PaperBLAST
PaperBLAST Hits for BRENDA::Q8RG11 D-lactate dehydrogenase (EC 1.1.1.28) (Fusobacterium nucleatum subsp. nucleatum) (335 a.a., MQKTKIIFFD...)
Show query sequence
>BRENDA::Q8RG11 D-lactate dehydrogenase (EC 1.1.1.28) (Fusobacterium nucleatum subsp. nucleatum)
MQKTKIIFFDIKDYDKEFFKKYGADYNFEMTFLKVRLTEETANLTKGYDVVCGFANDNIN
KETIDIMAENGIKLLAMRCAGFNNVSLKDVNERFKVVRVPAYSPHAIAEYTVGLILAVNR
KINKAYVRTREGNFSINGLMGIDLYEKTAGIIGTGKIGQILIKILRGFDMKVIAYDLFPN
QKVADELGFEYVSLDELYANSDIISLNCPLTKDTKYMINRRSMLKMKDGVILVNTGRGML
IDSADLVEALKDKKIGAVALDVYEEEENYFFEDKSTQVIEDDILGRLLSFYNVLITSHQA
YFTKEAVGAITVTTLNNIKDFVEGRPLVNEVPQNQ
Running BLASTp...
Found 250 similar proteins in the literature:
Q8RG11 D-lactate dehydrogenase (EC 1.1.1.28) from Fusobacterium nucleatum subsp. nucleatum (see 2 papers)
FN0511 D-lactate dehydrogenase from Fusobacterium nucleatum subsp. nucleatum ATCC 25586
100% identity, 100% coverage
- Diverse allosteric and catalytic functions of tetrameric d-lactate dehydrogenases from three Gram-negative bacteria
Furukawa, AMB Express 2014 - “...E. coli BL21(DE3) was isolated by ISOGEN (NIPPON GENE, Tokyo, Japan). The genes encoding the FN0511 (FNLDH), PA0927 (PALDH), and ECD_01352 (ECLDH) proteins (Genbank accession numbers: AAL94707.1, AAG04316.1, and ACT43236.1, respectively) were amplified via PCR using genomic DNA as templates. The primer pairs used were, 5-CGCTCGAGATGCAAAAAACTAAGATAATATTTTTTG-3...”
- “...CGGGATCCTCAGGCCCGGACCCGATTG-3 for the pa0927 gene, and 5-CGCATATGAAACTCGCCGTTTATAGC-3 and 5-CGGGATCCTTAAACCAGTTCGTTCGGGC-3 for the ecd_01352 gene. The amplified fn0511 , pa0927 , and ecd_01352 genes were inserted into T-vector pMD20 (TaKaRa Bio, Shiga, Japan). After purification of the plasmids carrying these genes, the plasmids were digested with restriction enzymes...”
5z21B / Q8RG11 The ternary structure of d-lactate dehydrogenase from fusobacterium nucleatum with nadh and oxamate (see paper)
100% identity, 99% coverage
- Ligand: 1,4-dihydronicotinamide adenine dinucleotide (5z21B)
BF638R_1473 2-hydroxyacid dehydrogenase from Bacteroides fragilis 638R
58% identity, 97% coverage
- New functions of pirin proteins and a 2-ketoglutarate: Ferredoxin oxidoreductase ortholog in Bacteroides fragilis metabolism and their impact on antimicrobial susceptibility to metronidazole and amixicile
Gough, MicrobiologyOpen 2024 - “...membrane; Kor1AB, 2Ketoglutarate ferredoxin oxidoreductase (BF638R_43214322); Kor2CDAEBG, 2Ketoglutarate ferredoxin oxidoreductase (BF638R_16601665); LdhA, d Lactate dehydrogenase (BF638R_1473); Lpd1, dihydrolipoamide dehydrogenaseE3 (BF638R_0023); Lpd2, dihydrolipoamide dehydrogenaseE3 (BF638R_1634); MaeB, malate dehydrogenase [oxaloacetatedecarboxylating NADP + dependent] (BF638R_3435); Mdh, malate dehydrogenase (BF638R_0537); MenD, 2Succinyl5enolpyruvyl6hydroxy3cyclohexene1carboxylicacid synthase (BF638R_1316); MenF, isochorismate synthase (BF638R_1315); MK, menaquinone;...”
BT1575 putative dehydrogenase from Bacteroides thetaiotaomicron VPI-5482
BT_1575, BT_RS07965 2-hydroxyacid dehydrogenase from Bacteroides thetaiotaomicron VPI-5482
57% identity, 98% coverage
- Investigation and Alteration of Organic Acid Synthesis Pathways in the Mammalian Gut Symbiont Bacteroides thetaiotaomicron
Porter, Microbiology spectrum 2022 - “...2.270.16 5.200.32 0.220.03 11.070.16** BT2955 /4738 b 15.611.17 0.010.00 ND** 6.630.33* 2.370.06 5.470.83 0.190.00** 11.250.73 BT1575 16.190.64 0.020.02 9.140.69 7.690.73 1.880.33 5.210.65 0.140.07 8.730.70 BT4455-7 15.990.34 0.020.00 8.620.81 9.760.19 2.260.11 4.640.15 0.140.03 8.820.53 BT1575 /4455-7 16.590.74 0.020.02 9.600.91 8.280.45 1.860.44 4.970.60 0.170.05 8.900.32 BT1450 16.480.70 0.010.00...”
- “...pyruvate to d -lactate while regenerating NAD + . Bt encodes one annotated lactate dehydrogenase (BT1575) with 50% amino acid identity to the E. coli ldhA gene. However, deletion of BT1575 only decreased lactate production to 75% of WT levels ( Fig.4B ), prompting us to...”
- Iron Deficiency Modulates Metabolic Landscape of Bacteroidetes Promoting Its Resilience during Inflammation
Lewis, Microbiology spectrum 2023 - “...BT145759 Response regulator transcription factor, histidine kinase 2.088 8E-04 BT_RS07480 BT1477 Fucose isomerase 2.23.0 5E-06 BT_RS07965 BT157577 2-Hydroxyacid dehydrogenase, pirin family protein, pyridoxamine 5-phosphate oxidase 3.241 0.002 BT_RS08050 BT1590 Hypothetical protein 5.921 0.25 BT_RS08070, feoB BT1592 Hypothetical protein, ferrous iron transport protein B 2.9 5E-08 BT_RS08100,...”
- Bacteroides thetaiotaomicron Fosters the Growth of Butyrate-Producing Anaerostipes caccae in the Presence of Lactose and Total Human Milk Carbohydrates
Chia, Microorganisms 2020 - “...stereospecific lactate dehydrogenase. The genome of B. thetaiotaomicron encoded only for a d -lactate dehydrogenase (BT_1575), leading to d -lactate production. The lactate-utilizing butyrate-producing bacteria (LUB) could subsequently convert acetate and lactate into butyrate. Our model organism, A. caccae , was reported to metabolize both d...”
BVU_2499 2-hydroxyacid dehydrogenase from Phocaeicola vulgatus ATCC 8482
BVU_2499 putative dehydrogenase from Bacteroides vulgatus ATCC 8482
59% identity, 98% coverage
- Genetic optimization of the human gut bacterium Phocaeicola vulgatus for enhanced succinate production
Gindt, Applied microbiology and biotechnology 2024 - “...propionate was effectively blocked. Furthermore, deletion of genes encoding the lactate dehydrogenase ( ldh , bvu_2499 ) and the pyruvate:formate lyase ( pfl , bvu_2880 ) eliminated the formation of fermentative end products lactate and formate. By overproducing the transketolase (TKT, BVU_2318) in the triple deletion...”
- “...the genome This study P. vulgatus mcm ldh P. vulgatus with bvu _ 0309-0310, and bvu_2499 deleted from the genome This study P. vulgatus mcm ldh pfl P. vulgatus with bvu _ 0309-0310 , bvu_2499 , and bvu_2880 deleted from the genome This study P. vulgatus...”
- Genetic tools for the redirection of the central carbon flow towards the production of lactate in the human gut bacterium Phocaeicola (Bacteroides) vulgatus
Lück, Applied microbiology and biotechnology 2022 - “...biochemically characterized D-LDH from E. coli (b1380) was performed resulting in the identification of protein BVU_2499 as a potential D-LDH in P. vulgatus. The corresponding gene ( ldh ) was amplified including 250 bp of the upstream region by PCR using Q5 High-fidelity DNA polymerase and...”
- “...for N-terminal fusion to a recombinant protein IBA Gttingen, Germany pASK5_ ldh pASK-IBA5 derivative containing BVU_2499 from P. vulgatus DSM 1447 This study pG106 Vector with erythromycin resistance cassette ( erm F and erm AM), f1 origin, MCS, repB-mob region for Bacteroides replication Jones et al....”
5z20F / Q9I530 The ternary structure of d-lactate dehydrogenase from pseudomonas aeruginosa with nadh and oxamate (see paper)
48% identity, 97% coverage
- Ligand: 1,4-dihydronicotinamide adenine dinucleotide (5z20F)
Q9I530 D-lactate dehydrogenase (EC 1.1.1.28) from Pseudomonas aeruginosa (see 2 papers)
PA14_52270 D-lactate dehydrogenase (fermentative) from Pseudomonas aeruginosa UCBPP-PA14
PA0927 D-lactate dehydrogenase (fermentative) from Pseudomonas aeruginosa PAO1
48% identity, 96% coverage
- The Pseudomonas aeruginosa Complement of Lactate Dehydrogenases Enables Use of d- and l-Lactate and Metabolic Cross-Feeding
Lin, mBio 2018 - “...genome for loci encoding 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 )....”
- Diverse allosteric and catalytic functions of tetrameric d-lactate dehydrogenases from three Gram-negative bacteria
Furukawa, AMB Express 2014 - “...BL21(DE3) was isolated by ISOGEN (NIPPON GENE, Tokyo, Japan). The genes encoding the FN0511 (FNLDH), PA0927 (PALDH), and ECD_01352 (ECLDH) proteins (Genbank accession numbers: AAL94707.1, AAG04316.1, and ACT43236.1, respectively) were amplified via PCR using genomic DNA as templates. The primer pairs used were, 5-CGCTCGAGATGCAAAAAACTAAGATAATATTTTTTG-3 and 5-GGGATCCATTTATTGATTTTGTGGAACTTC-3...”
- “...the pa0927 gene, and 5-CGCATATGAAACTCGCCGTTTATAGC-3 and 5-CGGGATCCTTAAACCAGTTCGTTCGGGC-3 for the ecd_01352 gene. The amplified fn0511 , pa0927 , and ecd_01352 genes were inserted into T-vector pMD20 (TaKaRa Bio, Shiga, Japan). After purification of the plasmids carrying these genes, the plasmids were digested with restriction enzymes and the...”
- A gacS deletion in Pseudomonas aeruginosa cystic fibrosis isolate CHA shapes its virulence
Sall, PloS one 2014 - “...CHA affects the GacS regulator. (A) Genetic organization of gacS (PA0928, 2778 bp) and ldhA (PA0927, 990 bp) in PAO1. A 426 bp deletion in the CHA chromosome leads to 3 truncated gacS * and 5 truncated ldhA gene. The two 11-tandem imperfect repeats located into...”
- Intraclonal genome diversity of Pseudomonas aeruginosa clones CHA and TB
Bezuidt, BMC genomics 2013 - “...global regulator gacS (PA0928) and the first 278 nucleotides of the adjacent lactate dehydrogenase ldhA (PA0927) . This two-gene spanning deletion generated a double mutant of key genes of lifestyle and metabolism of P. aeruginosa [ 35 , 36 ]. Table 4 Strain-specific losses of PAO1...”
- Response of Burkholderia cenocepacia H111 to micro-oxia
Pessi, PloS one 2013 - “...be used by P. aeruginosa to generate energy and survive during anoxic growth (PA0835-36 and PA0927) [19] . The genes necessary for the conversion of pyruvate to lactate, acetate, and succinate, i.e. the acetate kinase ackA , the phosphate acetyltransferase pta and the lactate dehydrogenase ldhA...”
- Microcolony formation by the opportunistic pathogen Pseudomonas aeruginosa requires pyruvate and pyruvate fermentation
Petrova, Molecular microbiology 2012 - “...fermentation b Oxygen-limiting conditions Arginine fermentation Gene Fold change Gene Fold change Gene Fold change PA0927, ldhA 6.73 PA1580, gltA 24.24 PA5170, arcD 6.68 PA1400 (PycA) 5.12 PA0795, prpC 13.64 PA5171, arcA 3.38 PA0854, fumC2 9.55 PA1562, acnA 39.69 PA5172, arcB 3.18 PA5046 (Mdh) 3.38 PA1787,...”
- Regulation and Function of Versatile Aerobic and Anaerobic Respiratory Metabolism in Pseudomonas aeruginosa
Arai, Frontiers in microbiology 2011 - “...and phosphotransacetylase encoded by the ackA-pta operon (PA08350836) and NADH-dependent lactate dehydrogenase encoded by ldhA (PA0927) are responsible for pyruvate fermentation. ATP is produced by the acetate kinase activity. Lactate dehydrogenase functions for reoxidation of NADH produced by the pyruvate dehydrogenase activity. ANR and the integration...”
- Membrane-bound nitrate reductase is required for anaerobic growth in cystic fibrosis sputum
Palmer, Journal of bacteriology 2007 - “...California, Berkeley PA3875 PA1174 PA0519 PA0523 PA3392 PA5171 PA0927 PA0836 PA0835 Genea 4452 PALMER ET AL. periments. The concentrations of nitrate observed...”
- Long-term anaerobic survival of the opportunistic pathogen Pseudomonas aeruginosa via pyruvate fermentation
Eschbach, Journal of bacteriology 2004 - “...metabolism were identified. The gacS-ldhA operon (PA0926 and PA0927), encoding the sensor kinase GacS of a GacA/GacS component regulatory system and a potential...”
YPO2329 D-lactate dehydrogenase from Yersinia pestis CO92
YPTB2248 D-lactate dehydrogenase from Yersinia pseudotuberculosis IP 32953
49% identity, 97% coverage
alr0058 D-lactate dehydrogenase from Nostoc sp. PCC 7120
50% identity, 96% coverage
NMB1685 D-lactate dehydrogenase from Neisseria meningitidis MC58
52% identity, 94% coverage
swp_4333 D-lactate dehydrogenase from Shewanella piezotolerans WP3
48% identity, 98% coverage
- Condition-Specific Molecular Network Analysis Revealed That Flagellar Proteins Are Involved in Electron Transfer Processes of Shewanella piezotolerans WP3
Ding, Genetics research 2021 - “...value KEGG pathways Members 1 15 0.67 2.85 E 05 Pyruvate metabolism swp_1380, swp_5027, swp_4752, swp_4333, swp_3528, swp_2388, swp_2216, swp_2215, swp_2213, swp_2053, swp_1378, swp_1379, swp_4077, swp_0481, swp_0360 2 12 0.56 1.56 E 04 Ribosome swp_2008, swp_2030, swp_4802, swp_3049, swp_2027, swp_2028, swp_2025, swp_2007, swp_0208, swp_1998, swp_0427, swp_1556...”
NGO1336 putative dehydrogenase, lactate from Neisseria gonorrhoeae FA 1090
52% identity, 94% coverage
C645_RS00700, WP_005672300 2-hydroxyacid dehydrogenase from Haemophilus influenzae
50% identity, 98% coverage
- Access to highly specialized growth substrates and production of epithelial immunomodulatory metabolites determine survival of Haemophilus influenzae in human airway epithelial cells
Hosmer, PLoS pathogens 2022 - “...lldD , C645_RS09865, WP_005657875.1) or two gene fragment ( dld , C645_RS09380, WP_046067851.1; ldhA , C645_RS00700, WP_005672300; guaB , C645_RS01605, WP_005660592.1) were cloned into pGEMT-Easy (Promega) or pBluescriptIISK (Stratagene), respectively, yielding pGEM-Hi lldD , pBlu-Hi ldhA , pBlu-Hi dld , and pBlu-Hi ImpDH . Suitable restriction...”
- “..., C645_RS09865, WP_005657875.1) or two gene fragment ( dld , C645_RS09380, WP_046067851.1; ldhA , C645_RS00700, WP_005672300; guaB , C645_RS01605, WP_005660592.1) were cloned into pGEMT-Easy (Promega) or pBluescriptIISK (Stratagene), respectively, yielding pGEM-Hi lldD , pBlu-Hi ldhA , pBlu-Hi dld , and pBlu-Hi ImpDH . Suitable restriction enzyme...”
ETAE_1771 D-lactate dehydrogenase from Edwardsiella tarda EIB202
47% identity, 89% coverage
BP1026B_I0581 2-hydroxyacid dehydrogenase from Burkholderia pseudomallei 1026b
47% identity, 96% coverage
Q8EI78 D-lactate dehydrogenase (EC 1.1.1.28) from Shewanella oneidensis (see paper)
SO_0968, WP_011071244 lactate dehydrogenase LdhA from Shewanella oneidensis MR-1
SO0968 D-lactate dehydrogenase from Shewanella oneidensis MR-1
49% identity, 98% 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 - “...there are two alternative pathways with NDHs function, 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,...”
- Roles of d-Lactate Dehydrogenases in the Anaerobic Growth of Shewanella oneidensis MR-1 on Sugars
Kasai, Applied and environmental microbiology 2019 - GeneRIF: LdhA (an NADH-dependent d-LDH) works in concert with Dld (a quinone-dependent d-LDH) to transfer electrons from NADH to quinones during sugar catabolism in S. oneidensis MR-1.
- “...NADH oxidation activity of LdhA. The ldhA gene (SO_0968) exhibits homology to fermentative D-LDH genes of fermentative bacteria (14) and is thought to be...”
- Roles of d-Lactate Dehydrogenases in the Anaerobic Growth of Shewanella oneidensis MR-1 on Sugars.
Kasai, Applied and environmental microbiology 2019 - GeneRIF: LdhA (an NADH-dependent d-LDH) works in concert with Dld (a quinone-dependent d-LDH) to transfer electrons from NADH to quinones during sugar catabolism in S. oneidensis MR-1.
- “...NADH oxidation activity of LdhA. The ldhA gene (SO_0968) exhibits homology to fermentative D-LDH genes of fermentative bacteria (14) and is thought to be...”
- Metabolic Characteristics of a Glucose-Utilizing Shewanella oneidensis Strain Grown under Electrode-Respiring Conditions
Nakagawa, PloS one 2015 - “...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 involved in pyruvate...”
- Pyruvate and lactate metabolism by Shewanella oneidensis MR-1 under fermentation, oxygen limitation, and fumarate respiration conditions
Pinchuk, Applied and environmental microbiology 2011 - “...fermentative lactate dehydrogenase (LDH) encoded by ldhA (SO_0968), which demonstrated NADH-dependent pyruvate reductase activity in vitro (21), is likely to be...”
- “...to SO_4511, and SO_4512 to SO_4515). LdhA (SO_0968), fermentative lactate dehydrogenase; PDH (SO_0424 to SO_0426), pyruvate dehydrogenase complex; PflB...”
- An empirical strategy for characterizing bacterial proteomes across species in the absence of genomic sequences
Turse, PloS one 2010 - “...to acetate under anaerobic growth conditions. Similar to 2-oxoglutarate, the enzyme lactate dehydrogenase ( dld; SO0968) was only observed in HRCR-1 and HRCR-4 when the S. oneidensis MR-1 genome sequence was used to identify proteins in the isolates. When the S. putrefaciens CN32 genome sequence was...”
- Hydrogen metabolism in Shewanella oneidensis MR-1
Meshulam-Simon, Applied and environmental microbiology 2007 - “...gene (pdh; SO0424 to SO0426), and the gene SO0968 that has recently been shown to encode a pyruvate reductase (prdA) (Grigoriy Pinchuk, personal communication)....”
- “...A third pyruvate-metabolizing enzyme, the pyruvate reductase (SO0968), was also identified (Fig. 8), and lactate formation from pyruvate was observed under...”
- Global transcriptome analysis of the cold shock response of Shewanella oneidensis MR-1 and mutational analysis of its classical cold shock proteins
Gao, Journal of bacteriology 2006 - “...formate acetyltransferase; 3.8-fold induction), lactate (so0968 [ldhA], D-lactate dehydrogenase; 4.5-fold), and aceto-lactate (so3262 [ilvB], acetolactate...”
THTE_3348 2-hydroxyacid dehydrogenase from Thermogutta terrifontis
50% identity, 95% coverage
BCAL3179 probable D-lactate dehydrogenase from Burkholderia cenocepacia J2315
48% identity, 96% coverage
- Identification of functions linking quorum sensing with biofilm formation in Burkholderia cenocepacia H111
Inhülsen, MicrobiologyOpen 2012 - “...n.d. BCAM2142 5.3 n.d. n.d. BCAM2143 ( bapA ) 5.1 2.6 Energy production and conversion BCAL3179 ( ldhA ) 3.4 2.6 n.d. BCAL3285 ( hmpA ) 25.8 n.d. n.d. Defense mechanisms BCAM0200 9.2 15.0 n.d. BCAM0393 4.1 5.6 n.d. BCAS0293 ( aidA ) 167.2 24.0 BCAS0292...”
- “...were found to be QS-regulated only in strain H111: BCAL0121, BCAL0510, BCAL1678BCAL1681, BCAL1813, BCAL1921, BCAL3178, BCAL3179, BCAL3285, BCAM0028, BCAM0030, BCAM0393, BCAM0835, BCAM2140BCAM2143, BCAM2308, BCAM2720, BCAS0236, and BCAS0498 ( Table 1 ). We found that a large proportion of the QS-regulated proteins was not among the QS-regulated...”
- Burkholderia cenocepacia differential gene expression during host-pathogen interactions and adaptation to the host environment
O'Grady, Frontiers in cellular and infection microbiology 2011 - “...Conserved hypothetical protein 2.19 BCAL3109 Urease accessory protein 1.69 BCAL3178 LysR family regulatory protein 1.72 BCAL3179 Probable d -lactate dehydrogenase 1.91 BCAL3211 Conserved hypothetical protein 1.66 BCAL3227 Conserved hypothetical protein 2.10 BCAL3231 Hypothetical protein 1.63 BCAL3234 Glycosyltransferase 1.69 BCAL3239 Glucosyltransferase 1.84 BCAL3368 Putative regulatory protein 1.85...”
PP1649, PP_1649 D-lactate dehydrogenase from Pseudomonas putida KT2440
46% identity, 94% coverage
WP_049588155 2-hydroxyacid dehydrogenase from Pseudomonas putida KT2440
46% identity, 96% coverage
Thicy_1457 2-hydroxyacid dehydrogenase from Thiomicrospira cyclica ALM1
50% identity, 98% coverage
- Complete genome sequence of the haloalkaliphilic, obligately chemolithoautotrophic thiosulfate and sulfide-oxidizing γ-proteobacterium Thioalkalimicrobium cyclicum type strain ALM 1 (DSM 14477(T))
Kappler, Standards in genomic sciences 2016 - “...oxaloacetate (PEP synthase, Thicy_1283, EC 2.7.9.2; PEP carboxylase, Thicy_1240, EC 4.1.1.31) or lactate (D-lactate dehydrogenase, Thicy_1457, 1.1.1.28) The TCA cycle of T. cyclicum is incomplete, with genes encoding the 2-oxoglutarate dehydrogenase or homologous enzymes (e.g. 2-oxoglutarate:ferredoxin oxidoreductase, KorAB) not having been identified in the genome. This...”
L21SP2_2897 2-hydroxyacid dehydrogenase from Salinispira pacifica
50% identity, 99% coverage
HtpH / b1380 D-lactate dehydrogenase (EC 1.1.1.28) from Escherichia coli K-12 substr. MG1655 (see 4 papers)
ldhA / P52643 D-lactate dehydrogenase (EC 1.1.1.28) from Escherichia coli (strain K12) (see 22 papers)
ldhA D-lactate dehydrogenase; EC 1.1.1.28 from Escherichia coli K12 (see 7 papers)
P52643 D-lactate dehydrogenase from Escherichia coli (strain K12)
NP_415898 D-lactate dehydrogenase from Escherichia coli str. K-12 substr. MG1655
b1380 D-lactate dehydrogenase from Escherichia coli str. K-12 substr. MG1655
47% identity, 98% coverage
- Systems biology approach for enhancing limonene yield by re-engineering Escherichia coli
Khanijou, NPJ systems biology and applications 2024 - “...study. CRISPR Cas9-assisted recombineering method as described previously 106 was used to delete ldhA (UniProt P52643) and adhE (UniProt P0A9Q7) genes from the E. coli MG1655 strain, resulting in LDH and ALDH-ADH knockouts, respectively. The ldhA and adhE regions of three successfully knockout strains were PCR...”
- Comparative genomics of the closely related fungal genera Cryptococcus and Kwoniella reveals karyotype dynamics and suggests evolutionary mechanisms of pathogenesis
Coelho, PLoS biology 2024 - “...proteins from C . neoformans (UniProt J9VFV7), Aspergillus fischeri (UniProt A1D163), and Escherichia coli (UniProt P52643) showing structural similarity. Pairwise structure alignments were performed and visualized in the Protein Data Bank (PDB) website ( https://www.rcsb.org/alignment ) using the JjFATCAT-rigid algorithm. The phylogenetic tree file is provided...”
- “...AlphaFold-predicted structures of Cryptococcus neoformans (UniProt J9VFV7), Aspergillus fischeri (UniProt A1D163), and Escherichia coli (UniProt P52643) are individually displayed at the top. Pairwise structure alignments with the C . neoformans protein were conducted with the JjFATCAT-rigid algorithm on the Protein Data Bank website ( https://www.rcsb.org/alignment )....”
- Comparative genomics of Cryptococcus and Kwoniella reveals pathogenesis evolution and contrasting karyotype dynamics via intercentromeric recombination or chromosome fusion.
Coelho, bioRxiv : the preprint server for biology 2024 - “...dehydrogenease proteins from C. neoformans (UniProt J9VFV7), Aspergillus fischeri (UniProt A1D163), and Escherichia coli (UniProt P52643) showing structural similarity. Pairwise structure alignments were performed and visualized in the Protein Data Bank (PDB) website ( https://www.rcsb.org/alignment ) using the JjFATCAT-rigid algorithm. Fig 9. Proposed model of chromosome...”
- A global analysis of function and conservation of catalytic residues in enzymes
Ribeiro, The Journal of biological chemistry 2020 (secret) - The Escherichia coli proteome: past, present, and future prospects
Han, Microbiology and molecular biology reviews : MMBR 2006 - “...5.11/44,335 5.15/44,053 4.70/22,351 5.15/43,951 5.00/74,518 IdhA P52643 D-Lactate IlvA P04968 IlvB P08142 IlvC dehydrogenase (DIGE 4.5-6.5) (DIGE 4.5-6.5)...”
- “...11, 2017 by University of California, Berkeley P52643 P04816 5.29/36,534.79 Experimentald LdhA LivK dehydrogenase pI/MW Theoreticalc ESCHERICHIA COLI PROTEOME...”
- ldhA-induced persister in Escherichia coli is formed through accidental SOS response via intracellular metabolic perturbation.
Yamamoto, Microbiology and immunology 2022 (PubMed)- GeneRIF: ldhA-induced persister in Escherichia coli is formed through accidental SOS response via intracellular metabolic perturbation.
- Stochastic expression of lactate dehydrogenase A induces Escherichia coli persister formation.
Yamamoto, Journal of bioscience and bioengineering 2018 (PubMed)- GeneRIF: LdhA-mediated persister formation pathway is different from previously reported persister formation via repression of aerobic metabolism.
- Production of succinate by a pflB ldhA double mutant of Escherichia coli overexpressing malate dehydrogenase.
Wang, Bioprocess and biosystems engineering 2009 (PubMed)- GeneRIF: The gene encoding malate dehydrogenase (MDH) was overexpressed in a pflB ldhA double mutant, NZN111, for succinic acid production.
- Eliminating side products and increasing succinate yields in engineered strains of Escherichia coli C.
Jantama, Biotechnology and bioengineering 2008 (PubMed)- GeneRIF: Deletion of the E. coli ldhA gene (together with deletions of other ferementation disruption genes) increased production of succinate
- FastKnock: an efficient next-generation approach to identify all knockout strategies for strain optimization
Hassani, Microbial cell factories 2024 - “...0.16 5.11 9.50 1.41E-2 b1241 LCADi_copy2 Double ADHEr, LDH_D 0.15 8.08 9.51 1.43E-2 b1241, b2133, b1380 LCADi_copy2 Triple ADHEr, LDH_D, PFL 0.12 11.08 12.73 1.53E-2 b1241, b2133, b1380, b3114, b0902, b3951 LCADi_copy, OBTFL Quadruple ADHEr, LDH_D, PFL, THD2 0.11 12.29 13.01 2.58E-2 b1241, b2133, b1380, b3114,...”
- “...b1602 LCADi_copy, OBTFL Quintuple ADHEr, LDH_D, GLUDy, PFL, THD2 0.10 12.34 13.06 2.61E-2 b1241, b2133, b1380, b1761, b3114, b0902, b3951, b1602 LCADi_copy, OBTFL Fig.2 Production envelopes for the best solutions presented in Table 3 regarding succinate production from single to quintuple reaction deletions in iJR904. Knocking...”
- Genetic tools for the redirection of the central carbon flow towards the production of lactate in the human gut bacterium Phocaeicola (Bacteroides) vulgatus
Lück, Applied microbiology and biotechnology 2022 - “...VA, USA). BLASTp analysis ( https://www.ncbi.nlm.nih.gov/ ) using the biochemically characterized D-LDH from E. coli (b1380) was performed resulting in the identification of protein BVU_2499 as a potential D-LDH in P. vulgatus. The corresponding gene ( ldh ) was amplified including 250 bp of the upstream...”
- NtrBC and Nac contribute to efficient Shigella flexneri intracellular replication
Waddell, Journal of bacteriology 2014 - “...flexneri genes regulated by Naca Annotationc b1380 Fermentative d-lactate dehydrogenase, NAD dependent Predicted protein potentially involved in detoxification...”
- “...involved in cellular respiration, such as ldhA (b1380), which encodes the NADdependent lactate dehydrogenase, and cybB (b1418), which encodes cytochrome b561....”
- 18th Congress of the European Hematology Association, Stockholm, Sweden, June 13–16, 2013
, Haematologica 2013 - Deletion of genes encoding cytochrome oxidases and quinol monooxygenase blocks the aerobic-anaerobic shift in Escherichia coli K-12 MG1655
Portnoy, Applied and environmental microbiology 2010 - “...b2925 b2097 b3919 b1779 b2926 b2779 b1380 b3713 b1004 b4151-b4154 b0721-b0724 b2288-b2276 Phosphoglucose isomerase 6-Phosphofructose kinase Fructose...”
- Differential gene expression for investigation of Escherichia coli biofilm inhibition by plant extract ursolic acid
Ren, Applied and environmental microbiology 2005 - “...0.0055 1.8 hycI b2717 1.3 0.0434 1.7 0.0103 1.2 ldhA narZ b1380 b1468 1.0 1.0 0.7186 0.8904 1.7 0.0008 1.4 0.0057 1.1 1.8 miaA b4171 1.4 0.0002 1.7 0.0189 1.1...”
- DNA microarray analyses of the long-term adaptive response of Escherichia coli to acetate and propionate
Polen, Applied and environmental microbiology 2003 - “...0.91 b1370 yi52_5 1 IS5 transposase 0.57* 0.47* 0.96 b1380 IdhA 1 Fermentative D-lactate dehydrogenase, NAD 3.27* 1.78 1.80* b1480 rpsV 1 30S ribosomal subunit...”
A0A140N893 D-lactate dehydrogenase (EC 1.1.1.28) from Escherichia coli (see 2 papers)
ECs2002 fermentative D-lactate dehydrogenase from Escherichia coli O157:H7 str. Sakai
UTI89_C1623 fermentative D-lactate dehydrogenase, NAD-dependent from Escherichia coli UTI89
Z2329 fermentative D-lactate dehydrogenase, NAD-dependent from Escherichia coli O157:H7 EDL933
ECD_01352 D-lactate dehydrogenase from Escherichia coli BL21(DE3)
47% identity, 98% coverage
- Gene expression induced in Escherichia coli O157:H7 upon exposure to model apple juice
Bergholz, Applied and environmental microbiology 2009 - “...Energy metabolism ECs0117 ECs0512 ECs1054 ECs1487 ECs1862 ECs2002 ECs2056 ECs2078 ECs2132 ECs2239 ECs2511 ECs2583 ECs3346 ECs3527 ECs4217 ECs4355 ECs4399...”
- Glycosuria Alters Uropathogenic Escherichia coli Global Gene Expression and Virulence
Islam, mSphere 2022 - “...0.0150 1.1007* 1.0980* Class 1 fructose-bisphosphatase Pyruvate metabolism UTI89_C0974 pflB 0.7838 1.6661* 2.4615* Formate C-acetyltransferase UTI89_C1623 ldhA 0.4059 2.1198* 1.7317* d -Lactate dehydrogenase UTI89_C1637 aldA 1.0333 1.7415* 2.7567* Aldehyde dehydrogenase UTI89_C2581 pta 0.4943 0.7184 1.2222* Phosphate acetyltransferase UTI89_C3247 0.5758 2.5276* 3.0862* Acetyl-CoA C-acetyltransferase UTI89_C4547 ppc 0.3527...”
- Characterizing the Escherichia coli O157:H7 proteome including protein associations with higher order assemblies
Pieper, PloS one 2011 - “...protein Z0009 mogA 21222 CY, Ho-3 9.39E-07 0 1939 81 cofactor biosynthesis C3 D-lactate dehydrogenase Z2329 ldhA 36519 CY 1.93E-05 92 2477 109 mixed acid fermentation C3 ureidoglycolate dehydrogenase Z0672 ylbC 37889 CY 7.88E-04 0 666 43 allantoin assimilation C3 D-glucuronate/galacturonate isomerase Z4445 uxaC 53927 CY...”
- Diverse allosteric and catalytic functions of tetrameric d-lactate dehydrogenases from three Gram-negative bacteria
Furukawa, AMB Express 2014 - “...by ISOGEN (NIPPON GENE, Tokyo, Japan). The genes encoding the FN0511 (FNLDH), PA0927 (PALDH), and ECD_01352 (ECLDH) proteins (Genbank accession numbers: AAL94707.1, AAG04316.1, and ACT43236.1, respectively) were amplified via PCR using genomic DNA as templates. The primer pairs used were, 5-CGCTCGAGATGCAAAAAACTAAGATAATATTTTTTG-3 and 5-GGGATCCATTTATTGATTTTGTGGAACTTC-3 for the fn0511...”
- “...gene, 5-CGCATATGCGCATCCTGTTCTTCAGCAG-3 and 5- CGGGATCCTCAGGCCCGGACCCGATTG-3 for the pa0927 gene, and 5-CGCATATGAAACTCGCCGTTTATAGC-3 and 5-CGGGATCCTTAAACCAGTTCGTTCGGGC-3 for the ecd_01352 gene. The amplified fn0511 , pa0927 , and ecd_01352 genes were inserted into T-vector pMD20 (TaKaRa Bio, Shiga, Japan). After purification of the plasmids carrying these genes, the plasmids were...”
SYNPCC7002_G0164 fermentative lactate dehydrogenase from Synechococcus sp. PCC 7002
48% identity, 98% coverage
- L-Lactate treatment by photosynthetic cyanobacteria expressing heterogeneous L-lactate dehydrogenase
Kato, Scientific reports 2023 - “...strains The pUC118-based vectors, harboring the trc promoter and homology arms for the ldhA gene (SYNPCC7002_G0164) in the pAQ7 plasmid of Synechococcus sp., were used to introduce the lldD and lldP genes from E. coli via homologous recombination. The codon-optimized genes of LldD (NP_418062.1) and LldP...”
- Transcription Profiling of the Model Cyanobacterium Synechococcus sp. Strain PCC 7002 by Next-Gen (SOLiD™) Sequencing of cDNA
Ludwig, Frontiers in microbiology 2011 - “...0.84 0.11 1.26 pntC Transhydrogenase, chain alpha, part 2 LACTATE DEHYDROGENASE, ALCOHOL DEHYDROGENASE AND HYDROGENASE SYNPCC7002_G0164 0.48 0.24 0.14 0.61 0.63 ldhA Fermentative lactate dehydrogenase SYNPCC7002_A1838 0.64 1.29 1.07 0.83 0.65 acsA Acetate-CoA ligase SYNPCC7002_A2015 0.77 2.37 0.46 0.19 0.94 acs Acetyl-CoA synthetase SYNPCC7002_A0868 0.59 1.10...”
- “...such a connection would provide to cells under fermentative conditions. Interestingly, transcript levels for ldhA (SYNPCC7002_G0164, d -lactate dehydrogenase), acsA (SYNPCC7002_A1838, acetyl-CoA ligase), acs (SYNPCC7002_A2015, acetyl-CoA synthetase), and two putative adh genes (alcohol dehydrogenases, SYNPCC7002_A0868 and SYNPCC7002_A2590) were similar under all conditions tested in this study....”
M634_18815 2-hydroxyacid dehydrogenase from Vibrio parahaemolyticus O1:Kuk str. FDA_R31
47% identity, 97% coverage
C9I78_22190 2-hydroxyacid dehydrogenase from Vibrio parahaemolyticus
47% identity, 97% coverage
4cukA / Q8Z780 Structure of salmonella d-lactate dehydrogenase in complex with nadh
46% identity, 98% coverage
- Ligand: 1,4-dihydronicotinamide adenine dinucleotide (4cukA)
slr1556 2-hydroxyaciddehydrogenase from Synechocystis sp. PCC 6803
48% identity, 98% coverage
- Review of recent advances in improvement strategies for biofuels production from cyanobacteria
Mescouto, Heliyon 2024 - “...al. (2013) [ 68 ] redirected carbon flow to acyl-ACP and overexpressed both slr0168 and slr1556 gene loci in Synechocystis sp. PCC 6803, which resulted in 1.3% dry cell weight, an increase by 8.3 times compared to the wild-type. Varman et al. (2012) [ 69 ]...”
- “...with the hpcB gene to improve isoprene production [ 68 ] Overexpression of slr0168 and slr1556 gene for alcohol production [ 69 ] Co-overexpression of slr1037 genes as well as sll0039 to increase the tolerance for production of isobutanol [ 71 ] Overexpression of sRNA Nc117...”
- Sustainable production of photosynthetic isobutanol and 3-methyl-1-butanol in the cyanobacterium Synechocystis sp. PCC 6803
Xie, Biotechnology for biofuels and bioproducts 2023 - “...used to generate strains in Fig.3B-E. P1 and P2 are integrative plasmids targeting ddh ( slr1556 ) site of Synechocystis chromosome. P3 and P4 are integrative plasmids targeting slr0168 site. P5 is a self-replicating plasmid. B The IB titer and IB production per cell on day...”
- “...carboxylase; PDH (encoded by slr1934 and sll1721 ), pyruvate dehydrogenase E1 component; Ddh (encoded by slr1556 ), D-lactate dehydrogenase; LeuA (encoded by slr0186 and sll1564 ), 2-isopropylmalate synthase. Abbreviations of intermediates: PEP, phosphoenolpyruvate. D The relative 3M1B titer of engineered Synechocystis strains HX56, HX61-63, HX78 and...”
- Regulation of organic acid and hydrogen production by NADH/NAD+ ratio in Synechocystis sp. PCC 6803
Akiyama, Frontiers in microbiology 2023 - “...by acetate kinase ( ackA ) (sll1299), lactate by d -lactate dehydrogenase ( ddh ) (slr1556), and four-carbon dicarboxylic acids by malate dehydrogenase (MDH) (encoded by citH ) (sll0891), fumarase ( fumC ) (slr0018), and succinate dehydrogenase ( sdhA, sdhB ) (slr1233, sll0823, sll1625) (as illustrated...”
- Mapping competitive pathways to terpenoid biosynthesis in Synechocystis sp. PCC 6803 using an antisense RNA synthetic tool
Rodrigues, Microbial cell factories 2023 - “...sqs sll0513 Squalene synthase FPP Hopanoids thiG slr0633 Thiamine synthase DXP Vitamin B 1 ddH slr1556 d - Lactate dehydrogenase Pyruvate Lactate pepc sll0920 Phosphoenolpyruvate carboxylase PEP Central-carbon metabolism atpB sll1324 -subunit of ATP synthase ADP+Pi ATP synthesis gpi slr1349 Glucose 6-phosphate isomerase F6P/G6P Sugar metabolism...”
- “...to the pyruvate consumption, we also included the gene encoding lactate dehydrogenase ( ddh , slr1556 ) in this exploratory study. A previously reported flux balance analysis (FBA) indicated a possible increase in isoprene production when reducing the carbon flow through the step catalysed by phosphoenolpyruvate...”
- Expressing 2-keto acid pathway enzymes significantly increases photosynthetic isobutanol production
Xie, Microbial cell factories 2022 - “...the N-terminal; Kivd S286T , IlvD , and Slr1192 OP expressed in the ddh ( slr1556 ) site of chromosome was Flag-tagged at the N-terminal; AlsS expressed in the ddh ( slr1556 ) site of chromosome was His-tagged at the N-terminal. B Growth curves of the...”
- “...N-terminal; IlvC, IlvD, Slr1192 OP , and Kivd S286T expressed in either the ddh ( slr1556 ) site or the slr0168 site of chromosome was Flag-tagged at the N-terminal. AlsS expressed in the ddh ( slr1556 ) site of chromosome was His-tagged at the N-terminal. B...”
- Insights into cyanobacterial alkane biosynthesis
Parveen, Journal of industrial microbiology & biotechnology 2022 - “...sp. PCC6803 Overexpression of two copies of native AAR and ADO in both slr0168 and slr1556 loci 11 mg/g DCW Wang et al. ( 2013 ) Heptadecane N. punctiforme PCC73102 Co-overexpression of extra copies of AAR and ADO encoded by Npun_F1710/Npun_F1711 and lipase encoded by Npun_F5141...”
- Genetic, Genomics, and Responses to Stresses in Cyanobacteria: Biotechnological Implications
Cassier-Chauvat, Genes 2021 - “...bisabolene [ 325 ] slr0168 and slr1193 Photoproduction of ethanol [ 326 ] slr0168 and slr1556 Photoproduction of alkanes [ 327 ] ndhB and slr0168 Photoproduction of ethanol [ 315 ] psbA1 and slr0168 Analysis of promoters [ 328 ] psbA2 and slr0168 Photoproduction of fatty-acids...”
- Expression of cyanobacterial genes enhanced CO2 assimilation and biomass production in transgenic Arabidopsis thaliana
Abbasi, PeerJ 2021 - “...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) were selected to construct a plant expression...”
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SPA1239 D-lactate dehydrogenase from Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150
46% identity, 98% coverage
- Identification of in vivo-induced bacterial proteins during human infection with Salmonella enterica serotype Paratyphi A
Alam, Clinical and vaccine immunology : CVI 2013 - “...nutrient acquisition, cellular processes SPA0489 SPA0608 SPA0652 SPA1239 SPA1734 SPA2362 SPA2948 SPA4117 Mobile and extrachromosomal element functions a SPA2397...”
- “...metabolism and cellular processes (SPA0489, SPA0608, SPA0652, SPA1239, SPA1734, SPA2362, SPA2948, and SPA4117), and anti- 714 cvi.asm.org microbial resistance...”
VPA0144 D-lactate dehydrogenase from Vibrio parahaemolyticus RIMD 2210633
47% identity, 97% coverage
- Insights into Vibrio parahaemolyticus CHN25 response to artificial gastric fluid stress by transcriptomic analysis
Sun, International journal of molecular sciences 2014 - “...Chn25A_1034 0.4695 Putative acyl-CoA thiolase VPA0611 Chn25A_1091 0.3706 Acetate kinase VPA0372 Chn25A_0367 3.9537 Phosphoenolpyruvate synthase VPA0144 Chn25A_0145 0.4364 d -lactate dehydrogenase VP2881 Chn25_2801 3.0293 Acetyl-CoA carboxylase, biotin carboxylase subunit VP2878 Chn25_2798 2.514 Acetyl-CoA synthetase VP2545 Chn25_2479 2.1607 Oxaloacetate decarboxylase subunit gamma VP2517 Chn25_2451 3.4256 Dihydrolipoamide dehydrogenase...”
CLNEO_28010 2-hydroxyacid dehydrogenase from Anaerotignum neopropionicum
50% identity, 98% coverage
VCA0192 D-lactate dehydrogenase from Vibrio cholerae O1 biovar eltor str. N16961
46% identity, 98% coverage
- Exploration of the effects of a degS mutant on the growth of Vibrio cholerae and the global regulatory function of degS by RNA sequencing
Huang, PeerJ 2019 - “...degradation VCA0007, VC2638, VCA0829 0.0328662 PATH:00620 Pyruvate metabolism VC1819, VC2738, VC0794, VC1304, VC0485, VC0432, VC2638, VCA0192, VC2646 0.0334527 Gene-Act network analysis To further explore the relationships among these differentially expressed genes, a Gene-Act network was constructed based on the genes and genetic relationships, including activation, binding,...”
- “...hydratase, class I), VC2090 (the succinate dehydrogenase hydrophobic membrane anchor protein), VC0794 (hypothetical protein) and VCA0192 (D-lactate dehydrogenase), were involved in multiple cellular metabolic pathways, as mentioned in Table 1 above. We also found that VCA0278 (serine hydroxymethyltransferase), VCA0666 (L-serine dehydratase 1), VCA0875 (D-serine dehydratase), VC0027...”
PN96_16785 2-hydroxyacid dehydrogenase from Vibrio natriegens NBRC 15636 = ATCC 14048 = DSM 759
45% identity, 97% coverage
- Metabolic engineering of Vibrio natriegens for anaerobic succinate production
Thoma, Microbial biotechnology 2022 - “...pfl genes encoding d lactate dehydrogenase, l lactate dehydrogenase and pyruvate formate lyase (locus tags: PN96_16785, PN96_16800 and PN96_08455) Hoffart etal . ( 2017 ) V. natriegens lldh dldh pfl ald V. natriegens lldh dldh pfl with additional deletion of the ald gene encoding alanine dehydrogenase...”
- Metabolic engineering of Vibrio natriegens
Thoma, Essays in biochemistry 2021 - “...optimized process conditions. For the anaerobic alanine production, the lldh and dldh genes (PN96_16800 and PN96_16785) encoding l - and d -lactate dehydrogenase, the pfl gene (PN96_08455) coding for the pyruvate formate lyase and the malate dehydrogenase encoding gene mdh (PN96_11695) were deleted, which avoided/reduced by-product...”
PHYSODRAFT_503916 hypothetical protein from Phytophthora sojae
48% identity, 98% coverage
- Insights into the adaptive response of the plant-pathogenic oomycete Phytophthora capsici to the fungicide flumorph
Pang, Scientific reports 2016 - “...protein PHYSODRAFT_284882 Nucleobase-containing compound metabolism 348677381 Hypothetical protein PHYSODRAFT_354553 Nucleobase-containing compound metabolism 348677150 hypothetical protein PHYSODRAFT_503916 Nucleobase-containing compound metabolism 348673952 Hypothetical protein PHYSODRAFT_286691 Nucleobase-containing compound metabolism 348672301 hypothetical protein PHYSODRAFT_547952 Nucleobase-containing compound metabolism 348671618 Hypothetical protein PHYSODRAFT_435859 Nucleobase-containing compound metabolism 348670008 hypothetical protein PHYSODRAFT_347790 Nucleobase-containing compound...”
SPAC186.07c hydroxyacid dehydrogenase (predicted) from Schizosaccharomyces pombe
46% identity, 95% coverage
ZMO_RS05565 2-hydroxyacid dehydrogenase from Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821
ZMO1237 D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding protein from Zymomonas mobilis subsp. mobilis ZM4
46% identity, 96% coverage
- Molecular mechanism of engineered Zymomonas mobilis to furfural and acetic acid stress
Shabbir, Microbial cell factories 2023 - “...in both strains (Additional file 1 : Tables S7, 8, S9, S10). ZMO_RS03395 (hydroxyacylglutathione hydrolase), ZMO_RS05565 (2-hydroxy acid dehydrogenase), ZMO_RS05445 (glucose-6-phosphate isomerase), ZMO_RS03970 (galactose-1-epimerase), and ZMO_RS05445 (glucose-6-phosphate isomerase) were up-regulated in ZM532 (Additional file 1 : Tables S7, S10). These genes may partly account for the...”
- Engineering Zymomonas mobilis for the Production of Xylonic Acid from Sugarcane Bagasse Hydrolysate
Herrera, Microorganisms 2021 - “...by homologous recombination. Target genes were ZMO_RS04375 (old locus tag ZMO0976, an aldo/keto reductase) and ZMO_RS05565 (old locus tag ZMO1237, a D-lactate dehydrogenase). Primers used for construction of gene deletion cassettes and to confirm events of integration and marker excision are listed in Table S1 ....”
- Improvement of Acetaldehyde Production in Zymomonas mobilis by Engineering of Its Aerobic Metabolism
Kalnenieks, Frontiers in microbiology 2019 - “...II respiratory NADH dehydrogenase CAGATGGCCGATACAGTTTTTGA AATGCAGGCGATAGAGCGAGTTA ldh (ZMO_RS01110) FAD-dependent respiratory lactate dehydrogenase TTGCGGCGAAATACGGAAAAGAT ATAACGCGGCAAGAAACTGACACG ldh (ZMO_RS05565) NAD-dependent lactate dehydrogenase ACTTCGGCATTGGCTTCGTC CGCGTCGCAATATTCAGTTCC ald (Zmob_1390) Aldehyde dehydrogenase CGTATCGCGGGACCGTATCTGA GCGCCCGCTTCTTCCAAAAC cat (ZMO_RS04105) Catalase TCGCCCTTTGAAAACGCATCCTA AACGGGCTTTTTCATCCTCTTTCA gap (ZMO_RS00775) Glyceraldehyde 3 P dehydrogenase ACCCCGGATGTCAGCCTTGTTG GGAGCTGTGCGGATCGGAGTAGAA glk (ZMO_RS01580) Glucokinase GCCGCTTTGGATCGCTTCTGCT ACCGACACCACCGCCAATAACAAC zwf...”
- Characterization and Application of the Sugar Transporter Zmo0293 from Zymomonas mobilis
Zhang, International journal of molecular sciences 2023 - “...ED pathway genes possess the same expression level, ZMO1236 ( adhA , encoding alcohol dehydrogenase), ZMO1237 ( ldhA , encoding D-lactate dehydrogenase), ZMO1570 ( pflB , encoding formate acetyltransferase), ZMO0178 ( pgk , encoding phosphoglycerate kinase), ZMO1240 ( gpmA , encoding 2,3-diphosphoglycerate-dependent phosphoglycerate mutase), and ZMO1496...”
- “...0.22 0.09 1.01 0.45 1.68 ZMO1236 adhA alcohol dehydrogenase 1 0.96 0.59 1 0.23 1.32 ZMO1237 ldhA D-Lactate dehydrogenase 1.06 0.9 0.51 1 0.97 6.14 ZM01754 ssdA aldehyde dehydrogenase (NAD + ) 1.05 1.14 0.73 1 1.53 4.85 ZMO1722 adhC class III alcohol dehydrogenase 0.91 0.39...”
- Metabolic engineering of Zymomonas mobilis for co-production of D-lactic acid and ethanol using waste feedstocks of molasses and corncob residue hydrolysate
Hu, Frontiers in bioengineering and biotechnology 2023 - “...al., 2019 ). Z. mobilis ZM4 has two homologous proteins encoding lactate dehydrogenase (ZMO0256 and ZMO1237) and can produce less than 1g/L lactate ( Yang et al., 2016 ; Martien et al., 2019 ). Lactate production can be further increased when heterologous lactate dehydrogenase genes were...”
- Engineering Zymomonas mobilis for the Production of Xylonic Acid from Sugarcane Bagasse Hydrolysate
Herrera, Microorganisms 2021 - “...genes were ZMO_RS04375 (old locus tag ZMO0976, an aldo/keto reductase) and ZMO_RS05565 (old locus tag ZMO1237, a D-lactate dehydrogenase). Primers used for construction of gene deletion cassettes and to confirm events of integration and marker excision are listed in Table S1 . Briefly, upstream and downstream...”
- “...by-product which is toxic to the cells [ 54 ]. To reduce other by-products formation, ZMO1237 was also deleted. This gene codes for a lactate dehydrogenase which produces lactate from pyruvate mainly under aerobioses [ 55 ], a condition that would benefit xylonic acid formation due...”
- Investigation of the impact of a broad range of temperatures on the physiological and transcriptional profiles of Zymomonas mobilis ZM4 for high-temperature-tolerant recombinant strain development
Li, Biotechnology for biofuels 2021 - “...8.5 ZMO0740 General stress protein CsbD 3.06 8.03 ZMO1113 FAD-dependent pyridine nucleotide-disulfide oxidoreductase 1.62 8.34 ZMO1237 Lactate dehydrogenase 2.82 9.39 ZMO1522 TonB-dependent receptor 1.01 3.88 ZMO1533 Hypothetical protein 3.01 12.07 ZMO1754 Succinate-semialdehyde dehydrogenase SSADH 3.95 11.33 ZMO1776 Aminopeptidase N 1.97 9.64 ZMO1940 Hypothetical protein 4.87 7.45...”
- The Magnesium Concentration in Yeast Extracts Is a Major Determinant Affecting Ethanol Fermentation Performance of Zymomonas mobilis
Li, Frontiers in bioengineering and biotechnology 2020 - “...protein 1.30 2.21 ZMO0740 General stress protein CsbD 1.44 2.56 ZMO1521 Hypothetical protein 1.70 2.41 ZMO1237 Lactate dehydrogenase 1.70 2.19 ZMO1289 Putative transglycosylase-associated protein 2.06 3.23 ZMO1522 TonB-dependent receptor 2.75 3.88 Down-regulated gene in ZM4 cultured in RM OXOID compared with RM BD ZMO0934 Secretion-related protein...”
- Establishment and application of a CRISPR-Cas12a assisted genome-editing system in Zymomonas mobilis
Shen, Microbial cell factories 2019 - “...target a sequence on the coding or noncoding strand of a lactate dehydrogenase encoding gene ZMO1237 ( ldh ). We next assayed the DNA cleavage activity of the exogenously introduced CRISPRCas12a system. To this end, the self-targeting plasmids were individually introduced into either ZM4 or ZM4-Cas12a...”
- “...Identification of edited genes To identify positive clones with nucleotide substitutions of the ldh ( ZMO1237 ) open reading frame, colony PCR was conducted using primers Ldh-check-F/R. PCR products were digested with Pst I. To confirm the deletion (or the replacement) of native gene, colonies with...”
- Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032
Yang, Biotechnology for biofuels 2018 - “...- wecH - tetA cassette was found to be inserted at the 3 end of ZMO1237 ( ldhA ). Interestingly in 2032, integration of P gap_xylA - xylB - yiaB - yiaA - wecH - tetA led to a duplication of xylA and partial duplication of...”
- “...to 708bp (in both 2032 and 8b) 10155321015532 Promoter of ZMO0998 C to T 12639841265916 ZMO1237 ( ldhA ) 11bp (CATGGGTCATA) deletion and 2881-bp duplicated Pgap-xylA xylB inserted into ZMO1237 (ldhA) 3-end, with ZMO1237 shorten from 996bp to 498bp 12659171266864 ZMO1237 ( ldhA ) Duplicated downstream...”
- Metabolic engineering of Zymomonas mobilis for 2,3-butanediol production from lignocellulosic biomass sugars
Yang, Biotechnology for biofuels 2016 - “...5 d). We had previously shown that the expression levels of the lactate dehydrogenase gene ZMO1237 were more abundant under aerobic conditions [ 63 ], and the expression of another d -lactate dehydrogenase gene, ZMO0256, was upregulated in the ethanol-treated cells during stationary phase [ 57...”
- “...9C, used in this study, is a derivative of Z. mobilis 8b in which the ZMO1237 gene was inactivated [ 37 ]. Therefore, ZMO1237 may play the major role in lactate production under aerobic conditions. However, another lactate dehydrogenase gene, ZMO0256, could also be activated under...”
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MAC_03964 putative dehydrogenase tr07 from Metarhizium acridum
47% identity, 92% coverage
- Role of MicroRNA-Like RNAs in the Regulation of Spore Morphological Differences in the Entomopathogenic Fungus Metarhizium acridum
Zhang, Polish journal of microbiology 2022 - “...selected six DEMs (bta-miR-150, bta-miR-328, cgr-miR-132, efu-miR-30b, efu-miR-7a, and sly-miR482c) and six DEGs (MAC_02738, MAC_03363, MAC_03964, MAC_07508, MAC_07780, and MAC_08938) to validate the accuracy of the milRNA and mRNA sequencing data using qRT-PCR. As shown in Fig. 7 , all expression patterns showed similar trends. The...”
tlr0711 D-lactate dehydrogenase from Thermosynechococcus elongatus BP-1
45% identity, 98% coverage
H16_A1681 D-Lactate dehydrogenase from Ralstonia eutropha H16
H16_A1682 D-Lactate dehydrogenase from Ralstonia eutropha H16
H16_A1681, H16_A1682 2-hydroxyacid dehydrogenase from Cupriavidus necator H16
44% identity, 98% coverage
- (R/S)-lactate/2-hydroxybutyrate dehydrogenases in and biosynthesis of block copolyesters by Ralstonia eutropha
Ishihara, Applied microbiology and biotechnology 2023 - “...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 , mob , P lac , lacZ Kovach et al. 1995 pBPP pBBR1MCS-2 derivative; P phaP1 , T...”
- “...were constructed. It should be noted that the two adjacent genes encoding predicted d -LDHs, h16_A1681 ( ldhA1 ) and h16_A1682 ( ldhA2 ), have a completely identical nucleotide sequence to each other, due to duplication of 1676 bp regions of 1,834,348-1,836,023 and 1,836,024-1,837,699 on chromosome...”
- (R/S)-lactate/2-hydroxybutyrate dehydrogenases in and biosynthesis of block copolyesters by Ralstonia eutropha
Ishihara, Applied microbiology and biotechnology 2023 - “...noted that the two adjacent genes encoding predicted d -LDHs, h16_A1681 ( ldhA1 ) and h16_A1682 ( ldhA2 ), have a completely identical nucleotide sequence to each other, due to duplication of 1676 bp regions of 1,834,348-1,836,023 and 1,836,024-1,837,699 on chromosome 1. The actual presence of...”
- “...PCR analysis. The knockout of LdhA1 and LdhA2 was conducted by removing both h16_A1681 and h16_A1682 along with the intergenic region. The genes h16_B0093 , h16_B0092 , and h16_B0091 , sharing 44.2%, 26.0%, and 40.1% identities to lutA , lutC , and lutB derived from Bacillus...”
SPAC186.02c hydroxyacid dehydrogenase (predicted) from Schizosaccharomyces pombe
45% identity, 95% coverage
- Identification of Aly1 and Aly2 as Modulators of Cytoplasmic pH in <i>Saccharomyces cerevisiae</i>
Liu, Current issues in molecular biology 2023 - “...protein phosphatase Sds21 16 V4-P28-81 (G9) SPCC794.10 YHL012W| YKL035W UTP-glucose-1-phosphate uridylyltransferase (predicted) 17 V4-P30-05 (A5) SPAC186.02c NONE hydroxyacid dehydrogenase (predicted) 18 V4-P33-74 (G2) SPBC29A3.21 NONE sequence orphan 19 V4-P34-95 (H11) SPBPB10D8.07c YPL092W membrane transporter (predicted) 20 V4-P35-39 (D3) SPCC162.11c YNR012W uridine kinase/uracil phosphoribosyltransferase (predicted) 21 V4-P35-50...”
- Php4 Is a Key Player for Iron Economy in Meiotic and Sporulating Cells
Brault, G3 (Bethesda, Md.) 2016 - “...153 SPAC869.08 pcm2 + Protein-L-isoaspartate O-methyltransferase Pcm2 (predicted) 3.633 2.488 447 a , 108 a SPAC186.02c Hydroxyacid dehydrogenase (predicted) 3.626 3.690 465 SPCC663. 13 C naa50 + NatA N-acetyltransferase subunit Naa50 (predicted) 3.471 3.694 948 a , 726 a SPCC663.14c trp663 + TRP-like ion channel (predicted)...”
- Role for cohesin in the formation of a heterochromatic domain at fission yeast subtelomeres
Dheur, Molecular and cellular biology 2011 - “...Locus imr1 dg1 SPAC869.10c SPAC186.01 SPAC186.02c SPAC186.04c SPAC186.05c SPAC186.06 SPAC750.07c act1 Forward Reverse TTTTGGACAGAATGGATGGA ACGGCATCGCTTGTACTTTT...”
- “...37C SPMIT.06 SPMIT.04 SPAC186.01 SPBC11C11.12 SPAC186.02c SPAPB8E5.05 SPBPJ4664.03 SPCC188.12 Reproducibilityb Location -Galactosidase (predicted) Cytochrome c...”
- Expression profiling of S. pombe acetyltransferase mutants identifies redundant pathways of gene regulation
Nugent, BMC genomics 2010 - “...SPCC1393.07c 2.23 4.88E-10 spk1 3.17 0.000216514 dak2 5.02 4.45E-12 SPAC513.06c 2.24 1.52E-09 mei2 3.25 0.000888516 SPAC186.02c 5.11 6.43E-15 SPCPB1C11.02 2.25 7.04E-07 SPAC977.05c 3.29 2.46E-05 eno102 5.11 3.01E-13 ste11 2.27 0.000335259 SPAC1F8.08 3.32 2.20E-09 SPAC3G9.11c 5.13 5.88E-11 wtf20 2.28 4.37E-06 SPAC3G6.07 3.33 1.53E-05 SPAC22G7.11c 5.22 4.34E-14 ppk33...”
- Transcription factors Pcr1 and Atf1 have distinct roles in stress- and Sty1-dependent gene regulation
Sansó, Eukaryotic cell 2008 - “...SPAC9E9.04 SPCC306.08c SPACUNK4.15 ght2 SPAC26F1.04c SPAC4H3.04c SPAC3G9.11c SPAC186.02c SPAC16A10.01 SPBC21H7.06c psi1 a WT, Unt atf1, Untb pcr1, Untb WT, KClb...”
8grvA / Q54UF7 Dictyostelium discoideum lactate dehydrogenase (dicldha)with NAD
45% identity, 94% coverage
- Ligand: nicotinamide-adenine-dinucleotide (8grvA)
4zgsA / B0LUZ5 Identification of the pyruvate reductase of chlamydomonas reinhardtii (see paper)
45% identity, 95% coverage
- Ligand: nicotinamide-adenine-dinucleotide (4zgsA)
J9VFV7 D-lactate dehydrogenase from Cryptococcus neoformans var. grubii serotype A (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487)
CNAG_00832 D-lactate dehydrogenase from Cryptococcus neoformans var. grubii H99
44% identity, 93% coverage
- Comparative genomics of the closely related fungal genera Cryptococcus and Kwoniella reveals karyotype dynamics and suggests evolutionary mechanisms of pathogenesis
Coelho, PLoS biology 2024 - “...(D) Overlay of AlphaFold predicted structures of D-lactate dehydrogenease proteins from C . neoformans (UniProt J9VFV7), Aspergillus fischeri (UniProt A1D163), and Escherichia coli (UniProt P52643) showing structural similarity. Pairwise structure alignments were performed and visualized in the Protein Data Bank (PDB) website ( https://www.rcsb.org/alignment ) using...”
- “...Structural comparison of D-lactate dehydrogenase proteins from AlphaFold predictions. AlphaFold-predicted structures of Cryptococcus neoformans (UniProt J9VFV7), Aspergillus fischeri (UniProt A1D163), and Escherichia coli (UniProt P52643) are individually displayed at the top. Pairwise structure alignments with the C . neoformans protein were conducted with the JjFATCAT-rigid algorithm...”
- Comparative genomics of Cryptococcus and Kwoniella reveals pathogenesis evolution and contrasting karyotype dynamics via intercentromeric recombination or chromosome fusion.
Coelho, bioRxiv : the preprint server for biology 2024 - “...highlighted. (D) Overlay of AlphaFold predicted structures of D-lactate dehydrogenease proteins from C. neoformans (UniProt J9VFV7), Aspergillus fischeri (UniProt A1D163), and Escherichia coli (UniProt P52643) showing structural similarity. Pairwise structure alignments were performed and visualized in the Protein Data Bank (PDB) website ( https://www.rcsb.org/alignment ) using...”
- Comparative genomics of the closely related fungal genera Cryptococcus and Kwoniella reveals karyotype dynamics and suggests evolutionary mechanisms of pathogenesis
Coelho, PLoS biology 2024 - “...from a BLASTP search against the NCBI clustered nr database, using the C . neoformans CNAG_00832 protein sequence as query and selecting the top 1,000 hits. The identified sequences in pathogenic Cryptococcus species were also included. Tree branches are colored as per the key, depicting major...”
- “...within the presumed Aspergilli donor lineage. (C) Domain organization of the protein sequence encoded by CNAG_00832 with identified InterPro (IPR) and Pfam (PF) domains highlighted. (D) Overlay of AlphaFold predicted structures of D-lactate dehydrogenease proteins from C . neoformans (UniProt J9VFV7), Aspergillus fischeri (UniProt A1D163), and...”
KK1H_CURCL / A0A348AXY0 D-lactate dehydrogenase kk1H; KK-1 biosynthesis cluster protein H; EC 1.1.1.- from Curvularia clavata (see 2 papers)
43% identity, 95% coverage
- function: D-lactate dehydrogenase; part of the gene cluster that mediates the biosynthesis of KK-1, a novel cyclic depsipeptide with 10 residues which is a promising active compound with high activity against many plant pathogens, especially Botrytis cinerea (PubMed:29686660, PubMed:37746209). Within the pathway, kk1H catalyzes in the synthesis of D-lactic acid from pyruvic acid, which is recognized by the A domain of the first kk1B module (Probable). The nonribosomal peptide synthetase (NRPS) kk1B catalyzes the elongation and cyclization of the decapeptide chain composed of 1 D-lactic acid residue (D-Lac), 1 pipecolic acid residue (Pip), 1 aspartic acid residue (Asp), 1 isoleucine residue (Ile), 1 glycine residue (Gly), 1 tyrosine residue (Tyr) and 4 valine residues (Val). The Asp, Ile and 3 Val residues are N-methylated by the 5 methyltransferase domains from the NRPS (found in modules 3, 5, 6, 7 and 9), whereas the Tyr residue is O-methylated by the cluster encoded O-methyltransferase kk1A. The thioesterase kk1J is likely to be involved in the corrective mechanism of peptide chain synthesis. The D-lactate dehydrogenase kk1H is involved in the synthesis of D-lactic acid from pyruvic acid, which is recognized by the A domain of the first kk1B module. The pyrroline-5- carboxylate reductase kk1I is involved in the synthesis of the L- pipecolic acid residue of KK-1 from delta-1-pyrroline-5-carboxylate (P5C), a metabolic intermediate of lysine. It still is unclear how kk1C and kk1D are involved in the production of KK-1 (Probable).
disruption phenotype: Abolishes completely the production of KK-1.
A1D163 D-lactate dehydrogenase, putative from Neosartorya fischeri (strain ATCC 1020 / DSM 3700 / CBS 544.65 / FGSC A1164 / JCM 1740 / NRRL 181 / WB 181)
44% identity, 94% coverage
SCO2118 D-lactate dehydrogenase from Streptomyces coelicolor A3(2)
43% identity, 96% coverage
- Occurrence of vanHAX and Related Genes beyond the Actinobacteria Phylum
Yushchuk, Genes 2022 - “...a 5-parameter distribution. The phylogeny of VanH proteins was built using 269 aa sequences, including SCO2118 (putative d -Lac dehydrogenase from S. coelicolor A3(2)) as an outgroup ( Supplementary FASTA File S1 ); the phylogeny of VanA was built using 265 aa sequences proteins, including SCO5560...”
- Genomic Insights into the Distribution and Phylogeny of Glycopeptide Resistance Determinants within the Actinobacteria Phylum
Andreo-Vidal, Antibiotics (Basel, Switzerland) 2021 - “...we used a dataset of 156 VanH proteins from actinobacteria and low G-C Gram-positives, with SCO2118 lactate dehydrogenase serving as an outgroup (see Section 4 ). It appeared that VanH proteins were quite conserved, and a branching pattern with completely reliable bootstrap support was difficult to...”
- Novel Two-Component System MacRS Is a Pleiotropic Regulator That Controls Multiple Morphogenic Membrane Protein Genes in Streptomyces coelicolor
Liu, Applied and environmental microbiology 2019 - “...a five-gene locus with their 135 flanking genes sco2118, sco2119, and sco2122, which encode, respectively, a probable D-lactate 136 dehydrogenase (Dldh2), a...”
- The metabolic switch can be activated in a recombinant strain of Streptomyces lividans by a low oxygen transfer rate in shake flasks
Gamboa-Suasnavart, Microbial cell factories 2018 - “...fermentative pathway was considered. In S. coelicolor , the presence of the lactate dehydrogenase gene (SCO2118) [ 43 ] has been reported. In S . griseus , lactate production has been reported, supporting the idea of a lactic acid fermentation mechanism [ 44 ]. Furthermore, it...”
- In vivo studies suggest that induction of VanS-dependent vancomycin resistance requires binding of the drug to D-Ala-D-Ala termini in the peptidoglycan cell wall
Kwun, Antimicrobial agents and chemotherapy 2013 - “...presumably synthesized by the VanH homologue Ddlh2 (SCO2118). The proportion of D-Ala-D-Ala-containing PG precursors relative to those containing D-Ala-D-Lac is...”
HADHA_ASPOR / Q2UH56 2-hydroxyacid dehydrogenase A; 2-HadhA; EC 1.1.1.272 from Aspergillus oryzae (strain ATCC 42149 / RIB 40) (Yellow koji mold) (see paper)
AO090023000577 No description from Aspergillus oryzae RIB40
43% identity, 94% coverage
SSIG_RS25800 2-hydroxyacid dehydrogenase from Streptomyces filamentosus NRRL 11379
41% identity, 96% coverage
F8A9V0 D-lactate dehydrogenase (EC 1.1.1.28) from Thermodesulfatator indicus (see paper)
42% identity, 95% coverage
fldH / G9EZR6 aromatic 2-oxoacid reductase (EC 1.1.1.110) from Clostridium sporogenes (strain ATCC 7955 / DSM 767 / NBRC 16411 / NCIMB 8053 / NCTC 8594 / PA 3679) (see 6 papers)
FLDH_CLOS3 / G9EZR6 Aromatic 2-oxoacid reductase; Phenyllactate dehydrogenase; EC 1.1.1.110 from Clostridium sporogenes (strain ATCC 7955 / DSM 767 / NBRC 16411 / NCIMB 8053 / NCTC 8594 / PA 3679) (see paper)
42% identity, 95% coverage
- function: Essential for the reductive metabolism of L-phenylalanine, L- tyrosine and L-tryptophan (By similarity). Catalyzes the conversion of phenylpyruvic acid to phenyllactic acid, 4-hydroxy-phenylpyruvic acid to 4-hydroxy-phenyllactic acid, and indolepyruvic acid to indolelactic acid (By similarity) (PubMed:10849007).
catalytic activity: (R)-3-phenyllactate + NAD(+) = 3-phenylpyruvate + NADH + H(+) (RHEA:38351)
catalytic activity: (2R)-2-hydroxy-3-(4-hydroxyphenyl)propanoate + NAD(+) = 3-(4- hydroxyphenyl)pyruvate + NADH + H(+) (RHEA:10780)
catalytic activity: 3-(indol-3-yl)lactate + NAD(+) = indole-3-pyruvate + NADH + H(+) (RHEA:20133)
FLDH_CLOS1 / J7SHB8 Aromatic 2-oxoacid reductase; Indolelactate dehydrogenase; EC 1.1.1.110 from Clostridium sporogenes (strain ATCC 15579) (see 2 papers)
CLOSPO_00316 hypothetical protein from Clostridium sporogenes ATCC 15579
42% identity, 95% coverage
- function: Essential for the reductive metabolism of L-phenylalanine, L- tyrosine and L-tryptophan (PubMed:29168502). Catalyzes the conversion of phenylpyruvic acid to phenyllactic acid, 4-hydroxy-phenylpyruvic acid to 4-hydroxy-phenyllactic acid, and indolepyruvic acid to indolelactic acid (PubMed:29168502, PubMed:4384683).
catalytic activity: (R)-3-phenyllactate + NAD(+) = 3-phenylpyruvate + NADH + H(+) (RHEA:38351)
catalytic activity: (2R)-2-hydroxy-3-(4-hydroxyphenyl)propanoate + NAD(+) = 3-(4- hydroxyphenyl)pyruvate + NADH + H(+) (RHEA:10780)
catalytic activity: 3-(indol-3-yl)lactate + NAD(+) = indole-3-pyruvate + NADH + H(+) (RHEA:20133)
disruption phenotype: Mutants are deficient in reductive metabolism of phenylalanine, tyrosine and tryptophan, and exhibit growth defects when cultured with amino acids as the sole carbon source. - Uncovering the specificity and predictability of tryptophan metabolism in lactic acid bacteria with genomics and metabolomics
Pan, Frontiers in cellular and infection microbiology 2023 - “...construct the fldH homologous protein in L. salivarius FWXBH185 and the experimentally verified fldH (Uniprot: J7SHB8) protein structure in C. sporogenes ATCC 15579. We used the Pairwise Structure Alignment function (algorithm, jFATCAT-rigid) provided by PDB ( https://www.rcsb.org ) to establish residue-residue correspondence between L. salivarius FWXBH185...”
- “...homology, constructed the protein structure and compared the protein structure similarity of the fldH (Uniprot: J7SHB8) of C. spologenes ATCC 15579 (here called reference fldH ) and type 1-4 fldH of L. salivarius FWXBH185, which was the largest production of ILA in all LAB. Type 1,...”
- Lacticaseibacillus rhamnosus Strain GG (LGG) Regulate Gut Microbial Metabolites, an In Vitro Study Using Three Mature Human Gut Microbial Cultures in a Simulator of Human Intestinal Microbial Ecosystem (SHIME)
Liu, Foods (Basel, Switzerland) 2023 - “...using the Clostridium sporogenes genes retrieved from the UniProt database (IDs: Q93AL8, Q93AL9, Q93AM0, Q93AM1, J7SHB8). Visualizations and statistical analysis were conducted in R [ 39 ] using the following packages: vegan, tidyverse, ggplot2, pheatmap, RColorBrewer, microViz, and factoextra. Multiple testing corrections for multivariate linear models...”
- A Cardiovascular Disease-Linked Gut Microbial Metabolite Acts via Adrenergic Receptors
Nemet, Cell 2020 - “...2017 ). E. coli CA434 (HB101/pRK24) harboring the pMTL007C-E2 with the specific sites retargeting fldH (CLOSPO_00316) or porA (CLOSPO_00147) were kindly provided from Justin Sonnenburg Lab. To introduce plasmid DNA into C. sporogenes , we performed bi-parental mating using a custom filter-mating-based approach. First 1 ml...”
- A gut bacterial pathway metabolizes aromatic amino acids into nine circulating metabolites
Dodd, Nature 2017 - “...flat files for subsequent analyses. Gene cluster searches The phenyllactate dehydratase gene cluster (CLOSPO_00306 to CLOSPO_00316) was used as the query to search annotated genomic scaffolds from HMP Reference Genomes (NCBI Bioproject PRJNA28331, downloaded from NCBI on 12 June 2016) using MultiGeneBlast 18 with the default...”
- “...been identified. The arylpyruvates are then converted to their corresponding aryllactates by phenyllactate dehydrogenase (FldH, CLOSPO_00316). The aryllactates are then dehydrated by phenyllactate dehydratase (FldBC, CLOSPO_00310-311) along with its activator (FldI, CLOSPO_00309). Previous studies indicate that the dehydration reaction requires the substrate to first be activated...”
SVXNc_0992 NAD(P)-dependent oxidoreductase from Candidatus Nanohalococcus occultus
39% identity, 94% coverage
- Functional diversity of nanohaloarchaea within xylan-degrading consortia
Reva, Frontiers in microbiology 2023 - “...complex (PDH) consisting of AcoAB, AceF, and Lpd enzymes (SVXNc_0064-67,0758 and BNXNv_0048-51,0239), lactate dehydrogenase LdhA (SVXNc_0992 and BNXNv_0542), NAD-dependent malic enzyme SfcA (SVXNc_0069 and BNXNv_0060), and a short-chain alcohol dehydrogenase FabG (SVXNc_1061 and BNXNv_0428). The PDH complex decarboxylates pyruvate to acetyl-CoA. An ADP-forming acetyl-CoA synthetase AcdA...”
A0A0R1RJ30 D-lactate dehydrogenase (EC 1.1.1.28) from Furfurilactobacillus rossiae (see 2 papers)
38% identity, 95% coverage
CAETHG_1147, CLAU_1108, CLJU_RS15865 D-isomer specific 2-hydroxyacid dehydrogenase family protein from Clostridium autoethanogenum DSM 10061
33% identity, 96% coverage
- Recent progress in engineering Clostridium autoethanogenum to synthesize the biochemicals and biocommodities
Wan, Synthetic and systems biotechnology 2024 - “...). The lactate is produced through direct reduction of pyruvate catalyzed by the lactate dehydrogenase (CAETHG_1147). The synthetic pathway for 2,3-BDO includes three key enzyme, acetolactate synthase (CAETHG_1740), acetolactate decarboxylase (CAETHG_2932) and 2,3-BDO dehydrogenase (CAETHG_0385), all of the genes for those enzymes have been identified in...”
- Clostridium autoethanogenum alters cofactor synthesis, redox metabolism, and lysine-acetylation in response to elevated H2:CO feedstock ratios for enhancing carbon capture efficiency
Davin, Biotechnology for biofuels and bioproducts 2024 - “...CAETHG_1740 Acetolactate synthase 0.479 0.14 CAETHG_2932 Alpha-acetolactate decarboxylase 0.002* 1.07 CAETHG_0385 (R,R)-Butanediol dehydrogenase 0.748 0.11 CAETHG_1147 D-Lactate dehydrogenase 0.040* 0.19 B12 Biosynthesis CAETHG_1110 Cob(I)alamin adenosyltransferase 0.005* 0.67 CAETHG_1111 GHMP kinase 0.002* 3.56 CAETHG_1112 Precorrin-6reductase 0.004* 0.79 CAETHG_1113 Sirohydrochlorin cobaltochelatase 0.023* 0.77 CAETHG_1114 Precorrin-3B C17-methyltransferase 0.256 0.50...”
- Required Gene Set for Autotrophic Growth of Clostridium autoethanogenum
Woods, Applied and environmental microbiology 2022 - “...there appears to be only one gene encoding each of the relevant functions (CLAU_2851 and CLAU_1108, respectively); in these cases, redundancy is unlikely to be the reason for their nonessential status, meaning it is more likely these are unnecessary biological routes. The successful application of TIS...”
- Transcriptomic profiles of Clostridium ljungdahlii during lithotrophic growth with syngas or H2 and CO2 compared to organotrophic growth with fructose
Aklujkar, Scientific reports 2017 - “...Clostridium autoethanogenum 32 , encoded by a gene that is not differentially expressed ( ldhA CLJU_RS15865). With no obvious mechanism to conserve energy from this exergonic reaction, the LdhA enzyme may function irreversibly, driving a cycle of pyruvate reduction and (R) -lactate reoxidation (Fig. 1 )....”
- Comparison of single-molecule sequencing and hybrid approaches for finishing the genome of Clostridium autoethanogenum and analysis of CRISPR systems in industrial relevant Clostridia
Brown, Biotechnology for biofuels 2014 - “...(BudA) CAETHG_2932, B 3 2,3-butanediol dehydrogenase (Bdh) CAETHG_0385, Lactate fermentation pathway. L Lactate dehydrogenase (Ldh) CAETHG_1147. Central pyruvate metabolism. P 1 Pyruvate:ferredoxin oxidoreductase (PFOR) CAETHG_0928, 3029, P 2 Pyruvate, phosphate dikinase (PPDK) CAETHG_2055, 2909, P 3 Pyruvate kinase (Pk) CAETHG_2440-41, P 4 Pyruvate carboxylase (Pyc) CAETHG_1594,...”
- Reconstruction of an acetogenic 2,3-butanediol pathway involving a novel NADPH-dependent primary-secondary alcohol dehydrogenase
Köpke, Applied and environmental microbiology 2014 - “...putative lactate dehydrogenase gene, ldhA (locus tag CAETHG_1147), was amplified from C. autoethanogenum genomic DNA by using primers Ldh-BamHI-F and Ldh-SalI-R...”
E0NDE9 D-lactate dehydrogenase (EC 1.1.1.28) from Pediococcus acidilactici (see paper)
35% identity, 98% coverage
WP_152689015 D-2-hydroxyacid dehydrogenase from Pediococcus acidilactici
35% identity, 98% coverage
OEOE_RS01985 D-2-hydroxyacid dehydrogenase from Oenococcus oeni PSU-1
OEOE_0413 Phosphoglycerate dehydrogenase or related dehydrogenase from Oenococcus oeni PSU-1
38% identity, 90% coverage
- Transcriptomic and Proteomic Analysis of Oenococcus oeni Adaptation to Wine Stress Conditions
Margalef-Català, Frontiers in microbiology 2016 - “...1.57 1.53 27.1 5.4 Aldehyde dehydrogenase OEOE_RS01550 1.21 (3) 1.59 (2) 52.5 4.9 Lactate dehydrogenase OEOE_RS01985 1.5 1.1 36.5 PTS mannose transporter subunit IIAB OEOE_RS02230 0.73 1.02 1.31 1.38 1.06 1.00 PTS mannose transporter subunit EIIAB OEOE_RS02230 2.4 0.7 35.6 HPr kinase/phosphorylase OEOE_RS02680 1.6 1.9 35.4...”
- Citrate metabolism in lactic acid bacteria: is there a beneficial effect for Oenococcus oeni in wine?
Eicher, Frontiers in microbiology 2023 - “..., the gene commonly linked to the lactate dehydrogenase is the ldhD gene (locus tag OEOE_0413 in PSU-1 genome; Kim et al., 2011 ; Yang et al., 2019 ). However, five other genes have been annotated as putative lactate dehydrogenases in this bacterium: OEOE_0025, OEOE_0701, OEOE_1182,...”
- Role of secondary transporters and phosphotransferase systems in glucose transport by Oenococcus oeni
Kim, Journal of bacteriology 2011 - “...57.3 59.3 60.3 54.7 55.3 55.3 55.3 OEOE_0413 OEOE_0413 OEOE_0006 OEOE_0006 OEOE_0478 OEOE_0478 OEOE_0819 OEOE_0819 OEOE_1574 OEOE_1574 OEOE_1766 OEOE_1766...”
- “...A; OEOE_0006) and ldhD (encoding lactate dehydrogenase; OEOE_0413) separately (7). Relative gene expression was determined by a relative quantification model,...”
LDHD_PEDAC / Q59642 D-lactate/D-glycerate dehydrogenase; D-LDH/GDH; D-specific 2-hydroxyacid dehydrogenase; EC 1.1.1.28; EC 1.1.1.29 from Pediococcus acidilactici (see paper)
ldhD / GI|897794 D-lactate dehydrogenase; EC 1.1.1.28; EC 1.1.1.81 from Pediococcus acidilactici (see paper)
35% identity, 98% coverage
- function: Has both D-lactate and D-glycerate dehydrogenase activities. Equally active on pyruvate and hydroxypyruvate.
catalytic activity: (R)-lactate + NAD(+) = pyruvate + NADH + H(+) (RHEA:16369)
catalytic activity: (R)-glycerate + NAD(+) = 3-hydroxypyruvate + NADH + H(+) (RHEA:17905)
subunit: Homodimer.
KSF55_09370 D-2-hydroxyacid dehydrogenase from Lactiplantibacillus pentosus
36% identity, 95% coverage
ldhD / Q88VJ2 D-lactate dehydrogenase subunit (EC 1.1.1.28) from Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1) (see paper)
C0LJH4 D-lactate dehydrogenase (EC 1.1.1.28) from Lactiplantibacillus plantarum subsp. plantarum (see paper)
Q88VJ2 D-lactate dehydrogenase from Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)
lp_2057 D-lactate dehydrogenase from Lactobacillus plantarum WCFS1
36% identity, 95% coverage
- Identification of key proteins and pathways in cadmium tolerance of Lactobacillus plantarum strains by proteomic analysis.
Zhai, Scientific reports 2017 - “...F9UTR4 ack2; acetate kinase 1.59 F9UM63 pox1; pyruvate oxidase 2.79 P59390 ldhL2; L-lactate dehydrogenase 3.36 Q88VJ2 ldhD; D-lactate dehydrogenase 1.69 F9URC8 pox3; pyruvate oxidase 8.87 F9UTJ5 pflB; formate C-acetyltransferase 1.85 P37063 pox5; pyruvate oxidase 4.19 Pentose phosphate pathway F9UN42 gntK; gluconokinase 1.99 F9URA8 tal1; Transaldolase 5.21...”
- Comparative study of sugar fermentation and protein expression patterns of two Lactobacillus plantarum strains grown in three different media.
Plumed-Ferrer, Applied and environmental microbiology 2008 - Unravelling the Reduction Pathway as an Alternative Metabolic Route to Hydroxycinnamate Decarboxylation in Lactobacillus plantarum
Santamaría, Applied and environmental microbiology 2018 - “...using an LIC strategy Amplification of a 62-bp lp_2057 (ldhD) fragment for RT-qPCR Amplification with oligo 1233 to corroborate the correct insertion of...”
- Transcriptional Reprogramming at Genome-Scale of Lactobacillus plantarum WCFS1 in Response to Olive Oil Challenge
Esteban-Torres, Frontiers in microbiology 2017 - “...1.8 1.01 lp_0009 rpsF 30S ribosomal protein S6 1.48 0.68 lp_2755 Membrane protein 1.34 0.45 lp_2057 ldhD D-lactate dehydrogenase 1.14 0.38 lp_2368 atpF H(+)-transporting two-sector ATPase, B subunit 0.95 3.04 lp_1449 Cell surface protein, CscB family 1.27 3.53 lp_2035 aroE 3-phosphoshikimate 1-carboxyvinyltransferase 1.34 3.71 lp_0265 pts5ABC...”
- Regulation of the activity of lactate dehydrogenases from four lactic acid bacteria
Feldman-Salit, The Journal of biological chemistry 2013 - “...L-LDH1 and lp_1101, L-LDH2) and one producing D-lactate (lp_2057, D-LDH) (6). (The LDH locus and 4 The abbreviations used are: LDH, lactate dehydrogenase; LAB,...”
C4XEL0 D-lactate dehydrogenase from Mycoplasmopsis fermentans (strain ATCC 19989 / NBRC 14854 / NCTC 10117 / PG18)
40% identity, 90% coverage
GFB67_00380 D-2-hydroxyacid dehydrogenase from Lactobacillus delbrueckii
35% identity, 96% coverage
CH_091795 D-lactate dehydrogenase; EC 1.1.1.28 from Lactobacillus pentosus (see 2 papers)
P26298 D-lactate dehydrogenase from Lactiplantibacillus pentosus
35% identity, 95% coverage
EF2295 D-specific alpha-keto acid dehydrogenase from Enterococcus faecalis V583
34% identity, 94% coverage
- Background Adjusted Alignment-Free Dissimilarity Measures Improve the Detection of Horizontal Gene Transfer
Tang, Frontiers in microbiology 2018 - “...607 815 688 605 854 1,001 511 EF2294 325 1,874 222 447 1,302 1,373 719 EF2295 138 855 109 219 1,169 1,273 520 EF2296 379 1,613 313 385 1,392 1,491 850 EF2297 618 2,638 665 1,245 1,117 1,165 551 EF2298 660 1,355 702 772 1,978 1,924...”
- Chlorhexidine Induces VanA-Type Vancomycin Resistance Genes in Enterococci
Bhardwaj, Antimicrobial agents and chemotherapy 2016 - “...Predicted protein ABC transporter system ATP-binding protein EF2293 EF2294 EF2295 19.0 15.4 104.3 78.7 82.6 6.4d 7.1d 8.4d 8.4d 61.1 37.1 58.9 7.6d 9.8d vanZ;...”
LDHD_LACDA / P26297 D-lactate dehydrogenase; D-LDH; D-specific 2-hydroxyacid dehydrogenase; EC 1.1.1.28 from Lactobacillus delbrueckii subsp. bulgaricus (strain ATCC 11842 / DSM 20081 / BCRC 10696 / JCM 1002 / NBRC 13953 / NCIMB 11778 / NCTC 12712 / WDCM 00102 / Lb 14) (see paper)
ldhA / OMNI|NTL01LD0096 D-lactate dehydrogenase; EC 1.1.1.28 from Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842 (see 3 papers)
Ldb0101 D-lactate dehydrogenase from Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842
WP_011543503 D-2-hydroxyacid dehydrogenase from Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842 = JCM 1002
35% identity, 96% coverage
- catalytic activity: (R)-lactate + NAD(+) = pyruvate + NADH + H(+) (RHEA:16369)
subunit: Homodimer. - Cloning of D-lactate dehydrogenase genes of Lactobacillus delbrueckii subsp. bulgaricus and their roles in D-lactic acid production
Huang, 3 Biotech 2017 - “...than other three strains. Further study revealed that Ldb0101 activity was down-regulated by the oxygen and, therefore, achieved a highest titer of <span...”
- “...">d</span>-lactate</sub>. Our results suggested that the enzyme Ldb0101 and Ldb1010 played a role of more importance in <span class="EmphasisTypeSmallCaps...”
- A global analysis of function and conservation of catalytic residues in enzymes
Ribeiro, The Journal of biological chemistry 2020 (secret) - Positive selection on D-lactate dehydrogenases of Lactobacillus delbrueckii subspecies bulgaricus
Zhang, IET systems biology 2015 (secret) - Enzymatic characterization of D-lactate dehydrogenase and application in alanine aminotransferase activity assay kit
Sun, Bioengineered 2021 - “...enzymatic properties directly determine sensitivity and accuracy of such kits. In this study, D-lactate dehydrogenase (WP_011543503, ld LDH) coding sequence derived from Lactobacillus delbrueckii was obtained from the NCBI database by gene mining. Ld LDH was expressed and purified in Escherichia coli , and its enzyme...”
- “...selected D-LDH derived from L. delbrueckii ( ld LDH) for further systematic studies. Ld LDH (WP_011543503) was expressed and purified in E. coli , and its enzymatic properties were characterized. To further improve storage stability, freeze-drying was performed. A total of 22 stabilizers belonging to the...”
1j49A / P26297 Insights into domain closure, substrate specificity and catalysis of d-lactate dehydrogenase from lactobacillus bulgaricus (see paper)
35% identity, 96% coverage
- Ligand: nicotinamide-adenine-dinucleotide (1j49A)
WP_005720611 D-2-hydroxyacid dehydrogenase from Lactobacillus crispatus
34% identity, 93% coverage
ldhA / Q188H7 4-methyl-2-oxopentanoate reductase (EC 1.1.1.345) from Clostridioides difficile (strain 630) (see 2 papers)
LDHA_CLODI / Q5U922 D-2-hydroxyacid dehydrogenase (NAD(+)); (R)-2-hydroxyisocaproate dehydrogenase; EC 1.1.1.345 from Clostridioides difficile (Peptoclostridium difficile) (see paper)
ldhA / GI|115249400 (R)-2-hydroxyisocaproate dehydrogenase from Clostridium difficile 630 (see paper)
CD0394 (R)-2-hydroxyisocaproate dehydrogenase from Clostridium difficile 630
CDR20291_0365 (R)-2-hydroxyisocaproate dehydrogenase from Clostridium difficile R20291
CD630_03940, CDIF630erm_00522, CDR20291_0365 D-2-hydroxyacid dehydrogenase from Clostridioides difficile 630
34% identity, 98% coverage
- function: Involved in the reductive branch of L-leucine fermentation (PubMed:16957230). Catalyzes the NADH-dependent reduction of 4-methyl- 2-oxopentanoate (2-oxoisocaproate) to (R)-2-hydroxy-4-methylpentanoate ((R)-2-hydroxyisocaproate) (PubMed:16957230). For the reverse reaction, the enzyme accepts (R)- but not (S)-2-hydroxy-4-methylpentanoate (PubMed:16957230). Can also use 2-oxopentanoate, 2-oxohexanoate and phenylpyruvate but not 2-oxoisovalerate and 2-oxobutyrate (PubMed:16957230). Cannot use NADPH (PubMed:16957230).
catalytic activity: a (2R)-2-hydroxycarboxylate + NAD(+) = a 2-oxocarboxylate + NADH + H(+) (RHEA:35643)
catalytic activity: (R)-2-hydroxy-4-methylpentanoate + NAD(+) = 4-methyl-2- oxopentanoate + NADH + H(+) (RHEA:10052)
subunit: Monomer. - Semiquantitative analysis of clinical heat stress in Clostridium difficile strain 630 using a GeLC/MS workflow with emPAI quantitation
Ternan, PloS one 2014 - “...eight proteins necessary for the reductive branch of the leucine fermentation pathway encoded by genes CD0394 CD0401 [38] with the sole exception of the ATP-dependent activator protein, hadI. We subsequently identified hadI (CD0396) in our iTRAQ investigation, where, like hadA (CD0395), hadB (CD0397) and hadC (CD0298),...”
- Pleiotropic role of the RNA chaperone protein Hfq in the human pathogen Clostridium difficile
Boudry, Journal of bacteriology 2014 - “...strain CDIP51. The expression of the ldhA gene (CD0394), the hadA operon (CD0395-CD0398), required for leucine reduction, and grdC (CD2349) involved in glycine...”
- Global transcriptional control by glucose and carbon regulator CcpA in Clostridium difficile
Antunes, Nucleic acids research 2012 - “...2 C). The expression of ldhA , hadA , hadI , acdB and etfB1 genes (CD0394, CD0395, CD0396, CD0399 and CD0400) required for the leucine reductive branch leading to the formation of isocaproate was 4-fold repressed by glucose by a CcpA-dependent mechanism ( Figure 7 )....”
- “...complex component C subunit ; grdD (CD2348), glycine reductase complex component C subunit ; ldhA (CD0394), 2-hydroxyisocaproate dehydrogenase; hadA (CD0395), 2-hydroxyisocaproate CoA transferase; hadI (CD0396), activator of dehydratase; acdB (CD0399), acyl-CoA dehydrogenase; gcvTPA (CD1657), bi-functional glycine dehydrogenase/aminomethyl transferase protein; gcvPB (CD1658), Glycine decarboxylase; CD1228, putative protease;...”
- Clostridioides difficile LuxS mediates inter-bacterial interactions within biofilms
Slater, Scientific reports 2019 - “...1.0229025 formate/nitrite transporter 9 CDR20291_0363 1.377088 radical SAM protein 10 CDR20291_0364 1.003595 hypothetical protein 11 CDR20291_0365 1.461207 (R)-2-hydroxyisocaproate dehydrogenase 12 CDR20291_0659 1.248536 radical SAM protein 13 CDR20291_1271 1.15672 hypothetical protein 14 CDR20291_1309 1.208811 phosphohydrolase 15 CDR20291_1400 1.833327 imidazole glycerol phosphate synthase subunit HisH 16 CDR20291_1834 1.411634...”
- Iron Regulation in Clostridioides difficile
Berges, Frontiers in microbiology 2018 - “...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 CDIF630erm_00524 hadI 2-hydroxyisocaproyl-CoA dehydratase activator -0.79 OFF -11 OFF CD630_03970 CDIF630erm_00525...”
- “...-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 CDIF630erm_00524 hadI 2-hydroxyisocaproyl-CoA dehydratase activator -0.79 OFF -11 OFF CD630_03970 CDIF630erm_00525 hadB...”
- Time-resolved amino acid uptake of Clostridium difficile 630Δerm and concomitant fermentation product and toxin formation
Neumann-Schaal, BMC microbiology 2015 - “...coding for genes of the classical reductive Stickland degradation ( ldhA and hadAIBC , locus-tag CD630_03940 to _03980) [ 31 ]. Though the specific function was assigned to leucine degradation, earlier in vitro studies showed an activity of the (R)-2-hydroxyisocaproate dehydrogenase (LdhA) for phenylpyruvate (corresponding to...”
LEUM_1756 D-lactate dehydrogenase, LdhA from Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
33% identity, 97% coverage
- Biological characterization of D-lactate dehydrogenase responsible for high-yield production of D-phenyllactic acid in Sporolactobacillus inulinus
Cheng, Microbial biotechnology 2022 - “...the aligned sequences using ESPript3. The amino sequences of LDH with high pyruvate reductase activity (LEUM_1756) from Leuconostoc mesenteroides ATCC 8293 and higher PPA reductase LDH (MH920335) from Pediococcus claussenii were used for comparison. Homology models of DLDH1 and DLDH2 were constructed using the SWISSMODEL online...”
- “...2675 0.8 40 50 1.87 Tokuda et al. ( 2003 ) Leucconostoc mesenteroides ATCC 8293 LEUM_1756 0.58 2900 5000 15.4 5646 366.62 7.53 Li et al. ( 2014 ) Pediococcus pentosaceus ATCC 25745 DLDH 0.49 320 658 1.73 173 100 15.20 Yu et al. ( 2012...”
- Autotrophic lactate production from H2 + CO2 using recombinant and fluorescent FAST-tagged Acetobacterium woodii strains
Mook, Applied microbiology and biotechnology 2022 - “...Bannam and Rood ( 1993 ) pJIR750_P tet _ldhD As pJIR750, P tet , ldhD (LEUM_1756, L. mesenteroides subsp. Mesenteroides ATCC 8293) Beck ( 2020 ) pMTL83251 ermB , ColE1 ori , pCB102 + , traJ , lacZ , MCS Heap et al. ( 2009 )...”
- Production of propionate using metabolically engineered strains of Clostridium saccharoperbutylacetonicum
Baur, Applied microbiology and biotechnology 2022 - “...and D -lactate dehydrogenase from L. mesenteroides subsp. mesenteroides (stoichiometrically incorrect). LdhD, D -lactate dehydrogenase (LEUM_1756); Pct, propionate CoA-transferase (CLNEO_17700); Lcd, lactoyl-CoA dehydratase (CLNEO_17730-17710); Acr, acryloyl-CoA reductase (CLNEO_21740-21760); ABE, acetone-butanol-ethanol Materials and methods Bacterial strains and cultivation Bacterial strains and plasmids used are listed in Table...”
- “...Furthermore, the well-characterized D -lactate dehydrogenase gene from L. mesenteroides subsp. mesenteroides ( ldhD ; LEUM_1756; Li et al. 2012 ) was inserted into the PSO. Previously, all mentioned genes except for acrA , acrB , and acrC were assembled on plasmid pMTL83151_P tet _3-HP_opt (Beck...”
- Engineered yeast tolerance enables efficient production from toxified lignocellulosic feedstocks
Lam, Science advances 2021 - “...Eurofins Genomics ( www.eurofinsgenomics.com ) from the amino acid sequence available from UniProt (gene entry LEUM_1756). For transcription termination, we either retained the CYC1 element from Mumberg or, from FY4/5 genomic DNA, cloned the 166 bp immediately following the stop codon of ADH1 or the 295...”
- Metabolic engineering and adaptive evolution for efficient production of D-lactic acid in Saccharomyces cerevisiae
Baek, Applied microbiology and biotechnology 2016 (PubMed)- “...highly stereospecific D-lactate dehydrogenase gene (ldhA, LEUM_1756) from Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293 in S. cerevisiae lacking...”
- “...and adaptive evolution. D -LDH gene (ldhA, LEUM_1756) from Leuconostoc mesenteroides subsp. mesenteroides American Type Culture Collection (ATCC) 8293, showing...”
- 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 - “...Bdh1 with C-terminal dockerin fusion, was previously reported 21 . p415GPD-ldhA 29 , containing ldhA (LEUM_1756, D-lactate dehydrogenase) gene from L. mesenteroides ATCC 8293, was used for lactate production. The PCR product encoding ldhA without stop codon was prepared by PCR amplification and cloned into p415GPD-Doc...”
- GSF2 deletion increases lactic acid production by alleviating glucose repression in Saccharomyces cerevisiae
Baek, Scientific reports 2016 - “...S. cerevisiae strain JHY5210 ( dld1jen1adh1gpd1gpd2pdc1::Lm.ldhA ) by expressing D-lactate dehydrogenase gene ( ldhA , LEUM_1756) from Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293 and by deleting DLD1 encoding D-lactate dehydrogenase, JEN1 encoding monocarboxylate transporter, and major competing pathways producing ethanol and glycerol 16 . In addition,...”
- Production of natural antimicrobial compound D-phenyllactic acid using Leuconostoc mesenteroides ATCC 8293 whole cells involving highly active D-lactate dehydrogenase
Li, Letters in applied microbiology 2014 (PubMed)- “...using resting cells. D-ldh, an enzyme encoded by the LEUM_1756 gene of Leuc. mesenteroides ATCC 8293, was found to be responsible for the conversion of PPA into...”
- “...related enzymes: LEUM_0373, LEUM_1837, LEUM_0445, LEUM_1233, LEUM_0503, LEUM_1756 and LEUM_2043. Our previous study showed that the LEUM_1756 gene was the most...”
- More
LBA0055 D-lactate dehydrogenase from Lactobacillus acidophilus NCFM
33% identity, 92% coverage
- Lactobacillus acidophilus-Rutin Interplay Investigated by Proteomics
Mazzeo, PloS one 2015 - “...DOWN(-1.8) pyruvate kinase kpyK LBA0957 Glycolysis / Gluconeogenesis / Pyruvate metabolism UP(1.8) D-lactate dehydrogenase ldhD LBA0055 Pyruvate metabolism DOWN(-1.7) isomerase LBA0651 Pentose phosphate pathway UP(1.6) AMINO ACIDS BIOSYNTESIS AND METABOLISM aspartate aminotransferase LBA0856 Lysine biosynthesis UP(1.6) branched-chain amino acid aminotransferase ilvE LBA1341 Valine, leucine and isoleucine...”
P30901 D-lactate dehydrogenase (EC 1.1.1.28) from Lactobacillus helveticus (see paper)
2dldA / P30901 D-lactate dehydrogenase complexed with nadh and oxamate
GB|CAA47255.1 D-lactate dehydrogenase; EC 1.1.1.28 from Lactobacillus helveticus (see 2 papers)
HUO_RS01270 D-2-hydroxyacid dehydrogenase from Lactobacillus helveticus
32% identity, 95% coverage
- Ligand: 1,4-dihydronicotinamide adenine dinucleotide (2dldA)
- Safety Assessment of Lactobacillus helveticus KLDS1.8701 Based on Whole Genome Sequencing and Oral Toxicity Studies
Li, Toxins 2017 - “...helveticus KLDS1.8701 genome. The genes encoding nitroreductase were HUO_RS07380 and HUO_RS08970 (pseudogene). d -lactate dehydrogenase (HUO_RS01270) was also found in the genome. However, the phenotypic results showed that the nitroreductase was not detected in the fermented supernatant and the optical purity of the produced lactic acid...”
- Engineering natural and noncanonical nicotinamide cofactor-dependent enzymes: design principles and technology development
King, Current opinion in biotechnology 2020 - “...Uniprot Native Cofactor Noncanonical Cofactor a CSR b Source D-lactate dehydrogenase ( L. helveticus ) P30901 NAD + NCD + 4.810 2 Liu et al, 2020 [ 5 ] Formate dehydrogenase ( Pseudomonas sp. 101) P33160 NAD + NCD + 4.7l0 2 Guo et al., 2020...”
- “...a Mutations CSR b RCE C RS d Source D-lactate dehydrogenase ( L. helveticus ) P30901 Bibliography, Saturation, Structure NAD + NCD + V152R-N213E 4.310 2.110 1 9.010 2 Liu et al., 2020 [ 5 ] V152R-I177K-N213I 4.210 3.110 1 8.810 2 Formate dehydrogenase ( Pseudomonas...”
- Bacteroides thetaiotaomicron Fosters the Growth of Butyrate-Producing Anaerostipes caccae in the Presence of Lactose and Total Human Milk Carbohydrates
Chia, Microorganisms 2020 - “...the genome. The homologous protein check against d -lactate dehydrogenase from Lactobacillus helveticus (UniProt identifier P30901) showed no match in the A. caccae genome except the general NAD-binding domain. Besides, no domain matching the lactate racemase from Lactobacillus plantarum (UniProt identifier F9USS9) was found in the...”
NP_964061 D-lactate dehydrogenase from Lactobacillus johnsonii NCC 533
34% identity, 93% coverage
SCO3594 D-lactate dehydrogenase from Streptomyces coelicolor A3(2)
32% identity, 90% coverage
- Heterologous Expression Reveals Ancient Properties of Tei3—A VanS Ortholog from the Teicoplanin Producer Actinoplanes teichomyceticus
Yushchuk, International journal of molecular sciences 2022 - “...pGJp and pGHp. DNA fragments including promoter regions of S. coelicolor vanJ (SCO3592) and vanH (SCO3594) genes were amplified from the chromosome DNA of S. coelicolor M512 using vanJp_KpnI_F/vanJp_SpeI_R and vanHp_KpnI_F/vanHp_SpeI_R primers pairs ( Table 2 ). The obtained amplicons for vanJp (321 bp) and vanHp...”
- Occurrence of vanHAX and Related Genes beyond the Actinobacteria Phylum
Yushchuk, Genes 2022 - “...spread among bacterial taxa. 2. Methods 2.1. van Genes Discovery Amino acid (aa) sequences of SCO3594, SCO3595, and SCO3596 (VanH, VanA, and VanX) from Streptomyces ( S .) coelicolor A3(2) were used as queries for BLASTP [ 56 ] against non-redundant protein sequence databases for each...”
- Genomic Insights into the Distribution and Phylogeny of Glycopeptide Resistance Determinants within the Actinobacteria Phylum
Andreo-Vidal, Antibiotics (Basel, Switzerland) 2021 - “...vlgs using BLASTP [ 74 ] with SCO3589 (VanS), SCO3590 (VanR), SCO3592 (VanJ), SCO3593 (VanK), SCO3594 (VanH), SCO3595 (VanA), SCO3596 (VanX) , CAG25753 (VanY) and ELS50663 (VanZ) as queries. These last sets of genomes were chosen to cover all the genera within a certain order and...”
O83080 D-lactate dehydrogenase (EC 1.1.1.28) from Treponema pallidum (see paper)
TP0037 D-specific D-2-hydroxyacid dehydrogenase from Treponema pallidum subsp. pallidum str. Nichols
31% identity, 98% coverage
- Biophysical and biochemical studies support TP0094 as a phosphotransacetylase in an acetogenic energy-conservation pathway in Treponema pallidum
Brautigam, PloS one 2023 - “...one of them: the D-lactate dehydrogenase encoded by gene tp0037 (TpDLD; 1.1.1.28; UniProt Acc. # O83080) [ 11 ]. 10.1371/journal.pone.0283952.g001 Fig 1 A putative acetogenic pathway in T . pallidum . Enzymes in the pathway are shown near the bottom of the figure as ovals; the...”
- Biophysical and biochemical studies support TP0094 as a phosphotransacetylase in an acetogenic energy-conservation pathway in Treponema pallidum
Brautigam, PloS one 2023 - “...have confirmed the activity of only one of them: the D-lactate dehydrogenase encoded by gene tp0037 (TpDLD; 1.1.1.28; UniProt Acc. # O83080) [ 11 ]. 10.1371/journal.pone.0283952.g001 Fig 1 A putative acetogenic pathway in T . pallidum . Enzymes in the pathway are shown near the bottom...”
- “...pyruvate:flavodoxin oxidoreductase (PFOR), Pta, and Ack. We have previously validated the structure and activity of TP0037 as the DLD (TpDLD; [ 11 ]). In this work, we have focused on the proposed Pta activity of TP0094. The structural and biochemical studies reported above were all compatible...”
- Biophysical and Biochemical Characterization of TP0037, a d-Lactate Dehydrogenase, Supports an Acetogenic Energy Conservation Pathway in Treponema pallidum
Deka, mBio 2020 - “...Washington, DC 7512555 32963009 mBio02249-20 10.1128/mBio.02249-20 Research Article Host-Microbe Biology Biophysical and Biochemical Characterization of TP0037, a d -Lactate Dehydrogenase, Supports an Acetogenic Energy Conservation Pathway in Treponema pallidum d -Lactate-Dependent Acetogenesis in T. pallidum Deka et al. Deka Ranjit K. a Liu Wei Z. a...”
- “...provides structural, biochemical, and biophysical evidence for the first T. pallidum enzyme in the pathway (TP0037; d -lactate dehydrogenase) requisite for the conversion of d -lactate to pyruvate. The findings represent the first experimental evidence to support a role for an acetogenic energy conservation pathway that...”
- Treponema pallidum, the syphilis spirochete: making a living as a stealth pathogen
Radolf, Nature reviews. Microbiology 2016 - “...drive the flagellar motor and nutrient uptake by symporters. T. pallidum uses lactate dehydrogenase (LDH (TP0037)) and the flavoprotein NADH oxidase-2 (NOX-2 (TP0921)) to resolve the first dilemma ( Fig. 2 ) 111 , 112 . Under low oxygen conditions, such as on mucosal surfaces, conversion...”
- Identification of the Treponema pallidum subsp. pallidum TP0092 (RpoE) regulon and its implications for pathogen persistence in the host and syphilis pathogenesis
Giacani, Journal of bacteriology 2013 - “...donors in the T. pallidum cytosol, such as TP0037 (lactate dehydrogenase) or TP0921 (a putative flavoprotein), might induce superoxide production in the...”
- Characterization and serologic analysis of the Treponema pallidum proteome
McGill, Infection and immunity 2010 - “...TP0662 66 67 TP0965 68 69 TP0249 TP0249 70 71 TP0662 TP0037 72 TP0319 73 73 TP0030 TP0574 74 TP0792 75 76 77 TP0868 TP0769 TP0868 78 79 80 81 TP0684 TP0792...”
- “...112 113 TP0769 TP0424 TP0769 TP0115 114 115 116 TP0971 TP0554 TP0037 117 TP0259 118 TP0349 119 120 TP0509 TP0568 121 122 123 124 125 126 127 128 129 TP0249...”
- Genome scale identification of Treponema pallidum antigens
McKevitt, Infection and immunity 2005 - “...TP0329; TP0127; TP0474; TP0220; TP0622; TP0604; TP0222; TP0037; TP0663; TP0767; TP0369; TP0655; TP0546; TP0856; TP0858; TP0240; TP0030; TP0606; TP0465; TP1010;...”
OEOE_1182 D-lactate dehydrogenase from Oenococcus oeni PSU-1
OEOE_RS05695 D-2-hydroxyacid dehydrogenase from Oenococcus oeni PSU-1
37% identity, 96% coverage
- Citrate metabolism in lactic acid bacteria: is there a beneficial effect for Oenococcus oeni in wine?
Eicher, Frontiers in microbiology 2023 - “...five other genes have been annotated as putative lactate dehydrogenases in this bacterium: OEOE_0025, OEOE_0701, OEOE_1182, OEOE_1672, and OEOE_1709. Nevertheless, only the products of the OEOE_0413 and OEOE_1672 genes have been detected in the proteome of the PSU-1 strain of O. oeni ( Zaunmller, 2008 )....”
- Transcriptomic and Proteomic Analysis of Oenococcus oeni Adaptation to Wine Stress Conditions
Margalef-Català, Frontiers in microbiology 2016 - “...1.43 1.23 0.97 Phosphocarrier protein hpr OEOE_RS03075 2.19 2.16 2.20 2.33 2.25 2.32 Lactate dehydrogenase OEOE_RS05695 1.20 0.93 1.10 1.22 1.14 1.37 PTS sugar transporter OEOE_RS05805 2.37 2.45 2.68 2.86 2.87 2.90 Glycerol-3-phosphate ABC transporter ATP-binding protein OEOE_RS07030 1.42 1.92 2.10 2.34 2.51 2.54 Glycerol-3-phosphate ABC...”
- “...pyruvate-protein phosphotransferase OEOE_RS03095 1.2 ND 63.2 5 Galactose mutarotase OEOE_RS04920 0.7 1.1 34.1 D-lactate dehydrogenase OEOE_RS05695 1.3 ND 36.5 5.74 UDP-glucose 4-epimerase OEOE_RS06755 1.1 0.7 36.9 Enolase OEOE_RS07960 1.54 1.387 0.7 1.8 48.4/47.3 4.6 Fructokinase OEOE_RS08245 1.2 ND 32.1 6.44 Lipid transport and metabolism ACP S-malonyltransferase...”
WP_013456296 2-hydroxyacid dehydrogenase from Mycoplasmopsis bovis
33% identity, 95% coverage
SERP2087 D-isomer specific 2-hydroxyacid dehydrogenase family protein from Staphylococcus epidermidis RP62A
34% identity, 93% coverage
WP_047132560 D-lactate dehydrogenase from Staphylococcus condimenti
34% identity, 93% coverage
LMB90_RS06670 D-2-hydroxyacid dehydrogenase from Limosilactobacillus reuteri
37% identity, 86% coverage
- Reconstructing the transcriptional regulatory network of probiotic L. reuteri is enabled by transcriptomics and machine learning
Josephs-Spaulding, mSystems 2024 - “...LMB90_RS06655 ) codes for hydroxymethylglutaryl-CoA synthase, while the three additional biosynthetic genes ( LMB90_RS06655 , LMB90_RS06670 , and LMB90_RS06715 ) code for 1-acyl-sn-glycerol-3-phosphate acyltransferase, D-2-hydroxy-acid dehydrogenase (also found in the sugar fermentation regulator iModulon), and RIP metalloprotease RseP , respectively. This cluster represents a group of...”
- “...genes identified in the T3PKS BGC, such as LMB90 _ RS06655 (involved in lipid biosynthesis), LMB90_RS06670 (part of the sugar fermentation regulator iModulon), and LMB90_RS06715 (potentially involved in polyketide synthesis signaling pathways), elucidate the intricate contributions to the metabolic versatility of L. reuteri . These findings...”
AORI_1471 D-lactate dehydrogenase VanH-Ao2 from Amycolatopsis keratiniphila
31% identity, 93% coverage
- Complete genome sequence and comparative genomic analyses of the vancomycin-producing Amycolatopsis orientalis
Xu, BMC genomics 2014 - “...for further exploration. The vcm cluster was annotated to encode a total of 35 enzymes (AORI_1471 to AORI_1505), including three vancomycin-resistance proteins (VanH, VanA, and VanX [ 7 , 8 ]), three large NRPSs, several post-assembly tailoring enzymes, and a series of biosynthetic proteins for the...”
- “...bal and cep AORI_CDS Gene name Annotation Best hit genes (NCBI accession no.) Identity % AORI_1471 vanH D-lactate dehydrogenase - - AORI_1472 vanA D-alanine-D-alanine ligase - - AORI_1473 vanX D-alanyl-D-alanine dipeptidase - - AORI_1474 Hypothetical protein - - AORI_1475 vtr Regulator protein lcl|Y16952.3_cdsid_CAG25754.1 83.33 AORI_1476 pdh...”
MAG1490 D-lactate dehydrogenase from Mycoplasma agalactiae PG2
33% identity, 95% coverage
- Genome-scale analysis of Mycoplasma agalactiae loci involved in interaction with host cells
Skapski, PloS one 2011 - “...deficient mutants selected on caprine cells (see panel B) [38] . Multiple COG proteins include MAG1490 and MAG2120, which fall into several COG categories (energy production and conversion, C-COG, coenzyme transport and metabolism, H-COG and general function prediction only, R-COG for MAG1490; general function prediction only,...”
- “...M MAG1430 E, F * 6 (3) 0.15 (+)/0.84 (+)/0.85 0.95 () HP M + MAG1490 F * 1 (1) 0.86 () ldhD D-lactate dehydrogenase (CHR) IM + MAG1500 F 2 (1) 0.56 (+) Esterase lipase (R) C MAG1540 F * 1 (1) 0.27 () tig...”
MMCAP2_0036 2-hydroxyacid dehydrogenase from Mycoplasma mycoides subsp. capri str. GM12
33% identity, 95% coverage
- Disruption of the S41 peptidase gene in mycoplasma mycoides capri impacts proteome profile, H(2)O(2) production, and sensitivity to heat shock
Allam, PloS one 2012 - “...L1 Inc 1.4170.051 <0.0013.01E04 MMCAP2_0810 50S ribosomal protein L11 Inc 1.5070.027 <0.0012.25E04 Metabolism: Amino acid MMCAP2_0036 D-lactate dehydrogenase Dec 0.6100.036 00 MMCAP2_0059 Alanine dehydrogenase Dec 0.6800.020 <0.0015.77E06 MMCAP2_0120 Threonine ammonia lyase Dec 0.6370.006 0.0010.002 MMCAP2_0225 Pyruvate dehydrogenase (acetyl-transferring) E1 component, alpha subunit Dec 0.8070.032 <0.0015.03E05 MMCAP2_0226...”
- “...Dec 0.5170.031 00 Metabolism: Other Amino Acids MMCAP2_0059 Alanine dehydrogenase Dec 0.6800.020 <0.0015.77E06 Metabolism: Carbohydrate MMCAP2_0036 D-lactate dehydrogenase Dec 0.6100.036 00 MMCAP2_0131 Fructose-1,6-bisphosphate aldolase, class II Dec 0.6670.064 0.0020.003 MMCAP2_0213 Phosphopyruvate hydratase Dec 0.6030.021 <0.0015.77E06 MMCAP2_0225 Pyruvate dehydrogenase (acetyl-transferring) E1 component, alpha subunit Dec 0.8070.032 <0.0015.03E05...”
vanH / Q7B609 D-lactate dehydrogenase (EC 1.1.1.28) from Enterococcus faecium (see paper)
VANH_ENTFC / Q05709 D-specific alpha-keto acid dehydrogenase; Vancomycin resistance protein VanH; EC 1.1.1.- from Enterococcus faecium (Streptococcus faecium) (see paper)
33% identity, 96% coverage
DHD2_LACPA / P17584 D-2-hydroxyacid dehydrogenase (NAD+); D-2-hydroxyisocaproate dehydrogenase; D-HicDH; EC 1.1.1.345 from Lacticaseibacillus paracasei (Lactobacillus paracasei) (see 2 papers)
P17584 D-2-hydroxyacid dehydrogenase (NAD+) (EC 1.1.1.345) from Lacticaseibacillus paracasei (see 2 papers)
CH_091798 D-2-hydroxyisocaproate dehydrogenase; EC 1.1.1.- from Lactobacillus paracasei (see 2 papers)
32% identity, 95% coverage
- function: Catalyzes the NADH-dependent reversible reduction of various 2-ketocarboxylic acids to the corresponding D-2-hydroxycarboxylic acids (Ref.2). In vitro can use various substrates, including 4-methyl-2- oxopentanoate (2-oxoisocaproate), 2-oxopentanoate, 2-oxohexanoate and phenylpyruvate (Ref.2).
catalytic activity: a (2R)-2-hydroxycarboxylate + NAD(+) = a 2-oxocarboxylate + NADH + H(+) (RHEA:35643)
catalytic activity: (R)-2-hydroxy-4-methylpentanoate + NAD(+) = 4-methyl-2- oxopentanoate + NADH + H(+) (RHEA:10052)
catalytic activity: (R)-3-phenyllactate + NAD(+) = 3-phenylpyruvate + NADH + H(+) (RHEA:38351)
subunit: Homodimer. - Expression and activity of heterologous hydroxyisocaproate dehydrogenases in Synechocystis sp. PCC 6803 ΔhoxYH.
Jurkaš, Engineering microbiology 2022 - “...20196 (UniProtKB ID: P14295) ( Schutteetal., 1984 ) and Lactobacillus paracasei DSM 20008 (UniProtKB ID: P17584) ( Hummeletal., 1985 ), respectively (hereafter L-HicDH and D-HicDH). It is noteworthy that, in contrast to literature reports ( Hummeletal., 1985 ; Schutteetal., 1984 ; Busto etal., 2016 , 2014...”
- Use of conserved randomly amplified polymorphic DNA (RAPD) fragments and RAPD pattern for characterization of Lactobacillus fermentum in Ghanaian fermented maize dough.
Hayford, Applied and environmental microbiology 1999
1dxyA / P17584 Structure of d-2-hydroxyisocaproate dehydrogenase (see paper)
32% identity, 95% coverage
- Ligands: nicotinamide-adenine-dinucleotide; 2-oxo-4-methylpentanoic acid (1dxyA)
LSEI_0145 Lactate dehydrogenase from Lactobacillus casei ATCC 334
32% identity, 98% coverage
MSC_0034 D-lactate dehydrogenase from Mycoplasma mycoides subsp. mycoides SC str. PG1
33% identity, 95% coverage
- Identification of genes coding for B cell antigens of Mycoplasma mycoides subsp. mycoides Small Colony (MmmSC) by using phage display
Miltiadou, BMC microbiology 2009 - “...MSC_0804 Prolipoprotein (Lpp) Yes (1) ND CAE77256 MSC_0635 D-lactate dehydrogenase (Ldh) Yes (2) ND CAE76687 MSC_0034 DNA gyrase subunit A (GyrA) Yes (2) ND CAE76660 MSC_0007 DNA gyrase subunit B (GyrB) Yes (1) ND CAE76659 MSC_0006 PTS system, glucose-specific, IIBC component (PtsG) Yes (4) ND CAE77485...”
- “...(GlpO) Yes (1) Yes (1) CAE76900 b MSC_0259 D-lactate dehydrogenase (Ldh) Yes (1) No CAE76687 MSC_0034 P115-like protein with SMC_C motif Yes (7) No CAE77104 MSC_0476 Ribose/Galactose ABC transporter, ATP-binding component (RbsA) Yes (3) No CAE76663 MSC_0010 Prolipoprotein B (LppB) Yes (2) Yes (5) CAE77147 b...”
Q6GDS2 D-lactate dehydrogenase from Staphylococcus aureus (strain MRSA252)
SAR2605 D-specific D-2-hydroxyacid dehydrogenase from Staphylococcus aureus subsp. aureus MRSA252
DA471_RS05580 D-lactate dehydrogenase from Staphylococcus aureus
34% identity, 93% coverage
P99116 D-lactate dehydrogenase from Staphylococcus aureus (strain N315)
34% identity, 93% coverage
CH51_RS14295 D-lactate dehydrogenase from Staphylococcus aureus
SACOL2535 D-isomer specific 2-hydroxyacid dehydrogenase family protein from Staphylococcus aureus subsp. aureus COL
34% identity, 93% coverage
- Staphylococcus aureus PhoU Homologs Regulate Persister Formation and Virulence
Shang, Frontiers in microbiology 2020 - “...0.37 0.52 0.12 CH51_RS01095 Acyl CoA:acetate/3-ketoacid CoA transferase 2.74 ND CH51_RS10975 Aldehyde dehydrogenase 2.84 ND CH51_RS14295 Lactate dehydrogenase 0.43 ND CH51_RS04930 CoA-disulfide reductase 2.32 ND CH51_RS09730 Acetate-CoA ligase 2.31 ND CH51_RS14750 Acetyl-CoA synthetase 2.17 1.91 0.61 Glycolysis/gluconeogenesis CH51_RS03355 Zinc-dependent alcohol dehydrogenase 0.24 ND CH51_RS10975 Aldehyde dehydrogenase...”
- “...kinase 0.36 ND CH51_RS14740 Malate:quinone oxidoreductase 0.49 ND CH51_RS04245 Aldehyde dehydrogenase 0.34 ND Pyruvate metabolism CH51_RS14295 D-Lactate dehydrogenase 3.11 ND CH51_RS01035 Pyruvate formate lyase 2.71 ND CH51_RS14750 2-Isopropylmalate synthase 0.49 ND Glycolysis/gluconeogenesis CH51_RS03355 Alcohol dehydrogenase 3.35 ND Pentose and glucuronate interconversions CH51_RS01190 2-C-Methyl-D-erythritol 4-phosphate cytidylyltransferase 0.39...”
- Transcriptomic and Metabolomic Analysis of a Fusidic Acid-Selected fusA Mutant of Staphylococcus aureus
Gupta, Antibiotics (Basel, Switzerland) 2022 - “...Microarray RT-PCR cap5E SACOL0140 10.4 2.1 adh1 SACOL0660 7.0 4.3 crtN SACOL2576 2.4 2.4 ddh SACOL2535 12.2 23.6 spa SACOL0095 8.9 1448.0 antibiotics-11-01051-t003_Table 3 Table 3 Functional category gene expression differences in SH10001st-2 compared to SH1000. Functional Category Upregulated Genes Downregulated Genes Number of Genes %...”
- “...(putative myosin-cross-reactive antigen) 12.27 SACOL1056 sspB cysteine protease precursor staphopain B 10.80 Central intermediary metabolism SACOL2535 ddh D-lactate dehydrogenase 12.16 SACOL2395 narG respiratory nitrate reductase, alpha subunit 13.51 Regulatory functions SACOL2399 nirR nitrite reductase transcriptional regulator NirR 10.86 Transport and binding proteins SACOL1144 smpB probable transmembrane...”
- Virulence and Metabolism
Richardson, Microbiology spectrum 2019 (secret) - Redox Imbalance Underlies the Fitness Defect Associated with Inactivation of the Pta-AckA Pathway in Staphylococcus aureus
Marshall, Journal of proteome research 2016 - “...S. aureus pta mutant. S. aureus possesses two L-lactate dehydrogenases (Ldh1/2) and two D-lactate dehydrogenases (SACOL2535 and SACOL2574). 30 , 45 , 46 However, these enzymes are generally not active under aerobic conditions. 31 Overexpression of ldh1 in the pta mutant using an inducible promoter partially...”
- Costs of life - Dynamics of the protein inventory of Staphylococcus aureus during anaerobiosis
Zühlke, Scientific reports 2016 - “...the most abundant fermentation enzyme even during long-lasting anaerobiosis. Ldh2 and the D-lactate producing LdhD (SACOL2535) are also produced in higher amounts after oxygen starvation but only to a level of 2,100 and 3,300 molecules per cell, respectively ( Fig. 5 ). In accordance lactate was...”
- Effect of oxygen on glucose metabolism: utilization of lactate in Staphylococcus aureus as revealed by in vivo NMR studies
Ferreira, PloS one 2013 - “...L-lactate dehydrogenases ( ldh1 [13] and the NO-inducible ldh2 [15] ), and two D-lactate dehydrogenases (SACOL2535 and SACOL2574). Although NAD + -dependent dehydrogenases are known to mediate the aerobic lactate oxidation in the fermentative bacterium Lactobacillus plantarum [34] , this is a rare event in nature....”
- Redox sensing by a Rex-family repressor is involved in the regulation of anaerobic gene expression in Staphylococcus aureus
Pagels, Molecular microbiology 2010 - “...306 Shift Up Up SACOL1535 srrA DNA-binding response regulator SrrA 103 Shift No change Up SACOL2535 (ddh) d -isomer specific 2-hydroxyacid dehydrogenase family protein 102 Shift SACOL2534 frp NAD(P)H-flavin oxidoreductase 185 [Shift] f SACOL0204 pflB Formate acetyltransferase 96 Shift Up Up SACOL0222 ldh1-1 l -lactate dehydrogenase...”
- Genetic changes that correlate with the pine-oil disinfectant-reduced susceptibility mechanism of Staphylococcus aureus
Lamichhane-Khadka, Journal of applied microbiology 2008 - “...expression (PS12 /COL) Gene Locus ID * Function * Microarray qRT- PCR Upregulated genes ddh SACOL2535 d -isomer specific 2-hydroxyacid dehydrogenase 2.37 3.7 phoR SACOL1739 sensory box histidine kinase PhoR 2.14 2.4 SACOL0722 phosphate transporter family protein 2.07 4.0 mvaS SACOL2561 hydroxymethylglutaryl-CoA synthase 2.00 3.0 SACOL2609...”
- A defect in menadione biosynthesis induces global changes in gene expression in Staphylococcus aureus
Kohler, Journal of bacteriology 2008 - “...were present in equal amounts in both strains (Ldh1, SACOL2535), other classically anaerobic enzymes seem to be present in higher amounts either in the hemB...”
- “...permease; SACOL2386, nitrate/nitrite extrusion protein; SACOL2535, D-specific D-2-hydroxyacid dehydrogenase (D-lactate dehydrogenase). 6360 KOHLER ET AL. J....”
- More
SAUSA300_2463 D-lactate dehydrogenase from Staphylococcus aureus subsp. aureus USA300_FPR3757
34% identity, 89% coverage
SA2312 2-hydroxyacid dehydrogenase from Staphylococcus aureus subsp. aureus N315
SAV2524 2-hydroxyacid dehydrogenase from Staphylococcus aureus subsp. aureus Mu50
34% identity, 89% coverage
- Proteomic and Membrane Lipid Correlates of Reduced Host Defense Peptide
Kohler, Antibiotics (Basel, Switzerland) 2019 - “...Increased in mutant IlvA1 (SA1271) Threonine/serine dehydrase 4.17 Ald1 (SA1272) -amino acid dehydrogenase 1.667 Ddh (SA2312) D-lactate dehydrogenase 1.006 antibiotics-08-00169-t002_Table 2 Table 2 Summary fatty acid compositional differences between parent and snoD mutant. Fatty Acid Species SH1000-98 * p value SH1000-WT * p value Aerobic Anaerobic...”
- The effect of skin fatty acids on Staphylococcus aureus
Neumann, Archives of microbiology 2015 - “...protein UreE 3.28 SA2098 Putative 2-hydroxyacid dehydrogenase SA2098 2.09 SA2311 Putative NAD(P)H nitroreductase SA2311 2.62 SA2312 Ddh d -lactate dehydrogenase 2.44 SA2336 ClpL ATP-dependent Clp proteinase chain clpL 2.26 SA2336 ClpL ATP-dependent Clp proteinase chain clpL 2.62 SA2400 Mqo2 Malate: quinone oxidoreductase 0.44 SA2400 Mqo2 Malate:...”
- Exposure of clinical MRSA heterogeneous strains to β-lactams redirects metabolism to optimize energy production through the TCA cycle
Keaton, PloS one 2013 - “...NADPH-dependent oxidoreductase Involved in maintenance of the cellular redox state and the disulfide stress response SA2312 ddh 10.8 D-lactate dehydroge-nase Catalyzes the formation of pyruvate from lactate SA0218 pflB 10.5 formate acetyltrans-ferase Catalyzes a key step in anaerobic glycolysis (conversion of pyruvate and CoA to formateacetyl-CoA)...”
- “...marked down-regulation of L-lactate dehydrogenase ( lctE , SA0232) and D-lactate dehydrogenase ( ddh , SA2312), which interconvert pyruvate and lactate. Genes encoding enzymes involved in gluconeogenesis were similarly down-regulated including pyruvate carboxylase ( pycA , SA0963), which catalyzes the conversion of pyruvate into oxaloacetate, and...”
- Induction of attachment-independent biofilm formation and repression of Hfq expression by low-fluid-shear culture of Staphylococcus aureus
Castro, Applied and environmental microbiology 2011 - “...alcohol dehydrogenase (SA0562); ddh, encoding D-lactate dehydrogenase (SA2312); and a hypothetical protein (SA2268). This consensus sequence is a binding site...”
- “...SA1013 SA1532 SA0455 SA2336 clpL 2.35 2.43 3.19 2.17 2.81 SA2312 ddh SA0562 adh1 SA2410 nrdD 2.31 2.27 2.09 SA0102 SA0570 SA0752 SA2268 2.14 2.14 2.07 4.45 argF...”
- Direct targets of CodY in Staphylococcus aureus
Majerczyk, Journal of bacteriology 2010 - “...SA1018 SA1019 SA1038 SA1039 SA1040 SA2144 SA2314 SA2312 SA2525 SA1144 SA2483 brnQ2-0303 brnQ1 SA2619 SA1963 SA0010, SA0011 SA0228-SA0232 Transcriptional...”
- Characterizing the effects of inorganic acid and alkaline shock on the Staphylococcus aureus transcriptome and messenger RNA turnover
Anderson, FEMS immunology and medical microbiology 2010 - “...ND SA2299 hypothetical protein sa_c5114s4412_a_at 17.7 2.5 ND SA2306 hypothetical protein sa_c5138s4434_a_at 2.6 2.5 2.5 SA2312 hypothetical protein sa_c5199s4501_a_at * 18.6 2.5 ND SA2328 hypothetical protein sa_c5211s4512_at 4.2 2.5 ND SA2331 hypothetical protein sa_c5219s4518_at 4.8 2.5 2.5 SA2333 hypothetical protein sa_c5223s4525_a_at * 2.0 2.5 2.5 SA2334...”
- Serial daptomycin selection generates daptomycin-nonsusceptible Staphylococcus aureus strains with a heterogeneous vancomycin-intermediate phenotype
Camargo, Antimicrobial agents and chemotherapy 2008 - “...0.49 0.42 0.52 0.22 0.54 0.21 0.56 2.16 SA2312 SA0997 ddh murI ABC transporter, ATP-binding protein ABC transporter, permease Glycine betaine transporter...”
- Characterizing the effect of the Staphylococcus aureus virulence factor regulator, SarA, on log-phase mRNA half-lives
Roberts, Journal of bacteriology 2006 - “...5 5 5 5 5 5 5 5 SA1075 SA1234 SA2312 SAS044 SA1305 SA2023 SA0353 SA1913 SA0182 SA0529 SA1528 Acyl carrier protein Major cold shock protein CspA D-Specific...”
- More
- The SAV1322 gene from Staphylococcus aureus: genomic and proteomic approaches to identification and characterization of gene function
Kim, BMC microbiology 2016 - “...Down A008 gi|15923216 Formate acetyltrasferase 1155 pflB SAV0226 Up A058 gi|15925514 D-lactate dehydrogenase 972 Ddh SAV2524 Up A078 gi|15925115 Fructose-bisphosphate aldolase 62 fbaA SAV2125 Up A281 gi|15923595 Alcohol dehydrogenase 1305 Adh SAV0605 Up Lipid metabolism A027 gi|15924291 Glycerol kinase 1037 glpK SAV1301 Down A054 gi|15923640 Dihydroxyacetone...”
MW2444 D-specific D-2-hydroxyacid dehydrogenase from Staphylococcus aureus subsp. aureus MW2
34% identity, 89% coverage
- Inhibition of Staphylococcus aureus biofilm formation by gurmarin, a plant-derived cyclic peptide
Chang, Frontiers in cellular and infection microbiology 2022 - “...genes in gurmarin treated S. aureus biofilm. TIGR ID Fold change Definition Gene symbol FDR MW2444 23.26 D-2-Hydroxyacid dehydrogenase ddh 0.01 SACOL2086 14.77 Transcriptional regulator, TenA family tenA 0.04 SACOL0842 14.04 Enolase eno 0.05 SACOL2076 11.24 Conserved hypothetical protein 0.01 SAV0181 9.21 Hypothetical protein yagU 0.04...”
- “...identified in the oxidoreductase category (induced). Gene ID (TIGR) Fold change Definition Gene symbol FDR MW2444 23.26 D-2-hydroxyacid dehydrogenase ddh 0.01 SAV1337 6.85 Guanosine 5-monophosphate oxidoreductase 0.03 SAV0382 5.17 Similar to nitro/flavin reductase 0.05 SACOL1245 4.54 3-oxoacyl-(acyl-carrier-protein) reductase fabG1 0.04 SACOL1068 3.44 Quinol oxidase, subunit III...”
- Rsp inhibits attachment and biofilm formation by repressing fnbA in Staphylococcus aureus MW2
Lei, Journal of bacteriology 2011 - “...3.9 3.8 2.3 2.9 2.3 clfA fnbA fnbB Metabolism MW2444 MW2198 MW2443 MW0358 MW2541 MW2594 MW0415 MW0414 MW2206 MW2207 MW2208 MW2212 MW2209 MW2210 MW2211 MW2157...”
D-ldh / P51011 D-lactate dehydrogenase subunit (EC 1.1.1.28) from Leuconostoc mesenteroides subsp. cremoris (see 3 papers)
CH_091801 D-lactate dehydrogenase; EC 1.1.1.28 from Leuconostoc mesenteroides subsp. cremoris (see paper)
32% identity, 97% coverage
HGDH_ACIFV / D2RJU7 (R)-2-hydroxyglutarate dehydrogenase; HGDH; EC 1.1.1.399 from Acidaminococcus fermentans (strain ATCC 25085 / DSM 20731 / CCUG 9996 / CIP 106432 / VR4) (see paper)
WP_012938338 2-hydroxyacid dehydrogenase from Acidaminococcus fermentans
31% identity, 98% coverage
WP_047131604 D-2-hydroxyacid dehydrogenase from Staphylococcus condimenti
32% identity, 93% coverage
NWMN_2459 D-lactate dehydrogenase from Staphylococcus aureus subsp. aureus str. Newman
SACOL2574 D-isomer specific 2-hydroxyacid dehydrogenase family protein from Staphylococcus aureus subsp. aureus COL
31% identity, 96% coverage
- Citrate serves as a signal molecule to modulate carbon metabolism and iron homeostasis in Staphylococcus aureus
Chen, PLoS pathogens 2024 - “...the Tn citB mutant led to markedly increased expression of genes, such as butA , NWMN_2459 , lctP1 , NWMN_1315 , NWMN_2026 , adh1 , pflB , and fdhA , associated with fermentation pathways [ 56 , 57 ] ( S5 Fig ). Additionally, in the...”
- Virulence and Metabolism
Richardson, Microbiology spectrum 2019 (secret) - Redox Imbalance Underlies the Fitness Defect Associated with Inactivation of the Pta-AckA Pathway in Staphylococcus aureus
Marshall, Journal of proteome research 2016 - “...pta mutant. S. aureus possesses two L-lactate dehydrogenases (Ldh1/2) and two D-lactate dehydrogenases (SACOL2535 and SACOL2574). 30 , 45 , 46 However, these enzymes are generally not active under aerobic conditions. 31 Overexpression of ldh1 in the pta mutant using an inducible promoter partially restored its...”
- Effect of oxygen on glucose metabolism: utilization of lactate in Staphylococcus aureus as revealed by in vivo NMR studies
Ferreira, PloS one 2013 - “...( ldh1 [13] and the NO-inducible ldh2 [15] ), and two D-lactate dehydrogenases (SACOL2535 and SACOL2574). Although NAD + -dependent dehydrogenases are known to mediate the aerobic lactate oxidation in the fermentative bacterium Lactobacillus plantarum [34] , this is a rare event in nature. Indeed, in...”
F8RPR8 D-lactate dehydrogenase (EC 1.1.1.28) from Weizmannia coagulans (see paper)
34% identity, 95% coverage
BAST_0909 D-2-hydroxyacid dehydrogenase from Bifidobacterium asteroides PRL2011
30% identity, 96% coverage
LSEI_2156 D-2-hydroxyacid dehydrogenase from Lacticaseibacillus paracasei ATCC 334
LSEI_2156 Lactate dehydrogenase related 2-hydroxyacid dehydrogenase from Lactobacillus casei ATCC 334
30% identity, 98% coverage
- Regulatory Mechanisms of L-Lactic Acid and Taste Substances in Chinese Acid Rice Soup (Rice-Acid) Fermented With a Lacticaseibacillus paracasei and Kluyveromyces marxianus
Liu, Frontiers in microbiology 2021 - “...C-acetyltransferase 2.30 2.35 LSEI_2110 [EC:2.1.3.15] K01963 acetyl-CoA carboxylase carboxyl transferase subunit beta 1.82 4.38 1.75 LSEI_2156 [EC:1.1.1.28] K03778 d-lactate dehydrogenase 4.99 4.63 LSEI_2172 [EC:2.7.2.1] K00925 acetate kinase 2.57 3.73 1.64 2.19 LSEI_2410 [EC:4.2.1.2] K01679 fumarate hydratase, class II 1.69 2.00 LSEI_2549 [EC:1.1.1.27] l-lactate dehydrogenase 1.89 1.61...”
- “...and four up-regulated genes on the third day of fermentation. The gene encoding d-lactate dehydrogenase (LSEI_2156, FC = 4.99) in the third day of fermentation showed the lower mRNA level than that on the first day in the group of the single inoculation of L. paracasei...”
SA2346 2-hydroxyacid dehydrogenase from Staphylococcus aureus subsp. aureus N315
31% identity, 96% coverage
O66939 D-lactate dehydrogenase (EC 1.1.1.28) from Aquifex aeolicus (see paper)
3kb6B / O66939 Crystal structure of d-lactate dehydrogenase from aquifex aeolicus complexed with NAD and lactic acid (see paper)
aq_727 D-lactate dehydrogenase from Aquifex aeolicus VF5
32% identity, 95% coverage
HPR_THEMA / Q9X1C1 Hydroxypyruvate reductase; HPR; EC 1.1.1.81 from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8) (see paper)
TM1401 D-3-phosphoglycerate dehydrogenase from Thermotoga maritima MSB8
41% identity, 74% coverage
KQ76_13385 D-lactate dehydrogenase from Staphylococcus aureus
30% identity, 96% coverage
4prlA Crystal structure of d-lactate dehydrogenase with NAD+ from lactobacillus jensenii (see paper)
33% identity, 90% coverage
- Ligand: nicotinamide-adenine-dinucleotide (4prlA)
SAK_0821 D-lactate dehydrogenase from Streptococcus agalactiae A909
gbs0668 Unknown from Streptococcus agalactiae NEM316
33% identity, 93% coverage
- The Role of Regulator Catabolite Control Protein A (CcpA) in Streptococcus agalactiae Physiology and Stress Response
Roux, Microbiology spectrum 2022 - “...), ptsI ( SAK_0946 ), budB ( SAK_1279 ), pfkA ( SAK_1036 ), ldhA ( SAK_0821 ), adhP ( SAK_0087 ), SAK_0674 , covR ( SAK_1639 ), pflB ( SAK_1735 ), and ahpF ( SAK_1854 ). The major part of the S. agalactiae CcpA regulon is...”
- “...phosphate dikinase; SAK_0179 , L-2-hydroxyisocaproate dehydrogenase; ldh ( SAK_1054 ), l -lactate dehydrogenase; ldhA ( SAK_0821 ), d -lactate deshydrogenase; budB ( SAK_1279 ), acetolactate synthase; budA ( SAK_1278 ), alpha-acetolactate decarboxylase; SAK_0674 , acetoin reductase; pta ( SAK_1177 ), phosphotransacetylase; SAK_1622 , acylphosphatase; ackA (...”
- Whole-Genome Comparison Uncovers Genomic Mutations between Group B Streptococci Sampled from Infected Newborns and Their Mothers
Almeida, Journal of bacteriology 2015 - “...gbs0476 (3= UTR) gbs1259 gbs1986 gbs1427 gbs1950 gbs1946 (5= UTR) gbs0668 gbs1038 gbs1946 (5= UTR) gbs1377 SNP SNP SNP Indel SNP SNP Indel SNP SNP SNP SNP SNP...”
- “...(ptsG), and both child strains were mutated in gbs0668 (D-lactate dehydrogenase) and gbs1038 (permease). The isolate from child 12-1 tested presented additional...”
- Transcriptomic and genomic evidence for Streptococcus agalactiae adaptation to the bovine environment
Richards, BMC genomics 2013 - “...lactose-specific iibc component NEM316 B gbs1330 lacE PTS family lactose porter iicb component NEM316 C gbs0668 D-lactate dehydrogenase NEM316 C gbs0789 Major facilitator superfamily protein NEM316 C gbs1264 Alpha-acetolactate decarboxylase NEM316 C gbs1332 lacT Transcription antiterminator NEM316 C gbs1508 4-alpha-glucanotransferase NEM316 C gbs1619 D-3-phosphoglycerate dehydrogenase NEM316...”
SAZ172_2659 D-lactate dehydrogenase from Staphylococcus aureus subsp. aureus Z172
30% identity, 96% coverage
- Protein CoAlation and antioxidant function of coenzyme A in prokaryotic cells
Tsuchiya, The Biochemical journal 2018 - “...200 SAZ172_2084 5-Amino-6-(5-phosphoribosylamino)uracil reductase 15.666 AFQILHEQYGC*K 51.727 gatB_2 Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B 53.656 C*DANISLRPYGQEK 76.574 SAZ172_2659 d -specific d -2-hydroxyacid dehydrogenase-like protein 37.264 DAVFVNC*AR 73.435 folP Dihydropteroate synthase 29.532 SEVAEAC*LK 115.33 AYM28_03210 Deoxyguanosinetriphosphate triphosphohydrolase 50.595 GGEVLLNNC*LK 164.22 Furthermore, the prevalence of hydrophobic and positively charged amino...”
TRQ7_RS07315 hydroxypyruvate reductase from Thermotoga sp. RQ7
41% identity, 74% coverage
- Adapted laboratory evolution of Thermotoga sp. strain RQ7 under carbon starvation
Gautam, BMC research notes 2022 - “...FlhB d11: AAAACAGGAAGTA Frame shift, truncation 1006296 TRQ7_RS05035 Alpha-amylase i1: TTA Frame shift, run-through 1426409 TRQ7_RS07315 2-hydroxyacid dehydrogenase i1: AGAGG Frame shift, truncation SNPs 205012 TRQ7_RS01075 Methylmalonyl-CoA carboxyltransferase Transversion: GT Silent: V360 262000 TRQ7_RS01400 Hypothetical protein Transition: GA Silent: L346 323128 TRQ7_RS01715 Queuosine precursor transporter Transition:...”
LRI_0357 D-2-hydroxyacid dehydrogenase from Limosilactobacillus reuteri I5007
31% identity, 98% coverage
SXYL_00325 D-lactate dehydrogenase from Staphylococcus xylosus
29% identity, 96% coverage
- Investigating Extracellular DNA Release in Staphylococcus xylosus Biofilm In Vitro
Leroy, Microorganisms 2021 - “...2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N -acetyltransferase, 4.1 * 2.5 * 4-hydroxy-tetrahydrodipicolinate reductase, synthase SXYL_02665 Dihydrodipicolinate synthase 2.0 3.2 SXYL_00325 ldhD d -lactate dehydrogenase 10.3 11.9 COFACTOR, VITAMIN SYNTHESIS SXYL_01097-100 ribDEBAH Riboflavin biosynthesis 2.8 * 3.7 * SXYL_00734-35 ecfA2T Energy-coupling factor transporter 2.2 * SXYL_01194 hemA Glutamyl-tRNA reductase 2.0 SXYL_01196...”
A4XJ21 D-3-phosphoglycerate dehydrogenase from Caldicellulosiruptor saccharolyticus (strain ATCC 43494 / DSM 8903 / Tp8T 6331)
34% identity, 54% coverage
PF1394 phosphoglycerate dehydrogenase from Pyrococcus furiosus DSM 3638
34% identity, 84% coverage
Athe_2125 phosphoglycerate dehydrogenase from Caldicellulosiruptor bescii DSM 6725
34% identity, 55% coverage
TEL01S_RS09140 D-2-hydroxyacid dehydrogenase from Pseudothermotoga elfii DSM 9442 = NBRC 107921
40% identity, 70% coverage
A0A0M3KL04 D-lactate dehydrogenase (EC 1.1.1.28) from Sporolactobacillus inulinus (see paper)
31% identity, 94% coverage
D805_0524 D-2-hydroxyacid dehydrogenase from Bifidobacterium thermophilum RBL67
29% identity, 96% coverage
4xkjA / A0A0M3KL04 A novel d-lactate dehydrogenase from sporolactobacillus sp
31% identity, 94% coverage
- Ligand: nicotinamide-adenine-dinucleotide (4xkjA)
TK1966 D-3-phosphoglycerate dehydrogenase from Thermococcus kodakaraensis KOD1
34% identity, 84% coverage
- Removal of phosphoglycolate in hyperthermophilic archaea
Michimori, Proceedings of the National Academy of Sciences of the United States of America 2024 - “...into account, we then searched for putative 2-hydroxyacid dehydrogenases. Three candidate genes (TK0551, TK0683, and TK1966), all encoding proteins of the d -lactate dehydrogenase (LDH) family, were found on the T. kodakarensis genome. TK0551 and TK0683 displayed 42% identity, TK0683 and TK1966 displayed 45% identity, and...”
- “...( 30 ), respectively. In addition, the T. kodakarensis genome harbors homologs of 3-phosphoglycerate dehydrogenase (TK1966), phosphoserine aminotransferase, and phosphoserine phosphatase. Using a TK1966 gene disruption strain, it was genetically demonstrated that 3-PGA is a precursor for serine biosynthesis ( 30 ). As T. kodakarensis harbors...”
- An archaeal ADP-dependent serine kinase involved in cysteine biosynthesis and serine metabolism
Makino, Nature communications 2016 - “...gene predicted to encode 3-phosphoglycerate dehydrogenase (SerA) is present on the genome ( Tk-serA : TK1966 (42% identical to SerA from E. coli )). We thus attempted to inactivate this pathway by disrupting the serA gene. As two other homologs with relatively high similarity, annotated as...”
- “...to glyA abolished the complementation effect by pyruvate ( Fig. 5e ), revealing that serA (TK1966) is the 3-phosphoglycerate dehydrogenase in T. kodakarensis , and that the cysteine auxotrophy observed in the serA ldhA1 ldhA2 serK -1 strain ( Fig. 2h ) was due to the...”
SERP2133 D-isomer specific 2-hydroxyacid dehydrogenase family protein from Staphylococcus epidermidis RP62A
28% identity, 91% coverage
MMP1588 D-3-phosphoglycerate dehydrogenase from Methanococcus maripaludis S2
37% identity, 46% coverage
A4XGF7 D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding protein from Caldicellulosiruptor saccharolyticus (strain ATCC 43494 / DSM 8903 / Tp8T 6331)
34% identity, 92% coverage
Q8TYK0 D-3-phosphoglycerate dehydrogenase from Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938)
35% identity, 57% coverage
HPR_BLAHS / C0CMQ8 Hydroxypyruvate reductase; EC 1.1.1.81 from Blautia hydrogenotrophica (strain DSM 10507 / JCM 14656 / S5a33) (Ruminococcus hydrogenotrophicus) (see paper)
33% identity, 76% coverage
- function: Involved in catabolism of D-apiose. Catalyzes the reduction of 3-hydroxypyruvate to glycerate.
catalytic activity: (R)-glycerate + NAD(+) = 3-hydroxypyruvate + NADH + H(+) (RHEA:17905) - Functional assignment of multiple catabolic pathways for D-apiose
Carter, Nature chemical biology 2018 - “...dehydrogenase), B9JN19 (D-erythrulose 4-phosphate isomerase), B9JN20 (L-eythrulose 1-phosphate isomerase), C0CMQ5/C0CMQ6 (3-oxo-isoapionate transketolase), C0CMQ7 (D-apionate oxidoisomerase), C0CMQ8 (hydroxypyruvate reductase), F8GV06 (D-apionate oxidoisomerase), Q2JZQ0 (3-oxo-isoapionate 4-phosphate decarboxylase), Q2JZQ5 (D-apiose binding SBP), Q6D5T7 (D-apiose isomerase), Q6D5T8 (D-apulose kinase), Q6D8V3 (D-apionate oxidoisomerase), Q6D8V4 (3-oxo-isoapionate decarboxylase), Q6D8V5 (L-erythrulose 1-phosphate isomerase), Q6D8V6...”
- “...(pH 8.0), 2 mM MgCl 2 , 0.16 mM NADH, and 3.65 10 8 M C0CMQ8 in a final volume of 200 L. Data were fit to the Michaelis-Menten equation (kinetic constants are shown in Supplementary Table 4 ). 1 H NMR Assay for Lactonase Activity...”
GKIL_0932 phosphoglycerate dehydrogenase from Gloeobacter kilaueensis JS1
29% identity, 58% coverage
- Cultivation and complete genome sequencing of Gloeobacter kilaueensis sp. nov., from a lava cave in Kīlauea Caldera, Hawai'i
Saw, PloS one 2013 - “...resistance pathway, revealed by the presence of vanB (GKIL_3597), vanX (GKIL_1509 and GKIL_1879), and serA (GKIL_0932). GVIO, however, only has a copy of vanX (gll1805) and serA (gvip294), and is missing vanB . Five essential gene products are in fact required for high-level vancomycin resistance, specifically...”
Q48534 D-2-hydroxyacid dehydrogenase (NAD+) (EC 1.1.1.345) from Lactobacillus delbrueckii (see paper)
30% identity, 96% coverage
BAB1_1697 ATP/GTP-binding site motif A (P-loop):Amino acid-binding ACT:D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain:... from Brucella melitensis biovar Abortus 2308
34% identity, 48% coverage
- Brucella abortus Depends on l-Serine Biosynthesis for Intracellular Proliferation
Révora, Infection and immunity 2020 (secret) - Evaluation of the effects of erythritol on gene expression in Brucella abortus
Rodríguez, PloS one 2012 - “...COG0683E BAB1_1794 0.56 0.38 Leu/Ile/Val-binding family protein COG0683E BAB2_0282 0.55 0.33 Leu/Ile/Val-binding family protein COG0683E BAB1_1697 2.67 7.98 D-3-phosphoglycerate dehydrogenase COG0111EH BAB1_1699 - 5.80 Phosphoserine aminotransferase COG1932EH BAB1_1502 2.15 2.57 Carbamoyl phosphate synthase small subunit COG0505EF BAB1_1508 2.11 2.54 Carbamoyl phosphate synthase large subunit COG0458EF BAB2_0640...”
- “...7.95 BAB1_1502 Carbamoyl phosphate synthase small subunit 3.65 BAB1_1508 Carbamoyl phosphate synthase large subunit 2.20 BAB1_1697 D-3-phosphoglycerate dehydrogenase 3.30 BAB1_1699 Phosphoserin aminotransferase 4.65 BAB1_1813 Putative transaldolase 4.40 BAB2_0364 Fructose-1,6-bisphosphatase 4.15 BAB2_0367 Triosephosphate isomerase 2 (TIM 2) 8.05 BAB2_0371 Erythritol-4-phosphate-dehydrogenase 9.25 BAB2_0375 Phosphoribulokinase ABC transporter ATPase 3.60...”
- Intracellular adaptation of Brucella abortus
Lamontagne, Journal of proteome research 2009 - “...synthesis SSU S17 34 BAB1_1699 AA synthesis SerC 35 BAB1_1236 Protein synthesis LSU L15p 35 BAB1_1697 AA synthesis SerA-1 36 BAB1_1259 Protein synthesis SSU S7 36 BAB1_1845 Stress response CtpA 37 BAB1_0811 Protein synthesis LSU L13 37 BAB1_2130 Stress response DnaJ 38 BAB1_1254 Protein synthesis LSU...”
2yq5C / Q1GAA2 Crystal structure of d-isomer specific 2-hydroxyacid dehydrogenase from lactobacillus delbrueckii ssp. Bulgaricus: NAD complexed form (see paper)
30% identity, 91% coverage
- Ligand: nicotinamide-adenine-dinucleotide (2yq5C)
Q1GAA2 D-lactate dehydrogenase (EC 1.1.1.28); D-2-hydroxyacid dehydrogenase (NAD+) (EC 1.1.1.345) from Lactobacillus delbrueckii subsp. bulgaricus (see 2 papers)
Ldb1010 D-isomer specific 2-hydroxyacid dehydrogenase from Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842
30% identity, 91% coverage
CC3215 D-3-phosphoglycerate dehydrogenase from Caulobacter crescentus CB15
CCNA_03322 D-3-phosphoglycerate dehydrogenase from Caulobacter crescentus NA1000
32% identity, 54% coverage
- Whole-genome transcriptional analysis of heavy metal stresses in Caulobacter crescentus
Hu, Journal of bacteriology 2005 - “...degradation CC0957 CC0958 CC0959 CC0960 Serine biosynthesis CC3215 CC3216 LPSa synthesis CC0118 CC1985 Annotation Chromate 8448 HU ET AL. ACKNOWLEDGMENTS This...”
- Transcriptional profiling of Caulobacter crescentus during growth on complex and minimal media
Hottes, Journal of bacteriology 2004 - “...dehydrogenase, putA 3.74 3.78 Serine synthesis CC3215, D-3-phosphoglycerate dehydrogenase, serA CC3216, phosphoserine aminotransferase, serC 0.23 0.27 0.22 0.24...”
- The complex logic of stringent response regulation in Caulobacter crescentus: starvation signalling in an oligotrophic environment
Boutte, Molecular microbiology 2011 - “...l ysA mar414 CCNA_02296 ( Huitema et al , 2006 ) 1166 NA1000 serA mar414 CCNA_03322 ( Huitema et al , 2006 ) 1164 NA1000 CCNA1419 mar414 CCNA_01419 ( Huitema et al , 2006 ) 1250 NA1000 gltB CCNA_03722 This work 1183 NA1000 cysE hMu CCNA_02734...”
Dhaf_1344 D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding from Desulfitobacterium hafniense DCB-2
DSY4020 hypothetical protein from Desulfitobacterium hafniense Y51
33% identity, 91% coverage
- vanI: a novel D-Ala-D-Lac vancomycin resistance gene cluster found in Desulfitobacterium hafniense
Kruse, Microbial biotechnology 2014 - “...homologues of these four genes were also found in the genomes of D. hafniense DCB-2 (Dhaf_1344, Dhaf_1980, Dhaf_2079 and Dhaf_2820) and D. hafniense DP7 (data not shown). The complete genomes of D. hafniense Y51 and DCB-2 (Nonaka et al ., 2006 ; Kim et al .,...”
- vanI: a novel D-Ala-D-Lac vancomycin resistance gene cluster found in Desulfitobacterium hafniense
Kruse, Microbial biotechnology 2014 - “...Previously, four genes have been proposed as potential vanH -encoding genes (DSY0996, DSY1673, DSY3442 and DSY4020) in the genome of D. hafniense Y51 (Kalan et al ., 2009 ). The homologues of these four genes were also found in the genomes of D. hafniense DCB-2 (Dhaf_1344,...”
- Noncanonical vancomycin resistance cluster from Desulfitobacterium hafniense Y51
Kalan, Antimicrobial agents and chemotherapy 2009 - “...2-hydroxyacid dehydrogenase genes (DSY0996, DSY1673, DSY3442, and DSY4020) are present in the genome of D. hafniense Y51. The organism exhibits high-level...”
Spy49_0919 D-lactate dehydrogenase from Streptococcus pyogenes NZ131
30% identity, 93% coverage
OEOE_1709 Lactate dehydrogenase from Oenococcus oeni PSU-1
29% identity, 97% coverage
Q8U3Y2 glyoxylate reductase (NADP+) (EC 1.1.1.79); hydroxypyruvate reductase (EC 1.1.1.81) from Pyrococcus furiosus (see paper)
PF0319 putative phosphoglycerate dehydrogenase from Pyrococcus furiosus DSM 3638
31% identity, 83% coverage
5aovA / Q8U3Y2 Ternary crystal structure of pyrococcus furiosus glyoxylate hydroxypyruvate reductase in presence of glyoxylate (see paper)
31% identity, 83% coverage
- Ligands: nadp nicotinamide-adenine-dinucleotide phosphate; glyoxylic acid (5aovA)
MSMEG_2378 D-3-phosphoglycerate dehydrogenase from Mycobacterium smegmatis str. MC2 155
A0QUY2 D-3-phosphoglycerate dehydrogenase from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)
MSMEG_2378, MSMEI_2318 phosphoglycerate dehydrogenase from Mycolicibacterium smegmatis MC2 155
33% identity, 46% coverage
- Interactome Analysis Identifies MSMEI_3879 as a Substrate of Mycolicibacterium smegmatis ClpC1
Ogbonna, Microbiology spectrum 2023 - “...acid metabolism A0QR33 hemL , MSMEG_0969, MSMEI_0943 Glutamate-1-semialdehyde 2,1-aminomutase (GSA) 0.09 0.02 A0QUY2 serA , MSMEG_2378, MSMEI_2318 d -3-Phosphoglycerate dehydrogenase (EC 1.1.1.95) 0.48 0.64 A0R6V5 gabT , MSMEG_6685, MSMEI_6505 4-Aminobutyrate transaminase (EC 2.6.1.19) 0.09 0.1 0.23 0.23 A0QZX1 hisG , MSMEG_4180, MSMEI_4082 ATP phosphoribosyltransferase (ATP-PRT) (ATP-PRTase)...”
- High throughput screen identifies small molecule inhibitors specific for Mycobacterium tuberculosis phosphoserine phosphatase
Arora, The Journal of biological chemistry 2014 - “...Rv2996c BCG_3017c MMAR_1715 ML1692 MUL_1952 MAF_30010 MSMEG_2378, MSMEI_2318 Rv3214 BCG_3241, BCG_3334 MMAR_1343 Rv0489 BCG_0530 MMAR_0814, MMAR_3747 ML2441c...”
- Regulation of the ald gene encoding alanine dehydrogenase by AldR in Mycobacterium smegmatis
Jeong, Journal of bacteriology 2013 - “...a molecular mass of 32 kDa and pI of 5.2, and MSMEG_2378 (SerA), with a molecular mass of 51 kDa and pI of 4.9. (B) Determination of the transcription levels of...”
- “...encoded by MSMEG_2659 (ald), MSMEG_3084 (gap), and MSMEG_2378 (serA), respectively. Since the synthesis of alanine dehydrogenase (Ald) was increased the most...”
- Mycobacterium smegmatis RoxY is a repressor of oxyS and contributes to resistance to oxidative stress and bactericidal ubiquitin-derived peptides
Daugherty, Journal of bacteriology 2011 - “...Annotationa Intermediary metabolism msmeg_2378 .........................D-3-Phosphoglycerate dehydrogenase msmeg_5121 .........................Aminotransferase,...”
- “...the wild type was reproducibly observed in the msmeg_2378 and msmeg_0642 (yliD) mutants (see Fig. S2C in the supplemental material). Since mycobacterial mutants...”
- Interactome Analysis Identifies MSMEI_3879 as a Substrate of Mycolicibacterium smegmatis ClpC1
Ogbonna, Microbiology spectrum 2023 - “...ClpC1 EQ Amino acid metabolism A0QR33 hemL , MSMEG_0969, MSMEI_0943 Glutamate-1-semialdehyde 2,1-aminomutase (GSA) 0.09 0.02 A0QUY2 serA , MSMEG_2378, MSMEI_2318 d -3-Phosphoglycerate dehydrogenase (EC 1.1.1.95) 0.48 0.64 A0R6V5 gabT , MSMEG_6685, MSMEI_6505 4-Aminobutyrate transaminase (EC 2.6.1.19) 0.09 0.1 0.23 0.23 A0QZX1 hisG , MSMEG_4180, MSMEI_4082 ATP...”
- Interactome Analysis Identifies MSMEI_3879 as a Substrate of Mycolicibacterium smegmatis ClpC1
Ogbonna, Microbiology spectrum 2023 - “...metabolism A0QR33 hemL , MSMEG_0969, MSMEI_0943 Glutamate-1-semialdehyde 2,1-aminomutase (GSA) 0.09 0.02 A0QUY2 serA , MSMEG_2378, MSMEI_2318 d -3-Phosphoglycerate dehydrogenase (EC 1.1.1.95) 0.48 0.64 A0R6V5 gabT , MSMEG_6685, MSMEI_6505 4-Aminobutyrate transaminase (EC 2.6.1.19) 0.09 0.1 0.23 0.23 A0QZX1 hisG , MSMEG_4180, MSMEI_4082 ATP phosphoribosyltransferase (ATP-PRT) (ATP-PRTase) 0.04...”
hprA / P73821 glycerate dehydrogenase (EC 1.1.1.29) from Synechocystis sp. (strain PCC 6803 / Kazusa) (see paper)
sll1908 phosphoglycerate dehydrogenase from Synechocystis sp. PCC 6803
31% identity, 47% coverage
- Regulatory Diversity and Functional Analysis of Two-Component Systems in Cyanobacterium Synechocystis sp. PCC 6803 by GC-MS Based Metabolomics
Shi, Frontiers in microbiology 2020 - “...acid 10.15 slr1124 gpmB , phosphoserine phosphatase, involved in glycine, serine and threonine metabolism 1.96 sll1908 serA , D-3-phosphoglycerate dehydrogenase / 2-oxoglutarate reductase 1.73 Pyruvic acid 3.76 slr0721 me , encoding a malic enzyme, involved in pyruvate metabolism 1.70 sll1721 pdhB , pyruvate dehydrogenase E1 component...”
- First proteomic study of S-glutathionylation in cyanobacteria
Chardonnet, Journal of proteome research 2015 (PubMed)- “...in oxidative stress tolerance and 3-phosphoglycerate dehydrogenase (Sll1908) acting on amino acids metabolism, was confirmed by biochemical studies on the...”
- “...(PrxII, Sll1621) and 3-phosphoglycerate dehydrogenase (PGDH, Sll1908), has been validated in vitro using recombinant proteins. Article EXPERIMENTAL SECTION...”
- Redox regulation by reversible protein S-thiolation in bacteria
Loi, Frontiers in microbiology 2015 - “...mapped by mass spectrometry. In addition, the peroxiredoxin PrxII (Sll1621) and the 3-phosphoglycerate dehydrogenase PGDH (Sll1908) could be S -glutathionylated by BioGSSG in vitro (Chardonnet et al., 2015 ). Figure 5 Redox proteomics methods to study protein S -glutathionylation at a global scale . Mass spectrometry-based...”
- 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 - “...g18360 slr0293 sll0171 slr0879 slr1096 sll1931 slr0006 sll1908 all4607 all4609 all4608 alr4745 alr4806 alr2765 alr1890 At4g33010 At1g11860 At2g35370 At3g17240...”
Dshi_3318 D-3-phosphoglycerate dehydrogenase from Dinoroseobacter shibae DFL 12
32% identity, 55% coverage
SMc00641 PUTATIVE D-3-PHOSPHOGLYCERATE DEHYDROGENASE PROTEIN from Sinorhizobium meliloti 1021
Q92MA3 D-3-phosphoglycerate dehydrogenase from Rhizobium meliloti (strain 1021)
32% identity, 55% coverage
ATU_RS17200 phosphoglycerate dehydrogenase from Agrobacterium fabrum str. C58
29% identity, 58% coverage
Dde_1681 Putative dehydrogenase from Desulfovibrio desulfuricans G20
32% identity, 80% coverage
alr1890 phosphoglycerate dehydrogenase from Nostoc sp. PCC 7120
30% identity, 53% coverage
- Proteomic De-Regulation in Cyanobacteria in Response to Abiotic Stresses
Babele, Frontiers in microbiology 2019 - “...of abiotic stresses. It was reported that the enzymes cysteine synthase (all2521) and D-3-phosphoglycerate dehydrogenase (alr1890) are drastically down-regulated under UV-B stress, which may negatively influence the amino acid biosynthesis pathway. In our study, we found down-regulation of D-3-phosphoglycerate dehydrogenase in Anabaena L31 under UV-B stress...”
- Induction and differential expression of certain novel proteins in Anabaena L31 under UV-B radiation stress
Babele, Frontiers in microbiology 2015 - “...7.6 110 IPR001926 Cysteine synthase/cystathionine beta-synthase P -phosphate-binding site 4.2.99.8 Down 12 D -3-phosphoglycerate dehydrogenase alr1890 17229382 526 55841.6 5.7 106 IPR006236 D -3-Phosphoglycerate_DH 1.1.1.95 Down Unknown proteins 11 Hypothetical protein all4050 all4050 17231542 324 37259.4 5 104 IPR007903 PRC_barrel Up 4 Hypothetical protein all3797 all3797...”
- “...of all living organisms. In this context, our data show that D -3-phosphoglycerate dehydrogenase ( alr1890) and cysteine synthase (all2521) are down regulated under UV-B stress and thus may adversely affect the amino acid biosynthesis pathway. Down regulation of D -3-phosphoglycerate dehydrogenase which catalyzes the formation...”
- 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 - “...all4607 all4609 all4608 alr4745 alr4806 alr2765 alr1890 At4g33010 At1g11860 At2g35370 At3g17240 At4g37930 At1g23310 At1g68010 At4g33010 (At3g16950*) slr1840...”
SYNPCC7002_A1246 D-3-phosphoglycerate dehydrogenase from Synechococcus sp. PCC 7002
29% identity, 55% coverage
MAB_3304c D-3-phosphoglycerate dehydrogenase (SerA) from Mycobacterium abscessus ATCC 19977
32% identity, 47% coverage
Dhaf_2820 Glyoxylate reductase from Desulfitobacterium hafniense DCB-2
35% identity, 58% coverage
Q03V58 D-2-hydroxyacid dehydrogenase (NAD+) (EC 1.1.1.345) from Leuconostoc mesenteroides subsp. mesenteroides (see paper)
34% identity, 78% coverage
gvip294 D-3-phosphoglycerate dehydrogenase from Gloeobacter violaceus PCC 7421
29% identity, 50% coverage
- Cultivation and complete genome sequencing of Gloeobacter kilaueensis sp. nov., from a lava cave in Kīlauea Caldera, Hawai'i
Saw, PloS one 2013 - “...GKIL_1879), and serA (GKIL_0932). GVIO, however, only has a copy of vanX (gll1805) and serA (gvip294), and is missing vanB . Five essential gene products are in fact required for high-level vancomycin resistance, specifically VanR, VanS, VanH, VanX, and either VanA, VanB or VanD [28] [30]...”
EMQU_2453 NAD(P)-dependent oxidoreductase from Enterococcus mundtii QU 25
29% identity, 98% coverage
RSP_1352 D-3-phosphoglycerate dehydrogenase from Rhodobacter sphaeroides 2.4.1
27% identity, 60% coverage
A7Z657 D-3-phosphoglycerate dehydrogenase from Bacillus velezensis (strain DSM 23117 / BGSC 10A6 / LMG 26770 / FZB42)
30% identity, 50% coverage
mru_0678 phosphoglycerate dehydrogenase SerA from Methanobrevibacter ruminantium M1
34% identity, 49% coverage
GYAR_THELN / Q9C4M5 Glyoxylate reductase; EC 1.1.1.26 from Thermococcus litoralis (strain ATCC 51850 / DSM 5473 / JCM 8560 / NS-C) (see paper)
Q9C4M5 glyoxylate reductase (EC 1.1.1.26) from Thermococcus litoralis (see paper)
OCC_02245 glyoxylate reductase from Thermococcus litoralis DSM 5473
33% identity, 85% coverage
- catalytic activity: glycolate + NAD(+) = glyoxylate + NADH + H(+) (RHEA:18229)
subunit: Homodimer. - Removal of phosphoglycolate in hyperthermophilic archaea
Michimori, Proceedings of the National Academy of Sciences of the United States of America 2024 - “...TK0551 and TK0683, proteins encoded by TK0683 homologs from Thermococcales have been biochemically characterized. The OCC_02245 protein from Thermococcus litoralis and the PH0597 protein from Pyrococcus horikoshii were described as reductases preferring glyoxylate ( 31 , 32 ), while another report concluded that the proteins encoded...”
Dhaf_2079 D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding from Desulfitobacterium hafniense DCB-2
32% identity, 76% coverage
DSY0996 hypothetical protein from Desulfitobacterium hafniense Y51
32% identity, 76% coverage
- vanI: a novel D-Ala-D-Lac vancomycin resistance gene cluster found in Desulfitobacterium hafniense
Kruse, Microbial biotechnology 2014 - “...al ., 2008 ). Previously, four genes have been proposed as potential vanH -encoding genes (DSY0996, DSY1673, DSY3442 and DSY4020) in the genome of D. hafniense Y51 (Kalan et al ., 2009 ). The homologues of these four genes were also found in the genomes of...”
- Noncanonical vancomycin resistance cluster from Desulfitobacterium hafniense Y51
Kalan, Antimicrobial agents and chemotherapy 2009 - “...cluster, four annotated D-isomer-specific 2-hydroxyacid dehydrogenase genes (DSY0996, DSY1673, DSY3442, and DSY4020) are present in the genome of D. hafniense...”
DET0599 D-3-phosphoglycerate dehydrogenase from Dehalococcoides ethenogenes 195
29% identity, 55% coverage
MA0592 phosphoglycerate dehydrogenase from Methanosarcina acetivorans C2A
30% identity, 50% coverage
C629_RS07285 phosphoglycerate dehydrogenase from Corynebacterium glutamicum SCgG2
cg1451 D-3-phosphoglycerate dehydrogenase from Corynebacterium glutamicum ATCC 13032
31% identity, 45% coverage
- Transcriptomic and enzymatic analysis reveals the roles of glutamate dehydrogenase in Corynebacterium glutamicum
Ge, AMB Express 2022 - “...were upregulated. In addition, the genes of serine synthesized from glyceric acid -3-P, including serA (C629_RS07285), serC (C629_RS05100), serB (C629_RS12565), and then glyA (C629_RS05820) of glycine synthesized from serine, were upregulated. Analysis of transcriptomic changes of C. glutamicum F343 elicited by gdhA gdhB double disruption When...”
- Comprehensive Analysis of C. glutamicum Anaplerotic Deletion Mutants Under Defined d-Glucose Conditions
Kappelmann, Frontiers in bioengineering and biotechnology 2020 - “...3.42e-23 CAF18800 cg0282 Conserved hypothetical protein 2.02 2.79e-08 CAF20737 cg3008 porA Porin 0.48 7.16e-06 CAF19986 cg1451 serA Phosphoglycerate dehydrogenase 0.43 5.03e-30 CAF19413 cg0812 dtsR1 Acetyl/ propionyl-CoA carboxylase beta chain 0.42 1.34e-13 All proteins with significant changes [p < 0.05, Log2(fold change) > 0.5 for upregulated proteins...”
- “...appear to accumulate intracellularly. This would also explain why the phosphoglycerate dehydrogenase encoded by serA (cg1451) was found to be significantly down-regulated in this mutant ( Table 3 ). The enzyme catalyzes the first step in the biosynthesis of l -glycine, l -serine and l -cysteine...”
- Protein S-mycothiolation functions as redox-switch and thiol protection mechanism in Corynebacterium glutamicum under hypochlorite stress
Chi, Antioxidants & redox signaling 2014 - “...Cg2862 PurLb Fructose-bisphosphate aldolase Phosphoglycerate Cg1451 SerAb dehydrogenase Cg3048 Pta Phosphate acetyltransferase Cg0147 XylB Sugar (pentulose...”
- Citrate utilization by Corynebacterium glutamicum is controlled by the CitAB two-component system through positive regulation of the citrate transport genes citH and tctCBA
Brocker, Journal of bacteriology 2009 - “...cg1581 cg1582 cg1583 cg3026 cg3027 cg3028 cg3029 cg1156 cg1451 cg0576 cg2894 cg1364 cg2157 cg1151 cg1386 cg0653 cg1147 cg1349 cg0825 cg0882 cg3420 cg2069 cg3351...”
- Functional genomics of pH homeostasis in Corynebacterium glutamicum revealed novel links between pH response, oxidative stress, iron homeostasis and methionine synthesis
Follmann, BMC genomics 2009 - “...subunit 0 -1.71 -1.11 1.1 4.2 3.4 3.3 4.9 4.7 4.0 4.0 2.5 SigH* 28 cg1451 serA Phosphoglycerate dehydrogenase 0 -0.22 -1.10 6.5 5.4 6.1 7.7 7.5 7.2 5.3 5.3 4.2 29 cg1537 ptsM PTS system mannose-specific EIIBCA component 10 -0.39 -1.06 2.6 3.5 1.8 5.9...”
- Co-ordinated regulation of gluconate catabolism and glucose uptake in Corynebacterium glutamicum by two functionally equivalent transcriptional regulators, GntR1 and GntR2
Frunzke, Molecular microbiology 2008 - “...0.99 0.90 cg1488 3-isopropylmalate dehydratase small subunit, leuD 0.10 1.23 1.09 1.27 1.15 0.98 0.98 cg1451 d -3-phosphoglycerate dehydrogenase, serA 0.12 1.10 0.86 1.00 1.09 0.67 1.14 cg2125 Uracil permease, uraA 0.14 1.11 1.22 0.86 1.10 1.03 0.98 cg0564 LSU ribosomal protein L1P 0.19 0.75 0.97...”
- Random mutagenesis in Corynebacterium glutamicum ATCC 13032 using an IS6100-based transposon vector identified the last unknown gene in the histidine biosynthesis pathway
Mormann, BMC genomics 2006 - “...proC (1) Pyrroline-5-carboxylate reductase Proline biosynthesis [98] 5 Methionine nd c nd c 13 Serine cg1451 serA (1) Phosphoglycerate dehydrogenase Serine biosynthesis [99] 17 Cysteine cg3118 cysI (2) Ferredoxin-sulfite reductase Assimilatory sulfate reduction [65] 14 Leucine cg1488 leuD (1) 3-Isopropylmalate dehydratase, small chain Leucine biosynthesis [100]...”
- Adaptation of Corynebacterium glutamicum to ammonium limitation: a global analysis using transcriptome and proteome techniques
Silberbach, Applied and environmental microbiology 2005 - “...cg0113 cg0115 cg0104 cg0104 cg0116 cg1256 cg0119 cg1437 cg0104 cg1451 cg1784 cg1783 cg1784 cg2280 cg1437 cg0303 cg1581 ureB glnA ocd ureG ureA ureC codAb codAb...”
- “...NCgl2451 NCgl1442 NCgl0625 NCgl0345 NCgl1926 NCgl0827 cg1203 cg1451 cg2361 cg0873 cg1814 cg1145 cg2453 cg3096 cg0482 cg2797 cg1693 cg0755 cg0422 cg2192 cg0984...”
MPNT_20138 phosphoglycerate dehydrogenase from Candidatus Methylacidithermus pantelleriae
29% identity, 55% coverage
DVU1412 D-isomer specific 2-hydroxyacid dehydrogenase family protein from Desulfovibrio vulgaris Hildenborough
30% identity, 80% coverage
- The primary pathway for lactate oxidation in Desulfovibrio vulgaris
Vita, Frontiers in microbiology 2015 - “...essential residue for enzymatic catalysis ( Dong et al., 1993 ). In addition, DVU0600 and DVU1412 were found to exhibit approximately 40 and 50% sequence identity with fermentative LDHs from Clostridium cellulolyticum ( Li et al., 2012 ) and S. oneidensis ( Pinchuk et al., 2009...”
- “...(1783) L -LdD DVU2784 Dehydrogenase, FMN-dependent family Fermentative LDHs DVU0600 L -lactate dehydrogenase D -LdhA DVU1412 D -isomer specific 2-hydroxyacid dehydrogenase family protein To obtain information on the functional role of LDH orthologs, expression of the corresponding encoding genes was measured in Dv H WT cells...”
- Metabolic modeling of a mutualistic microbial community
Stolyar, Molecular systems biology 2007 - “...annotated as a NAD + -dependent L -lactate dehydrogenase by TIGR (COG39, EC 1.1.1.27), and DVU1412, which was annotated as a NAD + -dependent D -isomer-specific 2-hydroxyacid dehydrogenase family protein by TIGR (COG1052, EC 1.1.1.29). To assess the potential importance of these putative reactions to the...”
Mchl_2132 D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding from Methylobacterium chloromethanicum CM4
32% identity, 76% coverage
P35136 D-3-phosphoglycerate dehydrogenase from Bacillus subtilis (strain 168)
BSU23070 D-3-phosphoglycerate dehydrogenase from Bacillus subtilis subsp. subtilis str. 168
29% identity, 50% coverage
TK0683 glyoxylate reductase from Thermococcus kodakaraensis KOD1
34% identity, 64% coverage
- Removal of phosphoglycolate in hyperthermophilic archaea
Michimori, Proceedings of the National Academy of Sciences of the United States of America 2024 - “...B ) GLDH activity from glycolate to glyoxylate in cell extracts from KU216, TK0551, and TK0683 strains. Gray or white bars indicate the specific activities in extracts from cells grown under anaerobic or microaerobic conditions, respectively. ( C ) GLDH activity from glyoxylate to glycolate in...”
- “...measured toward various phosphorylated metabolites. Dehydrogenase activities of the purified TK0551 ( C ) and TK0683 ( D ) proteins were examined toward various 2-hydroxyacids. Aminotransferase activities of the purified TK0186/TK1094 proteins with various amino donor compounds in the presence of glyoxylate as the amino acceptor...”
- An archaeal ADP-dependent serine kinase involved in cysteine biosynthesis and serine metabolism
Makino, Nature communications 2016 - “...as lactate dehydrogenases (LDHs), were also present ( Tk-ldhA1 : TK0551 (29% identical), Tk-ldhA2 : TK0683 (31% identical)), we constructed a triple gene disruption strain of these genes to ensure the complete shutdown of pathway Cys2. As a result, growth without Cys was not significantly affected...”
- “...tk1449 (TK1449, metC ), Tk - serA (TK1966), Tk - ldhA1 (TK0551), Tk - ldhA2 (TK0683), Tk-cysK (TK1687), Tk-serK (TK0378), Tk-glyA (TK0528) and Tk-tdh (TK0916), their coding regions along with about 1,000bps of 5- and 3-flanking regions were amplified by PCR using T. kodakarensis KOD1 genomic...”
Q972A9 phosphoglycerate dehydrogenase (EC 1.1.1.95) from Sulfurisphaera tokodaii (see paper)
ST1218 313aa long hypothetical D-3-phosphoglycerate dehydrogenase from Sulfolobus tokodaii str. 7
32% identity, 84% coverage
CLJU_c03860 phosphoglycerate dehydrogenase from Clostridium ljungdahlii DSM 13528
34% identity, 74% coverage
DSY1673 hypothetical protein from Desulfitobacterium hafniense Y51
33% identity, 58% coverage
- vanI: a novel D-Ala-D-Lac vancomycin resistance gene cluster found in Desulfitobacterium hafniense
Kruse, Microbial biotechnology 2014 - “...., 2008 ). Previously, four genes have been proposed as potential vanH -encoding genes (DSY0996, DSY1673, DSY3442 and DSY4020) in the genome of D. hafniense Y51 (Kalan et al ., 2009 ). The homologues of these four genes were also found in the genomes of D....”
- Noncanonical vancomycin resistance cluster from Desulfitobacterium hafniense Y51
Kalan, Antimicrobial agents and chemotherapy 2009 - “...four annotated D-isomer-specific 2-hydroxyacid dehydrogenase genes (DSY0996, DSY1673, DSY3442, and DSY4020) are present in the genome of D. hafniense Y51. The...”
2eklA / Q972A9 Structure of st1218 protein from sulfolobus tokodaii
32% identity, 84% coverage
- Ligand: nicotinamide-adenine-dinucleotide (2eklA)
KSF55_04355 D-2-hydroxyacid dehydrogenase from Lactiplantibacillus pentosus
29% identity, 96% coverage
MAP3033c SerA from Mycobacterium avium subsp. paratuberculosis str. k10
33% identity, 46% coverage
MAVA5_16825 phosphoglycerate dehydrogenase from Mycobacterium avium subsp. hominissuis A5
33% identity, 46% coverage
1wwkA / O50095 Crystal structure of phosphoglycerate dehydrogenase from pyrococcus horikoshii ot3
34% identity, 81% coverage
- Ligand: nicotinamide-adenine-dinucleotide (1wwkA)
ZMO1685 D-3-phosphoglycerate dehydrogenase from Zymomonas mobilis subsp. mobilis ZM4
30% identity, 61% coverage
- Comprehensive network of stress-induced responses in Zymomonas mobilis during bioethanol production: from physiological and molecular responses to the effects of system metabolic engineering
Asefi, Microbial cell factories 2024 - “...(AhpC). It was discovered that ZMNPs hydrolysate tolerance was influenced by increased cysteine production (including ZMO1685 (serA1), ZMO1684 (serC), and ZMO0748 (cysK)) and the activation of stress response genes [ 118 ]. In silico genome-scale metabolic modeling and mathematical modeling are two of the most potent...”
- Molecular mechanism of enhanced ethanol tolerance associated with hfq overexpression in Zymomonas mobilis
Tang, Frontiers in bioengineering and biotechnology 2022 - “...alpha chain 1.89 ZMO1000 metE 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase 2.12 2.56 ZMO1684 serC Phosphoserine aminotransferase 1.09 1.28 ZMO1685 serA1 D-3-phosphoglycerate dehydrogenase 1.55 1.83 Heat shock response ZMO0016 grpE GrpE protein 1.10 1.06 ZMO0246 hslV ATP-dependent protease subunit HslV 2.06 2.21 ZMO0247 hslU Heat shock protein atpase subunit HslU...”
- “...in ZM4- hfq was observed in other genes involved in cysteine biosynthesis, including serA1 ( ZMO1685 ) and serC ( ZMO1684 ) ( Table 1 ; Figure 2 , Supplementary Table S4 ). However, such upregulated gene cluster was not induced under the condition without ethanol...”
- A plasmid-free Zymomonas mobilis mutant strain reducing reactive oxygen species for efficient bioethanol production using industrial effluent of xylose mother liquor
Geng, Frontiers in bioengineering and biotechnology 2022 - “...expression results showed that three genes associated with cysteine synthesis were upregulated in ZMNP, including ZMO1685 ( serA1 ) and ZMO1684 ( serC ) for L-serine synthesis, and ZMO0748 ( cysK ) that could catalyze O-acety-L-serine and the sulfur assimilation product H 2 S to synthesize...”
- Model-driven analysis of mutant fitness experiments improves genome-scale metabolic models of Zymomonas mobilis ZM4
Ong, PLoS computational biology 2020 - “...ZMO1128, ZMO1182, ZMO1851 Isoprenoid Precursor biosynthesis M56 0.293 3 PGCD_f, PSERT_f, PSP_L_f 3 ZMO1137, ZMO1684, ZMO1685 Serine biosynthesis M57 0.247 6 ADEt2rpp_r, ADEtex_r , HPN1_f, HPN2_f, HPN3_f , EX_ade_e_f 3 ZMO0873, ZMO0874, ZMO0969 Hopanoid biosynthesis M60 0.119 11 ADCL_f, ADCS_f, AKP1_f, DHFS_f, DHNPA2r_f , DHPS2_f, EX_gcald_e_f...”
- Proteomic and metabolomic analysis of the cellular biomarkers related to inhibitors tolerance in Zymomonas mobilis ZM4
Chang, Biotechnology for biofuels 2018 - “...Of the 31 DEPs, 15 DEPs (ZMO1485, ZZM4_0141, ZMO0495, ZMO0472, Pgi, ZMO0070, ZMO0758, ZMO0487, Mfd, ZMO1685, CysH, ZMO0075, ZMO0474, LeuC, and ZMO1124) were simultaneously up-regulated; wherein, ZMO1485 showed the highest fold change with an average value of 11.95, followed by ZMO0472 with average 10.25-fold change and...”
- “...and LeuC have the maximal interaction numbers with other DEPs, followed by GabD, CysH, and ZMO1685. Here, proteinprotein interactions are determined if the two proteins have been documented to be neighborhood proteins, fusion proteins, co-expression proteins, etc. with a confidence score more than 0.40. Fig.4 Heat...”
- Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032
Yang, Biotechnology for biofuels 2018 - “...ZMO1657 G to A (K176K) 17150281715028 ZMO1659 ( ftsH ) G to A (V68I) 17392261739226 ZMO1685 ( serA ) A to G (T93A) 18900211890021 ZMO1842 ( nosX ) C to T (G277D) 18946041894604 ZMO1848 C to T (K347K) 19173601917360 ZMO1862 C to T (A33T) 19453901945390 ZMO1886...”
hprA / Q59516 hydroxypyruvate reductase subunit (EC 1.1.1.81) from Methylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1) (see 2 papers)
32% identity, 76% coverage
Ccel_3425 D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding from Clostridium cellulolyticum H10
32% identity, 79% coverage
Q608T2 hydroxypyruvate reductase (EC 1.1.1.81) from Methylococcus capsulatus (see paper)
30% identity, 85% coverage
serA / GB|AAC83943.1 phosphoglycerate dehydrogenase; EC 1.1.1.95 from Bacillus subtilis (see paper)
serA / AAC83943.1 phosphoglycerate dehydrogenase from Bacillus subtilis (see 3 papers)
29% identity, 50% coverage
MMP0870 2-hydroxyacid dehydrogenase, D-isomer specific from Methanococcus maripaludis S2
32% identity, 76% coverage
OEOE_0025 Lactate dehydrogenase related enzyme from Oenococcus oeni PSU-1
32% identity, 78% coverage
B7P3M8 D-3-phosphoglycerate dehydrogenase (Fragment) from Ixodes scapularis
28% identity, 64% coverage
XP_017888762 D-3-phosphoglycerate dehydrogenase isoform X2 from Ceratina calcarata
28% identity, 57% coverage
- The effect of maternal care on gene expression and DNA methylation in a subsocial bee
Arsenault, Nature communications 2018 - “...to genes encoding a STE20-like serine/threonine-protein kinase (SLK; Ccalc.v2_009097, XP_017892454), a D-3-phosphoglycerate dehydrogenase (PHGDH; Ccalc.v2_011692, XP_017888762), and a 6-phosphofructo-2-kinase (PFKFB1; Ccalc.v2_011841, XP_017879076). Each of these represents a candidate for localized involvement of DNA methylation in gene regulation associated with maternal care in C. calcarata . Discussion...”
BL02138 D-glycerate dehydrogenase from Bacillus licheniformis DSM 13 = ATCC 14580
33% identity, 63% coverage
- Metabolic engineering of Bacillus subtilis for growth on overflow metabolites
Kabisch, Microbial cell factories 2013 - “...much smaller extent (data not shown). B. licheniformis DSM13 possesses a putative glyoxylate reductase (ORF BL02138) which exhibits a 70% identity to a similar enzyme ( gyaR ) of Bacillus pumilus ATCC 7061. This putative glyoxylate reductase (ORF BL02138) could catalyze the reduction of glyoxylate to...”
A0A2R6X868 phosphoglycerate dehydrogenase (EC 1.1.1.95) from Marchantia polymorpha (see paper)
32% identity, 41% coverage
EF3141 D-isomer specific 2-hydroxyacid dehydrogenase family protein from Enterococcus faecalis V583
30% identity, 85% coverage
- Genomewide Profiling of the Enterococcus faecalis Transcriptional Response to Teixobactin Reveals CroRS as an Essential Regulator of Antimicrobial Tolerance
Darnell, mSphere 2019 - “...genes were involved in carbon metabolism, including 13 transporters (11 PTS transporters), 4 metabolic genes (EF3141 [9.9-fold], EF3142 [9.7-fold], EF3140 [9.4-fold], and EF0413 [9.7-fold]), and 1 regulator (EF2966 [9.3-fold]) ( Table2 ). The remaining two genes, EF2582 (9.0-fold) and EF2223 (8.8-fold), encode a chlorohydrolase/aminohydrolase and an...”
- “...138 10.9 PTS sugar transporter subunit IIC EF0412 2554 10.2 PTS mannitol transporter subunit IIA EF3141 136 9.9 2-Hydroxyacid dehydrogenase EF2965 2466 9.9 PTS sugar transporter subunit IIB EF3142 135 9.7 6-Phosphogluconate dehydrogenase EF0413 2553 9.7 Mannitol-1-phosphate 5-dehydrogenase EF3213 69 9.6 PTS mannose transporter subunit IID...”
CNC06220 glycerate-and formate-dehydrogenase from Cryptococcus neoformans var. neoformans JEC21
37% identity, 67% coverage
SH1200 D-3-phosphoglycerate dehydrogenase from Staphylococcus haemolyticus JCSC1435
29% identity, 47% coverage
- First Case of Staphylococci Carrying Linezolid Resistance Genes from Laryngological Infections in Poland
Michalik, Pathogens (Basel, Switzerland) 2021 - “...arcC allel 1; cfxE allel 1; hemH allel 1; leuB allel 1; RiboseABC allel 4; SH1200 allel 1; SH1431 allel 5) not applicable mecA only III fib, hla, hlb pathogens-10-00335-t002_Table 2 Table 2 Antimicrobial susceptibility profiles and antibiotic resistance genes of S. aureus and S. haemolyticus...”
- Incorporating Statistical Test and Machine Intelligence Into Strain Typing of Staphylococcus haemolyticus Based on Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry
Chung, Frontiers in microbiology 2019 - “...We defined the strain typing of S. haemolyticus by sequencing seven housekeeping genes, namely arc, SH1200, hemH, leuB, SH1431, cfxE , and RiboseABC (Panda et al., 2016 ). The sequencing results of these genes were used to assign the sequence types of S. haemolyticus throughout the...”
- Identification of Novel Sequence Types among Staphylococcus haemolyticus Isolated from Variety of Infections in India
Panda, PloS one 2016 - “...to NCBI GenBank under accession numbers KM985504KM985522 and KX073468KX073483 for arc, KM985523KM985541 and KX073484KX073499 for SH1200, KM985542KM985560 and KX073500KX073515 for hemH, KM985561KM985579 and KX073516KX073531 for leuB, KM985580 -KM985598 and KX073532KX073547 for SH1431, KM985599KM985617 and KX073548KX073563 for cfxE, KP019681KP019699 and KX073564KX073579 for Ribose ABC, respectively. Data Availability...”
- “...to NCBI GenBank under accession numbers KM985504KM985522 and KX073468KX073483 for arc, KM985523KM985541 and KX073484KX073499 for SH1200, KM985542KM985560 and KX073500KX073515 for hemH, KM985561KM985579 and KX073516KX073531 for leuB, KM985580 -KM985598 and KX073532KX073547 for SH1431, KM985599KM985617 and KX073548KX073563 for cfxE, KP019681KP019699 and KX073564KX073579 for Ribose ABC, respectively. Introduction Staphylococcus...”
- Analysis of nosocomial Staphylococcus haemolyticus by MLST and MALDI-TOF mass spectrometry
Kornienko, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2016 (PubMed)- “...novel variant of MLST scheme including the tpiA, pta, sh1200, rphE, tphK, mvaK1, and arc loki was tested. The discriminatory power was estimated by the...”
- “.... haemo lyticus clinical isolates in accordance ( tpiA pta sh1200 rphE tphK mvaK1 arcC ) MLST scheme: (a) clonal grouping of S . haemolyticus isolates based on...”
R2866_1089 2-hydroxyacid dehydrogenase from Haemophilus influenzae R2866
29% identity, 95% coverage
P9WNX3 phosphoglycerate dehydrogenase (EC 1.1.1.95) from Mycobacterium tuberculosis (see 5 papers)
Rv2996c PROBABLE D-3-PHOSPHOGLYCERATE DEHYDROGENASE SERA1 (PGDH) from Mycobacterium tuberculosis H37Rv
MT3074 D-3-phosphoglycerate dehydrogenase from Mycobacterium tuberculosis CDC1551
BCG_3017c putative D-3-phosphoglycerate dehydrogenase serA1 from Mycobacterium bovis BCG str. Pasteur 1173P2
YP_177916 D-3-phosphoglycerate dehydrogenase from Mycobacterium tuberculosis H37Rv
32% identity, 47% coverage
- The In Vivo Transcriptomic Blueprint of Mycobacterium tuberculosis in the Lung
Coppola, Frontiers in immunology 2021 - “...in vivo expressed genes 12 (Rv3418c, Rv3023c, Rv1199c, Rv0985c, Rv3115, Rv3022c, Rv2512c, Rv0299, Rv0294, Rv3018c, Rv2996c, and Rv1908c) were not previously described as IVE-TB genes or implemented in TB vaccines or diagnostics ( Figure S1 ). Taken together, these analyses show that most potent candidate TB...”
- One-Year Old Dormant, "Non-culturable" Mycobacterium tuberculosis Preserves Significantly Diverse Protein Profile
Trutneva, Frontiers in cellular and infection microbiology 2020 - “...regulatory protein MtrA Rv1436 Probable glyceraldehyde 3-phosphate dehydrogenase Gap (GAPDH) Rv3224 Possible iron-regulated short-chain dehydrogenase/reductase Rv2996c Probable D-3-phosphoglycerate dehydrogenase SerA1 (PGDH) Rv0860 Probable fatty oxidation protein FadB Rv3841 Bacterioferritin BfrB Rv0831c Conserved protein Rv0242c Probable 3-oxoacyl-[acyl-carrier protein] reductase FabG4 Rv2971 Probable oxidoreductase Rv3280 Probable propionyl-CoA carboxylase...”
- Activity-Based Protein Profiling Reveals That Cephalosporins Selectively Active on Non-replicating Mycobacterium tuberculosis Bind Multiple Protein Families and Spare Peptidoglycan Transpeptidases
Lopez, Frontiers in microbiology 2020 - “...subunit alpha P63677 Rv1310 atpD Yes PP: ATP synthase subunit beta Intermediary metabolism enzymes P0A544 Rv2996c serA Yes PP: D-3-phosphoglycerate dehydrogenase P60176 Rv3248c sahH Yes PP: adenosylhomocysteinase; thioester hydrolase P64178 Rv1436 gap Yes PP: glyceraldehyde-3-phosphate dehydrogenase P65149 Rv3001c ilvC Yes PP: ketol-acid reductoisomerase Q10530 Rv0896 gtlA2...”
- A High Throughput Whole Blood Assay for Analysis of Multiple Antigen-Specific T Cell Responses in Human Mycobacterium tuberculosis Infection
Whatney, Journal of immunology (Baltimore, Md. : 1950) 2018 - “...Unknown Pool 41 Rv2874 DipZ 2 Membrane Pool 42 Rv2875 MPT70 1 Secreted Pool 43 Rv2996c SerA1 2 Membrane Pool 44 Rv3012c GatC 4 Membrane Pool 45 Rv3015c Rv3015c 4 Cytoplasm Pool 46 Rv3018c PPE46 PPE family Unknown Pool 47 Rv3019c EsxR (TB10.3) 1 Predicted secreted...”
- D-3-Phosphoglycerate Dehydrogenase
Grant, Frontiers in molecular biosciences 2018 - “...tuberculosis , and Homo sapiens , the gene coding for PGDH is designated as serA1, Rv2996c , and PHGDH , respectively. In this review, the designation PGDH will be used to refer to this enzyme from any species. Figure 1 The l -serine biosynthetic pathway uses...”
- Cyclipostins and Cyclophostin analogs as promising compounds in the fight against tuberculosis
Nguyen, Scientific reports 2017 - “...AmiC Rv2888c 50.9 Amidase IM/R Amidase AmiB2 Rv1263 49.1 Amidase IM/R D-3-phosphoglycerate dehydrogenase (PGDH) SerA1 Rv2996c 54.5 in vitro Methyltransferase IM/R 32 Carboxylesterase A CaeA Rv2224c 55.9 Macrophage and in vitro growth Lipase/esterase CW/CP 49 , 51 2 Penicillin-binding protein Rv1730c 55.8 -lactamase CW/CP 30 Serine...”
- “...concomitant reduction of NAD; the putative L-lactate dehydrogenase LidD2 (Rv1872c) 31 ; the methyltransferase SerA1 (Rv2996c) involved in the L-serine biosynthetic process 32 ; glyA1 (Rv1093) annotated as a serine hydroxymethyltransferase with possible role in serine to glycine conversion 33 ; and UmaA (Rv0469) a S-adenosyl-L-methionine-dependent...”
- A genome-wide structure-based survey of nucleotide binding proteins in M. tuberculosis
Bhagavat, Scientific reports 2017 - “...Rv2855 NADPH-dependent mycothiol reductase Mtr ATP Rv2858c Probable aldehyde dehydrogenase AldC AMP ADP ATP GTP Rv2996c Probable D-3-phosphoglycerate dehydrogenase SerA1 (PGDH) ADP Rv3028c Probable electron transfer flavoprotein (alpha-subunit) FixB (alpha-ETF) (electron transfer flavoprotein large subunit) (ETFLS) GTP Rv3075c Conserved protein ATP GTP Rv3273 Probable transmembrane carbonic...”
- “...described in supplementary text B. Examples of proteins Rv1017c (prsA), Rv1098c (fum), Rv3676 (crp), Rv0998, Rv2996c (serA) and Rv3710 (leuA) are discussed with two possibilities of a) identifying a new additional location on the known allosteric protein, and b) suggesting a possible new allosteric modulator for...”
- Mycobacterium tuberculosis AtsG (Rv0296c), GlmU (Rv1018c) and SahH (Rv3248c) Proteins Function as the Human IL-8-Binding Effectors and Contribute to Pathogen Entry into Human Neutrophils
Dziadek, PloS one 2016 - “...arylsulfatase), GlmU (Rv1018c; bifunctional glucosamine-1-phosphate acetyltransferase and N-acetylglucosamine-1-phosphate uridyltransferase), SahH (Rv3248c; S-adenosyl-L-homocysteine hydrolase) and SerA (Rv2996c; D-3-phosphoglycerate dehydrogenase SerA1) were selected and subjected to further analysis. Proteins and peptides identification details are provided in S1 Table in supplementary materials related to this article. Analysis of Mtb...”
- More
- Neu-Laxova syndrome is a heterogeneous metabolic disorder caused by defects in enzymes of the L-serine biosynthesis pathway
Acuna-Hidalgo, American journal of human genetics 2014 - “...(RefSeq NP_496868.1), and Mycobacterium tuberculosis (UniProt ID P9WNX3) were obtained from UniProt and Entrez. The 3D structure of wild-type human PHGDH...”
- Enhanced specialized transduction using recombineering in Mycobacterium tuberculosis
Tufariello, mBio 2014 - “...( 17 ) to result in amino acid or vitamin auxotrophy: serA1 ( Rv2996c [ MT3074 ]), metA ( Rv3341 [ MT3444 ]), panC ( Rv3602c [ MT3707 ]), leuD ( Rv2987c [ MT3065 ]), and argB ( Rv1654 [ MT1692 ]), to induce auxotrophy for...”
- High throughput screen identifies small molecule inhibitors specific for Mycobacterium tuberculosis phosphoserine phosphatase
Arora, The Journal of biological chemistry 2014 - “...ML1837 (Pseudogene) MUL_0823 MAF_07380 Rv2996c BCG_3017c MMAR_1715 ML1692 MUL_1952 MAF_30010 MSMEG_2378, MSMEI_2318 Rv3214 BCG_3241, BCG_3334 MMAR_1343...”
- Crystal structure of Mycobacterium tuberculosis D-3-phosphoglycerate dehydrogenase: extreme asymmetry in a tetramer of identical subunits.
Dey, The Journal of biological chemistry 2005 (PubMed)- GeneRIF: Mycobacterium tuberculosis D-3-phosphoglycerate dehydrogenase has extreme asymmetry in a tetramer of identical subunits
- D-3-Phosphoglycerate dehydrogenase from Mycobacterium tuberculosis is a link between the Escherichia coli and mammalian enzymes.
Dey, The Journal of biological chemistry 2005 (PubMed)- GeneRIF: analysis of D-3-Phosphoglycerate dehydrogenase from Mycobacterium tuberculosis
3dc2A / P9WNX3 Crystal structure of serine bound d-3-phosphoglycerate dehydrogenase from mycobacterium tuberculosis (see paper)
32% identity, 47% coverage
Q9Z564 phosphoglycerate dehydrogenase (EC 1.1.1.95) from Streptomyces coelicolor (see paper)
SCO5515 probable D-3-phosphoglycerate dehydrogenase from Streptomyces coelicolor A3(2)
31% identity, 46% coverage
F6I5Y5 D-3-phosphoglycerate dehydrogenase from Vitis vinifera
33% identity, 36% coverage
LOC101246616 D-3-phosphoglycerate dehydrogenase 3, chloroplastic-like from Solanum lycopersicum
33% identity, 41% coverage
- Comparative Analyses of Tomato yellow leaf curl virus C4 Protein-Interacting Host Proteins in Healthy and Infected Tomato Tissues
Kim, The plant pathology journal 2016 - “...PREDICTED: Solanum lycopersicum asparagine--tRNA ligase, chloroplastic/mitochondrial-like (LOC101254276), mRNA XM_004236228.1 PREDICTED: Solanum lycopersicum d-3-phosphoglycerate dehydrogenase, chloroplastic-like (LOC101246616), mRNA NM_001246911.1 Solanum lycopersicum flavonoid biosynthesis oxidoreductase protein (LOC100736526), mRNA NM_001246909.1 Solanum lycopersicum carotenoid cleavage dioxygenase 1-2 (CCD1-2), mRNA KC184125.1 PREDICTED: Solanum lycopersicum 3-dehydroquinate synthase-like (LOC101252666), mRNA XM_004241576.1 PREDICTED: Solanum...”
HI1556 2-hydroxyacid dehydrogenase from Haemophilus influenzae Rd KW20
30% identity, 95% coverage
CHLNCDRAFT_56437 hypothetical protein from Chlorella variabilis
33% identity, 39% coverage
TON_0569 D-isomer specific 2-hydroxyacid dehydrogenase from Thermococcus onnurineus NA1
28% identity, 99% coverage
SMc01622 PUTATIVE OXIDOREDUCTASE PROTEIN from Sinorhizobium meliloti 1021
32% identity, 75% coverage
- Genetic characterization of a complex locus necessary for the transport and catabolism of erythritol, adonitol and L-arabitol in Sinorhizobium meliloti
Geddes, Microbiology (Reading, England) 2012 (PubMed)- “...necessary for both polyols (SMc01617, rbtC; SMc01618, rbtB; SMc01622, rbtA). Genetic and biochemical data show that in addition to utilizing erythritol as a...”
- “...was used to construct deletions of SMc01619, SMc01618, SMc01622 and SMc01617 to yield strains SRmD208, SRmD209, SRmD247 and SRmD249, respectively (House et al.,...”
lmo0078 similar to phosphoglycerate dehydrogenase from Listeria monocytogenes EGD-e
30% identity, 86% coverage
- Extreme genetic diversity in the type VII secretion system of Listeria monocytogenes suggests a role in bacterial antagonism
Bowran, Microbiology (Reading, England) 2021 - “...dehydrogenase family protein. Curiously this is the same predicted function as the gene encoded by lmo0078 in the invariant housekeeping cluster, although the two proteins have no detectable sequence identity. Two of the genes in the essC2 variable region 1 cluster encode related proteins (numbered 24...”
- Genomic dissection of the most prevalent Listeria monocytogenes clone, sequence type ST87, in China
Wang, BMC genomics 2019 - “...chromosomal loci adjacent to tRNA genes, including tRNA-CTT-Lys (ICDC-LM188 locus tag: A6K41_00440, the tRNA-Lys after lmo0078 ), tRNA-CGA-Ser (ICDC-LM188 locus tag: A6K41_03215, the tRNA-Ser after lmo0670 ), tRNA-CCG-Arg (ICDC-LM188 locus tag: A6K41_12845, the tRNA-Arg after lmo2466 ) and tRNA-GGT-Thr (ICDC-LM188 locus tag: A6K41_13515, the tRNA-Thr after...”
SERA2_ARATH / O04130 D-3-phosphoglycerate dehydrogenase 2, chloroplastic; PGDH; EC 1.1.1.95 from Arabidopsis thaliana (Mouse-ear cress) (see 3 papers)
O04130 phosphoglycerate dehydrogenase (EC 1.1.1.95) from Arabidopsis thaliana (see 3 papers)
NP_564034 D-3-phosphoglycerate dehydrogenase from Arabidopsis thaliana
AT1G17745 PGDH (3-PHOSPHOGLYCERATE DEHYDROGENASE); phosphoglycerate dehydrogenase from Arabidopsis thaliana
30% identity, 41% coverage
- function: Involved in the plastidial phosphorylated pathway of serine biosynthesis (PPSB).
catalytic activity: (2R)-3-phosphoglycerate + NAD(+) = 3-phosphooxypyruvate + NADH + H(+) (RHEA:12641)
disruption phenotype: No visible phenotype. - The rolB plant oncogene affects multiple signaling protein modules related to hormone signaling and plant defense
Bulgakov, Scientific reports 2018 - “...Required to activate the iron superoxide dismutases (FeSOD) 20.6 Chaperone Functions along with Cpn60 19 O04130 (SERA2_ARATH) D-3-phosphoglycerate dehydrogenase 2, chloroplastic Amino-acid biosynthesis 2.51 Primary metabolism 20 Q9M9K1 (PMG2_ARATH) 2,3-bisphosphoglycerate-independent phosphoglycerate mutase 2 Glycolysis 2.10.5 Primary metabolism 21 Q42592 (APXS_ARATH) L-ascorbate peroxidase S, chloroplastic/mitochondrial Plays a...”
- Iron-dependent modifications of the flower transcriptome, proteome, metabolome, and hormonal content in an Arabidopsis ferritin mutant
Sudre, Journal of experimental botany 2013 - “...metabolism 1 O80988 At2g26080 3.4 6.3 3.1 Glycine dehydrogenase 1 454/9/9 11 114.7/6.2 111.4/6.2 2 O04130 At1g17745 3.0 d -3-Phosphoglycerate-DH 625/12/8 17 66.8/5.8 71.3/5.7 3 Q9ZPF5 At4g08870 3.3 3.6 Putative arginase 834/36/18 48 38.1/5.9 35.4/6.2 Mn 4 F4I7I0 At1g17290 2.4 Alanine aminotransferase 723/15/13 28 60.4/5.9 56.5/5.6...”
- Biochemical insight into redox regulation of plastidial 3-phosphoglycerate dehydrogenase from Arabidopsis thaliana.
Yoshida, The Journal of biological chemistry 2020 - GeneRIF: Biochemical insight into redox regulation of plastidial 3-phosphoglycerate dehydrogenase from Arabidopsis thaliana.
- Novel regulatory mechanism of serine biosynthesis associated with 3-phosphoglycerate dehydrogenase in Arabidopsis thaliana
Okamura, Scientific reports 2017 - GeneRIF: In the present study, two Arabidopsis PGDH isoforms were inhibited by L-serine but were activated by L-amino acids such as L-homocysteine in vitro.
- “.... Accession numbers for each amino acid sequence are as follows: AtPGDH1, NP_195146 (EMBL/GenBank/DDBJ); AtPGDH2, NP_564034 (EMBL/GenBank/DDBJ); AtPGDH3, NP_566637 (EMBL/GenBank/DDBJ); AhPGDH, BAF91727.1 (EMBL/GenBank/DDBJ); MtPGDH, 1YGY chain A (PDB); RnPGDH, CAA66374.1 (EMBL/GenBank/DDBJ); HsPGDH, NP_006614.2 (EMBL/GenBank/DDBJ) and EcPGDH 1YBA chain A (PDB). Reagents Nicotine amide adenine dinucleotide (NAD)...”
- Functional characterization of the plastidial 3-phosphoglycerate dehydrogenase family in Arabidopsis.
Toujani, Plant physiology 2013 - GeneRIF: Data indicate that 3-phosphoglycerate dehydrogenases PGDH (At1g17745) and EDA9 (At4g34200) were expressed preferentially in roots while 3-PGDH (At3g19480) was expressed mainly in the aerial parts and was not expressed or very poorly in roots.
- Transcriptomic and Metabolomic Analysis of a Pseudomonas-Resistant versus a Susceptible Arabidopsis Accession
Orf, International journal of molecular sciences 2022 - “...( Supplementary Table S1 ). Increased expression of a G3P-consuming G3P dehydrogenase 2 ( PGDH2, AT1G17745 ; Supplementary Table S1 ) in Col-0 in only was observed. 3. Discussion Here, we report on the dynamic response of the metabolome and transcriptome of resistant (C24) and susceptible...”
- Stromal NADH supplied by PHOSPHOGLYCERATE DEHYDROGENASE3 is crucial for photosynthetic performance
Höhner, Plant physiology 2021 - “...respective metabolite or enzyme in WT and pgdh3 mutant plants. Accession numbers PGDH1 (At4g34200), PGDH2 (At1g17745), PGDH3 (At3g19480), pgdh3-1 mutant (SM_3_37584; Toujani etal., 2013 ), pgdh3-2 (GK-877F12; Toujani etal., 2013 ), npq4-1 (Li et al., 2000), npq2-1 aka aba1-6 CS3772 ( Niyogi etal., 1998 ). Supplemental...”
- Biochemical insight into redox regulation of plastidial 3-phosphoglycerate dehydrogenase from Arabidopsis thaliana
Yoshida, The Journal of biological chemistry 2020 (secret) - Target of Rapamycin Regulates Genome Methylation Reprogramming to Control Plant Growth in Arabidopsis
Zhu, Frontiers in genetics 2020 - “...ribosome in RAP vs. DMSO group. Gene id Methylation ratio Status Regions Annotation Carbon metabolism AT1G17745 0.0065 Hypo Promoter PGDH2| Allosteric substrate binding domain AT3G52200 0.3913 Hypo Exon/intron LTA3| 2-oxoacid dehydrogenase acyltransferase AT5G08300 0.5078 Hypo Promoter ATP-citrate lyase/succinyl-CoA ligase AT1G04410 0.5323 Hypo Promoter MDH1| Lactate dehydrogenase/glycoside...”
- Phosphoserine Aminotransferase1 Is Part of the Phosphorylated Pathways for Serine Biosynthesis and Essential for Light and Sugar-Dependent Growth Promotion
Wulfert, Frontiers in plant science 2018 - “...families. The Arabidopsis genome contains three genes for the PGDH ( At4g34200 , PGDH1 ; At1g17745 , PGDH2 ; At3g19480 , PGDH3 ), two genes for the PSAT ( At4g35630 , PSAT1 , and At2g17630 , PSAT2 ) and one gene for the PSP ( At1g18640...”
- Identification and Biochemical Characterization of the Serine Biosynthetic Enzyme 3-Phosphoglycerate Dehydrogenase in Marchantia polymorpha
Akashi, Frontiers in plant science 2018 - “...identity with MtPGDH. AtPGDH1 (At4g34200) and AtPGDH3 (At3g19480) are inhibited by L -serine, while AtPGDH2 (At1g17745) is not ( Benstein et al., 2013 ; Okamura and Hirai, 2017 ). The expression of genes encoding the three AtPGDH isozymes shows different organ specificity. AtPDGH1 is expressed in...”
- A Microsomal Proteomics View of H₂O₂- and ABA-Dependent Responses
Alqurashi, Proteomes 2017 - “...patterns between the two treatments. Three proteins, ubiquinol-cytochrome C reductase hinge (UQCRH, AT1G15120), D-3-phosphoglycerate dehydrogenase (AT1G17745) and NADH:cytochrome B5 reductase 1 (Cyt b 5R, AT5G17770), belonging to the molecular function category oxidoreductase activity ( Table S2 ), showed differential accumulation in response to either ABA or...”
- “...Number Protein Name ANOVA ( p -Value) FC 5 min FC 20 min 1. Metabolism AT1G17745 D-3-phosphoglycerate dehydrogenase 2 0.0089 0.1 0.1 AT5G26780 Serine hydroxymethyltransferase 2 0.036 2.1 13 AT3G61440 Cysteine synthase C1 0.00074 ns 5 AT4G14880 O-acetylserine (thiol) lyase isoform A1 0.015 0.1 7.9 AT5G23300...”
- Novel regulatory mechanism of serine biosynthesis associated with 3-phosphoglycerate dehydrogenase in Arabidopsis thaliana
Okamura, Scientific reports 2017 - “...domain. Arabidopsis thaliana expresses three PGDH isoforms and these are encoded by PGDH1 (At4g34200), PGDH2 (At1g17745), and PGDH3 (At3g19480) 1 (henceforth designated AtPGDH1 , AtPGDH2 , and AtPGDH3 , respectively). Although AtPGDH1 and AtPGDH3, but not AtPGDH2, are inhibited by l -serine 1 , the related...”
- “...dark) at 22C. Preparation of recombinant enzymes Full-length cDNA clones of AtPGDH1 (At4g34200) and AtPGDH2 (At1g17745) were obtained from RIKEN Bio Resource Center (accession code pda02295 and pda04481, respectively) 44 , 45 . Full-length cDNA of AtPGDH3 (At3g19480) was synthesized using a PrimeScript II High Fidelity...”
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Q6AWS3 SD23260p from Drosophila melanogaster
30% identity, 85% coverage
A9PEK1 D-3-phosphoglycerate dehydrogenase from Populus trichocarpa
33% identity, 39% coverage
A0A1Z4EAX3 phosphoglycerate dehydrogenase (EC 1.1.1.95) from Beta vulgaris (see paper)
32% identity, 38% coverage
HCBG_03370 glyoxylate reductase from Histoplasma capsulatum G186AR
32% identity, 85% coverage
- Insights Into Histoplasma capsulatum Behavior on Zinc Deprivation
Assunção, Frontiers in cellular and infection microbiology 2020 - “...2448 h DTPA 2448h HCBG_03816 Prefoldin subunit 4 0.34 0.05 HCBG_05072 Tyrosine-protein kinase 0.82 0.0000006 HCBG_03370 Glyoxylate reductase 0.83 0.0000019 Control 24 48 h, p values of the factor analysis for control conditions regulated over time. DTPA 24 48 h, p values of the factor analysis...”
- “...zinc deprivation. Zn Limitation and Pyridoxine Synthesis Factor analysis results revealed that the glyoxylate reductase (HCBG_03370) was induced during zinc deprivation at 24h when compared to cells in control condition. However, in 48h we observed an inversion in the abundancy of the enzyme, in which it...”
SMc02045 PUTATIVE OXIDOREDUCTASE PROTEIN from Sinorhizobium meliloti 1021
29% identity, 89% coverage
PITG_00133 phosphoserine aminotransferase, putative from Phytophthora infestans T30-4
29% identity, 8% coverage
E4T4B2 D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding protein from Paludibacter propionicigenes (strain DSM 17365 / JCM 13257 / WB4)
30% identity, 91% coverage
Q0W9V5 Glyoxylate/hydroxypyruvate reductase B from Yersinia pestis
29% identity, 73% coverage
- Metaproteomics reveals major microbial players and their biodegradation functions in a large-scale aerobic composting plant
Liu, Microbial biotechnology 2015 - “...sp. Actinobacteria Fructose-1,6-bisphosphatase class 1 C0QTP7 Glycolysis / Gluconeogenesis Persephonella marina Aquificae Glyoxylate/hydroxypyruvate reductase B Q0W9V5 Pyruvate metabolism Yersinia pestis Gammaproteobacteria Acetyl-coenzyme A synthetase Q9F7R5 Pyruvate metabolism uncultured marine gamma proteobacterium Gammaproteobacteria Acetyl-coenzyme A synthetase 1 Q9Z3R3 Pyruvate metabolism Sinorhizobium meliloti Alphaproteobacteria Pyruvate, phosphate dikinase Q59754...”
- “...Bacilli; Bacillales Pyruvate dehydrogenase E1 component Q59637 Pyruvate metabolism Pseudomonas aeruginosa Gammaproteobacteria Glyoxylate/hydroxypyruvate reductase B Q0W9V5 Pyruvate metabolism Yersinia pestis Gammaproteobacteria Acetyl-coenzyme A synthetase Q9F7R5 Pyruvate metabolism uncultured marine Gammaproteobacterium Gammaproteobacteria Acetyl-coenzyme A synthetase 1 Q9Z3R3 Pyruvate metabolism Sinorhizobium meliloti Alphaproteobacteria Malate dehydrogenase A5WGM2 TCA Psychrobacter...”
DSVG11_0256 D-2-hydroxyacid dehydrogenase from Desulfovibrio sp. G11
30% identity, 78% coverage
- The reductive glycine pathway allows autotrophic growth of Desulfovibrio desulfuricans
Sánchez-Andrea, Nature communications 2020 - “...transaminase DSVG11_0309 or other transaminases), subsequent reduction of hydroxypyruvate to glycerate (potentially by 2-hydroxyacid dehydrogenases DSVG11_0256 or DSVG11_0961) and finally the generation of phospho-glycerate by glycerate kinase (DSVG11_0656 or DSVG11_1884). During autotrophic growth, assimilation probably proceeds primarily via the glycine reduction route rather than the serine...”
c3405 2-hydroxyacid dehydrogenase from Escherichia coli CFT073
27% identity, 87% coverage
- PafR, a novel transcription regulator, is important for pathogenesis in uropathogenic Escherichia coli
Baum, Infection and immunity 2014 - “...demonstrated that the region that contains the genes c3405 to c3410 (c3405-c3410) is responsible for this attenuation (10). The c3405-c3409 genes appear to...”
- A unique arabinose 5-phosphate isomerase found within a genomic island associated with the uropathogenicity of Escherichia coli CFT073
Mosberg, Journal of bacteriology 2011 - “...March 2011 Previous studies showed that deletion of genes c3405 to c3410 from PAI-metV, a genomic island from Escherichia coli CFT073, results in a strain that...”
- “...to independently colonize the mouse kidney. Our analysis of c3405 to c3410 suggests that these genes constitute an operon with a role in the internalization and...”
- Comparative genomics of Escherichia coli strains causing urinary tract infections
Vejborg, Applied and environmental microbiology 2011 - “...absence call), the strain contained five of these genes (c3405 to c3409; c3410 was not on the microarray). The B2 commensal strain SE15 also carries this...”
- “...PAI-ICFT073 HPICFT073 c4491-c4581 c5143-c5216 c5371-c5386 hcp, clpB, c3405 to c3409 sisA, hlyA, pap, iha, sat, iutA, iucABCD, flu, kpsTM sisB pap_2...”
- Genomic islands of uropathogenic Escherichia coli contribute to virulence
Lloyd, Journal of bacteriology 2009 - “...are annotated as 2-hydroxyacid dehydrogenase (c3405); phosphosugar isomerase (c3406); beta-cystathionase (c3407); phosphotransferase system, maltose- and...”
- “...from E. coli K-12 (5). Indeed, we recently identified c3405 and c3408 as UPEC specific (44). APEC strains, the primary cause of colibacillosis in the poultry...”
- The Analysis of Multiple Genome Comparisons in Genus Escherichia and Its Application to the Discovery of Uncharacterised Metabolic Genes in Uropathogenic Escherichia coli CFT073
Bryant, Comparative and functional genomics 2009 - “...Lloyd et al. [ 18 ]), in which the SAC is restricted to the area c3405 to c3410. These genes are retained in all the UPEC, in E. coli E2348, and in E. coli SMS-3-5, but not in any other strain. Retention of the SorCDFBAME genes...”
- “...6 PTS system, cellobiose specific + + + + + + + + + 6 c3405 c3410 6 PTS system, maltose/glucose specific* + + + + + 7 c3750 c3756 7 5- or 6-carbon sugar metabolism + + + + + 8 c4013 c4018 6 Carbohydrate...”
- Multiple genes repress motility in uropathogenic Escherichia coli constitutively expressing type 1 fimbriae
Simms, Journal of bacteriology 2008 - “...(11) Metabolism ...................................tyrB, nrdF, c3405 DNA mismatch repair.................mutS (2) Transcriptional regulation ..........lrp,...”
- Defining genomic islands and uropathogen-specific genes in uropathogenic Escherichia coli
Lloyd, Journal of bacteriology 2007 - “...c2522 c2523 c2524 c2525 yfaL c3147 c3292 c3304 c3390 c3405 c3408 c3509 c3686 c3750 c3753 c3755 ygiK c3770 c3771 c3772 c3773 c3774 assT c4016 c4017 c4018 c4205...”
A2YVQ8 D-3-phosphoglycerate dehydrogenase from Oryza sativa subsp. indica
30% identity, 42% coverage
- TMT-based quantitative proteomics analysis of defense responses induced by the Bph3 gene following brown planthopper infection in rice
Qing, BMC plant biology 2024 - “...encoding up-regulated proteins (A2XFY5, B8B674, B8B186, A2WX74, A2WU38, B8BDJ3, A2YXK8, A28P7, B8AK41, B8ABR1, A2WP38, and A2YVQ8) were up-regulated, and 2 out of 3 genes encoding down-regulated proteins (A2XK95, A2WRZ6, and B8AQ36) were down-regulated at the mRNA level (Fig. 7 b). Following BPH infection of R582 for...”
MMAR_1715 D-3-phosphoglycerate dehydrogenase SerA1 from Mycobacterium marinum M
31% identity, 47% coverage
YPO1288 putative D-isomer specific 2-hydroxyacid dehydrogenase family protein from Yersinia pestis CO92
26% identity, 94% coverage
PAAG_05378 2-hydroxyacid dehydrogenase from Paracoccidioides lutzii Pb01
31% identity, 79% coverage
SERA_MOUSE / Q61753 D-3-phosphoglycerate dehydrogenase; 3-PGDH; A10; EC 1.1.1.95 from Mus musculus (Mouse) (see paper)
Q61753 phosphoglycerate dehydrogenase (EC 1.1.1.95) from Mus musculus (see 2 papers)
NP_058662 D-3-phosphoglycerate dehydrogenase from Mus musculus
28% identity, 52% coverage
- function: Catalyzes the reversible oxidation of 3-phospho-D-glycerate to 3-phosphonooxypyruvate, the first step of the phosphorylated L- serine biosynthesis pathway. Does not catalyze the reversible oxidation of 2-hydroxyglutarate to 2-oxoglutarate and the reversible oxidation of (S)-malate to oxaloacetate.
catalytic activity: (2R)-3-phosphoglycerate + NAD(+) = 3-phosphooxypyruvate + NADH + H(+) (RHEA:12641)
subunit: Homotetramer.
disruption phenotype: Decreased level of free serine, glycine, taurine, GABA, glutamine, and threonine in spinal cord and head. Impaired central nervous system (CNS) with shorter neural tube length and overall growth retardation. Severe atrophy at the thoracic level, particularly in the dorsal spinal cord. Poorly developed dorsal horn and adjacent mantle zone. Neurons fail to develop neurites, particularly commissural axonal fibers. - Lectin-Based Immunophenotyping and Whole Proteomic Profiling of CT-26 Colon Carcinoma Murine Model.
Faragó, International journal of molecular sciences 2024 - “...P16110 Galectin-3 73.50 P97310 DNA replication licensing factor MCM2 81.89 Q8K009 Mitochondrial 10-formyltetrahydrofolate dehydrogenase 82.70 Q61753 D-3-phosphoglycerate dehydrogenase 100 P25206 DNA replication licensing factor MCM3 100 P52927 High mobility group protein HMGI-C 100 P14069 Protein S100-A6 100 P70202 Latexin 100 Q64437 All-trans-retinol dehydrogenase [NAD(+)] ADH7 100...”
- Sertoli cell-enriched proteins in mouse and human testicular interstitial fluid
O'Donnell, PloS one 2023 - “...Q9DCJ9 Npl N-acetylneuraminate lyase No B2RQ13 Pald1 Paladin Yes Q921X9 Pdia5 Protein disulfide-isomerase A5 Yes Q61753 Phgdh D-3-phosphoglycerate dehydrogenase Yes Q9WTX2 Prkra Interferon-inducible double-stranded RNA-dependent protein kinase activator A Yes Q4VA55 Pwwp3b PWWP domain-containing DNA repair factor 3B Yes Q3UFN2 Qpct Glutaminyl-peptide cyclotransferase Yes Q4TU85 Rhox8...”
- Periostin Protects Against Alcohol-related Liver Disease by Activating Autophagy by Interacting With Protein Disulfide Isomerase.
Zhang, Cellular and molecular gastroenterology and hepatology 2023 - “...beta 7 2 2 Q61696 Hspa1a Heat shock 70 kDa protein 1A 21 11 4 Q61753 Phgdh D-3-phosphoglycerate dehydrogenase 4 2 2 Q62009 Postn Periostin 43 30 30 Q62267 Sprr1b Cornifin-B 5 1 1 Q68FD5 Cltc Clathrin heavy chain 1 4 6 6 Q6PDQ2 Chd4 Chromodomain-helicase-DNA-binding...”
- Identification and characterization of ARID1A-interacting proteins in renal tubular cells and their molecular regulation of angiogenesis.
Yoodee, Journal of translational medicine 2023 - “...E2R1I5 CCDC39 6.20 0.9 1/1 110.37 Cornifin-B P22528 SPRR1B 34.12 55.1 4/4 9.89 D-3-phosphoglycerate dehydrogenase Q61753 PHGDH 7.86 2.1 1/1 56.59 DCC-interacting protein 13-alpha Q8K3H0 APPL1 33.13 5.0 3/3 79.33 Desmoplakin P15924 DSP 21.59 1.0 2/2 331.77 Dolichyl-diphosphooligosaccharide protein glycosyltransferase 48kDa subunit Q29381 DDOST 28.26 2.5...”
- In-Depth Proteomic Analysis of De Novo Proteome in a Mouse Model of Alzheimer's Disease.
Wang, Journal of Alzheimer's disease : JAD 2023 - “...Actin-related protein 3B Q641P0 0.33 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 A2A5R2 0.33 D-3-phosphoglycerate dehydrogenase Q61753 0.38 Heat shock 70 kDa protein 1B P17879 0.40 Xaa-Pro aminopeptidase 1 Q6P1B1 0.53 Neurofascin Q810U3 0.58 Cholesterol 24-hydroxylase Q9WVK8 0.63 Phosphatidate cytidylyltransferase 2 Q99L43 0.64 Beta-adducin Q9QYB8 0.72 Engulfment...”
- Proteomic analysis reveals activation of platelet- and fibrosis-related pathways in hearts of ApoE-/- mice exposed to diesel exhaust particles.
Jung, Scientific reports 2023 - “...1.64 0.032 O88207 COL5A1 Collagen alpha-1(V) chain 1.62 0.018 Q80XB4 NRAP Nebulin-related-anchoring protein 1.62 0.044 Q61753 PHGDH D-3-phosphoglycerate dehydrogenase 1.61 0.002 P16110 LGALS3 Galectin-3 1.60 0.021 P18872 GNAO1 Guanine nucleotide-binding protein G(o) subunit alpha 1.60 0.008 Q7TQ62 PODN Podocan 1.60 0.003 P13595 NCAM1 Neural cell adhesion...”
- Intra- and Inter-individual Differences in the Human Intestinal Microbial Conversion of (-)-Epicatechin and Bioactivity of Its Major Colonic Metabolite 5-(3',4'-Dihydroxy-Phenyl)-γ-Valerolactone in Regulating Nrf2-Mediated Gene Expression.
Liu, Frontiers in nutrition 2022 - “...gamma 1, mitochondrial Idh3g 1.24 (0.265) 1.20 (0.330) P61222 ABCE1 Abce1 1.01 (0.916) 1.26 (0.074) Q61753 D-3-phosphoglycerate dehydrogenase Phgdh 1.05 (0.608) 1.20 (0.089) P39689 Cyclin-dependent kinase inhibitor 1 Cdkn1a 2.32 (0.513) 6.16 (0.093) P28033 CCAAT/enhancer-binding protein beta Cebpb 1.20 (0.427) 1.04 (0.868) O54790 Transcription factor MafG...”
- Myocardial Injury Caused by Chronic Alcohol Exposure-A Pilot Study Based on Proteomics.
Ma, Molecules (Basel, Switzerland) 2022 - “...Q3UIJ3 Uncharacterized protein Actc1 0.634 0.027 down V9GXQ2 Predicted gene 17087 Gm17087 0.710 0.027 down Q61753 D-3-phosphoglycerate dehydrogenase Phgdh 0.816 0.027 down O35604 NPC intracellular cholesterol transporter 1 Npc1 0.824 0.029 down Q8VDP3 [F-actin]-monooxygenase MICAL1 Mical1 0.832 0.032 down Q3TX70 t-SNARE coiled-coil homology domain-containing protein Stx6...”
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- Yap/Taz activity is associated with increased expression of phosphoglycerate dehydrogenase that supports myoblast proliferation.
Meinhold, Cell and tissue research 2024 - GeneRIF: Yap/Taz activity is associated with increased expression of phosphoglycerate dehydrogenase that supports myoblast proliferation.
- Phosphoglycerate dehydrogenase activates PKM2 to phosphorylate histone H3T11 and attenuate cellular senescence.
Wu, Nature communications 2023 - GeneRIF: Phosphoglycerate dehydrogenase activates PKM2 to phosphorylate histone H3T11 and attenuate cellular senescence.
- ZEB1 Transcriptionally Activates PHGDH to Facilitate Carcinogenesis and Progression of HCC.
Wang, Cellular and molecular gastroenterology and hepatology 2023 - GeneRIF: ZEB1 Transcriptionally Activates PHGDH to Facilitate Carcinogenesis and Progression of HCC.
- Low glucose metabolite 3-phosphoglycerate switches PHGDH from serine synthesis to p53 activation to control cell fate.
Wu, Cell research 2023 - GeneRIF: Low glucose metabolite 3-phosphoglycerate switches PHGDH from serine synthesis to p53 activation to control cell fate.
- Chemical Components of the Fruits of Morus nigra Linn.: Methyl Caffeate as a Potential Anticancer Agent by Targeting 3-Phosphoglycerate Dehydrogenase.
Wang, Journal of agricultural and food chemistry 2021 (PubMed)- GeneRIF: Chemical Components of the Fruits of Morus nigra Linn.: Methyl Caffeate as a Potential Anticancer Agent by Targeting 3-Phosphoglycerate Dehydrogenase.
- Downregulation of PHGDH expression and hepatic serine level contribute to the development of fatty liver disease.
Sim, Metabolism: clinical and experimental 2020 (PubMed)- GeneRIF: Reduced Phgdh expression and serine levels are closely associated with the development of Fatty Liver Disease.
- Inverse Data-Driven Modeling and Multiomics Analysis Reveals Phgdh as a Metabolic Checkpoint of Macrophage Polarization and Proliferation.
Wilson, Cell reports 2020 - GeneRIF: Inverse Data-Driven Modeling and Multiomics Analysis Reveals Phgdh as a Metabolic Checkpoint of Macrophage Polarization and Proliferation.
- Deletion of PHGDH in adipocytes improves glucose intolerance in diet-induced obese mice.
Okabe, Biochemical and biophysical research communications 2018 (PubMed)- GeneRIF: PHGDH-mediated serine biosynthesis has important roles in adipose tissue glucose metabolism and could be a therapeutic target for diabetes in humans
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NE1688 D-isomer specific 2-hydroxyacid dehydrogenase from Nitrosomonas europaea ATCC 19718
28% identity, 90% coverage
O58256 phosphoglycerate dehydrogenase (EC 1.1.1.95) from Pyrococcus horikoshii (see paper)
30% identity, 88% coverage
LOC100280688 uncharacterized protein LOC100280688 from Zea mays
30% identity, 42% coverage
GRMZM2G009323 D-3-phosphoglycerate dehydrogenase from Zea mays
34% identity, 37% coverage
Q6ZAA5 D-3-phosphoglycerate dehydrogenase from Oryza sativa subsp. japonica
30% identity, 42% coverage
SERA1_ARATH / O49485 D-3-phosphoglycerate dehydrogenase 1, chloroplastic; Protein EMBRYO SAC DEVELOPMENT ARREST 9; EC 1.1.1.95 from Arabidopsis thaliana (Mouse-ear cress) (see 2 papers)
O49485 phosphoglycerate dehydrogenase (EC 1.1.1.95) from Arabidopsis thaliana (see 4 papers)
NP_195146 D-3-phosphoglycerate dehydrogenase from Arabidopsis thaliana
AT4G34200 EDA9 (embryo sac development arrest 9); ATP binding from Arabidopsis thaliana
32% identity, 39% coverage
- function: Involved in the plastidial phosphorylated pathway of serine biosynthesis (PPSB). Required for mature pollen development.
catalytic activity: (2R)-3-phosphoglycerate + NAD(+) = 3-phosphooxypyruvate + NADH + H(+) (RHEA:12641)
disruption phenotype: Embryo lethal when homozygous. - Novel regulatory mechanism of serine biosynthesis associated with 3-phosphoglycerate dehydrogenase in Arabidopsis thaliana
Okamura, Scientific reports 2017 - “...42 , 43 . Accession numbers for each amino acid sequence are as follows: AtPGDH1, NP_195146 (EMBL/GenBank/DDBJ); AtPGDH2, NP_564034 (EMBL/GenBank/DDBJ); AtPGDH3, NP_566637 (EMBL/GenBank/DDBJ); AhPGDH, BAF91727.1 (EMBL/GenBank/DDBJ); MtPGDH, 1YGY chain A (PDB); RnPGDH, CAA66374.1 (EMBL/GenBank/DDBJ); HsPGDH, NP_006614.2 (EMBL/GenBank/DDBJ) and EcPGDH 1YBA chain A (PDB). Reagents Nicotine amide...”
- Functional characterization of the plastidial 3-phosphoglycerate dehydrogenase family in Arabidopsis.
Toujani, Plant physiology 2013 - GeneRIF: Data indicate that 3-phosphoglycerate dehydrogenases PGDH (At1g17745) and EDA9 (At4g34200) were expressed preferentially in roots while 3-PGDH (At3g19480) was expressed mainly in the aerial parts and was not expressed or very poorly in roots.
- Identification of the phosphoglycerate dehydrogenase isoform EDA9 as the essential gene for embryo and male gametophyte development in Arabidopsis.
Toujani, Plant signaling & behavior 2013 - GeneRIF: Genetic and molecular evidence were provided for the essential role of EDA9 for embryo and pollen development.
- Arabidopsis phosphoglycerate dehydrogenase1 of the phosphoserine pathway is essential for development and required for ammonium assimilation and tryptophan biosynthesis.
Benstein, The Plant cell 2013 - GeneRIF: PGDH1 is essential for Arabidopsis development.
- The Shared Proteome of the Apomictic Fern Dryopteris affinis ssp. affinis and Its Sexual Relative Dryopteris oreades
Ojosnegros, International journal of molecular sciences 2022 - “...195-2609_5_ORF2 Q41932 PSBQ2 Oxygen-evolving enhancer protein 3-2, chloroplastic 24 230 3.05 10 77 Reproduction 229414-114_3_ORF1 O49485 EDA9 D-3-phosphoglycerate dehydrogenase 1, chloroplastic 68 918 0 Reproduction 155382-187_1_ORF2 F4I6W4 PGM2 Phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) 68 915 0 Reproduction 40155-402_5_ORF3 Q38905 PRF5 Profilin-5 14 62 8.5 10 59 Reproduction 65126-313_6_ORF2 O81644...”
- Sexual and Apogamous Species of Woodferns Show Different Protein and Phytohormone Profiles
Fernández, Frontiers in plant science 2021 - “...At1g63130 1,010 62277-321_4_ORF2 90 Q9CAN0 3.09193E-32 2.00 5.1 7 D-3-phosphoglycerate dehydrogenase 1 918 229414-114_3_ORF1 68 O49485 0 1.00 23 14 DC1 domain-containing protein 919 167954-169_4_ORF1 68 O80763 8.1609E-154 1.58 5.4 3 Dihydrolipoyl dehydrogenase 1 867 143453-204_6_ORF2 [2] 63 A8MS68 0 1.58 13 9 Membrane-associated progesterone binding...”
- Disclosing proteins in the leaves of cork oak plants associated with the immune response to Phytophthora cinnamomi inoculation in the roots: A long-term proteomics approach
Coelho, PloS one 2021 - “...beta chain protein 2 ACLB2 O04499 0.098 0.195 0.009 0.9 2,3-bisphosphoglycerate-independent phosphoglycerate mutase 1 PMG1/iPGAM O49485 0.575 1.064 0.041 0.9 D-3-phosphoglycerate dehydrogenase 1, chloroplastic SERA1 Q9LF37 0.038 0.074 0.041 0.9 Chaperone protein ClpB3, chloroplastic CLPB3 Q9STX5 0.175 0.389 0.041 0.9 Endoplasmin homolog ENPL Q9M040 0.171 0.336...”
- Proteome Changes Reveal the Protective Roles of Exogenous Citric Acid in Alleviating Cu Toxicity in Brassica napus L.
Ju, International journal of molecular sciences 2021 - “...increased abundance, while NADP-dependent glyceraldehyde-3-phosphate dehydrogenase (P93338), two fructose-bisphosphate aldolases (P16096, O65581), D-3-phosphoglycerate dehydrogenase 1 (O49485), and glyceraldehyde-3-phosphate dehydrogenase A (P12858) were decreased ( Table 1 ). Under heavy metal stress, plants have developed complex and intricate regulatory network mechanisms to positively modulate the metabolic pathways...”
- “...ligase [ADP-forming] subunit beta (O82662), exhibited increased abundance under Cu stress, whereas D-3-phosphoglycerate dehydrogenase 1 (O49485) exhibited decreased abundance under a low concentration of Cu. Interestingly, however, exogenous CA treatment promoted the alleviation of Cu stress symptoms. A previous proteomic study in O. glazioviana subjected to...”
- Gel-based proteomic map of Arabidopsis thaliana root plastids and mitochondria
Grabsztunowicz, BMC plant biology 2020 - “...synthase 82, 83, 102 P47999, At2g43750 D-3-phosphoglycerate dehydrogenase 1 18, 2224, 30, 4547, 54, 55 O49485, At4g34200 Diaminopimelate decarboxylase 2 56 Q94A94, At5g11880 Diaminopimelate epimerase 86 Q9LFG2, At3g53580 Dihydroxy-acid dehydratase 30, 43, 45 Q9LIR4, At3g23940 Glutamine synthetase 55 Q43127, At5g35630 Homoserine kinase 83, 85 Q8L7R2, At2g17265...”
- iTRAQ-based quantitative proteomic analysis reveals the lateral meristem developmental mechanism for branched spike development in tetraploid wheat (Triticum turgidum L.)
Chen, BMC genomics 2018 - “...p -value=4.15E 03 ) (Additional file 4 : Table S4). Proteins of particular interest included O49485 (W5ASV5) and P25858 (W5HB91) because these proteins are involved in metabolic pathways and post-embryonic development according to the BP analysis ( p =3.26E 02 ) (Additional file 4 : Table...”
- “...tauschii Traes_1DL_FDB539EBE W5AJW7 0.439 0.376 Q6TBX7 carotene epsilon-monooxygenase, chloroplastic Aegilops tauschii Traes_2AL_608FCBC83 W5ASV5 0.476 0.531 O49485 D-3-phosphoglycerate dehydrogenase, chloroplastic Triticum urartu TRIAE_CS42_1DS_TGACv1_080841_AA0254500 W5ALP4 0.530 0.577 O22898 long chain acyl-CoA synthetase 1 Aegilops tauschii Traes_7AL_D93FC054C W5HB91 0.551 0.319 P25858 glyceraldehyde-3-phosphate dehydrogenase 1,cytosolic Aegilops tauschii Traes_4DL_852DF544C W5EJA0 0.568...”
- Cold and Heat Stress Diversely Alter Both Cauliflower Respiration and Distinct Mitochondrial Proteins Including OXPHOS Components and Matrix Enzymes
Rurek, International journal of molecular sciences 2018 - “...3 0.18 0.01 0.40 0.09 (+2.22) 0.21 0.01 (+1.17) 3-phosphoglycerate dehydrogenase-like protein; Arabidopsis; AM NP_195146.1 O49485 At4g34200 63.6 6.16 72 5.43 7707; 1.48 31 112; 266 4 0.11 0.01 0.15 0.01 (+1.36) 0.21 0.03 (+1.91) Phosphoglycerate kinase 1; Arabidopsis; CM NP_187884.1 Q9LD57 At3g12780 50.1 5.91 43...”
- “...8 0.17 0.02 0.64 0.19 (+3.76) 0.48 0.07 (+2.82) 3-phosphoglycerate dehydrogenase-like protein; Arabidopsis; AM NP_195146.1 O49485 At4g34200 63.6 6.16 73 5.56 6778; 1.74 30 88; 237 9 0.25 0.03 0.72 0.31 (+2.88) 0.72 0.16 (+2.88) 3-phosphoglycerate dehydrogenase-like protein; Arabidopsis; AM NP_195146.1 O49485 At4g34200 63.6 6.16 74...”
- The rolB plant oncogene affects multiple signaling protein modules related to hormone signaling and plant defense
Bulgakov, Scientific reports 2018 - “...metabolism 10 Q93ZC5 (AOC4_ARATH) Allene oxide cyclase 4, chloroplastic Jasmonic acid biosynthetic process 5.40.5 11 O49485 (SERA1_ARATH) D-3-phosphoglycerate dehydrogenase 1, chloroplastic L-serine biosynthetic process Embryo development Pollen development 2.60.5 Primary metabolism 12 Q8RWV0 (TKTC1_ARATH) Transketolase-1, chloroplastic Pentose-phosphate cycle 2.80.3 Primary metabolism 13 Q9C5Y9 (Q9C5Y9_ARATH) Initiation factor...”
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- Metabolic engineering of the serine/glycine network as a means to improve the nitrogen content of crops
Casatejada-Anchel, Plant biotechnology journal 2025 (no snippet) - New Insights on the Role of ß-Cyanoalanine Synthase CAS-C1 in Root Hair Elongation through Single-Cell Proteomics
Arenas-Alfonseca, Plants (Basel, Switzerland) 2023 - “...ubiquitin-activating enzyme 2 AT3G48340 CEP2 CEP2__Cysteine proteinases superfamily protein AT4G24800 ECIP1-MRF3 ECIP1 MA3 domain-containing protein AT4G34200 EDA9P-GDH1 EDA9 D-3-phosphoglycerate dehydrogenase AT1G29880 Glycyl-tRNA synthetase/glycine--tRNA ligase AT1G18500 IPMS1-MAML-4 IPMS1 methylthioalkylmalate synthase-like 4 AT1G53240 mMDH1 mMDH1 Lactate/malate dehydrogenase family protein AT3G04600 Nucleotidylyl transferase superfamily protein AT2G22780 PMDH1 PMDH1__peroxisomal NAD-malate...”
- DEFECTIVELY ORGANIZED TRIBUTARIES 5 is not required for leaf venation patterning in Arabidopsis thaliana
Vlad, The Plant journal : for cell and molecular biology 2022 - “...AT4G16230 GDSLlike lipase/acylhydrolase superfamily protein AtL er 4G62980.1 Deletion exon 4, premature stop codon Chr4 AT4g34200 PGDH1; phosphoglycerate dehydrogenase 1; EDA9 AtL er 5G70960.1 Deletion Chr5 AT5G56200 C2H2 type zinc finger transcription factor family AtL er 1G22980.1 Insertion exon 2 Chr1 Not annotated AtL er 1G47950.1...”
- Nitric oxide coordinates growth, development, and stress response via histone modification and gene expression
Ageeva-Kieferle, Plant physiology 2021 - “...hydrolase family protein, AT1G78060), auxin biosynthesis (tryptophan aminotransferase related 2, AT4G24670), serine biosynthesis (D-3-phosphoglycerate dehydrogenase, AT4G34200), and histone modification (histone-lysine N-methyltransferase SETD1B-like protein, AT5G03670; Figure 8 ; Supplemental Table S2 ). Under D conditions, only three genes are hyperacetylated and overexpressed in both mutants. One of...”
- “...related 2 TAR2 is required for reprogramming root architecture in response to low nitrogen conditions. AT4G34200 D-3-phosphoglycerate dehydrogenase AT3G50660 Cytochrome P450 superfamily protein Brassinosteroid biosynthetic pathway. AT5G03670 Histone-lysine N-methyltransferase SETD1B-like protein Histone methyltransferase that specifically methylates H3K4. ChIP-seq and RNA-seq datasets were integrated at the gene...”
- Proteins associated with the Arabidopsis thaliana plastid rhomboid-like protein RBL10
Lavell, The Plant journal : for cell and molecular biology 2021 - “...appears to influence growth and development is D-3-Phoshpoglycerate dehydrogenase 1 (PGDH1 or EDA9) encoded by At4g34200. PGDH1 catalyzes the first committed step of serine biosynthesis and out of three PGDH-encoding genes in Arabidopsis, this appears to be essential and induced under salt stress ( Rosa-Tellez et...”
- “...CPN60B, LEN1 - chaperonin 60 beta AT1G55490 64 1.906 2 11 EDA9 - D-3-phosphoglycerate dehydrogenase AT4G34200 63 1.906 2 12 SBPASE - sedoheptulose-bisphosphatase AT3G55800 42 1.906 2 13 CLPC1 - CLPC homologue 1 AT5G50920 103 1.906 2 14 ATPB - ATP synthase subunit beta ATCG00480 54...”
- Network Topological Analysis for the Identification of Novel Hubs in Plant Nutrition
Di, Frontiers in plant science 2021 - “...synthetase A0A0A0KCX8 Csa_6G077980 ARGAH1 (AT4G08900) 85% 590 34 1 0 4 Arginase A0A0A0LBW6 Csa_3G199630 EDA9 (AT4G34200) 83% 981 4 1,9E-02 33 7 D-3-phosphoglycerate dehydrogenase A0A0A0L0I0 Csa_4G285780 PA2 (AT5G06720) 53% 335 3,7 2,6E-02 33 3 1 3 Peroxidase A0A0A0KA81 Csa_6G088110 AT2G20420 88% 757 31 4 8 12...”
- High-throughput single-cell transcriptomics reveals the female germline differentiation trajectory in Arabidopsis thaliana
Hou, Communications biology 2021 - “.../ pAT4G13710: 3Venus construct, the promoter sequences of ER (AT2G26330), ERL1 (AT5G62230), ERL2 (AT5G07180) pPGDH1 (AT4G34200), and AT4G13710 were amplified, and PCR fragments were cloned into the pENTR/D-TOPO vector (Invitrogen) and the pPGDH1/AT4G13710 3Venus -N7 vectors. The pENTR clones were recombined into the destination vector pGWB604...”
- Stromal NADH supplied by PHOSPHOGLYCERATE DEHYDROGENASE3 is crucial for photosynthetic performance
Höhner, Plant physiology 2021 - “...of the respective metabolite or enzyme in WT and pgdh3 mutant plants. Accession numbers PGDH1 (At4g34200), PGDH2 (At1g17745), PGDH3 (At3g19480), pgdh3-1 mutant (SM_3_37584; Toujani etal., 2013 ), pgdh3-2 (GK-877F12; Toujani etal., 2013 ), npq4-1 (Li et al., 2000), npq2-1 aka aba1-6 CS3772 ( Niyogi etal., 1998...”
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B3KSC3 D-3-phosphoglycerate dehydrogenase from Homo sapiens
28% identity, 55% coverage
PHGDH / O43175 D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95) from Homo sapiens (see 3 papers)
SERA_HUMAN / O43175 D-3-phosphoglycerate dehydrogenase; 3-PGDH; 2-oxoglutarate reductase; Malate dehydrogenase; EC 1.1.1.95; EC 1.1.1.399; EC 1.1.1.37 from Homo sapiens (Human) (see 7 papers)
O43175 phosphoglycerate dehydrogenase (EC 1.1.1.95) from Homo sapiens (see 8 papers)
28% identity, 51% coverage
- function: Catalyzes the reversible oxidation of 3-phospho-D-glycerate to 3-phosphonooxypyruvate, the first step of the phosphorylated L- serine biosynthesis pathway. Also catalyzes the reversible oxidation of 2-hydroxyglutarate to 2-oxoglutarate and the reversible oxidation of (S)-malate to oxaloacetate.
catalytic activity: (2R)-3-phosphoglycerate + NAD(+) = 3-phosphooxypyruvate + NADH + H(+) (RHEA:12641)
catalytic activity: (R)-2-hydroxyglutarate + NAD(+) = 2-oxoglutarate + NADH + H(+) (RHEA:49612)
catalytic activity: (S)-malate + NAD(+) = oxaloacetate + NADH + H(+) (RHEA:21432)
subunit: Homotetramer. - Single-Cell Patch-Clamp/Proteomics of Human Alzheimer's Disease iPSC-Derived Excitatory Neurons Versus Isogenic Wild-Type Controls Suggests Novel Causation and Therapeutic Targets.
Ghatak, Advanced science (Weinheim, Baden-Wurttemberg, Germany) 2024 - “...in the TCA cycle not previously proposed, as discussed further below. Another upregulated protein, SERA (O43175, or D3phosphoglycerate dehydrogenase or PDGDH), catalyzes reversible oxidation of 3phosphoDglycerate to 3phosphonooxypyruvate, the first step of the phosphorylated l serine biosynthesis pathway, 2hydroxyglutarate to 2oxoglutarate, or (S)malate to oxaloacetate in...”
- A Proteomic Approach Identified TFEB as a Key Player in the Protective Action of Novel CB2R Bitopic Ligand FD22a against the Deleterious Effects Induced by β-Amyloid in Glial Cells.
Polini, Cells 2024 - “...1.20 1641 P68371 TUBB4B Tubulin beta-4B chain 142 31 13 4.79 50,255 0.0043 0.51 1725 O43175 PHGDH D-3-phosphoglycerate dehydrogenase 56 12 6 6.29 57,356 0.0005 1.81 1726 P28329 CHAT Choline O-acetyltransferase 73 9 8 8.9 83,852 0.0282 0.74 1730 P78371 CCT2 T-complex protein 1 subunit beta...”
- Downregulation of AHNAK2 inhibits cell cycle of lung adenocarcinoma cells by interacting with RUVBL1
Li, Thoracic cancer 2023 - “...smooth muscle (ACTA2) 228 0.25 10 P49411 Elongation factor Tu, mitochondrial (TUFM) 483 0.29 11 O43175 D3phosphoglycerate dehydrogenase (PHGDH) 429 0.18 12 P17844 Probable ATPdependent RNA helicase DDX5 (DDX5) 428 0.26 13.1 Q06830 Peroxiredoxin1 (PRDX1) 361 0.75 13.2 P32119 Peroxiredoxin2 (PRDX2) 214 0.33 14 O14980 Exportin1...”
- The mitotic surveillance pathway requires PLK1-dependent 53BP1 displacement from kinetochores
Burigotto, 2023 - Effects of Natural Products on Enzymes Involved in Ferroptosis: Regulation and Implications.
Zuo, Molecules (Basel, Switzerland) 2023 - “...3 [ 31 ] CS O75390 Citrate synthase [ 32 ] Glucose metabolism Inhibit PHGDH O43175 D-3-phosphoglycerate dehydrogenase [ 33 ] G6PD P11413 Glucose-6-phosphate 1-dehydrogenase [ 34 ] Promote PHKG2 P15735 Phosphorylase kinase subunit gamma-2 [ 35 ] Mevalonate pathway Promote SQLE Q14534 Squalene monooxygenase [...”
- Towards unravelling biological mechanisms behind radiation-induced oral mucositis via mass spectrometry-based proteomics.
Subedi, Frontiers in oncology 2023 - “...synthase 2 1,51 5,54E-03 9,16 4,75E-16 Q15646 OASL 2-5-oligoadenylate synthase-like protein 100 2,30E-16 4,26 9,31E-13 O43175 PHGDH D-3-phosphoglycerate dehydrogenase 0,418 3,77E-12 0,452 3,14E-05 P00749 PLAU Urokinase-type plasminogen activator 1,50 1,86E-02 1,89 3,89E-03 P06702 S100A9 Protein S100-A9 1,57 3,05E-03 1,55 3,91E-02 Q5K651 SAMD9 Sterile alpha motif domain-containing...”
- Analysis of local extracellular matrix identifies different aetiologies behind bicuspid and tricuspid aortic valve degeneration and suggests therapies.
Beusch, Cellular and molecular life sciences : CMLS 2023 - “...Signal transducer and activator of transcription 1-alpha/beta 8.5510 7 0.69 Q8TAD2 IL17D Interleukin-17D 0.0046 0.66 O43175 PHGDH D-3-phosphoglycerate dehydrogenase 0.0052 0.66 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 8.7410 4 0.65 P31150 GDI1 Rab GDP dissociation inhibitor alpha 5.2410 4 0.65 O60504 SORBS3 Vinexin 0.0035 0.64...”
- The effects of two gold-N-heterocyclic carbene (NHC) complexes in ovarian cancer cells: a redox proteomic study
Massai, Cancer chemotherapy and pharmacology 2022 - “...N.D N.D Others 10 Glutaredoxin-3 [Homo sapiens] O76003 No variation 510 14 d -3-phosphoglycerate dehydrogenase O43175 VVNCAR 10 25 19 * Programmed cell death 6-interacting protein CSDIVFAR N.D 10 23 Peflin Q9UBV8 N.D N.D 22 * Mitotic checkpoint protein BUB3 O43684 YQTRCIR N.D N.D 24 Band...”
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B9RYA3 D-3-phosphoglycerate dehydrogenase from Ricinus communis
XP_002518687 D-3-phosphoglycerate dehydrogenase 1, chloroplastic from Ricinus communis
32% identity, 39% coverage
- Proteomic Analysis of Embryo Isolated From Mature Jatropha curcas L. Seeds
Ramzan, Frontiers in plant science 2022 - “...AT2G33040.1 Jcr4S01672.20 Ferredoxin B9SCU0 AT2G27510.1 Jcr4S01794.30 Chlorophyll a-b binding protein B9SID9 AT5G54270.1 Jcr4S01456.10 Phosphoglycerate dehydrogenase B9RYA3 AT4G34200.1 We identified four cytosolic isoforms of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) (Jcr4S07385.10, Jcr4S00953.40, Jcr4S00273.150, and Jcr4S00205.140) that catalyze the formation of 1,3-bisphosphoglycerate (BPGA) from Gly-3-P. In rapeseeds, the specific expression of...”
- Domestication Syndrome Is Investigated by Proteomic Analysis between Cultivated Cassava (Manihot esculenta Crantz) and Its Wild Relatives
An, PloS one 2016 - “...beta, mitochondrial-like Brachypodium distachyon XP_003567942 59.12/6.00 1.100.08(-) 1.080.09(-) 215 d-3-phosphoglycerate dehydrogenase, putative R . communis XP_002518687 7.65/63.10 1.230.15(+) 1.160.10(+) 216 d-3-phosphoglycerate dehydrogenase, putative R . communis XP_002518687 7.65/63.10 1.100.09(+) 1.020.07(+) 217 * ATP synthase subunit beta, mitochondrial; P17614 5.95/59.86 1.550.16(+) 1.340.16(-) 218 ATP synthase subunit beta...”
- “...precursor, putative- R . communis XP_002526228 4.89/31.87 66/1 376 d-3-phosphoglycerate dehydrogenase, putative R . communis XP_002518687 7.65/63.10 421/4 385 ATP synthase subunit beta, mitochondrial P17614 5.95/59.86 342/2 386 Enolase 2 Q9LEI9 5.92/47.91 75/1 389 sinapyl alcohol dehydrogenase Populus tremuloides AAK58693 6.23/38.99 67/1 394 ADPglucose pyrophosphorylase Oryza...”
- Proteomic and biochemical analyses of the cotyledon and root of flooding-stressed soybean plants
Komatsu, PloS one 2013 - “...unguiculata] Glyma16g27210.1 ABB89042 54243 5.63 1795 168 35 880 55 d-3-phosphoglycerate dehydrogenase [Ricinus communis] Glyma10g40750.1 XP_002518687 62859 6.32 41 2 14 878 56 (No significant hits to report) 57 argininosuccinate synthase,putative [Ricinus communis] Glyma05g03190.1 XP_002521168 52641 6.55 16 2 13 774 58 pyruvate decarboxylase 1 [Lotus...”
MUL_1952 D-3-phosphoglycerate dehydrogenase SerA1 from Mycobacterium ulcerans Agy99
31% identity, 47% coverage
6biiA / F8AEA4 Crystal structure of pyrococcus yayanosii glyoxylate hydroxypyruvate reductase in complex with NADP and malonate (re-refinement of 5aow) (see paper)
32% identity, 76% coverage
- Ligand: nadp nicotinamide-adenine-dinucleotide phosphate (6biiA)
F8AEA4 glyoxylate reductase (NADP+) (EC 1.1.1.79); hydroxypyruvate reductase (EC 1.1.1.81) from Pyrococcus yayanosii (see paper)
PYCH_09300 glyoxylate reductase from Pyrococcus yayanosii CH1
32% identity, 76% coverage
- Removal of phosphoglycolate in hyperthermophilic archaea
Michimori, Proceedings of the National Academy of Sciences of the United States of America 2024 - “...another report concluded that the proteins encoded by PH0597, PF0319 from Pyrococcus furiosus , and PYCH_09300 from Pyrococcus yayanosii are actually HPRs ( 33 ). TK0551 homologs in Thermococcales have not yet been characterized and the physiological roles of TK0551 and TK0683 are still unclear. GLDH...”
NMA0274 glycerate dehydrogenase from Neisseria meningitidis Z2491
29% identity, 97% coverage
BPSL1577 2-ketogluconate reductase from Burkholderia pseudomallei K96243
33% identity, 73% coverage
Phgdh / O08651 3-phosphoglycerate dehydrogenase subunit (EC 1.1.1.95) from Rattus norvegicus (see paper)
SERA_RAT / O08651 D-3-phosphoglycerate dehydrogenase; 3-PGDH; EC 1.1.1.95 from Rattus norvegicus (Rat) (see paper)
O08651 phosphoglycerate dehydrogenase (EC 1.1.1.95) from Rattus norvegicus (see paper)
NP_113808 D-3-phosphoglycerate dehydrogenase from Rattus norvegicus
27% identity, 52% coverage
- function: Catalyzes the reversible oxidation of 3-phospho-D-glycerate to 3-phosphonooxypyruvate, the first step of the phosphorylated L- serine biosynthesis pathway. Does not catalyze the reversible oxidation of 2-hydroxyglutarate to 2-oxoglutarate and the reversible oxidation of (S)-malate to oxaloacetate.
catalytic activity: (2R)-3-phosphoglycerate + NAD(+) = 3-phosphooxypyruvate + NADH + H(+) (RHEA:12641)
subunit: Homotetramer. - Candidate proteins interacting with cytoskeleton in cells from the basal airway epithelium in vitro
Olatona, Frontiers in molecular biosciences 2024 - “...P22734 Comt Catechol O-methyltransferase 29.6 0.025 P18395 Csde1 Cold shock domain-containing protein E1 88.8 0.000 O08651 Phgdh D-3-phosphoglycerate dehydrogenase 56.5 0.351 Met-loss + Acetyl [N-Term] P55053 Fabp5 Fatty acid-binding protein 5 15.1 0.009 P05370 G6pdx Glucose-6-phosphate 1-dehydrogenase 59.3 0.526 Met-loss + Acetyl [N-Term] Q66H61 Qars1 Glutamine--tRNA...”
- Label-free proteomic analysis reveals the hepatoprotective mechanism of gypenosides in liver injury rats.
Chen, Frontiers in pharmacology 2024 - “...fibrosis ( Mackinnon et al., 2023 ). Psat1 (Uniprot ID: A0A0G2K931) and Phgdh (Uniprot ID: O08651) are critical enzymes involved in the de novo synthesis of serine, directing the glycolytic intermediate 3-phosphoglyceric acid into the pathway. Recent studies have revealed that in hepatocellular carcinoma, PHGDH has...”
- Carbonylated Proteins as Key Regulators in the Progression of Metabolic Syndrome.
Kitamura, Antioxidants (Basel, Switzerland) 2023 - “...(CAT) 16.9 7 1.46 1.39 989 Q68FS4 Cytosol aminopeptidase (LAP3) 7.9 3 2.39 2.58 999 O08651 D-3-phosphoglycerate dehydrogenase (PHGDH) 15.0 4 1.69 2.24 1598 O88989 Malate dehydrogenase (MDH1) 26.4 7 1.66 1.93 1888 Q9Z0V6 Thioredoxin-dependent peroxide reductase (PRDX3) 23.7 4 1.47 1.27 1907 P08010 Glutathione S-transferase...”
- Gephyrin Interacts with the K-Cl Cotransporter KCC2 to Regulate Its Surface Expression and Function in Cortical Neurons
Al, The Journal of neuroscience : the official journal of the Society for Neuroscience 2022 (secret) - Investigation into potential mechanisms of metabolic syndrome by integrative analysis of metabolomics and proteomics.
Chen, PloS one 2022 - “...mitochondrial Amino-acid biosynthesis. 1.475 0.0005 Pck1 P07379 Phosphoenolpyruvate carboxykinase, cytosolic [GTP] Gluconeogenesis 1.248 0.0062 Phgdh O08651 D-3-phosphoglycerate dehydrogenase Amino-acid biosynthesis 0.542 0.0037 Pycr3 Q5PQJ6 Pyrroline-5-carboxylate reductase 3 Amino-acid biosynthesis 0.77 0.0028 Retsat Q8VHE9 All-trans-retinol 13,14-reductase Retinol metabolic process 0.832 0.0024 Sdhd Q6PCT8 Succinate dehydrogenase [ubiquinone] Carbohydrate...”
- Fluoxetine Enhances Synaptic Vesicle Trafficking and Energy Metabolism in the Hippocampus of Socially Isolated Rats.
Filipović, International journal of molecular sciences 2022 - “...subunit A (PR 65), alpha isoform, isoform CRA_a Q5XI34 Ppp2r1a 1.58 10 10 D-3-phosphoglycerate dehydrogenase O08651 Phgdh 1.57 4 3 N-ethylmaleimide sensitive fusion protein, isoform CRA_b F1LQ81 Nsf 1.57 22 21 Heat shock cognate 71 kDa protein P63018 Hspa8 1.57 44 36 Heat shock 70 kDa...”
- Proteomic Analysis of the Spatio-temporal Based Molecular Kinetics of Acute Spinal Cord Injury Identifies a Time- and Segment-specific Window for Effective Tissue Repair
Devaux, Molecular & cellular proteomics : MCP 2016 - “...Q62669 Q68FY4 Q6MGC4 Q7TQ70 Cluster 5 B0BNM1 B2RYG6 O08651 Sec22b Protein name UV excision repair protein RAD23 homolog B Dihydropyrimidinase-related protein 3...”
- Influence of age on rat bone-marrow mesenchymal stem cells potential
Fafián-Labora, Scientific reports 2015 - “...and glycine-rich protein 1 7 1,0015 0,9815 1,0448 0,5131 1,2576 0,0488 0,6896 0,0389 1,2501 0,0705 O08651 D-3-phosphoglycerate dehydrogenase 3 0,8786 0,1902 0,7465 0,0308 1,1981 0,1105 1,1565 0,1448 1,0565 0,5069 Q5BJ93 Enolase 1, (Alpha) 23 1,0226 0,655 1,026 0,5722 1,054 0,2406 0,7412 0 1,2752 0,0123 Q8R4A1 ERO1-like...”
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- Phgdh serves a protective role in Il‑1β induced chondrocyte inflammation and oxidative‑stress damage.
Huang, Molecular medicine reports 2021 - GeneRIF: Phgdh serves a protective role in Il1beta induced chondrocyte inflammation and oxidativestress damage.
- Protective effects and potential mechanisms of Pien Tze Huang on cerebral chronic ischemia and hypertensive stroke
Zhang, Chinese medicine 2010 - “...CO3 -2.80 146 Complement C3 precursor Q9JHU0 NP_075412 DPYL5 -2.93 412 Dihydropyrimidinase-related protein 5 O08651 NP_113808 SERA -2.67 67 D-3-phosphoglycerate dehydrogenase P67779 NP_114039 PHB -2.13 561 Prohibitin P10860 NP_036702 DHE3 -2.03 443 Glutamate dehydrogenase 1, mitochondrial precursor Q63270 NP_059017 ACOC +2.00 154 Cytoplasmic aconitate hydratase *...”
BMMGA3_02750 D-2-hydroxyacid dehydrogenase from Bacillus methanolicus MGA3
28% identity, 86% coverage
XP_002283022 D-3-phosphoglycerate dehydrogenase 3, chloroplastic from Vitis vinifera
31% identity, 39% coverage
VC2504 2-hydroxyacid dehydrogenase family protein from Vibrio cholerae O1 biovar eltor str. N16961
29% identity, 76% coverage
- Exploration of the effects of a degS mutant on the growth of Vibrio cholerae and the global regulatory function of degS by RNA sequencing
Huang, PeerJ 2019 - “...gene P -value PATH:00010 Glycolysis/Gluconeogenesis VC1819, VC2000, VC2738,VC2013, VCA0843, VC0485, VC2638 0.0089266 PATH:01200 Carbon metabolism VC2504, VC2000, VC1942, VC2738, VC1304, VC2090, VCA0843, VCA0666, VC0485, VC0432, VC2638, VCA0278, VC2646, VC0027 0.0221534 PATH:00260 Glycine, serine and threonine metabolism VC2504, VC2036, VCA0875, VCA0666, VC2638, VCA0278, VC0027 0.0222798 PATH:00020 Citrate...”
B6SKK1 D-3-phosphoglycerate dehydrogenase from Zea mays
30% identity, 42% coverage
GOR1 / P53839 glyoxylate reductase 1 (EC 1.1.1.26) from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (see paper)
GOR1_YEAST / P53839 Glyoxylate reductase 1; EC 1.1.1.26; EC 1.1.1.79; EC 1.1.1.81 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 4 papers)
NP_014125 glyoxylate reductase from Saccharomyces cerevisiae S288C
YNL274C Glyoxylate reductase; null mutation results in increased biomass after diauxic shift; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies from Saccharomyces cerevisiae
31% identity, 73% coverage
- function: Glyoxylate reductase that reversibly reduces glyoxylate to glycolate, or alternatively hydroxypyruvate to D-glycerate, using either NADPH or NADH as a cosubstrate (PubMed:17173333). Does not act as a hydroxyisocaproate dehydrogenase even though it also has minor activity on alpha-ketoisocaproate (PubMed:17173333).
catalytic activity: glycolate + NAD(+) = glyoxylate + NADH + H(+) (RHEA:18229)
catalytic activity: glycolate + NADP(+) = glyoxylate + NADPH + H(+) (RHEA:10992)
catalytic activity: (R)-glycerate + NAD(+) = 3-hydroxypyruvate + NADH + H(+) (RHEA:17905)
catalytic activity: (R)-glycerate + NADP(+) = 3-hydroxypyruvate + NADPH + H(+) (RHEA:18657)
disruption phenotype: Leads to higher biomass concentration after diauxic shift. - The ORF YNL274c (GOR1) codes for glyoxylate reductase in Saccharomyces cerevisiae.
Rintala, Yeast (Chichester, England) 2007 (PubMed)- GeneRIF: GOR1 codes for glyoxalate reductase in Saccharomyces cerevisiae.
- Proteomics Answers Which Yeast Genes Are Specific for Baking, Brewing, and Ethanol Production
Davydenko, Bioengineering (Basel, Switzerland) 2020 - “...as ethanol or osmotic stress. In addition, we found genes with unknown function, YPR127W and YNL274C , with increased expression in ethanol-producing strains. Probably, the function of those genes is connected with yeast adaptation to toxic conditions during ethanol production. Proteomic analysis of brewers yeast showed...”
- “...ATPase D Subunit 2.30 RPL4A 60S ribosomal protein L4 2.27 YPR127W Putative pyridoxal reductase 2.20 YNL274C Putative 2-hydroxy acid dehydrogenase 2.20 NCL1 RNA (cytosine-5-)-methyltransferase 2.14 The Ethanol-Producing Strain ER in Relation to the Bakers LV7 NNR1 NADHX epimerase 10.36 TIF45 Eukaryotic translation initiation factor 4E 5.92...”
- Heme, A Metabolic Sensor, Directly Regulates the Activity of the KDM4 Histone Demethylase Family and Their Interactions with Partner Proteins
Konduri, Cells 2020 - “...6323635 Delta(24)-sterol C-methyltransferase COQ3, WBSCR27 + + ESS1 YJR017C 37362669 Peptidyl-prolyl cistrans isomerase PIN1 GOR1 YNL274C 6325144 Glyoxylate reductase GRHPR + + GPD2 YOL059W 6324513 Mitochondrial glycerol-3-phosphate dehydrogenase (NAD(+)) 2 GPD1 + + GRX2 YDR513W 6320720 Mitochondrial glutaredoxin-2 GLRX, GLRX2 GYP1 YOR070C 6324644 Cis-golgi GTPase-activating protein...”
- Yeast screen for modifiers of C9orf72 poly(glycine-arginine) dipeptide repeat toxicity
Chai, FEMS yeast research 2018 - “...YOR136W oxa1 YER154W rcf2 zwf1 YNR018W YNL241C gor1 YNL274C gpd2 YOL059W gph1 YPR160W stb5 YHR178W nnr2 ald6 YKL151C YPL061W yes Nucleotide biosynthetic pathway...”
- Cadmium-induced proteome remodeling regulated by Spc1/Sty1 and Zip1 in fission yeast
Guo, Toxicological sciences : an official journal of the Society of Toxicology 2012 - “...ZWF1 G6PD Q9UT59 SPAC513.07 GRE2 O14075 SPACUNK4.10 YNL274C O13326 SPBC428.11 MET25 P55306 O74402 SPCC757.07c SPBC4F6.17c CTT1 HSP78 Q10265 SPAC13G7.02c SSA1...”
- A genomewide screen for suppressors of Alu-mediated rearrangements reveals a role for PIF1
Chisholm, PloS one 2012 - “...0.010 none REC104 YHR157W 7.34 1.73 0.0009 none REC8 YPR007C 7.13 1.68 0.218 none GOR1 YNL274C 7.04 1.66 0.145 GRHPR TEL1 YBL088C 6.44 1.52 0.054 ATM Wild-type BY4742 4.24 1.00 a Unreported heterozygous mutations within each gene screened for in women with early breast and/or ovarian...”
- Construction and application of a protein and genetic interaction network (yeast interactome)
Stuart, Nucleic acids research 2009 - “...YIL087C 5.15 Hypothetical protein YKL150W MCR1 5.04 Mitochondrial NADH-cytochrome b5 reductase, involved in ergosterol biosynthesis YNL274C YNL274C 5.03 Putative hydroxyisocaproate dehydrogenase YER121W YER121W 5.01 Hypothetical protein YOR382W FIT2 5.01 Cell wall mannoprotein involved in the retention of siderophore-iron in the cell wall YPL281C ERR2 5.01 Protein...”
- Identification of coherent patterns in gene expression data using an efficient biclustering algorithm and parallel coordinate visualization
Cheng, BMC bioinformatics 2008 - “...YHR002W, YHR067W, YHR147C, YIL087C, YIL111W, YJL063C, YLL040C, YLR270W, YLR346C, YMR098C, YMR152W, YMR188C, YNL063W, YNL073W, YNL200C, YNL274C, YOL059W, YOL071W, YOR136W, YPR011C 18 bud neck contractile ring 6.08E-05 1.58E-03 YHR023W, YJR092W, YMR032W pre-autophagosomal structure 6.62E-04 1.72E-02 YBL078C, YDL113C 20 nuclear cohesin complex 3.74E-04 5.24E-03 YDL003W, YIL026C Table 11...”
- The ORF YNL274c (GOR1) codes for glyoxylate reductase in Saccharomyces cerevisiae
Rintala, Yeast (Chichester, England) 2007 (PubMed)- “...10.1002/yea.1434 Yeast Functional Analysis Report The ORF YNL274c (GOR1) codes for glyoxylate reductase in Saccharomyces cerevisiae Eija Rintala*, Juha-Pekka...”
- “...In this paper we show that GOR1 (ORF YNL274c) encodes a glyoxylate reductase and not a hydroxyisocaproate dehydrogenase in Saccharomyces cerevisiae, even though...”
- More
7dkmA / O43175 Phgdh covalently linked to oridonin (see paper)
29% identity, 76% coverage
- Ligands: (1beta,6beta,7beta,8alpha,9beta,10alpha,13alpha,14r,16beta)-1,6,7,14-tetrahydroxy-7,20-epoxykauran-15-one; nicotinamide-adenine-dinucleotide (7dkmA)
CTBP2_XENLA / Q9W758 C-terminal-binding protein 2; CtBP2; C-terminal-binding protein B; TCF-3 corepressor CtBP; XCtBP from Xenopus laevis (African clawed frog) (see paper)
30% identity, 65% coverage
Q5EAD2 D-3-phosphoglycerate dehydrogenase from Bos taurus
27% identity, 52% coverage
TM0327 phosphoglycerate dehydrogenase, putative from Thermotoga maritima MSB8
30% identity, 79% coverage
A0A1Z4EAX4 phosphoglycerate dehydrogenase (EC 1.1.1.95) from Beta vulgaris (see paper)
34% identity, 31% coverage
ML1692 D-3-phosphoglycerate dehydrogenase from Mycobacterium leprae TN
31% identity, 46% coverage
XP_018109636 C-terminal-binding protein 2 isoform X1 from Xenopus laevis
30% identity, 59% coverage
lpg0242 D-3-phosphoglycerate dehydrogenase from Legionella pneumophila subsp. pneumophila str. Philadelphia 1
31% identity, 76% coverage
LOC107808555 D-3-phosphoglycerate dehydrogenase 2, chloroplastic-like from Nicotiana tabacum
31% identity, 38% coverage
DSVG11_0961 phosphoglycerate dehydrogenase from Desulfovibrio sp. G11
34% identity, 56% coverage
- The reductive glycine pathway allows autotrophic growth of Desulfovibrio desulfuricans
Sánchez-Andrea, Nature communications 2020 - “...or other transaminases), subsequent reduction of hydroxypyruvate to glycerate (potentially by 2-hydroxyacid dehydrogenases DSVG11_0256 or DSVG11_0961) and finally the generation of phospho-glycerate by glycerate kinase (DSVG11_0656 or DSVG11_1884). During autotrophic growth, assimilation probably proceeds primarily via the glycine reduction route rather than the serine route, as...”
NWMN_1617 D-3-phosphoglycerate dehydrogenase from Staphylococcus aureus subsp. aureus str. Newman
SACOL1773 D-3-phosphoglycerate dehydrogenase from Staphylococcus aureus subsp. aureus COL
29% identity, 47% coverage
Q66KM4 Glyoxylate reductase/hydroxypyruvate reductase from Xenopus tropicalis
29% identity, 83% coverage
HVO_2968 D-3-phosphoglycerate dehydrogenase from Haloferax volcanii DS2
29% identity, 47% coverage
XP_042922996 uncharacterized protein from Chlamydomonas reinhardtii
30% identity, 42% coverage
NP_571789 C-terminal-binding protein 1 from Danio rerio
30% identity, 57% coverage
OEOE_0701 Lactate dehydrogenase or related 2-hydroxyacid dehydrogenase from Oenococcus oeni PSU-1
33% identity, 76% coverage
7cvpA / O43175 The crystal structure of human phgdh from biortus.
30% identity, 63% coverage
- Ligand: nicotinamide-adenine-dinucleotide (7cvpA)
SA1545 D-3-phosphoglycerate dehydrogenase from Staphylococcus aureus subsp. aureus N315
28% identity, 47% coverage
- Global transcriptome analysis of Staphylococcus aureus biofilms in response to innate immune cells
Scherr, Infection and immunity 2013 - “...SA1818 SA0155 SA2475 SA0712 SA0687 SA2278 SA1235 SA0024 SA1545 SA1553 SA0616 SA0024 SA2342 SA0409 SA0251 SA1825 SA0200 SA1401 SA1820 SA1596 SA1182 SA1435 SA1364...”
- Staphylococcal IgM enzyme-linked immunosorbent assay for diagnosis of periprosthetic joint infections
Artini, Journal of clinical microbiology 2011 - “...revised in 1983). SSPA from Staphylococcus strain SA1545 (a slime-producing clinical isolate) was prepared as previously reported, with important modifications...”
- Characterizing the effects of inorganic acid and alkaline shock on the Staphylococcus aureus transcriptome and messenger RNA turnover
Anderson, FEMS immunology and medical microbiology 2010 - “...diester phosphodiesterase sa_c2220s1920_a_at * 5.5 2.5 2.5 SA1514 glycerol-3-phosphate dehydrogenase, NAD-dependent sa_c2448s2032_a_at 2.5 2.5 2.5 SA1545 short chain dehydrogenase/reductase family oxidoreductase sa_c2493s2074_a_at 6.6 5 5 SA1560 2-oxoisovalerate dehydrogenase sa_c2497s2076_a_at 8.5 5 2.5 SA1561 2-oxoisovalerate dehydrogenase sa_c2501s2080_a_at 3.9 2.5 5 SA1562 2-oxoisovalerate dehydrogenase sa_c3114s2669_a_at 4.5 2.5 2.5...”
- Transcriptional signature following inhibition of early-stage cell wall biosynthesis in Staphylococcus aureus
O'Neill, Antimicrobial agents and chemotherapy 2009 - “...SA1235 SA1236 SA1238 SA1254 SA1255 SA1256 SA1257 SA1532 SA1545 SA1546 SA1691 SA1858 SA1859 SA1860 SA1861 SA1862 SA1863 SA1864 SA1865 SA1866 SA2112 SA2221 SA2235...”
- Transcriptome analysis of the responses of Staphylococcus aureus to antimicrobial peptides and characterization of the roles of vraDE and vraSR in antimicrobial resistance
Pietiäinen, BMC genomics 2009 - “...4.2 5.3 3.3 VraSR, VCM Hypothetical protein SA1517 citC 4.9 5.8 3.1 VCM Isocitrate dehydrogenase SA1545 serA 4.6 2.5 VCM Similar to soluble hydrogenase 42 kD subunit SA1549 htrA 2.9 3.0 2.0 VraSR, VCM Similar to serine proteinase Do, heat-shock protein HtrA SA1599 3.2 2.4 Similar...”
SAR1801 D-3-phosphoglycerate dehydrogenase from Staphylococcus aureus subsp. aureus MRSA252
DA471_RS00355 phosphoglycerate dehydrogenase from Staphylococcus aureus
28% identity, 47% coverage
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 789,361 different protein sequences to 1,256,019 scientific articles. Searches against EuropePMC were last performed on January 10 2025.
PaperBLAST builds a database of protein sequences that are linked
to scientific articles. These links come from automated text searches
against the articles in EuropePMC
and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot,
BRENDA,
CAZy (as made available by dbCAN),
BioLiP,
CharProtDB,
MetaCyc,
EcoCyc,
TCDB,
REBASE,
the Fitness Browser,
and a subset of the European Nucleotide Archive with the /experiment tag.
Given this database and a protein sequence query,
PaperBLAST uses protein-protein BLAST
to find similar sequences with E < 0.001.
To build the database, we query EuropePMC with locus tags, with RefSeq protein
identifiers, and with UniProt
accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use
queries of the form "locus_tag AND genus_name" to try to ensure that
the paper is actually discussing that gene. Because EuropePMC indexes
most recent biomedical papers, even if they are not open access, some
of the links may be to papers that you cannot read or that our
computers cannot read. We query each of these identifiers that
appears in the open access part of EuropePMC, as well as every locus
tag that appears in the 500 most-referenced genomes, so that a gene
may appear in the PaperBLAST results even though none of the papers
that mention it are open access. We also incorporate text-mined links
from EuropePMC that link open access articles to UniProt or RefSeq
identifiers. (This yields some additional links because EuropePMC
uses different heuristics for their text mining than we do.)
For every article that mentions a locus tag, a RefSeq protein
identifier, or a UniProt accession, we try to select one or two
snippets of text that refer to the protein. If we cannot get access to
the full text, we try to select a snippet from the abstract, but
unfortunately, unique identifiers such as locus tags are rarely
provided in abstracts.
PaperBLAST also incorporates manually-curated protein functions:
- Proteins from NCBI's RefSeq are included if a
GeneRIF
entry links the gene to an article in
PubMed®.
GeneRIF also provides a short summary of the article's claim about the
protein, which is shown instead of a snippet.
- Proteins from Swiss-Prot (the curated part of UniProt)
are included if the curators
identified experimental evidence for the protein's function (evidence
code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that
describe the protein's function are shown (with bold headings).
- Proteins from BRENDA,
a curated database of enzymes, are included if they are linked to a paper in PubMed
and their full sequence is known.
- Every protein from the non-redundant subset of
BioLiP,
a database
of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself
does not include descriptions of the proteins, those are taken from the
Protein Data Bank.
Descriptions from PDB rely on the original submitter of the
structure and cannot be updated by others, so they may be less reliable.
(For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every
ligand is represented among a group of structures with similar sequences, but for
PaperBLAST, we use the non-redundant set provided by BioLiP.)
- Every protein from EcoCyc, a curated
database of the proteins in Escherichia coli K-12, is included, regardless
of whether they are characterized or not.
- Proteins from the MetaCyc metabolic pathway database
are included if they are linked to a paper in PubMed and their full sequence is known.
- Proteins from the Transport Classification Database (TCDB)
are included if they have known substrate(s), have reference(s),
and are not described as uncharacterized or putative.
(Some of the references are not visible on the PaperBLAST web site.)
- Every protein from CharProtDB,
a database of experimentally characterized protein annotations, is included.
- Proteins from the CAZy database of carbohydrate-active enzymes
are included if they are associated with an Enzyme Classification number.
Even though CAZy does not provide links from individual protein sequences to papers,
these should all be experimentally-characterized proteins.
- Proteins from the REBASE database
of restriction enzymes are included if they have known specificity.
- Every protein with an evidence-based reannotation (based on mutant phenotypes)
in the Fitness Browser is included.
- Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators)
with experimentally-determined DNA binding sites from the
PRODORIC database of gene regulation in prokaryotes.
- Putative transcription factors from RegPrecise
that have manually-curated predictions for their binding sites. These predictions are based on
conserved putative regulatory sites across genomes that contain similar transcription factors,
so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
- Coding sequence (CDS) features from the
European Nucleotide Archive (ENA)
are included if the /experiment tag is set (implying that there is experimental evidence for the annotation),
the nucleotide entry links to paper(s) in PubMed,
and the nucleotide entry is from the STD data class
(implying that these are targeted annotated sequences, not from shotgun sequencing).
Also, to filter out genes whose transcription or translation was detected, but whose function
was not studied, nucleotide entries or papers with more than 25 such proteins are excluded.
Descriptions from ENA rely on the original submitter of the
sequence and cannot be updated by others, so they may be less reliable.
Except for GeneRIF and ENA,
the curated entries include a short curated
description of the protein's function.
For entries from BioLiP, the protein's function may not be known beyond binding to the ligand.
Many of these entries also link to articles in PubMed.
For more information see the
PaperBLAST paper (mSystems 2017)
or the code.
You can download PaperBLAST's database here.
Changes to PaperBLAST since the paper was written:
- November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
- February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
- June 2022: incorporated some coding sequences from ENA with the /experiment tag.
- March 2022: incorporated BioLiP.
- April 2020: incorporated TCDB.
- April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
- February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
- January 2018: incorporated BRENDA.
- December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
- September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.
Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.
PaperBLAST cannot provide snippets for many of the papers that are
published in non-open-access journals. This limitation applies even if
the paper is marked as "free" on the publisher's web site and is
available in PubmedCentral or EuropePMC. If a journal that you publish
in is marked as "secret," please consider publishing elsewhere.
Many important articles are missing from PaperBLAST, either because
the article's full text is not in EuropePMC (as for many older
articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an
article that characterizes a protein's function but is missing from
PaperBLAST, please notify the curators at UniProt
or add an entry to GeneRIF.
Entries in either of these databases will eventually be incorporated
into PaperBLAST. Note that to add an entry to UniProt, you will need
to find the UniProt identifier for the protein. If the protein is not
already in UniProt, you can ask them to create an entry. To add an
entry to GeneRIF, you will need an NCBI Gene identifier, but
unfortunately many prokaryotic proteins in RefSeq do not have
corresponding Gene identifers.
References
PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.
Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.
Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.
UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.
BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.
The MetaCyc database of metabolic pathways and enzymes.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.
CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.
The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.
The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.
REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
R. J. Roberts et al (2015). Nucleic Acids Research, 10.1093/nar/gku1046.
Deep annotation of protein function across diverse bacteria from mutant phenotypes.
M. N. Price et al (2016). bioRxiv, 10.1101/072470.
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory