
25% identity, 51% coverage

• mutant phenotype: Specific phenotype: utilization of D-Lactate, Glycerol. The phenotype on glycerol is not explained (is there is a side pathway via glycerate?)

MSMEG_5045 D-2-hydroxyglutarate dehydrogenase from Mycobacterium smegmatis str. MC2 155
27% identity, 90% coverage

• Conserved Evolutionary Trajectory Can Be Perturbed to Prevent Resistance Evolution under Norfloxacin Pressure by Forcing Mycobacterium smegmatis on Alternate Evolutionary Paths
  Akanksha,, ACS infectious diseases 2024 (PubMed)
  • “...minimum inhibitory concentration (MIC). A combination of three mutations in the genes, lfrR, MSMEG_1959, and MSMEG_5045, was conserved across multiple lineages, leading to high-level resistance and preceding the appearance of drug target mutations. Interestingly, in populations evolved from parental strains lacking the lfrA efflux pump, the...”
• MadR mediates acyl CoA-dependent regulation of mycolic acid desaturation in mycobacteria
  Cooper, Proceedings of the National Academy of Sciences of the United States of America 2022
  • “...down-regulated upon madR deletion were genes encoding putative acyl-CoA dehydrogenases ( MSMEG_0323 , MSMEG_2650 , MSMEG_5045 , MSMEG_6585 , and MSMEG_6686 ). This may suggest that fatty acid -oxidation is reduced in madR cells, although mycobacterial genomes encode multiple enzymes for each step of -oxidation (...”

SMUL_0787 FAD-binding and (Fe-S)-binding domain-containing protein from Sulfurospirillum multivorans DSM 12446
25% identity, 47% coverage

• Hydrogen production by Sulfurospirillum species enables syntrophic interactions of Epsilonproteobacteria
  Kruse, Nature communications 2018
  • “...we observed a high abundance of a membrane-bound flavin and Fe-S cluster-containing protein (encoded by SMUL_0787, among the 15 highest abundant proteins in both proteomes) and lactate utilization proteins ABC (encoded by SMUL_10331035, in the top 40% abundant proteins) described to oxidize lactate in the related...”

B2WHR3 D-lactate dehydrogenase 2, mitochondrial from Pyrenophora tritici-repentis (strain Pt-1C-BFP)
27% identity, 81% coverage

• Two D-2-hydroxy-acid dehydrogenases in Arabidopsis thaliana with catalytic capacities to participate in the last reactions of the methylglyoxal and beta-oxidation pathways
  Engqvist, The Journal of biological chemistry 2009
  • “...K. lactis (Q6CL48); N. crassa (Q7RYX6); P. tritici-repentis (B2WHR3); A. fulmigatus (Q4WE96); and N. fischeri (A1D092). SEPTEMBER 11, 2009 * VOLUME 284 * NUMBER...”

Rv0161 / O07406 trans-delta20-39-hydroxy-40-methyl-C60:1-[acp] oxidoreductase from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (see paper)
Mb0166 PUTATIVE OXIDOREDUCTASE from Mycobacterium bovis AF2122/97
Rv0161 POSSIBLE OXIDOREDUCTASE from Mycobacterium tuberculosis H37Rv
26% identity, 90% coverage

• Microsatellite polymorphism across the M. tuberculosis and M. bovis genomes: implications on genome evolution and plasticity
  Sreenu, BMC genomics 2006
  • “...(833) II) Muation leading to premature termination (13) C7 8 Oxido-reductase *Rv0161 (449) MT0170 (pt) Mb0166 (449) T5 4 umaA1 *Rv0469 (286) MT0485 (pt) Mb0478 (286) G4 3 Cysteine synthase *Rv0848 (372) MT0871 (pt) Mb0871 (372) G3 2 Membrane transport *Rv0849 (419) MT0872 (pt) Mb0872 (419)...”
• Comprehensive Essentiality Analysis of the Mycobacterium tuberculosis Genome via Saturating Transposon Mutagenesis
  DeJesus, mBio 2017
  • “...sites within a window of 150 to +70 bp around the transcriptional start site for Rv0161). (N) Essentiality state assignment from the HMM of essentiality. Download TABLES2, XLSX file, 3.1 MB . Copyright 2017 DeJesus et al. 2017 DeJesus et al. This content is distributed under...”
• Mycobacterium tuberculosis Transcriptome Profiling in Mice with Genetically Different Susceptibility to Tuberculosis
  Skvortsov, Acta naturae 2013
  • “...sugB, Rv1431, Rv1667c, Rv2136c, Rv2203, efpA, rip, Rv2963, lpqF CWaCP cell wall and cell processes Rv0161, ndhA, Rv0526, menH, Rv0805, lipU, glyA1, dapE, atpF, atpH, Rv1432, frdB, cmk, plcD, lipJ, cobK, cobS, cysK1, cysE, gdh, gabT, miaA, ilvC, guaB2, cyp142, hsaD, Rv0089, Rv0331, aspC, hemA, Rv0567,...”
• Pathway to synthesis and processing of mycolic acids in Mycobacterium tuberculosis
  Takayama, Clinical microbiology reviews 2005
  • “...122, 123 41 31, 123 31, 123 39, 42 41 Rv0161 Rv0162c Rv3057c Alcohol dehydrogenaseb -- No No No No No accD4 accD5 fadD32 pks13 Rv3799c Rv3280 Rv3801c Rv3800c...”
  • “...analysis showed that an oxidoreductase/oxygenase encoded by Rv0161 is functionally linked with all methytransferases, indicating that Rv0161 is a possible...”
• CD8+-T-cell responses of Mycobacterium-infected mice to a newly identified major histocompatibility complex class I-restricted epitope shared by proteins of the ESAT-6 family
  Majlessi, Infection and immunity 2003
  • “...Proteins with unknown localizations Rv0065 Rv0127 Rv0140 Rv0161 Rv0164 Rv0393, Rv0397 RYPHSPRLI WYAGRNREL SYYSVTTDA RYRGRASAL RYASRMPVL TYVTTPGSA GYAGTLQSL c...”

MSMEG_2492 D-lactate dehydrogenase from Mycobacterium smegmatis str. MC2 155
27% identity, 44% coverage

• Protein Composition of Mycobacterium smegmatis Differs Significantly Between Active Cells and Dormant Cells With Ovoid Morphology
  Trutneva, Frontiers in microbiology 2018
  • “...lactate like in fermenting bacteria. However, fermentative lactate dehydrogenase (in contrast to FAD-dependent lactate dehydrogenase (MSMEG_2492) is not annotated in the Msm genome. LDH activity was not detected experimentally, however, NADH dependent reduction of pyruvate was observed ( Table 2 ). In this context, extracellular accumulation...”

Q72FG1 D-lactate dehydrogenase (cytochrome) from Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)
DVU0253 oxidoreductase, FAD/iron-sulfur cluster-binding domain protein from Desulfovibrio vulgaris Hildenborough
25% identity, 48% coverage

• Combining metabolic flux analysis with proteomics to shed light on the metabolic flexibility: the case of Desulfovibrio vulgaris Hildenborough.
  Marbehan, Frontiers in microbiology 2024
  • “...6 D-lactate dehydrogenase (Dld-II family) Q72F25 DVU_0390 48.2 25 51 17 D-lactate dehydrogenase (Dld-II family) Q72FG1 DVU_0253 103 88 62 52 L-lactate dehydrogenase (LldG family) Q72B57 DVU_1781 23.9 L-lactate dehydrogenase (LldH family) Q72B56 DVU_1782 52.6 4 8 4 Lactate permeases, putative Q72B55 DVU_1783 27.4 3 14...”
• Pyridoxal 5'-phosphate synthesis and salvage in Bacteria and Archaea: predicting pathway variant distributions and holes.
  Denise, Microbial genomics 2023
  • “...Fig. 5 , panel A). Desulfovibrio vulgaris str. Hildenborough encodes five paralogs, DVU0253 (UniProt ID Q72FG1), DVU0390 (UniProt ID Q72F25), DVU0827 (UniProt ID Q72DV2), DVU3027 (UniProt ID Q72659), and DVU3071 (UniProt ID Q726N5). The genes encoding DVU0827 and DVU3027 are each in an operon with a...”
  • “...DVU3027 (UniProt ID Q726S9); green node, DVU0390 (UniProt ID Q72F25); magenta node, DVU0253 (UniProt ID Q72FG1); cyan node, DVU03071 (UniProt ID Q726N5). Panel (b). Genome context () for the paralogs in Desulfovibrio vulgaris str. Hildenborough (NC_002937.3), colour coding for five paralogs conserved between the two panels....”
• Combining metabolic flux analysis with proteomics to shed light on the metabolic flexibility: the case of Desulfovibrio vulgaris Hildenborough
  Marbehan, Frontiers in microbiology 2024
  • “...) were detected with confidence ( Table 1 ). In addition, two paralogs (DVU0390 and DVU0253) of the D-LDH located in the luo operon ( Vita et al., 2015 ) and one ortholog of the L-LDH (DVU2789) from Escherichia coli ( Dong et al., 1993 )...”
• Pyridoxal 5'-phosphate synthesis and salvage in Bacteria and Archaea: predicting pathway variant distributions and holes
  Denise, Microbial genomics 2023
  • “...in Desulfovibrionales ( Fig. 5 , panel A). Desulfovibrio vulgaris str. Hildenborough encodes five paralogs, DVU0253 (UniProt ID Q72FG1), DVU0390 (UniProt ID Q72F25), DVU0827 (UniProt ID Q72DV2), DVU3027 (UniProt ID Q72659), and DVU3071 (UniProt ID Q726N5). The genes encoding DVU0827 and DVU3027 are each in an...”
  • “...panel B). DVU0390 is in an operon with genes encoding a putative amino acid transporter. DVU0253 and DVU0371 are multidomain proteins with additional FAD-binding and iron-sulphur domains. The only subgroup with relevant neighbourhood information revealed by the Gene Neighbourhood Network (GNN), was the linking of members...”
• Proteomic and Isotopic Response of Desulfovibrio vulgaris to DsrC Perturbation
  Leavitt, Frontiers in microbiology 2019
  • “...reductase-like subunit of a flavin adenine dinucleotide (FAD) oxidoreductase, was less abundant in the mutant (DVU0253, 1.39 0.05) ( Figure 6 and Supplementary Figure S5 ). FIGURE 6 Schematic representation of possible DsrC interacting proteins and their arrangement according to each gene cluster. These proteins belong...”
• The primary pathway for lactate oxidation in Desulfovibrio vulgaris
  Vita, Frontiers in microbiology 2015
  • “...into several groups ( Table 4 ). The first group included DVU0826-27, DVU3071, DVU0390, and DVU0253, which are paralogs of DVU3027-28 in the Dld-II family. The second group included DVU1781-82-83, which is a paralog of DVU3032-33 in the LldEFG family. A schematic representation of these Dld-II...”
  • “...putative (0827) DVU3071 Oxidoreductase, FAD/iron-sulfur cluster-binding domain protein DVU0390 Glycolate oxidase, subunit GlcD, putative Dld-II DVU0253 Oxidoreductase, FAD/iron-sulfur cluster-binding domain protein L -lactate dehydrogenase DVU3032-33 Conserved hypothetical protein (3032) Iron-sulfur cluster-binding protein (3033) LldEFG DVU1781-83 Conserved hypothetical protein (1781) Iron-sulfur cluster-binding protein (1782) Cysteine-rich domain protein...”
• Characterization of NaCl tolerance in Desulfovibrio vulgaris Hildenborough through experimental evolution
  Zhou, The ISME journal 2013
  • “...ES DVU Nos. DVU3107 DVU0624 DVU0625 DVU0702 DVU1817 DVU0253 DVU2645 DVU2103 DVU2104 DVU0531 DVU0532 DVU0533 DVU0534 DVU0535 DVU0536 DVU0305 (fd II) DVU0384...”
• Temporal transcriptomic analysis as Desulfovibrio vulgaris Hildenborough transitions into stationary phase during electron donor depletion
  Clark, Applied and environmental microbiology 2006
  • “...as putative lactate dehydrogenase genes (DVU0600, DVU2784, and DVU0253) in the D. vulgaris genome. The levels of two of these genes were elevated during...”

Dhaf_3228 D-lactate dehydrogenase (cytochrome) from Desulfitobacterium hafniense DCB-2
24% identity, 45% coverage

• Genome sequence of Desulfitobacterium hafniense DCB-2, a Gram-positive anaerobe capable of dehalogenation and metal reduction
  Kim, BMC microbiology 2012
  • “...Dhaf_1622, Dhaf_3294. 3 . pyruvate, phosphate dikinase; Dhaf_1046, Dhaf_4240, Dhaf_4251. 4 . D-lactate dehydrogenase (cytochrome); Dhaf_3228, Dhaf_4382. 5 . L-lactate dehydrogenase; Dhaf_1965. 6 . PEP carboxykinase; Dhaf_1134. 7 . malate dehydrogenase (NADP + ); Dhaf_0902, Dhaf_3085. 8 . pyruvate carboxyltransferase; Dhaf_1012, Dhaf_1059. 9 . pyruvate formate-lyase;...”

PA14_63100 putative ferredoxin from Pseudomonas aeruginosa UCBPP-PA14
25% identity, 48% coverage

• Transcriptional profiling of Pseudomonas aeruginosa and Staphylococcus aureus during in vitro co-culture
  Tognon, BMC genomics 2019
  • “...second lactate dehydrogenase operon including lldD , the adjacent lldP lactate permease gene (3-fold) and PA14_63100 coding for a cytochrome type lactate dehydrogenase (Table 3 and Additionalfile 4 : Table S2), strongly suggests that P. aeruginosa takes up lactate secreted by S. aureus to use it...”
  • “...RNA RNA synthesis/modif. PA14_62060 5.05 23S ribosomal RNA RNA synthesis/modif. PA14_61830 4.88 tRNA-Met RNA synthesis/modif. PA14_63100 4.38 cytochrome type D-lactate DH (4Fe-4S) metabolism narK1 3.95 nitrite extrusion protein I transport PA14_24780 3.87 Amoonium transporter transport lldD 3.64 L-lactate dehydrogenase metabolism PA14_60150 3.26 tRNA-Lys RNA synthesis/modif. popN...”
• The Pseudomonas aeruginosa Complement of Lactate Dehydrogenases Enables Use of d- and l-Lactate and Metabolic Cross-Feeding
  Lin, mBio 2018
  • “...lactate dehydrogenases. PA14 contains four genes with the following annotation: ldhA (PA14_52270), lldD (PA14_63090), lldE (PA14_63100), and lldA (PA14_33860) ( Fig.1 ). ldhA encodes a lactate dehydrogenase that reduces pyruvate to lactate during anaerobic pyruvate fermentation ( 7 ) ( Fig.1 ). According to computational prediction...”

Q726N5 Oxidoreductase, FAD/iron-sulfur cluster-binding domain protein from Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)
DVU3071 oxidoreductase, FAD/iron-sulfur cluster-binding domain protein from Desulfovibrio vulgaris Hildenborough
27% identity, 30% coverage

• Pyridoxal 5'-phosphate synthesis and salvage in Bacteria and Archaea: predicting pathway variant distributions and holes.
  Denise, Microbial genomics 2023
  • “...(UniProt ID Q72F25), DVU0827 (UniProt ID Q72DV2), DVU3027 (UniProt ID Q72659), and DVU3071 (UniProt ID Q726N5). The genes encoding DVU0827 and DVU3027 are each in an operon with a gene encoding their iron-sulphur subunits, DVU0826, and DVU3028, respectively ( Fig. 5 , panel B). DVU0390 is...”
  • “...DVU0390 (UniProt ID Q72F25); magenta node, DVU0253 (UniProt ID Q72FG1); cyan node, DVU03071 (UniProt ID Q726N5). Panel (b). Genome context () for the paralogs in Desulfovibrio vulgaris str. Hildenborough (NC_002937.3), colour coding for five paralogs conserved between the two panels. AA_Transporter_ATP, Amino Acid ABC transporter ATPase...”
• Pyridoxal 5'-phosphate synthesis and salvage in Bacteria and Archaea: predicting pathway variant distributions and holes
  Denise, Microbial genomics 2023
  • “...ID Q72FG1), DVU0390 (UniProt ID Q72F25), DVU0827 (UniProt ID Q72DV2), DVU3027 (UniProt ID Q72659), and DVU3071 (UniProt ID Q726N5). The genes encoding DVU0827 and DVU3027 are each in an operon with a gene encoding their iron-sulphur subunits, DVU0826, and DVU3028, respectively ( Fig. 5 , panel...”
• The primary pathway for lactate oxidation in Desulfovibrio vulgaris
  Vita, Frontiers in microbiology 2015
  • “...classify these orthologs into several groups ( Table 4 ). The first group included DVU0826-27, DVU3071, DVU0390, and DVU0253, which are paralogs of DVU3027-28 in the Dld-II family. The second group included DVU1781-82-83, which is a paralog of DVU3032-33 in the LldEFG family. A schematic representation...”
  • “...protein (3028) DVU0826-27 Glycolate oxidase, iron-sulfur subunit, putative (0826) Glycolate oxidase, subunit GlcD, putative (0827) DVU3071 Oxidoreductase, FAD/iron-sulfur cluster-binding domain protein DVU0390 Glycolate oxidase, subunit GlcD, putative Dld-II DVU0253 Oxidoreductase, FAD/iron-sulfur cluster-binding domain protein L -lactate dehydrogenase DVU3032-33 Conserved hypothetical protein (3032) Iron-sulfur cluster-binding protein (3033)...”
• Identification of key components in the energy metabolism of the hyperthermophilic sulfate-reducing archaeon Archaeoglobus fulgidus by transcriptome analyses
  Hocking, Frontiers in microbiology 2014
  • “...AF0809, may facilitate a multimeric complex that functions as monomeric homologs encoded in other species (Dvu3071, Figures 3 , 5 ). The presence of a gene cluster with identical arrangement in the lactate utilizing A. sulfaticallidus and A. fulgidus , supports a potential role of the...”

Q88DT2 D-2-hydroxyacid dehydrogenase (quinone) (EC 1.1.5.10); D-lactate dehydrogenase (quinone) (EC 1.1.5.12) from Pseudomonas putida (see paper)
PP4737, PP_4737 D-lactate dehydrogenase, putative from Pseudomonas putida KT2440
24% identity, 48% coverage

• Fatty Acid and Alcohol Metabolism in Pseudomonas putida: Functional Analysis Using Random Barcode Transposon Sequencing
  Thompson, Applied and environmental microbiology 2020 (secret)
• FinR Regulates Expression of nicC and nicX Operons, Involved in Nicotinic Acid Degradation in Pseudomonas putida KT2440
  Xiao, Applied and environmental microbiology 2018
  • “...PP_4434 PP_4435 PP_4548 PP_4625 PP_4626 PP_4735 PP_4736 PP_4737 PP_5029 PP_5030 PP_5031 PP_5032 PP_5033 PP_5036 PP_5073 PP_5269 PP_5270 PP_5338 PP_5549 Log2...”
• A Bacterial Multidomain NAD-Independent d-Lactate Dehydrogenase Utilizes Flavin Adenine Dinucleotide and Fe-S Clusters as Cofactors and Quinone as an Electron Acceptor for d-Lactate Oxidization
  Jiang, Journal of bacteriology 2017
  • “...analysis of Fe-S D-iLDH. The Fe-S D-iLDH-encoding gene lldE (pp4737) is located in the four-gene lactate utilization operon pp4734 to pp4737 in the P. putida...”
• The metabolic response of P. putida KT2442 producing high levels of polyhydroxyalkanoate under single- and multiple-nutrient-limited growth: highlights from a multi-level omics approach
  Poblete-Castro, Microbial cell factories 2012
  • “...regulatory protein -3.4 -3.6 PP2149 Glyceraldehyde 3-phospate dehydrogenase 1.5 -3.7 PP4715 Triosephosphate isomerase 1.9 -3.3 PP4737 D-lactate dehydrogenase putative -2.6* -3.1 PP0545 Aldehyde dehydrogenase family protein -1.9 -3.1 PP1083 Bacterioferritin-associated ferredoxin putative 1.4 2.9 PP3071 Acetoacetyl-CoA synthetase putative 1.1 -2.6 PP4736 L- lactate dehydrogenase -1.1 -2.5...”

ADAS_DICDI / O96759 Alkyldihydroxyacetonephosphate synthase; Alkyl-DHAP synthase; Alkylglycerone-phosphate synthase; EC 2.5.1.26 from Dictyostelium discoideum (Social amoeba) (see paper)
O96759 alkylglycerone-phosphate synthase (EC 2.5.1.26) from Dictyostelium discoideum (see paper)
21% identity, 69% coverage

• function: Catalyzes the exchange of an acyl for a long-chain alkyl group and the formation of the ether bond in the biosynthesis of ether phospholipids.
  catalytic activity: a long chain fatty alcohol + a 1-acylglycerone 3-phosphate = a 1-O-alkylglycerone 3-phosphate + a long-chain fatty acid + H(+) (RHEA:36171)
  cofactor: FAD
  subunit: Homodimer.

PA4772 probable ferredoxin from Pseudomonas aeruginosa PAO1
25% identity, 48% coverage

• The Effects of Sub-inhibitory Antibiotic Concentrations on Pseudomonas aeruginosa: Reduced Susceptibility Due to Mutations
  Ramsay, Frontiers in microbiology 2021
  • “...1.0 DUN-036-1 Ceftazidime 1 1.5 Ciprofloxacin 1 1.0 Meropenem 1 ^ 6.3 PA2441 (P233H (CCCCAC); PA4772 (+1bp, bp 6) Tobramycin 1 2.0 * Fold change of MIC over time; Average value of up to three Etest replicates. ^ Etest performed in replicate. # Etest performed in...”
• The AraC-Type Transcriptional Regulator GliR (PA3027) Activates Genes of Glycerolipid Metabolism in Pseudomonas aeruginosa
  Kotecka, International journal of molecular sciences 2021
  • “...kinase/response regulator 19 intra 25,030 PA4610 3.03 2.56 5,276,490 HUU copper transporter 20 term 26,025 PA4772 1.83 3.09 5,480,812 EM FAD-binding oxidoreductase 21 intra 28,310 PA5208 3.54 3.28 5,982,827 HUU TIGR00153 family protein 22 intra 28,490 PA5243 1.56 3.49 6,024,153 BCPGC porphobilinogen synthase 23 prom 28,760...”
• Structural and Molecular Mechanism of CdpR Involved in Quorum-Sensing and Bacterial Virulence in Pseudomonas aeruginosa
  Zhao, PLoS biology 2016
  • “...binds to some selected target regions in vitro. The chosen promoter regions (for opdC , PA4772 , PA4087 , PA0440 , PA3388 , cysG , recC , pscC , PA5146 , and PA1271valS , PA0159 , PA4541 , selB , serS , PA3992 , PA5114 ,...”
• Dissection of the cis-2-decenoic acid signaling network in Pseudomonas aeruginosa using microarray technique
  Rahmani-Badi, Frontiers in microbiology 2015
  • “...rubB napCF, nuoD, aer, ubiA, ercS, norD, etfB, hemE, PA0510, PA0516, PA0918, PA1779, PA3025, PA3491, PA4772, PA5491 Bacteriophage production PA0616-PA0623, PA0627, PA063 Tricarboxylic acid (TCA) cycle fumC1, acnA N -AHLs and PQS QS-dependent genes and Virulence lasIR, rhlI, qscR, rsaL, vfr, pqsR (mvfR), pchR, gacA,pqsBCDEH, antAB,...”
• Protein-to-mRNA ratios are conserved between Pseudomonas aeruginosa strains
  Kwon, Journal of proteome research 2014
  • “...binding protein component of ABC transporter PA4771| lldD 10.5 29.6 709.5 1772.5 l -lactate dehydrogenase PA4772 0.7 10.8 933.5 2008.0 probable ferredoxin PA4778 0.0 9.7 266.5 1392.5 probable transcriptional regulator PA5261| algR 6.6 1.1 207.0 100.0 alginate biosynthesis regulatory protein AlgR PA5289 5.0 0.0 655.0 190.5...”
• Transcriptome profiling defines a novel regulon modulated by the LysR-type transcriptional regulator MexT in Pseudomonas aeruginosa
  Tian, Nucleic acids research 2009
  • “...protein PA4770 lldP 43 46 l -lactate permease PA4771 lldD 28 70 l -lactate dehydrogenase PA4772 7.0 19 Probable ferredoxin PA4881 751 <2 Hypothetical protein a Gene number from the Pseudomonas Genome Project ( http://www.pseudomonas.com ). b Fold change in gene expression of PAO1 (pME6032- mexT...”
• Cystic fibrosis sputum supports growth and cues key aspects of Pseudomonas aeruginosa physiology
  Palmer, Journal of bacteriology 2005
  • “...PA4231 PA4471 PA4498 PA4514 PA4570 PA4633 PA4770 PA4771 PA4772 PA4811 PA4834 PA4835 PA4836 PA4837 PA4838 PA4929 PA5303 PA5532 PA5534 PA5535 PA5536 PA5538 PA5539...”

PST_3340 D-lactate dehydrogenase, putative from Pseudomonas stutzeri A1501
24% identity, 47% coverage

• Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea
  Pfeiffer, Genes 2021
  • “...probably 33% PST_3339 O4VPR7 [ 317 ] 25917905 partial match 9f HVO_1697 - unclear 24% PST_3340 O4VPR8 [ 317 ] 25917905 9f HVO_1696 lctP probably 44% PST_3336 O4VPR4 [ 317 ] 25917905 9g HVO_B0300 pucL1 yes 49% BSU32450 O32141 [ 318 ] 20168977 Bacillus : bifunctional,...”

MAP2004 hypothetical protein from Mycobacterium avium subsp. paratuberculosis str. k10
27% identity, 80% coverage

• Key role for the alternative sigma factor, SigH, in the intracellular life of Mycobacterium avium subsp. paratuberculosis during macrophage stress
  Ghosh, Infection and immunity 2013
  • “...MAP2175c MAP2642 MAP3763c MAP2174c MAP2178 MAP3740 MAP3764c MAP2004 MAP2873c MAP1555c Rv0215c Rv3504 Rv1193 Rv2486 Rv1136 Rv3556c Rv1346 Rv1345 Rv2382c Rv1665...”

I3LDY5 D-lactate dehydrogenase (cytochrome) from Sus scrofa
26% identity, 51% coverage

• Metabolomics and proteomics insights into hepatic responses of weaned piglets to dietary Spirulina inclusion and lysozyme supplementation
  Martins, BMC veterinary research 2024
  • “...1 1 0.0159 -0.4588 A0A0B8RTA8 Acyl-CoA dehydrogenase, very long chain ACADVL 3 1 0.0212 -0.4541 I3LDY5 Lactate dehydrogenase D LDHD 1 2 0.0317 -0.4457 F1RMV5 ETHE1, persulfide dioxygenase ETHE1 1 2 0.0317 -0.4449 F1SCF0 Alpha-1-antitrypsin SERPINA1 3 2 0.0159 -0.4410 F1SMW9 Proteasome 26S subunit, non-ATPase 1...”

Dde_3604 FAD-binding and (Fe-S)-binding domain-containing protein from Oleidesulfovibrio alaskensis G20
Dde_3604 Oxidoreductase/iron-sulfur cluster-binding protein from Desulfovibrio desulfuricans G20
24% identity, 47% coverage

• Influence of Copper on Oleidesulfovibrio alaskensis G20 Biofilm Formation
  Thakur, Microorganisms 2024
  • “...energy to support cell growth through anaerobic respiration. In addition, lactate dehydrogenases ( ldh , Dde_3604) had the highest expression level (log2FC = 2.642) in 15 M-biofilm samples. Ldh allow Desulfovibrio sp. to maintain energy balance and metabolic flexibility, enabling the bacteria to adapt to the...”
• Integration of text mining and biological network analysis: Identification of essential genes in sulfate-reducing bacteria
  Saxena, Frontiers in microbiology 2023
  • “...(shown in Figure 4A ). The enriched genes (dde_0276, dde_0528, dde_1112, dde_1258, dde_2115, dde_2271, dde_3081, dde_3604, cysQ , and sucD ) were not only unconstrained to sulfate metabolism but a strong network to three other pathways- cysteine and methionine metabolism, selenocompound metabolism, and secondary metabolite synthesis...”
  • “...dde_1109, dde_1110, dde_0527, dde_0526, dde_2271, dde_3081, dde_1112, dde_2115, dde_2265, dde_3080, and dde_0528 dde_1789, sucD , dde_3604, and, dde_1258 dde_0123, dde_0276 12 4 2 18 Ribosome synthesis rpsM, rpsE, rpsD, fbp, rpsR, rpsK, bamD, rpmJ, rplO, rplQ, rpmD, rplS, rpsP, rplF, polA, rplR, rpsH, secY, tsaD, rplI,...”
• Shotgun proteomic analysis of nanoparticle-synthesizing Desulfovibrio alaskensis in response to platinum and palladium
  Capeness, Microbiology (Reading, England) 2019
  • “...membrane-bound oxidoreductase 0.64 Dde_3240 Protein of unknown function DUF224 0.55 Dde_1633 Gamma-glutamyl phosphate reductase 0.55 Dde_3604 d -lactate dehydrogenase (cytochrome) 0.65 Dde_2272 Hdr menaquinol oxidoreductase 0.56 Dde_2979 Carbonic anhydrase 0.57 Dde_2201 Polyprenyl synthetase 0.65 Dde_0990 H + transporting two-sector ATPase B/B' subunit 0.56 Dde_3520 Molybdate-transporting ATPase...”
• Flexibility of syntrophic enzyme systems in Desulfovibrio species ensures their adaptation capability to environmental changes
  Meyer, Journal of bacteriology 2013
  • “.../ / / / Dde_0750 / / / / Dde_3604 Dde_0182 Dde_1681 / / / / / / / / / Dde_1842-Dde_1844 Dde_3239-Dde_3240 Dde_1085-Dde_1087 Dde_3241 Dde_3242 Dde_1273...”

AAY72_06850 FAD-binding and (Fe-S)-binding domain-containing protein from Alishewanella sp. WH16-1
23% identity, 51% coverage

• Identification of a Novel Chromate and Selenite Reductase FesR in Alishewanella sp. WH16-1
  Zhou, Frontiers in microbiology 2022
  • “...distribution or reproduction is permitted which does not comply with these terms. A ferredoxin protein (AAY72_06850, named FesR) was identified to associate with chromate [Cr(VI)] resistance in Alishewanella sp. WH16-1. FesR and its similar proteins were phylogenetically separated from other reductase families. Unlike the reported Cr(VI)...”
  • “...gene was identified by Tn 5 transposon mutagenesis, and the accession number of FesR was AAY72_06850 . In this study, we comprehensively analyzed the Cr(VI) and Se(IV) reduction mechanism of FesR. Materials and Methods Bacterial Strains and Growth Condition The strains and plasmids used in this...”
• The Cytochrome bd Complex Is Essential for Chromate and Sulfide Resistance and Is Regulated by a GbsR-Type Regulator, CydE, in Alishewanella Sp. WH16-1
  Xia, Frontiers in microbiology 2018
  • “...S 2- can be used for FeS cluster synthesis. A potential Cr(VI) reductase (4Fe4S ferredoxin, AAY72_06850) was also identified by the Tn 5 transposon mutagenesis in this study. Previously, ferredoxin and hydrogenase, which contain the FeS cluster as the active group, were reported to be associated...”

Dde_0312 Oxidoreductase, putative from Desulfovibrio desulfuricans G20
37% identity, 16% coverage

• New model for electron flow for sulfate reduction in Desulfovibrio alaskensis G20
  Keller, Applied and environmental microbiology 2014
  • “...G20 abundance Log2 R (I2/G20) Ab Dde_0182 Dde_0312 Dde_0750 Dde_1087 Dde_3238 Dde_3239 Dde_3240 GlcD COG-GlcD LdlD COG-GlcD LldP GlcD LdhB (S)-2-Hydroxy...”
• Flexibility of syntrophic enzyme systems in Desulfovibrio species ensures their adaptation capability to environmental changes
  Meyer, Journal of bacteriology 2013
  • “...pair) Gene locus tag(s) Dde_1207-Dde_1213 Dde_3523-Dde_3530 Dde_3245 Dde_0312 Dde_3540 M. maripaludis M. hungatei M. maripaludis M. hungatei Mutant growth c 1...”
  • “...results of mutants for the uncharacterized HdrD homologue, Dde_0312 (additional FAD group containing), and the NADH oxidase, Nox. In association, both proteins...”

VPARA_27740 FAD-binding oxidoreductase from Variovorax paradoxus
26% identity, 91% coverage

• The catabolism of 3,3'-thiodipropionic acid in Variovorax paradoxus strain TBEA6: A proteomic analysis
  Heine, PloS one 2019
  • “...with TDP as the only carbon source. Deletion mutants lacking VPARA_05540, VPARA_05550, VPARA_21730, VPARA_24900, or VPARA_27740 showed no change in growth with TDP (not shown). Still, they might be involved in the general sulfur metabolism (e. g. amino acid biosynthesis, detoxification) due the high abundance of...”
  • “...Fig 3 ) to important genes of the TDP metabolism. For the other genes (VPARA_21730, VPARA_27740, VPARA_27760), no connections to the TDP catabolism were identified. Enoyl-CoA hydratases (VPARA_05520, VPARA_05530) and a crotonase family protein (VPARA_05510) Ech-20 and Ech-30 were of special interest, as they seemed to...”

YN53_SCHPO / Q9C1X2 Putative D-lactate dehydrogenase C713.03, mitochondrial; EC 1.1.2.4 from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) (see paper)
24% identity, 83% coverage

• catalytic activity: (R)-lactate + 2 Fe(III)-[cytochrome c] = 2 Fe(II)-[cytochrome c] + pyruvate + 2 H(+) (RHEA:13521)
  cofactor: FAD

BCAS0201 putative FAD dependent oxidoreductase from Burkholderia cenocepacia J2315
29% identity, 86% coverage

• Role of Burkholderia cenocepacia afcE and afcF genes in determining lipid-metabolism-associated phenotypes
  Subramoni, Microbiology (Reading, England) 2013 (PubMed)
  • “...regulator, and ShvR-regulated genes BCAS0208 and BCAS0201 (designated afcE and afcF, respectively) affect colony morphotype, biofilm and pellicle...”
  • “...Tpr K56-2 with pGSVTp-luxCDABE inserted in BCAS0204; Tpr BCAS0201 : : lux, K56-2 with pGSVTp-luxCDABE inserted in BCAS0201; Tpr Spontaneous shv morphotype...”
• Burkholderia cenocepacia ShvR-regulated genes that influence colony morphology, biofilm formation, and virulence
  Subramoni, Infection and immunity 2011
  • “...containing a mutation in the catalytic site. BCAS0201, encoding a putative flavin adenine dinucleotide (FAD)-dependent oxidoreductase, and BCAS0207, encoding a...”
  • “...of biofilm formation and virulence. Both BCAS0208 and BCAS0201 contribute to pellicle formation, although individual mutations in each of these genes had no...”

VCA0985 oxidoreductase/iron-sulfur cluster-binding protein from Vibrio cholerae O1 biovar eltor str. N16961
25% identity, 43% coverage

• Regulatory Effects of CsrA in Vibrio cholerae
  Butz, mBio 2021
  • “...iron-containing proteins, such as ferritin (VC0078), ferredoxin (VC0311), and iron-sulfur cluster-containing proteins (VC1512, VC2088, and VCA0985), were repressed. This suggests that CsrA may be critical for restricting the influx of free, unchelated iron during stationary phase growth, while sequestering any excess intracellular iron. Another significantly overrepresented...”
• Transcriptomics reveals a cross-modulatory effect between riboflavin and iron and outlines responses to riboflavin biosynthesis and uptake in Vibrio cholerae
  Sepúlveda-Cisternas, Scientific reports 2018
  • “...1.135 VCA0968 hypothetical protein 1.527 1.190 VCA0979 methyl-accepting chemotaxis protein 1.006 VCA0981 hypothetical protein 1.008 VCA0985 oxidoreductase/iron-sulfur cluster-binding protein 1.381 VCA0988 methyl-accepting chemotaxis protein 1.119 VCA1006 organic hydroperoxide resistance protein putative 1.130 VCA1007 hypothetical protein 1.064 VCA1009 hypothetical protein 1.260 VCA1010 conserved hypothetical protein 3.403 VCA1014...”
• Genes induced late in infection increase fitness of Vibrio cholerae after release into the environment
  Schild, Cell host & microbe 2007
  • “...family 3.0 7.6 10.1 17.3 5.8 1.7 2.3 VCA0985 VCA09845 oxidoreductase-iron-sulfur cluster-binding protein 13.0 22.3 43.3 88.0 6.7 2.0 3.9 Early infection-induced...”

HVO_1697 FAD-linked oxidase domain protein from Haloferax volcanii DS2
32% identity, 18% coverage

• Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea
  Pfeiffer, Genes 2021
  • “...19201793 9f HVO_1693 (cont.) probably 33% PST_3339 O4VPR7 [ 317 ] 25917905 partial match 9f HVO_1697 - unclear 24% PST_3340 O4VPR8 [ 317 ] 25917905 9f HVO_1696 lctP probably 44% PST_3336 O4VPR4 [ 317 ] 25917905 9g HVO_B0300 pucL1 yes 49% BSU32450 O32141 [ 318 ]...”
• Splicing Endonuclease Is an Important Player in rRNA and tRNA Maturation in Archaea
  Schwarz, Frontiers in microbiology 2020
  • “...IucD HVO_B0045 4.5 Diaminobutyrate decarboxylase HVO_1228 4.2 DUF5059 domain HVO_B0043 4.1 Probable N4-hydroxy-1-aminopropane O-acetyltransferase, IucB HVO_1697 4.1 FAD-dependent oxidoreductase (GlcD/DLD_GlcF/GlpC domain fusion protein) HVO_B0047 4.0 ABC-type transport system periplasmic substrate-binding protein (probable substrate iron-III) HVO_B0046 3.9 Diaminobutyrate decarboxylase diaminobutyrate-2-oxoglutarate aminotransferase HVO_B0197 3.8 ABC-type transport system periplasmic...”
  • “...This gene is encoded in a bicistronic operon together with the gene for FAD-dependent oxidoreductase (HVO_1697), which is also up-regulated. Six of the most up-regulated genes are located in a cluster on pHV3 (HVO_B0042-HVO_B0047) and are related to iron metabolism. Altogether, 11 transport related proteins and...”

DFE_3147 FAD-binding and (Fe-S)-binding domain-containing protein from Desulfovibrio ferrophilus
25% identity, 46% coverage

• Proteomic study of Desulfovibrio ferrophilus IS5 reveals overexpressed extracellular multi-heme cytochrome associated with severe microbiologically influenced corrosion
  Chatterjee, Scientific reports 2021
  • “...biosynthesis of lipid A DFE_2738 Uncharacterized protein 2.1 0.049 Unknown Yes, Lipoprotein signal peptide (Sec/SPII) DFE_3147 Oxidoreductase, FAD/4Fe-4S ferredoxin-binding protein 2.1 0.034 Electron transfer DFE_2290 Uncharacterized protein 2.1 0.035 Unknown DFE_3364 4Fe-4S ferredoxin 1.6 0.069 Electron transfer Yes, TAT signal peptide DFE_3267 Putative redox-active protein (C_GCAxxG_C_C...”

HFX_1789 FAD-binding and (Fe-S)-binding domain-containing protein from Haloferax mediterranei ATCC 33500
31% identity, 19% coverage

• Small RNAs of Haloferax mediterranei: Identification and Potential Involvement in Nitrogen Metabolism
  Payá, Genes 2018
  • “...-Value p -adj HM16_M CHR - 2661497-2661554 57 Intergenic HFX_1537 , pgk, HFX_1505 , trkA, HFX_1789 8.6985 5.05 10 259 8.09 10 258 HM7_S CHR + 2620188-2620373 185 Intergenic HFX_0627 , acnA, HFX_1005 , arsR, HFX_3006 1.7547 1.29 10 24 1.03 10 23 HM52_V CHR -...”

AT730_01475 FAD-binding and (Fe-S)-binding domain-containing protein from Vibrio alginolyticus
22% identity, 44% coverage

• Exogenous maltose enhances Zebrafish immunity to levofloxacin-resistant Vibrio alginolyticus
  Jiang, Microbial biotechnology 2020
  • “...S1 ) identified eight mutations, five of which occurred in the following gene coding regions: AT730_01475 , aceF , cpxP , cpxA and gyrB . Of these, gyrB is the only gene previously associated with fluoroquinolone resistance (Tables S1 and S2 ). While cpxP harbours a...”
  • “...Raivio et al. , 2013 ; Zhang et al. , 2019 ). The functions of AT730_01475 and aceF in antibiotic resistance have not yet been elucidated. Fig. 1 Zebrafish response to LevR. A. The MIC of levofloxacinsensitive V.alginolyticus (LevS) and levofloxacinresistant bacteria (LevR). 0.125g levofloxacin, which...”

CCO0259 probable oxidoreductase Cj1585c from Campylobacter coli RM2228
22% identity, 46% coverage

• Differences in the Transcriptomic Response of Campylobacter coli and Campylobacter lari to Heat Stress
  Riedel, Frontiers in microbiology 2020
  • “...Category Up-regulated Down-regulated Energy production and conversion aspA , cydA , hydA2 , ldh , CCO0259, CCO0482, CCO1660 fliI Amino acid transport and metabolism bisZ , dapA , glnA , hisH , potA , proB , serB , CCO1002, CCO1668 ilvE , proC , CCO0338, CCO0845,...”

Rmet_5443 FAD-binding oxidoreductase from Cupriavidus metallidurans CH34
25% identity, 78% coverage

• Adaptation of Cupriavidus metallidurans CH34 to Toxic Zinc Concentrations Involves an Uncharacterized ABC-Type Transporter
  Van, Microorganisms 2021
  • “...coding for a putative glycerol uptake operon antiterminator regulatory protein (Rmet_5442), a putative akylglycerone-phosphate synthase (Rmet_5443), and a Major Facilitator Superfamily (MFS) transporter (Rmet_5446). However, none of the genes in this second glp locus are differentially expressed in CH34 ZnR . Furthermore, as glycerol can still...”

YP_002344954 oxidoreductase from Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819
Cj1585c putative oxidoreductase from Campylobacter jejuni subsp. jejuni NCTC 11168
21% identity, 46% coverage

• Two respiratory enzyme systems in Campylobacter jejuni NCTC 11168 contribute to growth on L-lactate.
  Thomas, Environmental microbiology 2011 (PubMed)
  • GeneRIF: A cj0075c cj1585c double mutant showed no L-lactate oxidase activity and did not utilize or grow on L-lactate; D-lactate-dependent growth was unaffected.
• Phylogenetic Association and Genetic Factors in Cold Stress Tolerance in Campylobacter jejuni
  Hur, Microbiology spectrum 2022
  • “...domain-containing protein cj1420c Class I SAM-dependent methyltransferase Energy production and conversion cj0490 ald Aldehyde dehydrogenase cj1585c FAD-binding oxidoreductase Nucleotide transport and metabolism cj0766 Pseudogene Putative arylsulfate sulfotransferase cj0381c pyrF Orotidine-5-phosphate decarboxylase General function prediction only cj0054c TIGR00730 family Rossman fold protein cj1555c NAD(P)-dependent oxidoreductase Lipid transport...”
• A Genome-Wide Association Study to Identify Diagnostic Markers for Human Pathogenic Campylobacter jejuni Strains
  Buchanan, Frontiers in microbiology 2017
  • “...1.21E-15 Cj1255 Putative isomerase 11168_01309 5.30E-15 1.04E-11 Cj1365c Putative secreted serine protease 11168_01519 4.29E-10 8.39E-07 Cj1585c Putative oxidoreductase 11168_01610 4.29E-10 8.38E-07 Cj1679 Hypothetical protein 06_2866_00597 6.89E-28 1.36E-24 Di-/tripeptide transporter 06_7515_00723 4.19E-16 8.24E-13 Prophage Lp2 protein 6 07_0675_00227 2.62E-11 5.15E-08 tetO Elongation factor G 1 p -value...”
• A Bacterial Multidomain NAD-Independent d-Lactate Dehydrogenase Utilizes Flavin Adenine Dinucleotide and Fe-S Clusters as Cofactors and Quinone as an Electron Acceptor for d-Lactate Oxidization
  Jiang, Journal of bacteriology 2017
  • “...respectively, while the purified enzyme from C. jejuni (Cj1585c) exhibited higher activity with D-lactate than with L-lactate (17, 18). In the case of P....”
  • “...purified Fe-S D-iLDH. In accordance with the results using Cj1585c, Fe-S D-iLDH from P. putida KT2440 exhibits activity with both D- and L-lactate, although the...”
• [Multilocus Sequence Typing analysis of human Campylobacter coli in Granada (Spain)]
  Carrillo-Ávila, Revista espanola de quimioterapia : publicacion oficial de la Sociedad Espanola de Quimioterapia 2016 (PubMed)
  • “...strains of Campylobacter coli. Nineteen genetic markers were amplified for MLST analysis: AnsB, DmsA, ggt, Cj1585c, CJJ81176-1367/1371, Tlp7, cj1321-cj1326, fucP, cj0178, cj0755/cfrA, ceuE, pldA, cstII, cstIII. After comparing the obtained sequences with the Campylobacter MLST database, the allele numbers, sequence types (STs) and clonal complexes (CCs)...”
• Genomic insights from whole genome sequencing of four clonal outbreak Campylobacter jejuni assessed within the global C. jejuni population
  Clark, BMC genomics 2016
  • “...A A G secreted serine protease Cj1365c 1515973 A A A A C D-lactate dehydrogenase Cj1585c 1630514 C C C C T 2-isopropylmalate synthase Cj1719c Fig. 3 Phylogenetic tree of C. jejuni sequenced in this study compared with publicly available C. jejuni . The tree was...”
• Defining the metabolic requirements for the growth and colonization capacity of Campylobacter jejuni
  Hofreuter, Frontiers in cellular and infection microbiology 2014
  • “...respective mutants with lactate (Thomas et al., 2011 ). However, a second L-iLDH, the oxidoreductase Cj1585c, was identified and demonstrated to be responsible for the observed redundancy in the catabolism of L-lactate. Only a double mutation inactivating cj0075c and cj1585c abolished the growth of C. jejuni...”
  • “...source but it did not affect in the utilization of D-lactate. The gene locus of cj1585c is not conserved in C. jejuni (Hofreuter et al., 2006 ) and is replaced by a dimethyl sulfoxide reductase ( dmsABC ) gene cluster encoding for an anaerobic dimethyl sulfoxide...”
• Identification of the genes that contribute to lactate utilization in Helicobacter pylori
  Iwatani, PloS one 2014
  • “...the stereoisomer specificity of this enzyme is somewhat controversial as the orthologue in C. jejuni (Cj1585c) was identified as L-iLDH but not D-iLDH [17] . Cj1585c is one of the highly similar orthologues of HP1222 sharing ca. 50% identity with each other. This similarity may explain...”
• Discrimination of multilocus sequence typing-based Campylobacter jejuni subgroups by MALDI-TOF mass spectrometry
  Zautner, BMC microbiology 2013
  • “...combination of MLST with isolate-profiling for sixteen genetic markers: ansB , dmsA , ggt , cj1585c , cjj81176-1367/71 ( cj1365c ), tlp7 m+c ( cj0951c plus cj0952c ), cj1321-cj1326 , fucP , cj0178 , cj0755/cfrA , ceuE , pldA , cstII , and cstIII lead to...”
  • “...major clusters, the overall majority of isolates is positive for the marker genes cj1365c , cj1585c , cj1321-6 , fucP , cj0178 , and cj0755 positive but dmsA -, ansB - and ggt -negative (different shades of yellow); B1 : one cluster of dmsA + ,...”
• More

Mb2275 POSSIBLE FLAVOPROTEIN from Mycobacterium bovis AF2122/97
MT2311 alkyl-dihydroxyacetonephosphate synthase, putative from Mycobacterium tuberculosis CDC1551
BCG_2269 putative flavoprotein from Mycobacterium bovis BCG str. Pasteur 1173P2
26% identity, 87% coverage

• Circulating Mycobacterium bovis peptides and host response proteins as biomarkers for unambiguous detection of subclinical infection
  Lamont, Journal of clinical microbiology 2014
  • “...MB0862 MB1482c MB2883c MB1929 MB1886c MB1192 MB2441c MB2275 MB2122c MB1672c MB1554c (pks5) MB1895c MB3729c MB1268 MB3017c Transcriptional regulator (LuxR...”
• Microsatellite polymorphism across the M. tuberculosis and M. bovis genomes: implications on genome evolution and plasticity
  Sreenu, BMC genomics 2006
  • “...with overlaping orf (8) G4 5 Flavo protein, electron acceptor, Rv2251A (139) *Rv2251(475) MT2311 (529) Mb2275 (529) G5 6 Conserved hypothetical protein *Rv2879c (189) Rv2880c (275) MT2947 (364) Mb2904c (364) G4 3 Conserved hypothetical protein *Rv0740 (175) MT0765 (82), MT0766 (120) 31791926 (175) G3 2 fusA2...”
• Feedback for the Seventh International AIDS conference, Florence 1991
  , Genitourinary medicine 1991
• Microsatellite polymorphism across the M. tuberculosis and M. bovis genomes: implications on genome evolution and plasticity
  Sreenu, BMC genomics 2006
  • “...c) Fission with overlaping orf (8) G4 5 Flavo protein, electron acceptor, Rv2251A (139) *Rv2251(475) MT2311 (529) Mb2275 (529) G5 6 Conserved hypothetical protein *Rv2879c (189) Rv2880c (275) MT2947 (364) Mb2904c (364) G4 3 Conserved hypothetical protein *Rv0740 (175) MT0765 (82), MT0766 (120) 31791926 (175) G3...”
• InbR, a TetR family regulator, binds with isoniazid and influences multidrug resistance in Mycobacterium bovis BCG
  Yang, Scientific reports 2015
  • “...hypothetical protein BCG_2267c 2.28 Rv2249c glpD1 glycerol-3-phosphate dehydrogenase glpd1 BCG_2268c 2.11 Rv2250c transcriptional regulatory protein BCG_2269 2.16 Rv2251 flavoprotein BCG_2270 2.20 Rv2252 diacylglycerol kinase BCG_2271 1.36 1.47 Rv2253 hypothetical protein 18 BCG_2651c 1.69 2.18 Rv2624c hypothetical protein BCG_2652c 2.00 2.32 Rv2625c transmembrane alanine and leucine rich...”

Rv2251 POSSIBLE FLAVOPROTEIN from Mycobacterium tuberculosis H37Rv
NP_216767 flavoprotein from Mycobacterium tuberculosis H37Rv
25% identity, 83% coverage

• Transcriptomic profile of the most successful Mycobacterium tuberculosis strain in Aragon, the MtZ strain, during exponential and stationary growth phases
  Comín, Microbiology spectrum 2023
  • “...related to cholesterol metabolism, and Rv1592c ), and lipid metabolism ( fadB2 , fadE5 , Rv2251 , Rv2277 , fadE35 , and lipU ) were upregulated in MtZ strain. Similar to the exponential growth phase, the molybdopterin biosynthesis pathway ( moaC3 , moaA1 , Rv3324A ,...”
• Extracellular Vesicles in Mycobacterial Infections: Their Potential as Molecule Transfer Vectors
  Wang, Frontiers in immunology 2019
  • “...Rv1488, Rv2091c, Rv1410c, Hup, MihF, Can, Enolase, MmsA, Rv0315, Gnd2, IlvX, AtpD, Rv0296c, gmdA, Rv0248c, Rv2251, Rv3671c, aldC, icd2, Rv0063, Rv0148, AtsA, MycP3, AtpA, Qor, Ag85A, FadA3, Ag85C, AccA3, Ag85B, MPT51, FadA2, EchA21, FadD13, Rv1544, FadE4, maA4, FadB, SodB, HspX, EphG, Rv3722c, Rv0831c, Rv2159c, ppe41, Rv3099c,...”
• Resuscitation of Dormant "Non-culturable" Mycobacterium tuberculosis Is Characterized by Immediate Transcriptional Burst
  Salina, Frontiers in cellular and infection microbiology 2019
  • “...dioxygenase Rv3161c, oxidoreductases Rv3352c, Rv0369c, and Rv0370c as well as electron acceptors flavoproteins Rv2250A and Rv2251 was also upregulated, indicating intensification of redox processes in the early resuscitation phase. The pyrE (Rv0382c) gene for orotate phosphoribosyl transferase involved in pyrimidine biosynthesis was also significantly activated. The...”
• T cell recall response of two hypothetical proteins (Rv2251 and Rv2721c) from Mycobacterium tuberculosis in healthy household contacts of TB - Possible subunit vaccine candidates
  Santhi, The Journal of infection 2016 (PubMed)
  • “...hypothetical proteins (Rv2251 and Rv2721c) from Mycobacterium tuberculosis in healthy household contacts of TB Possible subunit vaccine candidates...”
  • “...and functional profiles of two novel mycobacterial antigens Rv2251 and Rv2721c during T cell recall response via multi-color flow cytometry. Healthy household...”
• InbR, a TetR family regulator, binds with isoniazid and influences multidrug resistance in Mycobacterium bovis BCG
  Yang, Scientific reports 2015
  • “...BCG_2267c 2.28 Rv2249c glpD1 glycerol-3-phosphate dehydrogenase glpd1 BCG_2268c 2.11 Rv2250c transcriptional regulatory protein BCG_2269 2.16 Rv2251 flavoprotein BCG_2270 2.20 Rv2252 diacylglycerol kinase BCG_2271 1.36 1.47 Rv2253 hypothetical protein 18 BCG_2651c 1.69 2.18 Rv2624c hypothetical protein BCG_2652c 2.00 2.32 Rv2625c transmembrane alanine and leucine rich protein BCG_2653c...”
• In silico analysis of potential human T Cell antigens from Mycobacterium tuberculosis for the development of subunit vaccines against tuberculosis
  Devasundaram, Immunological investigations 2014 (PubMed)
  • “...T cell antigens Rv0733 (97.24%), Rv0462 (96.9%) and Rv2251 (96.3%). The prediction results were experimentally tested by in vitro stimulation of these novel T...”
  • “...in the present study. Three antigens (Rv0733, Rv0462 and Rv2251) were found to have highest percentage of binding and population coverage and are selected for...”
• Key role for the alternative sigma factor, SigH, in the intracellular life of Mycobacterium avium subsp. paratuberculosis during macrophage stress
  Ghosh, Infection and immunity 2013
  • “...Rv1345 Rv2382c Rv1665 Rv3820c Rv2381c Rv2384 Rv0035 Rv1180 Rv2251 Rv2247 Rv1344 90.65 65.58 75.89 75.39 55.55 61.05 84.55 75.09 78.87 60.23 66.73 52.68 76.87...”
• Immunoproteomic identification of human T cell antigens of Mycobacterium tuberculosis that differentiate healthy contacts from tuberculosis patients
  Deenadayalan, Molecular & cellular proteomics : MCP 2010
  • “...(BfrB, GgtB, LpdC, MmsA, Pks13, Rv1910c, Rv1558, Rv2204c, Rv2251, and Rv2721c) are reported here as potentially novel human T cell antigens. Mass spectrometric...”
  • “...T T T Gene number Rv1558 Rv1910c Rv2204c Rv2251 Rv2626c Rv2721c Rv3169 Rv3716c Rv3248c Rv3846 Rv1448c Rv2185c Rv2140c Rv0462 Rv1174c Rv1932 Rv3914 Rv2145c...”
• More
• T cell recall response of two hypothetical proteins (Rv2251 and Rv2721c) from Mycobacterium tuberculosis in healthy household contacts of TB - Possible subunit vaccine candidates.
  Santhi, The Journal of infection 2016 (PubMed)
  • GeneRIF: Rv2251 and Rv2721c antigen specific IFN-gamma, TNF-alpha and IL-2 response was also significantly high in latent household contacts when compared to the active pulmonary tuberculosis

5adzC / P97275 Ether lipid-generating enzyme agps in complex with inhibitor 1a (see paper)
25% identity, 47% coverage

• Ligands: flavin-adenine dinucleotide; (3s)-3-(2-fluorophenyl)-n-((2-oxo-2,3-dihydro-1h-benzo[d]imidazol-5-yl)methyl)butanamide) (5adzC)

A0KLK7 FAD linked oxidases, C-terminal domain protein from Aeromonas hydrophila subsp. hydrophila (strain ATCC 7966 / DSM 30187 / BCRC 13018 / CCUG 14551 / JCM 1027 / KCTC 2358 / NCIMB 9240 / NCTC 8049)
AHA_2649 FAD linked oxidases, C-terminal domain protein from Aeromonas hydrophila subsp. hydrophila ATCC 7966
22% identity, 41% coverage

• Quantitative Proteomics Analysis Reveals the Effect of a MarR Family Transcriptional Regulator AHA_2124 on Aeromonas hydrophila
  Li, Biology 2023
  • “...proteins are A0KEL7 (gene ID: AHA_0149 ), A0KID3 ( AHA_1496 ), A0KLH4 ( AHA_2616 ), A0KLK7 ( AHA_2649 ), A0KN49 ( AHA_3209 ), EutE, FrdA, Icd, IlvB-2, LeuA-1, LeuB, PpsA, RnpA, RplF, RpmA, RpmG, RpmH, RpsB, RpsF, and YfiA-1, and most of them were involved in...”
• Quantitative Proteomics Analysis Reveals the Effect of a MarR Family Transcriptional Regulator AHA_2124 on Aeromonas hydrophila
  Li, Biology 2023
  • “...A0KEL7 (gene ID: AHA_0149 ), A0KID3 ( AHA_1496 ), A0KLH4 ( AHA_2616 ), A0KLK7 ( AHA_2649 ), A0KN49 ( AHA_3209 ), EutE, FrdA, Icd, IlvB-2, LeuA-1, LeuB, PpsA, RnpA, RplF, RpmA, RpmG, RpmH, RpsB, RpsF, and YfiA-1, and most of them were involved in ribosome function,...”

Q4QLD4 Conserved FAD/FMN-containing dehydrogenase from Haemophilus influenzae (strain 86-028NP)
NTHI1331 conserved FAD/FMN-containing dehydrogenase from Haemophilus influenzae 86-028NP
22% identity, 41% coverage

• Correction: Beta- Lactam Antibiotics Stimulate Biofilm Formation in Non-Typeable Haemophilus influenzae by Up-Regulating Carbohydrate Metabolism
  , PloS one 2014
  • “...NTHI0735 Q4QMU6 -1.64 0.0005 Predicated membrane protein NTHI1330 Q4QLD5 -1.64 0.001 Conserved FAD/FMN-containing dehydrogenase NTHI1331 Q4QLD4 -1.77 0.001 NTHI1505 Q4QKY1 -2.25 0.001 NTHI1511 Q4QKX6 -2.54 0.0007 DNA replication NTHI1528 Q4QKW1 -2.17 0.0005 NTHI1534 Q4QKV5 -1.84 0.002 NTHI1635 Q4QKL4 -4.08 0.001 Catalytic activity NTHI1721 Q4QKD8 -3.11 0.001...”
• Beta- lactam antibiotics stimulate biofilm formation in non-typeable haemophilus influenzae by up-regulating carbohydrate metabolism
  Wu, PloS one 2014
  • “...NTHI0735 Q4QMU6 1.64 0.0005 Predicated membrane protein NTHI1330 Q4QLD5 1.64 0.001 Conserved FAD/FMN-containing dehydrogenase NTHI1331 Q4QLD4 1.77 0.001 NTHI1505 Q4QKY1 2.25 0.001 NTHI1511 Q4QKX6 2.54 0.0007 DNA replication NTHI1528 Q4QKW1 2.17 0.0005 NTHI1534 Q4QKV5 1.84 0.002 NTHI1635 Q4QKL4 4.08 0.001 Catalytic activity NTHI1721 Q4QKD8 3.11 0.001...”
• Correction: Beta- Lactam Antibiotics Stimulate Biofilm Formation in Non-Typeable Haemophilus influenzae by Up-Regulating Carbohydrate Metabolism
  , PloS one 2014
  • “...0.0004 NTHI0735 Q4QMU6 -1.64 0.0005 Predicated membrane protein NTHI1330 Q4QLD5 -1.64 0.001 Conserved FAD/FMN-containing dehydrogenase NTHI1331 Q4QLD4 -1.77 0.001 NTHI1505 Q4QKY1 -2.25 0.001 NTHI1511 Q4QKX6 -2.54 0.0007 DNA replication NTHI1528 Q4QKW1 -2.17 0.0005 NTHI1534 Q4QKV5 -1.84 0.002 NTHI1635 Q4QKL4 -4.08 0.001 Catalytic activity NTHI1721 Q4QKD8 -3.11...”
• Beta- lactam antibiotics stimulate biofilm formation in non-typeable haemophilus influenzae by up-regulating carbohydrate metabolism
  Wu, PloS one 2014
  • “...0.0004 NTHI0735 Q4QMU6 1.64 0.0005 Predicated membrane protein NTHI1330 Q4QLD5 1.64 0.001 Conserved FAD/FMN-containing dehydrogenase NTHI1331 Q4QLD4 1.77 0.001 NTHI1505 Q4QKY1 2.25 0.001 NTHI1511 Q4QKX6 2.54 0.0007 DNA replication NTHI1528 Q4QKW1 2.17 0.0005 NTHI1534 Q4QKV5 1.84 0.002 NTHI1635 Q4QKL4 4.08 0.001 Catalytic activity NTHI1721 Q4QKD8 3.11...”

FNLLGLLA_01898 FAD-binding and (Fe-S)-binding domain-containing protein from Veillonella parvula
23% identity, 45% coverage

• Identification of <i>Veillonella parvula</i> and <i>Streptococcus gordonii</i> adhesins mediating co-aggregation and its impact on physiology and mixed biofilm structure
  Dorison, mBio 2024
  • “...upregulated, while genes related to the L- and D-lactate dehydrogenases were downregulated ( lutA-lutC , FNLLGLLA_01898, and fucO ). Genes involved in iron or other metal uptake through the inner membrane were also both upregulated and downregulated. We also compared specifically all coculture conditions compared to...”

LINJ_30_0120 alkyldihydroxyacetonephosphate synthase from Leishmania infantum JPCM5
21% identity, 69% coverage

• Unravelling the proteomic signature of extracellular vesicles released by drug-resistant Leishmania infantum parasites
  Douanne, PLoS neglected tropical diseases 2020
  • “...10.0 no no (0.493) no 21 LINJ_30_3430 Phosphoglycerate kinase 10.0 no no (0.501) no 22 LINJ_30_0120 Alkyl dihydroxy acetone phosphate synthase O 9.3 no no (0.400) no 23 LINJ_32_3200 Leucine-rich repeat protein-putative 9.3 no no (0.568) no 24 LINJ_22_1390 AlaninetRNA ligase 9.0 no no (0.324) no...”

NP_766254 alkyldihydroxyacetonephosphate synthase, peroxisomal from Mus musculus
28% identity, 32% coverage

• Blind sterile 2 (bs2), a hypomorphic mutation in Agps, results in cataracts and male sterility in mice.
  Liegel, Molecular genetics and metabolism 2011
  • GeneRIF: Linkage analysis mapped the bs2 locus to mouse chromosome 2

ADAS_MOUSE / Q8C0I1 Alkyldihydroxyacetonephosphate synthase, peroxisomal; Alkyl-DHAP synthase; Alkylglycerone-phosphate synthase; EC 2.5.1.26 from Mus musculus (Mouse) (see paper)
Q8C0I1 alkylglycerone-phosphate synthase (EC 2.5.1.26) from Mus musculus (see paper)
28% identity, 34% coverage

• function: Catalyzes the exchange of the acyl chain in acyl- dihydroxyacetonephosphate (acyl-DHAP) for a long chain fatty alcohol, yielding the first ether linked intermediate, i.e. alkyl- dihydroxyacetonephosphate (alkyl-DHAP), in the pathway of ether lipid biosynthesis.
  catalytic activity: a long chain fatty alcohol + a 1-acylglycerone 3-phosphate = a 1-O-alkylglycerone 3-phosphate + a long-chain fatty acid + H(+) (RHEA:36171)
  catalytic activity: hexadecan-1-ol + 1-hexadecanoylglycerone 3-phosphate = 1-O- hexadecylglycerone 3-phosphate + hexadecanoate + H(+) (RHEA:40659)
  catalytic activity: 1-hexadecanoylglycerone 3-phosphate + a long-chain fatty acid = a 1-acylglycerone 3-phosphate + hexadecanoate (RHEA:40727)
  cofactor: FAD
  subunit: Homodimer.
• Proteomic Analysis of Mouse Kidney Tissue Associates Peroxisomal Dysfunction with Early Diabetic Kidney Disease
  Tserga, Biomedicines 2022
  • “...wt 0.0071 0.119 NO NO Q3UBX0 Transmembrane protein 109 0.014 0.590 0.0289 0.289 NO YES Q8C0I1 Alkyldihydroxyacetonephosphate synthase, peroxisomal 0.0157 0.297 0.000682 0.08254 YES YES P03930 ATP synthase protein 8 0.0173 0.353 0.0287 0.0285 NO NO P28825 Meprin A subunit alpha 0.0205 0.326 0.000155 0.424 YES...”
• Flotillin proteins recruit sphingosine to membranes and maintain cellular sphingosine-1-phosphate levels.
  Riento, PloS one 2018
  • “...carrier family 38 member 4 Slc38a4 0.65785 0.98883 0.93633 P18572 Basigin Bsg 0.64210 0.53755 1.02380 Q8C0I1 Alkylglycerone-phosphate synthase Agps 0.69536 0.99206 0.94860 Q80YX1 Tenascin Tnc 0.70862 0.95785 0.44446 Q91VH2 Sorting nexin-9 Snx9 0.77664 0.88207 0.81726 P15379 CD44 Cd44 0.77357 0.80821 0.51437 O08573 Galectin-9 Lgals9 0.79942 0.86333...”

PA1416 hypothetical protein from Pseudomonas aeruginosa PAO1
26% identity, 84% coverage

• Control of a programmed cell death pathway in Pseudomonas aeruginosa by an antiterminator
  Peña, Nature communications 2021
  • “...regulated by AlpA and appear to result from bypassing intrinsic transcription terminators, such as anti-sense PA1416 and cyaA (Fig. 5b, c ), the fact that the relA mutation does not appear to influence the expression of the gene(s) upstream of the terminator (Supplementary Table 2 )...”
• Pseudomonas aeruginosa D-arabinofuranose biosynthetic pathway and its role in type IV pilus assembly
  Harvey, The Journal of biological chemistry 2011
  • “...pEX18Ap pilT::GmFRT pBADGr AWX pBADGr PsPA7_6248 pBADGr PA1416 pBADGr MSMEG6382 pBADGr Rv3790 pUCP20 6245-6251 pUCP20 6247-6251 pUCP20 6245-6249 pUCP20...”
  • “...gene Complementation construct carrying the PAO1 PA1416 gene Complementation construct carrying the M. smegmatis MSMEG6392 gene Complementation construct...”
• Functional genomics enables identification of genes of the arginine transaminase pathway in Pseudomonas aeruginosa
  Yang, Journal of bacteriology 2007
  • “...*PA0265 *PA0266 *PA0296 *PA0297 *PA0298 *PA0299 PA1415 PA1416 PA1417 PA1418 PA1419 PA1420 PA1421 PA2310 PA2311 PA2312 PA2313 PA2862 PA2863 PA3690 PA3862...”
  • “...from microarray data (Table 2). Among these genes, PA1416 and PA1417 were annotated to encode a flavin adenine dinucleotide-linked oxidase and a decarboxylase,...”

ADAS_CAVPO / P97275 Alkyldihydroxyacetonephosphate synthase, peroxisomal; Alkyl-DHAP synthase; Alkylglycerone-phosphate synthase; EC 2.5.1.26 from Cavia porcellus (Guinea pig) (see 4 papers)
P97275 alkylglycerone-phosphate synthase (EC 2.5.1.26) from Cavia porcellus (see paper)
27% identity, 33% coverage

• function: Catalyzes the exchange of the acyl chain in acyl- dihydroxyacetonephosphate (acyl-DHAP) for a long chain fatty alcohol, yielding the first ether linked intermediate, i.e. alkyl- dihydroxyacetonephosphate (alkyl-DHAP), in the pathway of ether lipid biosynthesis.
  catalytic activity: a long chain fatty alcohol + a 1-acylglycerone 3-phosphate = a 1-O-alkylglycerone 3-phosphate + a long-chain fatty acid + H(+) (RHEA:36171)
  catalytic activity: hexadecan-1-ol + 1-hexadecanoylglycerone 3-phosphate = 1-O- hexadecylglycerone 3-phosphate + hexadecanoate + H(+) (RHEA:40659)
  catalytic activity: 1-hexadecanoylglycerone 3-phosphate + a long-chain fatty acid = a 1-acylglycerone 3-phosphate + hexadecanoate (RHEA:40727)
  cofactor: FAD
  subunit: Homodimer.
• Mass Spectrometry and Computer Simulation Predict the Interactions of AGPS and HNRNPK in Glioma.
  Zhou, BioMed research international 2021
  • “...Use Discovery Studio v3.5's MODELER program to model HNRNPK with HNRNPK amino acid (UniProt ID: P97275) as the target sequence. Briefly, download the HNRNPK sequence from the NCBI database as a template, and use the similarity search tool BLAST to search the protein database RCSB-PDB for...”
• Prediction of FAD binding sites in electron transport proteins according to efficient radial basis function networks and significant amino acid pairs.
  Le, BMC bioinformatics 2016
  • “...Q9YHT1 P07342 P38038 Q0QLF4 Q709F0 Q9AL95 P55931 O53355 P39662 Q28943 Q7SID9 C6ELC9 A3KEZ1 O54050 P41367 P97275 Q7WZ62 D0VWY5 O60341 P45954 Q2GBV9 Q7X2H8 O52582 P0A6U3 P47989 Q389T8 Q7ZA32 Q9RSY7 P15651 P49748 Q47PU3 Q8DMN3 Q9UBK8 P19920 P55789 Q52437 Q8X1D8 Q9UKU7 P07872 P09622 Q9HJI4 Q9HKS9 Q9HTK9 Sequence information Sequence...”

5adzA / P97275 Ether lipid-generating enzyme agps in complex with inhibitor 1a (see paper)
27% identity, 39% coverage

• Ligands: flavin-adenine dinucleotide; (3s)-3-(2-fluorophenyl)-n-((2-oxo-2,3-dihydro-1h-benzo[d]imidazol-5-yl)methyl)butanamide) (5adzA)

I3LM15 Alkylglycerone-phosphate synthase from Sus scrofa
26% identity, 31% coverage

• Proteome changes in the small intestinal mucosa of growing pigs with dietary supplementation of non-starch polysaccharide enzymes
  Zhang, Proteome science 2016
  • “...- [F1RNR6_PIG] HPD 31 1 0.35 0.0391 Aromatic amino acid family metabolic process Lipid metabolism I3LM15 Uncharacterized protein OS=Sus scrofa GN=AGPS PE=4 SV=1 - [I3LM15_PIG] AGPS 48.77 1 0.36 0.0019 Lipid biosynthetic process Q9GJX2 Diazepam binding inhibitor (Fragment) OS=Sus scrofa GN=DBI PE=2 SV=1 - [Q9GJX2_PIG] DBI...”

APL_1422 hypothetical protein from Actinobacillus pleuropneumoniae L20
20% identity, 41% coverage

• Comparative profiling of the transcriptional response to iron restriction in six serotypes of Actinobacillus pleuropneumoniae with different virulence potential
  Klitgaard, BMC genomics 2010
  • “...Quinol dehydrogenase membrane component C -1.14 APL_1426 napB Nitrate reductase cytochrome c-type subunit C -1.60 APL_1422 napC Nitrate/TMAO reductase C -1.42 APL_1379 mauG # Cytochrome c peroxidase P -1.95 APL_1367 + ccmF Cytochrome c-type biogenesis protein O -0.54 APL_1337 hypG Hydrogenase maturation factor O -0.68 APL_1336...”

ADAS_RAT / Q9EQR2 Alkyldihydroxyacetonephosphate synthase, peroxisomal; Alkyl-DHAP synthase; Alkylglycerone-phosphate synthase; EC 2.5.1.26 from Rattus norvegicus (Rat) (see 2 papers)
27% identity, 34% coverage

• function: Catalyzes the exchange of the acyl chain in acyl- dihydroxyacetonephosphate (acyl-DHAP) for a long chain fatty alcohol, yielding the first ether linked intermediate, i.e. alkyl- dihydroxyacetonephosphate (alkyl-DHAP), in the pathway of ether lipid biosynthesis.
  catalytic activity: a long chain fatty alcohol + a 1-acylglycerone 3-phosphate = a 1-O-alkylglycerone 3-phosphate + a long-chain fatty acid + H(+) (RHEA:36171)
  catalytic activity: hexadecan-1-ol + 1-hexadecanoylglycerone 3-phosphate = 1-O- hexadecylglycerone 3-phosphate + hexadecanoate + H(+) (RHEA:40659)
  catalytic activity: 1-hexadecanoylglycerone 3-phosphate + a long-chain fatty acid = a 1-acylglycerone 3-phosphate + hexadecanoate (RHEA:40727)
  cofactor: FAD
  subunit: Homodimer.

AGPS / O00116 alkylglycerone-phosphate synthase (EC 2.5.1.26) from Homo sapiens (see 24 papers)
ADAS_HUMAN / O00116 Alkyldihydroxyacetonephosphate synthase, peroxisomal; Alkyl-DHAP synthase; Aging-associated gene 5 protein; Alkylglycerone-phosphate synthase; EC 2.5.1.26 from Homo sapiens (Human) (see 4 papers)
O00116 alkylglycerone-phosphate synthase (EC 2.5.1.26) from Homo sapiens (see 7 papers)
NP_003650 alkyldihydroxyacetonephosphate synthase, peroxisomal precursor from Homo sapiens
27% identity, 33% coverage

• function: Catalyzes the exchange of the acyl chain in acyl- dihydroxyacetonephosphate (acyl-DHAP) for a long chain fatty alcohol, yielding the first ether linked intermediate, i.e. alkyl- dihydroxyacetonephosphate (alkyl-DHAP), in the pathway of ether lipid biosynthesis.
  catalytic activity: a long chain fatty alcohol + a 1-acylglycerone 3-phosphate = a 1-O-alkylglycerone 3-phosphate + a long-chain fatty acid + H(+) (RHEA:36171)
  catalytic activity: hexadecan-1-ol + 1-hexadecanoylglycerone 3-phosphate = 1-O- hexadecylglycerone 3-phosphate + hexadecanoate + H(+) (RHEA:40659)
  catalytic activity: 1-hexadecanoylglycerone 3-phosphate + a long-chain fatty acid = a 1-acylglycerone 3-phosphate + hexadecanoate (RHEA:40727)
  cofactor: FAD
  subunit: Homodimer.
• The presence of plasmenyl ether lipids in Capsaspora owczarzaki suggests a premetazoan origin of plasmalogen biosynthesis in animals
  , Heliyon 2024
  • “...C. owczarzaki XP_004364531, H. sapiens NP_055051; AGPS: T. harzianum KKP00238, C. owczarzaki KJE89098, H. sapiens NP_003650; DHRS7B: L. elongata KAF9292753, C. owczarzaki XP_004348163, H. sapiens NP_056325; EPT1: F. alba XP_9494251, T. harzianum XP_024774613, Linnemannia zychae KAF9922440, Blastocladiella britannica KAI9222539, S. arctica XP_014158253, C. owczarzaki XP_011269962, H....”
• TrkA promotes MDM2-mediated AGPS ubiquitination and degradation to trigger prostate cancer progression.
  Zhang, Journal of experimental & clinical cancer research : CR 2024
  • GeneRIF: TrkA promotes MDM2-mediated AGPS ubiquitination and degradation to trigger prostate cancer progression.
• Mass Spectrometry and Computer Simulation Predict the Interactions of AGPS and HNRNPK in Glioma.
  Zhou, BioMed research international 2021
  • GeneRIF: Mass Spectrometry and Computer Simulation Predict the Interactions of AGPS and HNRNPK in Glioma.
• The effect of benzyl isothiocyanate and its computer-aided design derivants targeting alkylglycerone phosphate synthase on the inhibition of human glioma U87MG cell line.
  Zhu, Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine 2015 (PubMed)
  • GeneRIF: we optimized the BITC construction targeting alkylglycerone phosphate synthase (AGPS) by computer-aided design, and the derivants also showed anti-tumor potential in vitro.
• Alkylglyceronephosphate synthase (AGPS) alters lipid signaling pathways and supports chemotherapy resistance of glioma and hepatic carcinoma cell lines.
  Zhu, Asian Pacific journal of cancer prevention : APJCP 2014 (PubMed)
  • GeneRIF: AGPS overexpression could be a causation of chemotherapy agent resistance of cancer cells. AGPS silencing could lead to drug uptake and cell cycle arrest and apoptotic cell death.
• Role and mechanism of the alkylglycerone phosphate synthase in suppressing the invasion potential of human glioma and hepatic carcinoma cells in vitro.
  Zhu, Oncology reports 2014 (PubMed)
  • GeneRIF: Results demonstrated that AGPS negatively regulated the invasion potential of glioma and hepatic carcinoma cells by modulating the expression of relevant genes and activity of the MAPK pathway.
• Ether lipid generating enzyme AGPS alters the balance of structural and signaling lipids to fuel cancer pathogenicity.
  Benjamin, Proceedings of the National Academy of Sciences of the United States of America 2013
  • GeneRIF: AGPS, in addition to maintaining ether lipids, also controls cellular utilization of fatty acids, favoring the generation of signaling lipids necessary for promoting the aggressive features of cancer.
• Functional characterization of novel mutations in GNPAT and AGPS, causing rhizomelic chondrodysplasia punctata (RCDP) types 2 and 3.
  Itzkovitz, Human mutation 2012 (PubMed)
  • GeneRIF: Novel mutations in AGPS (alkylglycerone-phosphate synthase) cause rhizomelic chondrodysplasia punctata (RCDP) type 3.
• More
• Understanding the activating mechanism of the immune system against COVID-19 by Traditional Indian Medicine: Network pharmacology approach.
  Thirumal, Advances in protein chemistry and structural biology 2022
  • “...615437 Q86YB8 ERP44 ERP44 ENSG00000023318 18311 23071 609170 Q9BS26 AGPS AGPS ENSG00000018510 327 8540 603051 O00116 FKBP10 FKBP10 ENSG00000141756 18169 60681 607063 Q96AY3 FKBP15 FKBP15 ENSG00000119321 23397 23307 617398 Q5T1M5 MEPCE MEPCE ENSG00000146834 20247 56257 611478 Q7L2J0 FKBP7 FKBP7 ENSG00000079150 3723 51661 607062 Q9Y680 BCKDK BCKDK...”
• Regulation of the HTRA2 Protease Activity by an Inhibitory Antibody-Derived Peptide Ligand and the Influence on HTRA2-Specific Protein Interaction Networks in Retinal Tissues
  Schmelter, Biomedicines 2021
  • “...11.4 50.6 - 49 Q04760 Lactoylglutathione lyase GLO1 3.3 2 2 12.5 20.8 - 50 O00116 Alkyldihydroxyacetonephosphate synthase, peroxisomal AGPS 10.3 1 1 2.6 72.9 n.d. 51 Q9ULC4 Malignant T-cell-amplified sequence 1 MCTS1 4.5 1 1 10.5 20.6 n.d. : Proteins fulfilled filtering criteria ( p...”
• A metabolic modeling approach reveals promising therapeutic targets and antiviral drugs to combat COVID-19.
  Santos-Beneit, Scientific reports 2021
  • “...proteins were generated using the SWISS-MODEL cloud based modeling tool 59 in the cases of: O00116 (template PDB ID 4BC7), O95573 (template PDB ID 5MSS), Q2TAA5 (template PDB ID Q2TAA5), Q8WUY8 (template PDB ID 5L7J), Q9Y673 (template PDB ID 5MLZ), O14975 (template PDB ID 3A9V) and...”
• Secretory Carrier Membrane Protein 3 Interacts with 3A Viral Protein of Enterovirus and Participates in Viral Replication.
  Lu, Microbiology spectrum 2021
  • “...3 6.63 Q9NUQ2 AGPAT5 1-Acyl- sn -glycerol-3-phosphate acyltransferase epsilon 42.0 115.0 3 3 4 9.07 O00116 AGPS Alkyl-dihydroxyacetone-phosphate synthase, peroxisomal 72.9 539.6 9 9 12 17.02 P30837 ALDH1B1 Aldehyde dehydrogenase X, mitochondrial 57.2 480.8 7 7 12 16.83 Q9BT22 ALG1 Chitobiosyldiphosphodolichol beta-mannosyltransferase 52.5 266.1 8 8...”
• Proteomic analysis reveals dysregulated cell signaling in ejaculated spermatozoa from infertile men.
  Samanta, Asian journal of andrology 2019
  • “...regulatory subunit 6A P17980 49 22.7 20.7 13.0 3.0 Alkyl dihydroxyacetone phosphate synthase, peroxisomal precursor O00116 73 22.7 5.0 0.0 0.0 Mitochondrial import receptor subunit TOM22 homolog Q9NS69 16 22.7 10.7 0.0 0.0 Anterior gradient protein 2 homolog precursor O95994 20 22.3 6.7 0.7 0.0 Gamma-glutamyltranspeptidase...”
• Identification of proteins interacting with the mitochondrial small heat shock protein Hsp22 of Drosophila melanogaster: Implication in mitochondrial homeostasis
  Dabbaghizadeh, PloS one 2018
  • “...0 Danj homolog subfamily C member 11 (Q9NVH1) 0.237 0 0 0 0 Alkyldihydroxyacetonephosphate synthase (O00116) 0.2 0 0 0 0 Succinyl-CoA ligase subunit alpha, mitochondrial (P53597) 0.2 0.12 0 0 0 Protein-glutamine gamma-glutamyltransferase 2 (P21980) 0.2 0.02 0.2 0.3 Putative ribosome-binding factor A, mitochondrial (Q8N0V3)...”
• Probing the prostate tumour microenvironment II: Impact of hypoxia on a cell model of prostate cancer progression
  Tonry, Oncotarget 2017
  • “...v AI Up 3 P49321 NASP_HUMAN 13.1 5.2 8 Hour AS v AI Up 3 O00116 ADAS_HUMAN 6.2 5.3 8 Hour AS v AI Up 3 Q8TEM1 PO210_HUMAN 5.4 7.9 8 Hour AS v AI Up 3 O75795 UDB17_HUMAN 6.9 8.2 8 Hour AS v AI...”
• The proteome signature of the inflammatory breast cancer plasma membrane identifies novel molecular markers of disease.
  Suárez-Arroyo, American journal of cancer research 2016
• More

O97157 alkylglycerone-phosphate synthase (EC 2.5.1.26) from Trypanosoma brucei (see paper)
AAD19697.1 alkyl-dihydroxyacetonephosphate synthase from Trypanosoma brucei (see paper)
24% identity, 68% coverage

PFCIRM129_08935, RM25_RS01945 FAD-binding and (Fe-S)-binding domain-containing protein from Propionibacterium freudenreichii subsp. freudenreichii
23% identity, 48% coverage

• Aerobic adaptation and metabolic dynamics of <i>Propionibacterium freudenreichii</i> DSM 20271: insights from comparative transcriptomics and surfaceome analysis
  Loivamaa, mSystems 2024
  • “...and nitrate reduction. Among other genes encoding proteins predicted to be involved in lactate utilization, RM25_RS01945, which encodes a putative FAD-dependent D-lactate dehydrogenase, was expressed 3.8-fold higher under anaerobic conditions compared to aerobic conditions at sampling point III. These findings suggest that lactate metabolism is more...”
• Mutation of the Surface Layer Protein SlpB Has Pleiotropic Effects in the Probiotic Propionibacterium freudenreichii CIRM-BIA 129
  do, Frontiers in microbiology 2018
  • “...b46.a1 PFCIRM129_08280 Elongation factor G (EF-G) CYT J 76.5 5.4 2 2 0.2 b48 b48.a1 PFCIRM129_08935 FAD linked oxidase domain protein CYT C 100.4 18.2 5 3 0.2 b49 b49.a1 PFCIRM129_08300 DNA-directed RNA polymerase beta chain (RNAP beta subunit) (Transcriptase beta chain) (RNA polymerase subunit beta)...”

Q57252 D-2-hydroxyglutarate dehydrogenase from Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
HI1163 conserved hypothetical protein from Haemophilus influenzae Rd KW20
21% identity, 41% coverage

• Functional annotation of conserved hypothetical proteins from Haemophilus influenzae Rd KW20
  Shahbaaz, PloS one 2013
  • “...P45083 Thioesterase 179. HP HI1162 950122 P44116 Restriction endonuclease type II-like 180. HP HI1163 950119 Q57252 FAD-linked oxidoreductase 181. HP HI1165 949810 P45085 Glutaredoxin (electron carrier) 182. HP HI1173 950125 P44119 Zinc metal-binding SPRT metallopeptidase 183. HP HI1189 950138 P45097 Methyltransferase (radical SAM protein) 184. HP...”
• Functional annotation of conserved hypothetical proteins from Haemophilus influenzae Rd KW20
  Shahbaaz, PloS one 2013
  • “...HI1161 950121 P45083 Thioesterase 179. HP HI1162 950122 P44116 Restriction endonuclease type II-like 180. HP HI1163 950119 Q57252 FAD-linked oxidoreductase 181. HP HI1165 949810 P45085 Glutaredoxin (electron carrier) 182. HP HI1173 950125 P44119 Zinc metal-binding SPRT metallopeptidase 183. HP HI1189 950138 P45097 Methyltransferase (radical SAM protein)...”
• Nontypeable Haemophilus influenzae gene expression induced in vivo in a chinchilla model of otitis media
  Mason, Infection and immunity 2003
  • “...stress response protein Hypothetical or unknown proteins HI0094 HI1163 HI1063 HI0665 HI1292 HI1064 8.3 2.3 2.7 2.8 2.6 2.6 Hypothetical protein Conserved...”
• Gene expression changes triggered by exposure of Haemophilus influenzae to novobiocin or ciprofloxacin: combined transcription and translation analysis
  Gmuender, Genome research 2001
  • “...hi0503 hi1152 hi1193 hi0538 hi1033 hi1632 hi1227 hi1041 hi1163 hi0117 hi1022 hi0563 hi0539 hi1201 hi1682 hi1065 hi1545 hi1383 hi0078 hi1263 hi0419 hi1106 hi1507...”
  • “...protein h1159 Conserved hypothetical protein hi1163 D-Lactate dehydrogenase hi1190 Conserved hypothetical protein hi1191 Conserved hypothetical protein...”

2uuuA / O96759 Alkyldihydroxyacetonephosphate synthase in p212121 (see paper)
24% identity, 42% coverage

• Ligands: flavin-adenine dinucleotide; hexadecan-1-ol (2uuuA)

MXAN_1676 oxidase, FAD binding from Myxococcus xanthus DK 1622
24% identity, 48% coverage

• Plasmalogens and Photooxidative Stress Signaling in Myxobacteria, and How it Unmasked CarF/TMEM189 as the Δ1'-Desaturase PEDS1 for Human Plasmalogen Biosynthesis
  Padmanabhan, Frontiers in cell and developmental biology 2022
  • “...The M. xanthus genome also revealed a three-gene operon ( Figure 3B ) comprising: 1) MXAN_1676 , whose product is 42% identical (92% coverage) in sequence to human AGPS, which acts in the second peroxisomal step of ether lipid biosynthesis ( Figure 2 ); 2) MXAN_1,675...”
  • “...a putative NAD-dependent epimerase/dehydratase family protein, like ElbA and ElbE. The similarities of MXAN_1,675 and MXAN_1676 to eukaryotic enzymes and their possible implication in M. xanthus ether lipid biosynthesis had been noted and suggested, but not established, in an earlier study ( Curtis et al., 2006...”
• Development versus predation: Transcriptomic changes during the lifecycle of Myxococcus xanthus
  Pérez, Frontiers in microbiology 2022
  • “...for enzymes required for ether lipid synthesis in M. xanthus , such as MXAN_1675 and MXAN_1676, are upregulated during predation. However, since these genes also seem to be involved also in the biosynthesis of homospermidine lipids, which have antibacterial properties ( Hoffmann et al., 2018 ),...”
• Light-Triggered Carotenogenesis in Myxococcus xanthus: New Paradigms in Photosensory Signaling, Transduction and Gene Regulation
  Padmanabhan, Microorganisms 2021
  • “...that differ from those in the M. xanthus VEPE). Furthermore, deleting genes ( elbD and MXAN_1676) implicated in synthesis of the precursor AEPE ( Figure 3 c) impaired light-induced carotenogenesis, but was rescued by exogenous plasmalogen or by AEPE, which CarF converted to VEPE [ 23...”
• Neutral and Phospholipids of the Myxococcus xanthus Lipodome during Fruiting Body Formation and Germination
  Ahrendt, Applied and environmental microbiology 2015
  • “...highly conserved in myxobacteria. The homolog MXAN_1676, encoding alkyl dihydroxyacetone phosphate synthase, known from eukaryotic ether lipid biosynthesis,...”
• Transcription factor MrpC binds to promoter regions of hundreds of developmentally-regulated genes in Myxococcus xanthus
  Robinson, BMC genomics 2014
  • “...function as energy storage compounds and signals during development [ 104 , 105 ]. Since MXAN_1676, 1675 ( plsB2 ), the likely co-transcribed 1674, and/or the separately transcribed 5208 ( socA1 ) had been proposed to be involved in ether lipid synthesis [ 106 , 107...”
  • “...], these genes were on our list of potentially interesting genes (Additional file 6 ). MXAN_1676 and socA1 have putative MrpC binding sites located at +8 and -61 relative to their predicted TSCs, respectively (Additional file 3 ), suggesting these genes might be regulated by MrpC....”

FTN_0649 4Fe-4S ferredoxin, FAD dependent from Francisella tularensis subsp. novicida U112
21% identity, 42% coverage

• The Drosophila melanogaster host model
  Igboin, Journal of oral microbiology 2012
  • “...biosynthesis) htrA (stress response protease) zmpA (zinc metalloprotease) zmpB (zinc metalloprotease) Francisella novicida Adult (SI) FTN_0649 (FAD-dependent 4Fe-4S ferrodoxin) ( 268 ) * FTN_0869 (putative transglutaminase) FTN_0889 (putative transcriptional regulator) glpD (anaerobic glycerol-3-phosphate dehydrogenase) nadC (nicotinate-nucleotide pyrophosphorylase) OxyR (oxidative stress transcriptional regulator) pmrA response regulator udp...”
• Francisella-arthropod vector interaction and its role in patho-adaptation to infect mammals
  Akimana, Frontiers in microbiology 2011
  • “...mutM FTN_0623 2-C-methyl- d -erythritol 4-phosphate cytidylyltransferase ispD FTN_0627 Chitinase, glycosyl hydrolase family 18 chiA FTN_0649 FAD-binding family protein, pseudogene FTN_0651 Cytidine deaminase cdd FTN_0652 Uridine phosphorylase udp FTN_0653 tRNA-(ms(2)io(6)a)-hydroxylase miaE FTN_0655 Methylase FTN_0660 Cytosol aminopeptidase pepA FTN_0664 Type IV pili fiber building block protein FTN_0666...”
• Reciprocal analysis of Francisella novicida infections of a Drosophila melanogaster model reveal host-pathogen conflicts mediated by reactive oxygen and imd-regulated innate immune response
  Moule, PLoS pathogens 2010
  • “...measured by disk diffusion assay. Error bars represent standard error. pmrA, FTN_0889, udp, glpD and FTN_0649 are statistically significantly different from U112 with 2-tailed t-test P values of 0.0299, 0.0041, 0.0495, 0.0065 and 0.0447 respectively. FTN_0869 and nadC are not significantly different than wild-type U112, with...”
  • “...glpD which is an anaerobic glycerol-3-phosphate dehydrogenase, the nicotinate-nucleotide pyrophosphorylase nadC, a uridine phosphorylase udp, FTN_0649, a FAD-dependent 4Fe-4S ferrodoxin, and FTN_0869, a hypothetical protein that encodes a putative transglutaminase that is regulated by the virulence factor mglA [28] . Since the imd pathway has been...”

GYD1 / A8J2E9 glycolate dehydrogenase (EC 1.1.99.14) from Chlamydomonas reinhardtii (see 4 papers)
A8J2E9 D-lactate dehydrogenase (cytochrome) from Chlamydomonas reinhardtii
34% identity, 16% coverage

• Quantitative Phosphoproteomic and System-Level Analysis of TOR Inhibition Unravel Distinct Organellar Acclimation in Chlamydomonas reinhardtii
  Roustan, Frontiers in plant science 2018
  • “...to mitochondria such as ATP synthase (A8IQU3), gamma carbonic anhydrase (A8JFK6) and a (D)-2-hydroxyglutarate dehydrogenase (A8J2E9) were down-regulated. Nevertheless, a mitochondrial ubiquinol-cytochrome c oxidoreductase subunit (A8JC51) increased over rapamycin treatment. Similarly, proteins related to purine metabolism were found to be significantly up-regulated during rapamycin treatment (A8JGY3,...”

Q0ZAZ1 D-lactate dehydrogenase (cytochrome) from Chlamydomonas reinhardtii
34% identity, 16% coverage

• Quantitative proteomics of a B₁₂ -dependent alga grown in coculture with bacteria reveals metabolic tradeoffs required for mutualism
  Helliwell, The New phytologist 2018
  • “...1.4.4.2) 1.15 Q6SA05 RCA1 Rubisco activase 1.23 P23489 RA Ribulose bisphosphate carboxylase/oxygenase activase, chloroplastic 1.36 Q0ZAZ1 GDH Glycolate dehydrogenase 1.37 A8HP84 GAP3 Glyceraldehyde3phosphate dehydrogenase (EC 1.2.1.12) (EC 4.3.2.1) 1.47 A8IPI7 HPR1 Hydroxypyruvate reductase 1.51 A8IRK4 SEBP1 Sedoheptulose1,7bisphosphatase (EC 3.1.3.37) 1.53 A8IKW6 RPE1 Ribulosephosphate 3epimerase (EC 5.1.3.1)...”

FTH_1443 bifunctional FAD/FMN dehydrogenase/Fe-S oxidoreductase from Francisella tularensis subsp. holarctica OSU18
21% identity, 42% coverage

• Use of magnetic hydrazide-modified polymer microspheres for enrichment of Francisella tularensis glycoproteins
  Horák, Soft matter 2012
  • “...translocase SecA subunit 103.56/5.29 cyt, MLS cyt FTH_1424 M41 family endopeptidase FtsH/HflB 70.74/5.42 CM TMH FTH_1443 Bifunctional FAD/FMN dehydrogenase/FeS oxidoreductase 114.57/8.64 cyt cyt FTH_1487 Polyribonucleotide nucleotidyltransferase 75.53/5.68 cyt cyt FTH_1488 Ribosomal protein S15 10.36/10.13 cyt cyt FTH_1489 Peptidoglycan glycosyltransferase 62.73/8.77 CM TMH FTH_1492 Probable acyl-coenzyme A...”
  • “...Probable capsule biosynthesis protein 44.90/7.41 CM TMH FTH_1424 M41 family endopeptidase FtsH/HflB 70.74/5.42 CM TMH FTH_1443 Bifunctional FAD/FMN dehydrogenase/FeS oxidoreductase 114.57/8.64 cyt cyt FTH_1462 MFS family major facilitator transporter, glycerol-3-phosphate uniporter 48.02/8.51 CM cyt FTH_1487 Polyribonucleotide nucleotidyltransferase 75.53/5.68 cyt cyt FTH_1488 Ribosomal protein S15 10.36/10.13 cyt...”

PP_4493 D-2-hydroxyglutarate dehydrogenase (EC 1.1.99.39) from Pseudomonas putida KT2440
ydiJ / Q88EH0 (R)-2-hydroxyglutarate dehydrogenase (EC 1.1.99.39) from Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440) (see paper)
D2HDH_PSEPK / Q88EH0 D-2-hydroxyglutarate dehydrogenase; D2HGDH; EC 1.1.99.39 from Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440) (see paper)
PP_4493 oxidoreductase, putative from Pseudomonas putida KT2440
22% identity, 42% coverage

• mutant phenotype: Specifically important in carbon source D-Lysine; carbon source L-Lysine; carbon source DL-2-Aminoadipic acid. This is part of the pathway from D-lysine to 2-oxoglutarate. For detailed rationale, see PMC6509195.
• function: Catalyzes the oxidation of D-2-hydroxyglutarate (D-2-HGA) to 2-oxoglutarate (Probable). Is involved in a D-lysine catabolic pathway (PubMed:31064836).
  catalytic activity: (R)-2-hydroxyglutarate + A = AH2 + 2-oxoglutarate (RHEA:38295)
  cofactor: [4Fe-4S] cluster (Binds 1 [4Fe-4S] cluster.)
  cofactor: FAD
  disruption phenotype: Deletion mutant cannot grow on D-lysine as a sole carbon source and shows attenuated growth on L-lysine (PubMed:31064836). Mutant accumulates D-2-hydroxyglutarate (PubMed:31064836).
• Nitrogen Metabolism in Pseudomonas putida: Functional Analysis Using Random Barcode Transposon Sequencing
  Schmidt, Applied and environmental microbiology 2022 (secret)
• Massively Parallel Fitness Profiling Reveals Multiple Novel Enzymes in Pseudomonas putida Lysine Metabolism
  Thompson, mBio 2019
  • “...dehydrogenases, oxidoreductases, glycolate dehydrogenases, and aminotransferases implies a metabolic function similar to that of PP_5260. PP_4493 putatively oxidizes d- 2HG to 2KG and connects d- lysine to central metabolism. In the CoA-independent route of glutarate metabolism, LghO oxidizes l -2HG to 2KG; however, this enzyme is...”
  • “...data ( Fig.S1a ). A putative flavin adenine dinucleotide (FAD)-dependent and 4Fe-4S cluster-containing glycolate dehydrogenase, PP_4493, did show fitness defects on both d- lysine and l -lysine (fitness scores of 5.4 and 2.7, respectively) ( Fig.1A ). Glycolate dehydrogenases are members of a larger family of...”

MA4410 hypothetical protein (multi-domain) from Methanosarcina acetivorans C2A
27% identity, 20% coverage

• Deconstructing Methanosarcina acetivorans into an acetogenic archaeon
  Schöne, Proceedings of the National Academy of Sciences of the United States of America 2022
  • “...activity ( SI Appendix , Fig. S6 ). Instead, its genome contains two conspicuous loci, MA4410 and MA4630-MA4631, which could be responsible for the anabolic requirement of CoM-S-S-CoB. The loci encode putative enzymes consisting of a (N-terminal domain of a) FAD/FMN-containing dehydrogenase (COG0277) and a (C-terminal...”
  • “...reaction in which the thiols HS-CoM and HS-CoB serve as electron donors for fumarate reduction, MA4410 and/or MA4630-MA4631 would use CoM-S-S-CoB as an electron acceptor for an oxidation reaction. Using CoM-S-S-CoB both as the terminal catabolic as well as an anabolic electron acceptor offers a simple...”

HSUHS5_RS01825 FAD-binding and (Fe-S)-binding domain-containing protein from Helicobacter suis HS5
21% identity, 64% coverage

• Oral glutathione supplementation drastically reduces Helicobacter-induced gastric pathologies
  De, Scientific reports 2016
  • “...dehydrogenase (NC.000915.1, gene ID 898825) is also present in the H. suis genome (locus tag HSUHS5_RS01825) 21 , allowing the conversion of lactate to pyruvate. Pyruvate can subsequently be converted to acetyl-CoA by pyruvate synthase. For H. pylori, it has been described that the main route...”

UTI89_C3136 hypothetical protein from Escherichia coli UTI89
22% identity, 84% coverage

• DFI-seq identification of environment-specific gene expression in uropathogenic Escherichia coli
  Madelung, BMC microbiology 2017
  • “...protein H; flagellum-specific ATP synthase 4 2.177048 fliE flagellar hook-basal body protein FliE 1 2.158562 UTI89_C3136 Hypothetical protein (FAD-linked oxidoreductase) 1 1.979745 ybeK Hypothetical protein (hydrolase) 1 1.857649 nadC quinolinate phosphoribosyltransferase 1 1.789156 nagA N-acetylglucosamine-6-phosphate deacetylase 1 1.739815 menE ; menC; menB O-succinylbenzoic acid-CoA ligase; O-succinylbenzoate...”

F1P5J7 Alkylglycerone-phosphate synthase from Gallus gallus
26% identity, 34% coverage

• Comprehensive Proteome and Acetyl-Proteome Atlas Reveals Hepatic Lipid Metabolism in Layer Hens with Fatty Liver Hemorrhagic Syndrome.
  Zhang, International journal of molecular sciences 2023
  • “...RPL21 Up 3.876 A0A3Q2U825 77 16 RPS28 Up 2.786 F1NNV2 76 633 ACSL5 Up 1.789 F1P5J7 76 150 AGPS Up 2.049 F1NC38 76 339 ACADL Up 2.901 F1NPD3 76 12 RPL18A Up 2.174 F1NY85 76 152 MRPL2 Down 0.398 Q5ZLD1 75 58 FH Down 0.409 F1NQU7...”

CAA05690.1 alkyl-dihydroxyacetonephosphate synthase from Caenorhabditis elegans (see paper)
21% identity, 69% coverage

YgcV / b4463 putative FAD-containing dehydrogenase from Escherichia coli K-12 substr. MG1655 (see paper)
22% identity, 84% coverage

EC958_3037 FAD-binding oxidoreductase from Escherichia coli O25b:H4-ST131
22% identity, 84% coverage

• Sequential Acquisition of Virulence and Fluoroquinolone Resistance Has Shaped the Evolution of Escherichia coli ST131
  Ben, mBio 2016
  • “...482 yfeA Hypothetical protein 3030230 G G T T T T T T T KN EC958_3037 192 Hypothetical protein 3798899 G G A A A A A A A Syn EC958_3771 208 yhfW Hypothetical protein 3802091 G G T T T T T T T 3823737...”

SMc04384 (R)-2-hydroxyglutarate dehydrogenase (EC 1.1.99.39) from Sinorhizobium meliloti 1021
28% identity, 50% coverage

• mutant phenotype: Specifically important for L-lysine utilization. This is part of lysine catabolism via 2-aminoadipate and D-2-hydroxyglutarate synthase (also known as 2-oxoadipate dioxygenase/decarboxylase; SMc04383).

PSPPH_2690 oxidoreductase, FAD-binding, putative from Pseudomonas syringae pv. phaseolicola 1448A
22% identity, 41% coverage

• Transcriptional profile of P. syringae pv. phaseolicola NPS3121 at low temperature: physiology of phytopathogenic bacteria
  Arvizu-Gómez, BMC microbiology 2013
  • “...transcriptional regulator, GntR family 1.53 PSPPH_2580 transcriptional regulator, LysR family 1.97 PSPPH_2620 5-methyltetrahydrofolate--homocysteine methyltransferase 1.85 PSPPH_2690 oxidoreductase, FAD-binding, putative 1.56 PSPPH_2781 TspO/MBR family protein 1.99 PSPPH_2840 sodium/hydrogen exchanger family protein 1.55 PSPPH_2847 general secretion pathway protein GspK, putative 1.89 PSPPH_3045 transporter, AcrB/AcrD/AcrF family 1.64 PSPPH_3252 glycolate...”

SCO7572 oxidoreductase from Streptomyces coelicolor A3(2)
38% identity, 15% coverage

• Effects of carbon ion beam-induced mutagenesis for the screening of RED production-deficient mutants of Streptomyces coelicolor JCM4020
  Yanagisawa, PloS one 2022
  • “...195G>T S hypothetical protein JCM4020_47210 SCO4587 99.5 5 Mt 204003 8,370,142 843C>T S oxidoreductase JCM4020_75780 SCO7572 99.7 6,935,841 379_381delCGC del_Arg127 D hypothetical protein JCM4020_63500 SCO6192 99.7 2,858,275 555G>T Gln185His M chitinase precursor JCM4020_26770 SCO2503 98.7 2,828,233 G>T UTR 2,240,012 783C>T S hydrolase JCM4020_21170 SCO1968 99.6 305,254...”

glcD2 / P74033 glycolate dehydrogenase 2 (EC 1.1.99.14) from Synechocystis sp. (strain PCC 6803 / Kazusa) (see 4 papers)
P74033 glycolate dehydrogenase (EC 1.1.99.14) from Synechocystis sp. PCC 6803 (see paper)
slr0806 unknown protein from Synechocystis sp. PCC 6803
33% identity, 34% coverage

• Computational metabolic engineering strategies for growth-coupled biofuel production by Synechocystis
  Shabestary, Metabolic engineering communications 2016
  • “...-dependent oxidase activity ( Eisenhut et al., 2006 ). A second glycolate dehydrogenase/oxidase GlcD2 ( slr0806 ) was identified in Synechocystis, but its activity was not characterized ( Eisenhut et al., 2008 ), so it is not known if GlcD2 has oxygen-dependent glycolate oxidase activity. The...”
• Expression profiling of the bloom-forming cyanobacterium Nodularia CCY9414 under light and oxidative stress conditions
  Kopf, The ISME journal 2015
  • “...(e 178) Slr1223 (e 130) None Slr2006HL (e 49) Slr0806 (e 138) None Slr0426HL (1e 98) None None Slr0721 (0.0) Sll0454 (0.0) Abbreviations: ASC, analysis of...”
• The photorespiratory glycolate metabolism is essential for cyanobacteria and might have been conveyed endosymbiontically to plants
  Eisenhut, Proceedings of the National Academy of Sciences of the United States of America 2008
  • “...search in the Synechocystis genome identified a gene, slr0806, potentially coding an alternative GlcD. The amino acid sequence of Slr0806 shares 46% similarity...”
  • “...from Synechocystis and from Escherichia coli. Also, Slr0806 harbors a conserved consensus sequence GXGXXG [supporting information (SI) Fig. S1] thought to...”
• Mutation of a gene encoding a putative glycoprotease leads to reduced salt tolerance, altered pigmentation, and cyanophycin accumulation in the cyanobacterium Synechocystis sp. strain PCC 6803
  Zuther, Journal of bacteriology 1998
  • “...psaJ, does not show any similarities to known proteins (slr0806 [22]). In mutant 549, about 75 amino acid residues of its C-terminal part are missing (Fig. 1)....”

PA3026 hypothetical protein from Pseudomonas aeruginosa PAO1
28% identity, 33% coverage

• The AraC-Type Transcriptional Regulator GliR (PA3027) Activates Genes of Glycerolipid Metabolism in Pseudomonas aeruginosa
  Kotecka, International journal of molecular sciences 2021
  • “...of P. aeruginosa PAO1161 overexpressing PA3027 revealed a spectacular increase in the mRNA levels of PA3026 - PA3024 (divergent to PA3027 ), PA3464 , and PA3342 genes encoding proteins potentially involved in glycerolipid metabolism. Concomitantly, chromatin immunoprecipitation-sequencing (ChIP-seq) analysis revealed that at least 22 regions are...”
  • “...promoter-reporter assays in a heterologous host showed the PA3027-dependent activation of the promoter of the PA3026 - PA3024 operon. Two motifs representing the preferred binding sites for PA3027, one localized upstream and one overlapping with the 35 promoter sequence, were identified in PA3026 p and our...”
• Quantitative proteomics analysis of proteins involved in alkane uptake comparing the profiling of Pseudomonas aeruginosa SJTD-1 in response to n-octadecane and n-hexadecane
  Zhou, PloS one 2017
  • “...dehydrogenase PA0316 serA 2.11 1.5 gi|15598528 Uncharacterized PhzA/B-like protein PA3332 2.02 2.23 gi|15598222 Uncharacterized protein PA3026 0.5 0.57 Note: a Proteins with fold changes of 2 or 0.5 (label free) and 1.5 or 0.65 (iTRAQ) are considered significantly more or less abundant in the presence of...”

AF0868 alkyldihydroxyacetonephosphate synthase from Archaeoglobus fulgidus DSM 4304
27% identity, 41% coverage

• Identification of key components in the energy metabolism of the hyperthermophilic sulfate-reducing archaeon Archaeoglobus fulgidus by transcriptome analyses
  Hocking, Frontiers in microbiology 2014
  • “...Surprisingly, the genes corresponding to d -lactate dehydrogenase (AF0394) and a putative d-lactate dehydrogenase gene (AF0868) (Reed and Hartzell, 1999 ; Pagala et al., 2002 ) were induced during growth with T-H 2 /CO 2 . The gene AF0394 was up-regulated by a minor fold (<1.5)...”
• The Archaeoglobus fulgidus D-lactate dehydrogenase is a Zn(2+) flavoprotein
  Reed, Journal of bacteriology 1999
  • “...expression of A. fulgidus genes. The ORFs AF0394 and AF0868 were amplified by PCR with A. fulgidus chromosomal DNA as a template. The oligonucleotide primers 5...”
  • “...PstI sites (underlined) designed to generate an in-frame fusion between AF0868 and malE. The conditions for PCR were 30 cycles consisting of 30 s at 95C, 30 s...”

SO1521 D-lactate:flavin oxidoreductase from Shewanella oneidensis MR-1
24% identity, 46% coverage

• Transcriptional analysis of Shewanella oneidensis MR-1 with an electrode compared to Fe(III)citrate or oxygen as terminal electron acceptor
  Rosenbaum, PloS one 2012
  • “...SO1495 putative glycosyl hydrolase 0.0005 3.021139 SO1520 Fe-S oxidoreductase, L-lactate dehydrogenase 0.0296 Lactate metabolism 1.413225 SO1521 D-lactate dehydrogenase (dld) 0.0035 Lactate metabolism 1.487265 SO1538 isocitrate dehydrogenase 0.0000 TCA-cycle 1.61607 SO1678 methylmalonate-semialdehyde dehydrogenase 0.0132 1.572969 SO1748 hypothetical protein 0.0075 One type c heme binding motif 2.960933 SO1776...”
  • “...at the electrode ( Figure 1 Cellular Processes). Two recently identified lactate dehydrogenases (SO1520 and SO1521) [39] also showed higher expression with the electrode than with soluble iron(III) as electron acceptor, as did many of the core enzymes of the TCA-cycle (see Table 2 ), indicating...”
• Shewanella oneidensis MR-1 sensory box protein involved in aerobic and anoxic growth
  Sundararajan, Applied and environmental microbiology 2011
  • “...to SO1520 encodes an L-lactate dehydrogenase and SO1521 encodes a D-lactate dehydrogenase (40). In our study, these Downloaded from http://aem.asm.org/ on...”
  • “...SO0583 (bfd) SO0768 SO1329 (cyaA) SO1427 SO1519 SO1520 SO1521 SO1522 SO1927 (sdhC) SO1928 (sdhA) SO1929 (sdhB) SO1930 (sucA) SO1931 (sucB) SO1932 (sucC) SO2097...”
• An empirical strategy for characterizing bacterial proteomes across species in the absence of genomic sequences
  Turse, PloS one 2010
  • “...in S. oneidensis MR-1 [51] , and we observed protein components (LldF, SO1519 and Lld-II, SO1521) of this second pathway in all isolates. While orthologs featuring similar topology for this second lactate utilization pathway exist in S. putrefaciens CN32, we only observed these orthologs in HRCR-1,...”
• A universal TagModule collection for parallel genetic analysis of microorganisms
  Oh, Nucleic acids research 2010
  • “...SO3180, SO3182, SO3183, SO3185, SO3188 and SO3190). In addition, we identified mutations in SO1518 and SO1521 as having fitness defects in minimal media. These genes were recently shown to encode d-lactate dehydrogenase (SO1521) and a subunit of l-lactate dehydrogenase (SO1518) ( 29 ). These results are...”
• Identification of protein-protein interactions and topologies in living cells with chemical cross-linking and mass spectrometry
  Zhang, Molecular & cellular proteomics : MCP 2009
  • “...G (FusA-1) SO3064, amidophosphoribosyltransferase (PurF) SO1521, iron-sulfur cluster-binding protein SO0608, ubiquinol-cytochrome c SO4410, glutamine...”
• In vivo identification of the outer membrane protein OmcA-MtrC interaction network in Shewanella oneidensis MR-1 cells using novel hydrophobic chemical cross-linkers
  Zhang, Journal of proteome research 2008
  • “...SO4749 SO1142 SO4747 SO2638 SO0314 SO3032 SO1679 SOA0112 SO1521 SO3532 SO0021 SO0256 SO4030 SO1295 SO3440 SO1779 SO3542 C denotes cytoplasmic, and OM denotes...”
• Genomic analysis of carbon source metabolism of Shewanella oneidensis MR-1: Predictions versus experiments
  Serres, Journal of bacteriology 2006
  • “...that two genes, designated by locus tags SO1520 and SO1521, are located adjacent to the lactate permease gene. One codes for an ironsulfur protein, and the...”

dld-II / Q8EGS3 D-lactate dehydrogenase Dld-II (EC 1.1.2.5) from Shewanella oneidensis (strain MR-1) (see paper)
SO_1521 FAD-binding and (Fe-S)-binding domain-containing protein from Shewanella oneidensis MR-1
24% identity, 45% coverage

• Supplementation with Amino Acid Sources Facilitates Fermentative Growth of Shewanella oneidensis MR-1 in Defined Media
  Ikeda, Applied and environmental microbiology 2023 (secret)
• Reconstruction of a Genome-Scale Metabolic Network for Shewanella oneidensis MR-1 and Analysis of its Metabolic Potential for Bioelectrochemical Systems
  Luo, Frontiers in bioengineering and biotechnology 2022
  • “...including 1) LdhA (pyruvate reductase encoded by SO_0968, EC: 1.1.1.28) and Dld (lactate dehydrogenase by SO_1521, EC: 1.1.2.4) ( Figure 8B ); 2) ProC (pyrroline-5-carboxylate reductase encoded by SO_3354, EC: 1.5.1.2) and PutA (proline dehydrogenase encoded by SO_3774, EC: 1.5.5.2) ( Figure 8C ). The former...”
• Electrochemically active bacteria sense electrode potentials for regulating catabolic pathways
  Hirose, Nature communications 2018
  • “...this study Process Locus tag Gene Annotation Log 2 FC a Lactate and pyruvate oxidation SO_1521 dld Respiratory FAD-dependent d -lactate dehydrogenase 2.32 SO_0425 aceF Dihydrolipoamide acetyltransferase 1.52 Formate oxidation SO_0101 fdnG Nitrate-inducible formate dehydrogenase molybdopterin-binding subunit 2.97 SO_0102 fdnH Nitrate-inducible formate dehydrogenase iron-sulfur subunit 3.33...”
• CRP Regulates D-Lactate Oxidation in Shewanella oneidensis MR-1
  Kasai, Frontiers in microbiology 2017
  • “...organic compounds, including lactate. Here, we investigated transcriptional mechanisms for the lldP (SO_1522) and dld (SO_1521) genes, which encode putative lactate permease and D -lactate dehydrogenase, respectively, and demonstrate that CRP regulates their expression in MR-1. We found that a crp -deletion mutant of MR-1 (...”
  • “...the lldEFG genes (SO_1520 to SO_1518), whereas D -LDH is encoded by the dld gene (SO_1521), a distant homolog of a FAD-dependent LDH gene in yeast ( Pinchuk et al., 2009 ). A previous study has also demonstrated that LlpR (L- lactate-positive regulator, SO_3460) is required...”
• Investigation of a spontaneous mutant reveals novel features of iron uptake in Shewanella oneidensis
  Dong, Scientific reports 2017
  • “...putative lactate transporters, SO_1522 and SO_0827; the former is clustered with metabolizing genes ( dld (SO_1521), D-lactate dehydrogenase; lldEFG (SO_1518-20), L-lactate dehydrogenase) for both D- and L-lactate, while the latter is located somewhere on the chromosome. However, a sequence comparison analysis revealed that SO_0827 is likely...”
• Regulation of Gene Expression in Shewanella oneidensis MR-1 during Electron Acceptor Limitation and Bacterial Nanowire Formation
  Barchinger, Applied and environmental microbiology 2016
  • “...metabolism SO_0101 SO_0102 SO_0103 SO_1483 SO_1484 SO_1520 SO_1521 SO_2098 SO_2099 SO_2912 SO_2913 SO_3920 SO_3921 SO_4508 SO_4509 SO_4510 SO_4511 fdnG fdnH...”
• Metabolic Characteristics of a Glucose-Utilizing Shewanella oneidensis Strain Grown under Electrode-Respiring Conditions
  Nakagawa, PloS one 2015
  • “...S . oneidensis MR-1 is predicted to have two D-lactate dehydrogenase (D-LDH) genes, i.e., dld-II (SO_1521) and ldhA (SO_0968). Previous studies have reported that, while Dld-II functions as the respiratory D-LDH required for D-lactate oxidation to pyruvate in MR-1 [ 15 ], this enzyme is also...”
• Utilization of D-Lactate as an Energy Source Supports the Growth of Gluconobacter oxydans
  Sheng, Applied and environmental microbiology 2015
  • “...(similar to E. coli D-iLDH) and dld-II (similar to SO_1521 of S. oneidensis MR-1) (32), but their respective functions in these strains have not been reported....”
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D2HDH_PANAA / A0A0H3KZS3 D-2-hydroxyglutarate dehydrogenase; D2HGDH; EC 1.1.99.39 from Pantoea ananatis (strain AJ13355) (see paper)
21% identity, 41% coverage

• function: Catalyzes the oxidation of D-2-hydroxyglutarate (D-2-HGA) to 2-oxoglutarate. Appears to be the only D2HGDH in P.ananatis, providing the way to recycle D-2-HGA produced during L-serine synthesis by SerA, by converting it back to 2-oxoglutarate. Is involved in the utilization of D-2-HGA, that can support the growth of P.ananatis as a sole carbon source, although it barely serves as a good substrate. The physiological molecule that functions as the primary electron acceptor during D-2-HGA oxidation by YdiJ in P.ananatis is unknown. Shows strict substrate specificity towards D-2-HGA, since it has no detectable activity on L-2-hydroxyglutarate, L-malate, D-malate, L-lactate, D- lactate, L-tartrate, D-tartrate, L-glycerate, D-glycerate, glutarate, or pyruvate.
  catalytic activity: (R)-2-hydroxyglutarate + A = AH2 + 2-oxoglutarate (RHEA:38295)
  cofactor: [4Fe-4S] cluster
  cofactor: FAD
  subunit: Homotetramer.
  disruption phenotype: Disruption of this gene leads to the significant accumulation of D-2-HGA, and thus impairs D-2-HGA utilization.

RSc0454 PUTATIVE OXIDOREDUCTASE PROTEIN from Ralstonia solanacearum GMI1000
34% identity, 10% coverage

• Metagenomic and Culturomics Analysis of Microbial Communities within Surface Sediments and the Prevalence of Antibiotic Resistance Genes in a Pristine River: The Zaqu River in the Lancang River Source Region, China
  Yan, Microorganisms 2024
  • “...]. The most prevalent pathogen genes included RpoB (belonging to Acinetobacter baumannii ), followed by RSc0454 and speC ( Ralstonia solanacearum ), as well as CcoN2 and rmlA ( Pseudomonas aeruginosa ). Among the pathogens carrying the most diverse genes, the top 10 species were Xanthomonas...”
• Involvement of a FAD-Linked Oxidase RSc0454 for Expression of the Type III Secretion System and Pathogenicity in Ralstonia solanacearum
  Chen, Molecular plant-microbe interactions : MPMI 2021 (PubMed)
  • “...Ralstonia solanacearum RSc0454 is predicted as a FAD-linked oxidase based on protein homologies, while it contains distinct domains of lactate dehydrogenase and succinate dehydrogenase. A previous study demonstrated that RSc0454 exhibits lactate dehydrogenase...”
  • “...substrates, and is essential for pathogenicity of R. solanacearum. Here, we genetically characterized involvement of RSc0454 on bacterial growth and expression of genes for the type III secretion system (T3SS, a pathogenicity determinant) in R. solanacearum. The RSc0454 mutant grew normally in rich medium but grew...”
• The RSc0454-Encoded FAD-Linked Oxidase Is Indispensable for Pathogenicity in Ralstonia solanacearum GMI1000
  Hu, Molecular plant-microbe interactions : MPMI 2019 (PubMed)
  • “...agent of bacterial wilt disease. Here, we report that a large FAD-linked oxidase encoded by RSc0454 in GMI1000 is required for pathogenicity. The FAD-linked oxidase encoded by RSc0454 is composed of 1,345 amino acids, including DUF3683, lactate dehydrogenase (LDH), and succinate dehydrogenase (SDH) domains. The RSc0454...”
  • “...LDH and SDH activities. To investigate its role in pathogenicity, a deletion mutant of the RSc0454 gene was constructed in GMI1000, which was impaired in its ability to cause bacterial wilt disease in tomato. A single DUF3683, LDH, or SDH domain was insufficient to restore bacterial...”

YdiJ / b1687 putative FAD-linked oxidoreductase YdiJ from Escherichia coli K-12 substr. MG1655 (see 4 papers)
ydiJ / P77748 D-2-hydroxyglutarate dehydrogenase (EC 1.1.99.39) from Escherichia coli (strain K12) (see 5 papers)
D2HDH_ECOLI / P77748 D-2-hydroxyglutarate dehydrogenase; D2HGDH; EC 1.1.99.39 from Escherichia coli (strain K12) (see 2 papers)
b1687 predicted FAD-linked oxidoreductase from Escherichia coli str. K-12 substr. MG1655
21% identity, 41% coverage

• function: Catalyzes the oxidation of D-2-hydroxyglutarate (D-2-HGA) to 2-oxoglutarate. Appears to be the only D2HGDH in E.coli, providing the way to recycle D-2-HGA produced during L-serine synthesis by SerA, by converting it back to 2-oxoglutarate. The physiological molecule that functions as the primary electron acceptor during D-2-HGA oxidation by YdiJ in E.coli is unknown. Shows strict substrate specificity towards D-2-HGA, since it has no detectable activity on L-2-hydroxyglutarate, L-malate, D-malate, L-lactate, D-lactate, L-tartrate, D-tartrate, L- glycerate, D-glycerate, glutarate, or pyruvate.
  catalytic activity: (R)-2-hydroxyglutarate + A = AH2 + 2-oxoglutarate (RHEA:38295)
  cofactor: [4Fe-4S] cluster
  cofactor: FAD
  subunit: Homotetramer.
  disruption phenotype: Disruption of this gene leads to the significant accumulation of D-2-HGA.
• Functional Prediction of Biological Profile During Eutrophication in Marine Environment
  Sbaoui, Bioinformatics and biology insights 2022
  • “...to acid resistance with formate dehydrogenase/DMSO reductase YdgF P69212 Multidrug/spermidine efflux pump membrane subunit YdiJ P77748 Putative FAD-linked oxidoreductase YdiL P76196 Conserved hypothetical protein YdjX P76219 DedA family protein YehT P0AFT5 DNA-binding transcriptional dual regulator yfaL P45508 Serine protease autotransporter YfbQ , P0A959 Glutamatepyruvate aminotransferase YfdM...”
• Identification of Iron-Sulfur (Fe-S) Cluster and Zinc (Zn) Binding Sites Within Proteomes Predicted by DeepMind's AlphaFold2 Program Dramatically Expands the Metalloproteome
  Wehrspan, Journal of molecular biology 2022
  • “...provided experimental evidence implicating two of them as being 4Fe-4S cluster-containing proteins: YdiJ (UniProt ID: P77748 ) and YhcC (UniProt ID: P0ADW6 ). Interestingly, both of those proteins are also successfully identified here, although YdiJ is predicted here to contain two 4Fe-4S clusters and one 2Fe-2S...”
• The Escherichia coli proteome: past, present, and future prospects
  Han, Microbiology and molecular biology reviews : MMBR 2006
  • “...P77804 P76177 P0AC69 P77552 P0ACX3 P0A8A4 P77748 P76206 P0ACY1 P39173 P76256 5.38/59,928.8 5.07/54,689 9.1/31,910.83 4.75/12,878.76 4.96/9,928 (4.5-5.5)...”
• Genetic snapshots of the Rhizobium species NGR234 genome
  Viprey, Genome biology 2000
  • “...12g02 AAC75037 920 05a01 P94437 865 15e04 P52049 920a 05g06 overlaps clone 05a01 866 15f04 P77748 921 06c04 P94937 867 16f04 BAA31826 922 06e01 AAB72069 868 17c04 P23522 923 04h03 O32272 869 18g09 AAA83544 924 07f08 AAB35255 870 18h06 AAC74284 925 08a08 BAA06611 871 18h11 P77368...”
• 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)
• 18th Congress of the European Hematology Association, Stockholm, Sweden, June 13–16, 2013
  , Haematologica 2013
• Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions
  Orth, BMC systems biology 2012
  • “...(R) IV cysH (b2762) 3.00E-12 R06613 (F) II ybiU (b0821) 1.6 R07164 (R) III ydiJ (b1687) 0.9 R07165 (R) III ydiJ (b1687) 0.9 R07176 (R) IV global orphan R07463 (F) IV dadA (b1189) 2.00E-18 R07613 (R) II ydbL (b0600) 7.00E-26 ydcR (b1439) 6.00E-15 R08553 (R) IV...”

cce_3707 glycolate oxidase subunit from Cyanothece sp. ATCC 51142
22% identity, 55% coverage

• Proteome analyses of strains ATCC 51142 and PCC 7822 of the diazotrophic cyanobacterium Cyanothece sp. under culture conditions resulting in enhanced H₂ production
  Aryal, Applied and environmental microbiology 2013
  • “...genome sequence comparison (13). SbtA (cce_2939), GlcE (cce_3707), and the ParA family chromosome-partitioning protein (cce_2448) also decreased in the presence...”

Caur_2133 FAD linked oxidase domain protein from Chloroflexus aurantiacus J-10-fl
23% identity, 86% coverage

• Complete genome sequence of the filamentous anoxygenic phototrophic bacterium Chloroflexus aurantiacus
  Tang, BMC genomics 2011
  • “...III (ACIII) actABCDEFG (Caur_0621 to Caur_0627) encoding C p (subscript p stands for photosynthesis) ACIII Caur_2133 to Caur_2144 (12 genes) encoding C r (subscript r stands for respiration) ACIII NADH:quinone oxido-reductase (complex I, EC 1.6.5.3) nuoA to nuoN (Caur_2896 to Caur_2909) nuoA (Caur_1987), nuoB (Caur_1986), muoC...”
  • “...(Caur_1977 and Caur_1978) and nuoN (Caur_1976) The proposed C r ACIII operon contains 12 genes (Caur_2133 to 2144) encoding a putative FAD-dependent oxidase (component K, actK , Caur_2133), D-lactate dehydrogenase (component L, actL , Caur_2134), a Cys-rich protein with Fe-S binding motifs (component M, actM ,...”

CV_3027 probable ferredoxin from Chromobacterium violaceum ATCC 12472
Q7NTM7 D-lactate dehydrogenase (cytochrome) from Chromobacterium violaceum (strain ATCC 12472 / DSM 30191 / JCM 1249 / CCUG 213 / NBRC 12614 / NCIMB 9131 / NCTC 9757 / MK)
28% identity, 25% coverage

• GeLC-MS-based proteomics of Chromobacterium violaceum: comparison of proteome changes elicited by hydrogen peroxide
  Lima, Scientific reports 2016
  • “...NADH + that will feed the oxidative phosphorylation increasing the production of ATP. The ORF CV_3027, which is annotated as a likely ferredoxin, decreased its abundance in 3.7 fold, being the most reduced expression ( Table 2 ). In the C. violaceum genome, it appears to...”
  • “...Q7P1P4 fad H 3, 1 2,4-dienoyl-CoA reductase FadH1 Q7NYM4 CV_1250 3, 4 UPF0246 protein Q7NTM7 CV_3027 3, 7 Probable ferredoxin These proteins presented the most significant changes in their abundance (p<0.01). A positive fold change indicates a higher abundancy in the treatment condition....”
• GeLC-MS-based proteomics of Chromobacterium violaceum: comparison of proteome changes elicited by hydrogen peroxide
  Lima, Scientific reports 2016
  • “...dehydrogenase Q7P1P4 fad H 3, 1 2,4-dienoyl-CoA reductase FadH1 Q7NYM4 CV_1250 3, 4 UPF0246 protein Q7NTM7 CV_3027 3, 7 Probable ferredoxin These proteins presented the most significant changes in their abundance (p<0.01). A positive fold change indicates a higher abundancy in the treatment condition....”

ETH_00007785 uncharacterized protein from Eimeria tenella
26% identity, 32% coverage

• Dynamically expressed genes provide candidate viability biomarkers in a model coccidian
  Tucker, PloS one 2021
  • “...hypothetical protein and a gene encoding a homologous hypothetical protein in E . tenella ( ETH_00007785 ) was also up-regulated in immature oocysts [ 12 ]. Each protein resembled LDH in E . necatrix and peroxisomal alkyldihydroxyacetonephosphate synthase in C . cayetanensis . The GO terms...”
• RNA Seq analysis of the Eimeria tenella gametocyte transcriptome reveals clues about the molecular basis for sexual reproduction and oocyst biogenesis
  Walker, BMC genomics 2015
  • “...protease ETH_00034420 722.78 thioredoxin oxidoreductase ETH_00033360 475.71 gmc oxidoreductase oxidoreductase ETH_00032305 438.54 peroxidoxin 2 oxidoreductase ETH_00007785 343.29 alkyldihydroxyacetonephosphate synthase, peroxisomal oxidoreductase ETH_00025705 332.68 thioredoxin oxidoreductase ETH_00028385 311.75 amiloride-sensitive amine oxidase, copper-containing oxidoreductase ETH_00027865 282.95 peroxiredoxin 3 oxidoreductase ETH_00027760 79.18 mannitol 2-dehydrogenase oxidoreductase ETH_00015660 153.33 UDP-glucose 4-epimerase...”

lpg1634 oxidase from Legionella pneumophila subsp. pneumophila str. Philadelphia 1
28% identity, 18% coverage

• bdhA-patD operon as a virulence determinant, revealed by a novel large-scale approach for identification of Legionella pneumophila mutants defective for amoeba infection
  Aurass, Applied and environmental microbiology 2009
  • “...lpg1441 lpg1466 lpg1469 lpg1507 lpg1596 lpg1610 lpg1615 lpg1634 lpg1638 lpg1653 lpg1665 lpg1702 lpg1762 lpg1805 lpg1843 lpg1925 lpg1974 lpg2011 lpg2031 lpg2032...”

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How It Works

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.

Secrets

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.

Omissions from the PaperBLAST Database

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