PaperBLAST

PaperBLAST Hits for reanno::HerbieS:HSERO_RS17015 sorbitol dehydrogenase (EC 1.1.1.14); xylitol dehydrogenase (EC 1.1.1.9) (Herbaspirillum seropedicae SmR1) (345 a.a., MQALVLEATR...)

Show query sequence

>reanno::HerbieS:HSERO_RS17015 sorbitol dehydrogenase (EC 1.1.1.14); xylitol dehydrogenase (EC 1.1.1.9) (Herbaspirillum seropedicae SmR1)
MQALVLEATRELKLREIDLPQQMGAQDVRIRIHTVGICGSDLHYYTHGSIGPFKVEAPMV
LGHEASGTVIEVGSAVSHLKVGDRVCMEPGIPRLDSPATLRGMYNLDPAVRFWATPPIHG
CLTGSVVHPAAFTYRLPDNVSFAEGAIVEPLSIGLQAATKARMKPGDTAVVIGAGTIGAM
TALAALAGGAARVILADVVAEKLAHFADNPAVITVDVTRETLTDVVRQATDGWGADVVFE
ASGHAGVYQTLLDLVCPGGCAVLVGMPPAPVALDVVAMQTKEVRLESVFRYANIFPRALA
LISSGMIDVKPFISRKFPFSQSIRAFEEAASGRPQDVKIQIEMEG

Running BLASTp...

Found 251 similar proteins in the literature:

HSERO_RS17015 sorbitol dehydrogenase (EC 1.1.1.14); xylitol dehydrogenase (EC 1.1.1.9) from Herbaspirillum seropedicae SmR1
100% identity, 100% coverage

• mutant phenotype: Specifically important for utilizing Xylitol. Automated validation from mutant phenotype: the predicted function (1.1.1.14, 1.1.1.9) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

Q2K0Q7 D-xylulose reductase (EC 1.1.1.9) from Rhizobium etli (see paper)
61% identity, 99% coverage

PhaeoP88_01862 NAD(P)-dependent alcohol dehydrogenase from Phaeobacter inhibens
60% identity, 98% coverage

• Trajectories and Drivers of Genome Evolution in Surface-Associated Marine Phaeobacter
  Freese, Genome biology and evolution 2017
  • “...( fig. 5 , insert) probably due to the exclusive presence of a D-xylulose reductase (PhaeoP88_01862, K05351) and xylokinase (PhaeoP88_01866, K00854). Fig. 5. Principal component analysis of the utilization patterns of 190 substrates determined for the 32 Phaeobacter strains on OmniLog PM01 and PM02A plates. Strains...”

A9H073 Putative D-xylulose reductase from Gluconacetobacter diazotrophicus (strain ATCC 49037 / DSM 5601 / CCUG 37298 / CIP 103539 / LMG 7603 / PAl5)
GDI_3142 NAD(P)-dependent alcohol dehydrogenase from Gluconacetobacter diazotrophicus PA1 5
63% identity, 99% coverage

• Arabidopsis thaliana exudates induce growth and proteomic changes in Gluconacetobacter diazotrophicus
  Dos, PeerJ 2020
  • “...Porin oprB 9.00 2,838.53 0.46 A9H577 Sugar ABC transporter substrate-binding protein GDI0354 8.00 4,390.16 0.47 A9H073 Alcohol dehydrogenase GroES domain protein GDI_3142 4.00 1,094.65 0.48 A9HRF1 Succinate--CoA ligase (ADP-forming) subunit alpha sucD 5.00 2,866.13 0.51 A9HPH9 10 kDa chaperonin groS 5.00 4,835.59 0.54 A9HNP0 D-xylose ABC...”
• Arabidopsis thaliana exudates induce growth and proteomic changes in Gluconacetobacter diazotrophicus
  Dos, PeerJ 2020
  • “...Sugar ABC transporter substrate-binding protein GDI0354 8.00 4,390.16 0.47 A9H073 Alcohol dehydrogenase GroES domain protein GDI_3142 4.00 1,094.65 0.48 A9HRF1 Succinate--CoA ligase (ADP-forming) subunit alpha sucD 5.00 2,866.13 0.51 A9HPH9 10 kDa chaperonin groS 5.00 4,835.59 0.54 A9HNP0 D-xylose ABC transporter, periplasmic substrate-binding protein xylF 18.00...”

Dshi_0551 D-xylulose reductase (EC 1.1.1.9) from Dinoroseobacter shibae DFL-12
61% identity, 99% coverage

• mutant phenotype: Specifically important for utilizing Xylitol. Automated validation from mutant phenotype: the predicted function (1.1.1.9) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

BAD_RS01695 NAD(P)-dependent alcohol dehydrogenase from Bifidobacterium adolescentis ATCC 15703
56% identity, 99% coverage

• Combining of transcriptome and metabolome analyses for understanding the utilization and metabolic pathways of Xylo-oligosaccharide in Bifidobacterium adolescentis ATCC 15703
  Yang, Food science & nutrition 2019
  • “...ko01100/ko00040 BAD_RS06365 1.23 exgA Betaglucosidase 1,112.17 475.02 ko00500 BAD_RS06400 1.19 bgaB Betagalactosidase 45.11 19.79 ko00052 BAD_RS01695 1.18 Sulfurtransferase 20.92 9.24 ko01100/ko00040 BAD_RS02400 1.16 malL Alphaglucosidase 76.25 34.21 ko01100/ko00500/ko00052 BAD_RS06090 1.14 cscA Beta(12)fructofuranosidase 47.64 21.63 ko01100/ko00500/ko00052 BAD_RS05480 1.11 BAD_1030 Mannan endo1,4betamannosidase 29.85 13.79 ko00051 BAD_RS01580 1.08 murB...”

BKKJ1_0339 NAD(P)-dependent alcohol dehydrogenase from Bifidobacterium catenulatum subsp. kashiwanohense
55% identity, 99% coverage

• Metabolism of the predominant human milk oligosaccharide fucosyllactose by an infant gut commensal
  James, Scientific reports 2019
  • “...BKKJ1_0208 BKKJ1_0208 putative gluconokinase 17.21 BKKJ1_0336 BKKJ1_0336 hypothetical protein 16.99 BKKJ1_0338 BKKJ1_0338 hypothetical protein 27.69 BKKJ1_0339 BKKJ1_0339 xylitol (sorbitol) dehydrogenase 34.61 BKKJ1_0340 BKKJ1_0340 transcriptional regulator 36.34 BKKJ1_0341 BKKJ1_0341 aldehyde-alcohol dehydrogenase 2 22.03 BKKJ1_0429 fumG L-1,2-propanediol oxidoreductase 5.90 BKKJ1_2066 lacS galactoside symporter 5.35 BKKJ1_2067 lacA beta-galactosidase 6.47...”

GFR01_RS14945 NAD(P)-dependent alcohol dehydrogenase from Gluconobacter frateurii
64% identity, 99% coverage

• D-Allulose (D-Psicose) Biotransformation From Allitol by a Newly Found NAD(P)-Dependent Alcohol Dehydrogenase From Gluconobacter frateurii NBRC 3264 and the Enzyme Characterization
  Wen, Frontiers in microbiology 2022
  • “...the GenBank National Center for Biotechnology Information (NCBI) 1 . The adh gene locus_tag was GFR01_RS14945 and the ADH protein ID number was WP_099183078.1. The optimization and synthesis of the gene encoding NAD(P)-dependent alcohol dehydrogenase (ADH) were made by a company named Boshang (Jinan, China). The...”

NRBB01_1662 NAD(P)-dependent alcohol dehydrogenase from Bifidobacterium breve
53% identity, 99% coverage

• Comparative genomics and genotype-phenotype associations in Bifidobacterium breve
  Bottacini, Scientific reports 2018
  • “.... 22 B7017_1842/ NRBB01_1661 Transcriptional regulator, AraC family PF12833 Bottacini et al . 22 B7017_1843/ NRBB01_1662 Alcohol dehydrogenase X PF08240 Bottacini et al . 22 B7017_1844/ NRBB01_1663 transporter, major facilitator family protein PF07690 Bottacini et al . 22 B7017_1845/ NRBB01_1664 Transcriptional regulator, ROK family PF00480 Bottacini...”

A4I8R5 Putative d-xylulose reductase from Leishmania infantum
LINJ_33_0530 putative d-xylulose reductase from Leishmania infantum JPCM5
52% identity, 99% coverage

• A Computational Approach Using Bioinformatics to Screening Drug Targets for Leishmania infantum Species
  Chávez-Fumagalli, Evidence-based complementary and alternative medicine : eCAM 2018
  • “...E 60 37 A4HY37 Gamma-glutamylcysteine synthetase 0,623 8 E 104 47 8 E 104 47 A4I8R5 Putative d-xylulose reductase 0,611 3 E 79 41 1 E 80 42 E9AG23 D-3-phosphoglycerate dehydrogenase-like protein 0,549 8 E 51 34 2 E 51 34 A4IAM3 D-isomer specific 2-hydroxyacid dehydrogenase-like...”
• Distinct gene expression patterns in vector-residing Leishmania infantum identify parasite stage-enriched markers
  Coutinho-Abreu, PLoS neglected tropical diseases 2020
  • “...3 DE genes between these two stages were a GP63 (LINJ_10_0530), a putative d-xylulose reductase (LINJ_33_0530) and glucose transporter (LINJ_36_6540). As expected, only six genes displayed significant expression differences between leptomonads at day 6 (6d) and leptomonds at day 8 (8d) ( Fig 1C ) in...”
  • “...-1.433 -0.605 0.867 XM_001465134.2 LINJ_20_1220 XP_001465171.2 putative calpain-like cysteine peptidase 0 -9.404 -0.903 0.781 XM_001468097.1 LINJ_33_0530 XP_001468134.1 putative d-xylulose reductase 0 -0.833 -1.751 0.701 log2 FC PRO2d vs MET14d log2 FC NEC4d vs MET14d log2 FC LEP8d vs MET14d MET14d XM_003392269.1 LINJ.12.0666 XP_003392317.1 putative surface antigen...”

Q59545 xylitol dehydrogenase (EC 1.1.1.9) from Morganella morganii (see paper)
Q59545 D-xylulose reductase from Morganella morganii
56% identity, 96% coverage

• Simulating the evolutionary trajectories of metabolic pathways for insect symbionts in the genus Sodalis
  Hall, Microbial genomics 2020
  • “...between the S. praecaptivus orthologue, AFW03778/Sant_3108, and the M. morganii subsp. morganii protein, UniProt ID Q59545). The cluster contains a xylulose reductase as the second enzyme required to convert d -xylitol to the central metabolite d -xylulose-5-phosphate (Fig. S1c) and a complete ABC transporter that is...”

DHSO_RAT / P27867 Sorbitol dehydrogenase; SDH; L-iditol 2-dehydrogenase; Polyol dehydrogenase; Xylitol dehydrogenase; XDH; EC 1.1.1.-; EC 1.1.1.14; EC 1.1.1.9 from Rattus norvegicus (Rat) (see 5 papers)
41% identity, 95% coverage

• function: Polyol dehydrogenase that catalyzes the reversible NAD(+)- dependent oxidation of various sugar alcohols (By similarity). Is active with D-sorbitol (D-glucitol) leading to the C2-oxidized product D-fructose (PubMed:6862079). Is a key enzyme in the polyol pathway that interconverts glucose and fructose via sorbitol, which constitutes an important alternate route for glucose metabolism. May play a role in sperm motility by using sorbitol as an alternative energy source for sperm motility (By similarity).
  catalytic activity: keto-D-fructose + NADH + H(+) = D-sorbitol + NAD(+) (RHEA:33031)
  catalytic activity: xylitol + NAD(+) = D-xylulose + NADH + H(+) (RHEA:20433)
  catalytic activity: L-iditol + NAD(+) = keto-L-sorbose + NADH + H(+) (RHEA:10160)
  cofactor: Zn(2+) (Binds 1 zinc ion per subunit.)
  subunit: Homotetramer; dimer of dimers.
• Sugar alcohol degradation in Archaea: uptake and degradation of mannitol and sorbitol in Haloarcula hispanica
  Ortjohann, Extremophiles : life under extreme conditions 2024
  • “...sorbitol in RnSorDH are conserved in HhSorDH (). UniProt accession: HsSorDH, Q00796; OaSorDH, P07846; RnSorDH, P27867; BsSorDH, Q06004; LrMtlDH, Q6ECH5; LpMtlDH, Q83VI5; TbMtlDH, Q1ACW3; HhSorDH, G0I050; HhMtlDH, G0I059 Besides sorbitol and mannitol dehydrogenases (Riveros-Rosas et al. 2003 ; Ceccaroli et al. 2007 ), the PDH family...”
  • “...H. hispanica , G0I050; B. argentifolii , O96496; M. musculus , Q64442; R. norvegicus , P27867; O. aries , P07846; H. sapiens , Q00796; H. gibbonsii , M0HN94; H. rarus , WP_256422950.1; H. marismortui , Q5V6U8; MtlDH: H. hispanica , G0I059; H. marismortui , Q5V6V7; T....”
• iTRAQ-based quantitative proteomics analysis of the hepatoprotective effect of melatonin on ANIT-induced cholestasis in rats.
  Wang, Experimental and therapeutic medicine 2021
  • “...family 2A, dehydroepiandrosterone (DHEA)-preferring, member 6 (SULT2A6) 2.1173 0.0255 P25093 Fumarylacetoacetate hydrolase (FAH) 1.6438 0.0894 P27867 Sorbitol dehydrogenase (SORD) 1.5653 0.0658 P36201 Cysteine-rich protein 2 (CRIP2) 0.6203 0.0038 P37397 Calponin 3 (CNN3) 0.5362 0.0339 P50123 Glutamyl aminopeptidase (ENPEP) 1.5400 0.1557 P50237 Sulfotransferase family 1C member 3...”
• Functional proteomic analysis of corticosteroid pharmacodynamics in rat liver: Relationship to hepatic stress, signaling, energy regulation, and drug metabolism.
  Ayyar, Journal of proteomics 2017
  • “...UP P12928 Pklr Pyruvate kinase Glycolysis - transfer of phosphate from phosphoenolpyruvate to ADP UP/DOWN P27867 Sord Sorbitol dehydrogenase Carbohydrate metabolism - converts sorbitol to fructose UP P50137 Tkt Transketolase Pentose phosphate pathway - transfers glycoaldehyde from ketose-donor to aldose-acceptor sugars UP P48500 Tpi1 Triosephosphate isomerase...”
• Peptidomic Analysis of Rat Plasma: Proteolysis in Hemorrhagic Shock.
  Aletti, Shock (Augusta, Ga.) 2016
  • “...chymotrypsin-like KESTLHLVL 1.61 F1LML2 Ubc chymotrypsin-like AADISQWAGPLSL P31044 Pebp1 chymotrypsin-like AALQERLDNVSHTPSSY Q5U2Z3 Nap1l4 chymotrypsin-like AAPAKGENLSL P27867 Sord chymotrypsin-like AAVVLENGVLSRKLSDFGQETSY P04176 Pah chymotrypsin-like AEFYGSLEHPQTHY Q7TMC7 Tf chymotrypsin-like AETDVQTLFSQY P04638 Apoa2 chymotrypsin-like AEVTGLSPGVTYLFKVF P04937 Fn1 chymotrypsin-like AGQAFRKFLPLF P26772 Hspe1 chymotrypsin-like AGQAFRKFLPLFDRVL P26772 Hspe1 chymotrypsin-like AGVLSRDAPDIESIL O89000 Dpyd chymotrypsin-like...”
  • “...x x Protein Shfm1 D3ZHW9 Shfm1 x Protein Smyd1 D4A3D2 Smyd1 x x Sorbitol dehydrogenase P27867 Sord x x Q9R095-2 Spef2 x Stathmin P13668 Stmn1 x x Sem. ves. Secr. protein 4 P02783 Svs4 x Sem. ves. Secr. prot. 5 P04812 Svs5 x Serotransferrin Q7TMC7 Tf...”
• Gender-specific effects of intrauterine growth restriction on the adipose tissue of adult rats: a proteomic approach
  de, Proteome science 2015
  • “...3 81 11 2.44 36634/6.16 P18422 Proteasome subunit -type 3 4 86 15 1.93 28633/5.29 P27867 Sorbitol dehydrogenase 2 94 7 2.05 38790/7.14 P68370 Tubulin -1A chain 3 121 9 2.37 50800/4.94 Q9Z2L0 Voltage-dependent anion-selective channel protein 1 2 60 8 2.16 30853/8.62 Q9Z2L0 Voltage-dependent anion-selective...”
• Changes of the Cytoplasmic Proteome in Response to Alcoholic Hepatotoxicity in Rats.
  Kim, International journal of molecular sciences 2015
  • “...protein SA (p40) 32,824/4.8 729 P38983 0.0832 0.0406 0.49 0.028 318 Sorbitol dehydrogenase 42,835/6.8 9459 P27867 0.1499 0.0766 0.51 0.002 361 Sideroflexin1 (Tricarboxylate carrier protein, Sfx1) 35,547/9.2 401 Q63965 0.0550 0.0000 0.00 0.012 389 Thiosulfate sulfurtransferase (Rhodanese) 33,177/7.8 1537 P24329 0.4404 0.3192 0.72 0.037 433 Carbonic...”
• Modulation of nitro-fatty acid signaling: prostaglandin reductase-1 is a nitroalkene reductase
  Vitturi, The Journal of biological chemistry 2013
  • “...protein. Reference Protein P97584 P00481 Q63276 P27867 B5DF65 P00884 B6DYP8 P09034 P07824 P12346-1 Prostaglandin reductase-1 Ornithine carbamoyltransferase Bile...”
• Proteomic profiling and pathway analysis of the response of rat renal proximal convoluted tubules to metabolic acidosis
  Schauer, American journal of physiology. Renal physiology 2013
  • “...subunit 4 RCG21481, isoform CRA_b Accession Number P34058 P27867 Control Acute acidosis Chronic acidosis 1 1 1 1 Peptide Sequence Modified Site*...”
• More

XP_017446963 sorbitol dehydrogenase isoform X1 from Rattus norvegicus
41% identity, 96% coverage

• SORD-deficient rats develop a motor-predominant peripheral neuropathy unveiling novel pathophysiological insights.
  Rebelo, Brain : a journal of neurology 2024 (PubMed)
  • GeneRIF: SORD-deficient rats develop a motor-predominant peripheral neuropathy unveiling novel pathophysiological insights.
• Sorbitol dehydrogenase: structure, function and ligand design.
  El-Kabbani, Current medicinal chemistry 2004 (PubMed)
  • GeneRIF: Sorbitol dehydrogenase is expressed almost ubiquitously in all mammalian tissues.
• Gene expression of enzymes comprising the polyol pathway in various rat tissues determined by the competitive RT-PCR method.
  Maekawa, Japanese journal of pharmacology 2002 (PubMed)
  • GeneRIF: Gene expression of enzymes comprising the polyol pathway in various rat tissues determined by the competitive RT-PCR method.

DHSO_MOUSE / Q64442 Sorbitol dehydrogenase; SDH; SORD; L-iditol 2-dehydrogenase; Polyol dehydrogenase; Xylitol dehydrogenase; XDH; EC 1.1.1.-; EC 1.1.1.14; EC 1.1.1.9 from Mus musculus (Mouse) (see 3 papers)
NP_666238 sorbitol dehydrogenase from Mus musculus
40% identity, 95% coverage

• function: Polyol dehydrogenase that catalyzes the reversible NAD(+)- dependent oxidation of various sugar alcohols (By similarity). Is active with D-sorbitol (D-glucitol) leading to the C2-oxidized product D-fructose (PubMed:6852349). Is a key enzyme in the polyol pathway that interconverts glucose and fructose via sorbitol, which constitutes an important alternate route for glucose metabolism (By similarity). May play a role in sperm motility by using sorbitol as an alternative energy source for sperm motility and protein tyrosine phosphorylation (PubMed:18799757). Has no activity on ethanol. Cannot use NADP(+) as the electron acceptor (PubMed:6852349).
  catalytic activity: keto-D-fructose + NADH + H(+) = D-sorbitol + NAD(+) (RHEA:33031)
  catalytic activity: xylitol + NAD(+) = D-xylulose + NADH + H(+) (RHEA:20433)
  catalytic activity: L-iditol + NAD(+) = keto-L-sorbose + NADH + H(+) (RHEA:10160)
  cofactor: Zn(2+) (Binds 1 zinc ion per subunit.)
  subunit: Homotetramer.
• Sugar alcohol degradation in Archaea: uptake and degradation of mannitol and sorbitol in Haloarcula hispanica
  Ortjohann, Extremophiles : life under extreme conditions 2024
  • “...S. cerevisiae , P35497; H. hispanica , G0I050; B. argentifolii , O96496; M. musculus , Q64442; R. norvegicus , P27867; O. aries , P07846; H. sapiens , Q00796; H. gibbonsii , M0HN94; H. rarus , WP_256422950.1; H. marismortui , Q5V6U8; MtlDH: H. hispanica , G0I059; H....”
• Protein Targets of Acetaminophen Covalent Binding in Rat and Mouse Liver Studied by LC-MS/MS.
  Geib, Frontiers in chemistry 2021
  • “...0 1 Q63836 Selenium-binding protein 2 C8 C * GPGYPTPLEAMK 2 0 2 0 1 Q64442 Sorbitol dehydrogenase C106 EVDEYC * K 2 0 0 0 1 P10639 Thioredoxin C73 C * MPTFQFYK 2 0 2 2 1 * APAP modification site. Underlined peptides (or modification...”
• Protein Expression Profile of Twenty-Week-Old Diabetic db/db and Non-Diabetic Mice Livers: A Proteomic and Bioinformatic Analysis
  Guzmán-Flores, Biomolecules 2018
  • “...subunit beta, mitochondrial Suclg2 Q9Z2I8 136 35 6.58 +4.2 Citrate cycle 2 Sorbitol dehydrogenase Sord Q64442 69 33 6.60 +1.7 Fructose metabolism 17 Fumarylacetoacetase Fah P35505 100 27 6.70 +2.4 Amino-acid degradation 60 Triosephosphate isomerase Tpi1 P17751 128 33 6.90 +2.7 Gluconeogenesis 41 Phosphatidylethanolamine-binding protein 1...”
• 2D DIGE proteomic analysis reveals fasting-induced protein remodeling through organ-specific transcription factor(s) in mice
  Kamata, FEBS open bio 2018
  • “...aspartate dehydrogenase Q9DCQ2 Aspdh Mm.88478 66 39% 9/38 30479 6.45 53 1.39 0.009 Sorbitol dehydrogenase Q64442 Sord Mm.371580 108 35% 9/22 38795 6.56 54 1.38 0.016 Glutathione S transferase 1 P19157 Gstp1 Mm.299292 73 44% 10/42 23765 7.68 51 1.37 0.004 Cytosolic 10formyltetrahydrofolate dehydrogenase Q8R0Y6 Aldh1l1...”
• Protein identification in imaging mass spectrometry through spatially targeted liquid micro-extractions.
  Ryan, Rapid communications in mass spectrometry : RCM 2018
  • “...2 P51667 Myosin regulatory light chain 2 Q9QXD6 Fructose-1,6-bisphosphatase 1 P52825 Carnitine O-palmitoyltransferase 2, mitochondrial Q64442 Sorbitol dehydrogenase P70694 Estradiol 17 beta-dehydrogenase 5 Cerebellum Q8VHQ9 Acyl-coenzyme A thioesterase 11 Q924X2 Carnitine O-palmitoyltransferase 1, muscle isoform Q62203 Splicing factor 3A subunit 2 Q3UZA1 CapZ-interacting protein Q3TMP8 Trimeric...”
• Transcriptome-wide profiling and posttranscriptional analysis of hematopoietic stem/progenitor cell differentiation toward myeloid commitment
  Klimmeck, Stem cell reports 2014
  • “...0.42 0.0360 no P09671 ENSMUSG00000006818 Sod2 superoxide dismutase [Mn], mitochondrial 0.81 0.0203 0.60 0.0068 no Q64442 ENSMUSG00000027227 Sord sorbitol dehydrogenase 0.68 0.0629 0.63 0.0108 yes Q64105 ENSMUSG00000033735 Spr sepiapterin reductase 0.67 0.0762 0.87 0.0068 yes Q9WUM5 ENSMUSG00000052738 Suclg1 succinyl-CoA ligase [GDP-forming] subunit alpha, mitochondrial 0.64 0.0855...”
• Identification and quantification of the basal and inducible Nrf2-dependent proteomes in mouse liver: biochemical, pharmacological and toxicological implications.
  Walsh, Journal of proteomics 2014
  • “...ATP-dependent dihydroxyacetone kinase/FAD-AMP lyase (cyclizing) 77 1.60 0.039 P24472 Glutathione S-transferase A4 8 1.58 0.003 Q64442 Sorbitol dehydrogenase 36 1.58 <0.001 Q64458 Cytochrome P450 2C29 26 1.56 0.029 P52760 Ribonuclease UK114 35 1.55 <0.001 O70570 Polymeric immunoglobulin receptor 3 1.55 <0.001 Q9EQK5 Major vault protein 14...”
• Renal proteome in mice with different susceptibilities to fluorosis
  Carvalho, PloS one 2013
  • “...dehydrogenase [NADP+] 38/7.51 36.5/6.9 17/775 129(0.049) Q9JII6 Metabolism 189 Sorbitol dehydrogenase 40.5/6.885 38.2/6.6 13/853 129(0.041) Q64442 Metabolism 209 Isovaleryl-CoA dehydrogenase, mitochondrial 42.5/6.6 43/6.3 12/535 129(0.000) Q9JHI5 Metabolism 233 Ornithine aminotransferase, mitochondrial 45/5.72 45.8/5.7 10/255 129(0.024) P29758 Metabolism 237 Creatine kinase U-type, mitochondrial 45/8.05 43.2/7.3 9/133 129(0.033)...”
  • “...oxidase 2 37/8.1 38.7/7.6 11/529 129(0.003) Q9NYQ2 Metabolism 184 Sorbitol dehydrogenase 40.5/6.805 38.2/6.56 10/586 129(0.003) Q64442 Metabolism 210 Aminoacylase-1 42.5/5.92 45.8/5.9 18/831 129(0.006) Q99JW2 Metabolism 217/221 Medium-chain specific acyl-CoA dehydrogenase, mitochondrial 41.5/8.22 43.6/7.69 15/715 129(0.009) P45952 Metabolism 269 Homogentisate 1,2-dioxygenase 49/7.41 50/6.85 6/105 129(0.002) O09173 Metabolism...”
• More
• Natural antioxidant flavonoids in formalin-induced mice paw inflammation; inhibition of mitochondrial sorbitol dehydrogenase activity.
  Mohammad, Journal of biochemical and molecular toxicology 2017 (PubMed)
  • GeneRIF: flavonoids induced marked improvement in paw licking time, paw edema %, malondialdehyde content, superoxide dismutase, and sorbitol dehydrogenase activities, with slight progress in paw interlukin-1beta. Additionally, silymarin augmented brain content of dopamine and norepinephrine.
• Protein profile screening: reduced expression of Sord in the mouse epididymis induced by nicotine inhibits tyrosine phosphorylation level in capacitated spermatozoa.
  Dai, Reproduction (Cambridge, England) 2016 (PubMed)
  • GeneRIF: Nicotine-induced reduced expression of Sord could be involved in impaired secretory functions of the epididymis.
• Caloric restriction counteracts age-related changes in the activities of sorbitol metabolizing enzymes from mouse liver.
  Hagopian, Biogerontology 2009
  • GeneRIF: Caloric restriction counteracts age-related changes in the activities of sorbitol metabolizing enzymes from mouse liver.
• ZAC1 is up-regulated by hypertonicity and decreases sorbitol dehydrogenase expression, allowing accumulation of sorbitol in kidney cells.
  Lanaspa, The Journal of biological chemistry 2009
  • GeneRIF: The zinc-finger protein ZAC1 is up-regulated under hypertonic stress and negatively regulates expression of sorbitol dehydrogenase, allowing for accumulation of sorbitol as a compatible organic osmolyte.
• Redox state-dependent and sorbitol accumulation-independent diabetic albuminuria in mice with transgene-derived human aldose reductase and sorbitol dehydrogenase deficiency.
  Ii, Diabetologia 2004 (PubMed)
  • GeneRIF: Knockout mice had the highest sorbitol content among various genetic types including mice wwith human aldose reductase.

DHSO_BOVIN / Q58D31 Sorbitol dehydrogenase; SDH; L-iditol 2-dehydrogenase; Polyol dehydrogenase; Xylitol dehydrogenase; XDH; EC 1.1.1.-; EC 1.1.1.14; EC 1.1.1.9 from Bos taurus (Bovine) (see paper)
40% identity, 96% coverage

• function: Polyol dehydrogenase that catalyzes the reversible NAD(+)- dependent oxidation of various sugar alcohols. Is mostly active with xylitol, D-sorbitol (D-glucitol) and L-iditol as substrates, leading to the C2-oxidized products D-xylulose, D-fructose and L-sorbose, respectively (PubMed:9143345). Is a key enzyme in the polyol pathway that interconverts glucose and fructose via sorbitol, which constitutes an important alternate route for glucose metabolism. May play a role in sperm motility by using sorbitol as an alternative energy source for sperm motility (By similarity). Cannot use NADP(+) as the electron acceptor. Has no activity on ethanol, methanol, glycerol, galactitol and fructose 6-phosphate (PubMed:9143345).
  catalytic activity: xylitol + NAD(+) = D-xylulose + NADH + H(+) (RHEA:20433)
  catalytic activity: keto-D-fructose + NADH + H(+) = D-sorbitol + NAD(+) (RHEA:33031)
  catalytic activity: L-iditol + NAD(+) = keto-L-sorbose + NADH + H(+) (RHEA:10160)
  cofactor: Zn(2+) (Binds 1 zinc ion per subunit.)
  subunit: Homotetramer.

XP_004010700 sorbitol dehydrogenase from Ovis aries
40% identity, 96% coverage

• X-ray crystal structure and small-angle X-ray scattering of sheep liver sorbitol dehydrogenase.
  Yennawar, Acta crystallographica. Section D, Biological crystallography 2011
  • GeneRIF: The X-ray crystal structure of sheep liver sorbitol dehydrogenase has been determined using the crystal structure of human sorbitol dehydrogenase (hSDH) as a molecular-replacement model.
• Catalytic mechanism of Zn2+-dependent polyol dehydrogenases: kinetic comparison of sheep liver sorbitol dehydrogenase with wild-type and Glu154-->Cys forms of yeast xylitol dehydrogenase.
  Klimacek, The Biochemical journal 2007
  • GeneRIF: Results compare the catalytic mechanism of sheep liver sorbitol dehydrogenase with wild-type and Glu154-->Cys forms of yeast xylitol dehydrogenase.

3qe3A / P07846 Sheep liver sorbitol dehydrogenase (see paper)
40% identity, 97% coverage

• Ligands: zinc ion; glycerol (3qe3A)

NP_001280132 sorbitol dehydrogenase from Gallus gallus
40% identity, 96% coverage

• Steady-state kinetic properties of sorbitol dehydrogenase from chicken liver.
  Karacaoğlan, Comparative biochemistry and physiology. Part B, Biochemistry & molecular biology 2005 (PubMed)
  • GeneRIF: steady-state kinetic properties of partially purified chicken liver sorbitol dehydrogenase (SDH) were determined spectrophotometrically
  • GeneRIF: Comparison of assayed steady-state constants of chicken SORD with previously published steady-state constants of human, sheep, bovine, and horse SORDs.
  • GeneRIF: Authors discuss differences in steady-state kinetics of chicken SORD and some mammalian species, with respect to changes in experimental pH and temperature
• Bacterial endotoxins and the pathogenesis of fatty liver--haemorrhagic syndrome in the laying hen.
  Pearson, Research in veterinary science 1981 (PubMed)
  • GeneRIF: fatty liver-haemorrhagic syndrome caused by a high energy maize diet for layers is associated with low SDH activity

V9HW89 Sorbitol dehydrogenase from Homo sapiens
41% identity, 92% coverage

• Urinary protein biomarkers based on LC-MS/MS analysis to discriminate vascular dementia from Alzheimer's disease in Han Chinese population
  Chen, Frontiers in aging neuroscience 2023
  • “...OX=9,606 GN=NARS1 PE=1 SV=1 K01893 NARS, asnS 2.224 1.153 0.01706 up 1.732 0.7924 0.02091 up V9HW89 Epididymis secretory sperm binding protein Li 95n OS=Homo sapiens OX=9,606 GN=HEL-S-95n PE=2 SV=1 K00008 SORD, gutB 6.035 2.593 0.01929 up 2.758 1.464 0.01519 up Q99816 Tumor susceptibility gene 101 protein...”
  • “...Q4JM47 AGR2 OS=Homo sapiens OX=9,606 GN=AGR2 PE=4 SV=1 K20356 AGR2 0.645 0.107 0.124 0.435 0.856 V9HW89 Epididymis secretory sperm binding protein Li 95n OS=Homo sapiens OX=9,606 GN=HEL-S-95n PE=2 SV=1 K00008 SORD, gutB 0.652 0.104 0.107 0.448 0.857 A0A5C2GLK7 IG c58_heavy_IGHV3-23_IGHD5-18_IGHJ4 (Fragment) OS=Homo sapiens OX=9,606 PE=2 SV=1...”
• Quantitative Phosphoproteomic Comparison of Lens Proteins in Highly Myopic Cataract and Age-Related Cataract.
  Zhang, BioMed research international 2021
  • “...ARC-C Actin, cytoplasmic 1 ACTA2 P60709 111.6 _GYS(ph)FTTTAER_ 199 NaN 0.006 Alcohol dehydrogenase 1A ADH1A V9HW89 93.73 _SGGTLVLVGLGS(ph)EMTTVPLLHAAIR_ 277 NaN 0.024 Alcohol dehydrogenase 1A ADH1A V9HW89 82.89 _EIGADLVLQISKES(ph)PQEIAR_ 228 NaN 0.001 Alcohol dehydrogenase 1A ADH1A V9HW89 105.8 _S(ph)GGTLVLVGLGSEMTTVPLLHAAIR_ 266 NaN 0.001 Cysteine protease ATG4D B4DZK0 64.3...”
  • “...E7EX29 55.885 _DICNDVLS(ph)LLEK_ 99 NaN 0.003 Phosphosites exclusively detected in ARC-C Alcohol dehydrogenase 1A ADH1A V9HW89 124.19 _AMGAAQVVVTDLSATRLS(ph)K_ 211 NaN 0.048 Alcohol dehydrogenase 2A ADH1A V9HW89 82.885 _EIGADLVLQISKES(ph)PQEIAR_ 228 NaN 0.001 Carbonyl reductase (NADPH) 1 CBR1 P16152 75.462 _LFS(ph)GDVVLTAR_ 30 NaN 0.001 Alpha-crystallin B chain CRYAA...”

1pl6A / Q00796 Human sdh/nadh/inhibitor complex (see paper)
41% identity, 93% coverage

• Ligands: zinc ion; nicotinamide-adenine-dinucleotide; 4-[2-(hydroxymethyl)pyrimidin-4-yl]-n,n-dimethylpiperazine-1-sulfonamide (1pl6A)

DHSO_HUMAN / Q00796 Sorbitol dehydrogenase; SDH; (R,R)-butanediol dehydrogenase; L-iditol 2-dehydrogenase; Polyol dehydrogenase; Ribitol dehydrogenase; RDH; Xylitol dehydrogenase; XDH; EC 1.1.1.-; EC 1.1.1.4; EC 1.1.1.14; EC 1.1.1.56; EC 1.1.1.9 from Homo sapiens (Human) (see 8 papers)
NP_003095 sorbitol dehydrogenase from Homo sapiens
41% identity, 92% coverage

• function: Polyol dehydrogenase that catalyzes the reversible NAD(+)- dependent oxidation of various sugar alcohols. Is mostly active with D- sorbitol (D-glucitol), L-threitol, xylitol and ribitol as substrates, leading to the C2-oxidized products D-fructose, L-erythrulose, D- xylulose, and D-ribulose, respectively (PubMed:3365415). Is a key enzyme in the polyol pathway that interconverts glucose and fructose via sorbitol, which constitutes an important alternate route for glucose metabolism. The polyol pathway is believed to be involved in the etiology of diabetic complications, such as diabetic neuropathy and retinopathy, induced by hyperglycemia (PubMed:12962626, PubMed:25105142, PubMed:29966615). May play a role in sperm motility by using sorbitol as an alternative energy source for sperm motility (PubMed:16278369). May have a more general function in the metabolism of secondary alcohols since it also catalyzes the stereospecific oxidation of (2R,3R)-2,3-butanediol. To a lesser extent, can also oxidize L-arabinitol, galactitol and D-mannitol and glycerol in vitro. Oxidizes neither ethanol nor other primary alcohols. Cannot use NADP(+) as the electron acceptor (PubMed:3365415).
  catalytic activity: keto-D-fructose + NADH + H(+) = D-sorbitol + NAD(+) (RHEA:33031)
  catalytic activity: L-threitol + NAD(+) = L-erythrulose + NADH + H(+) (RHEA:48760)
  catalytic activity: xylitol + NAD(+) = D-xylulose + NADH + H(+) (RHEA:20433)
  catalytic activity: ribitol + NAD(+) = D-ribulose + NADH + H(+) (RHEA:20053)
  catalytic activity: (R,R)-butane-2,3-diol + NAD(+) = (R)-acetoin + NADH + H(+) (RHEA:24340)
  catalytic activity: L-iditol + NAD(+) = keto-L-sorbose + NADH + H(+) (RHEA:10160)
  cofactor: Zn(2+) (Binds 1 zinc ion per subunit.)
  subunit: Homotetramer.
• Sugar alcohol degradation in Archaea: uptake and degradation of mannitol and sorbitol in Haloarcula hispanica
  Ortjohann, Extremophiles : life under extreme conditions 2024
  • “...involved in binding of sorbitol in RnSorDH are conserved in HhSorDH (). UniProt accession: HsSorDH, Q00796; OaSorDH, P07846; RnSorDH, P27867; BsSorDH, Q06004; LrMtlDH, Q6ECH5; LpMtlDH, Q83VI5; TbMtlDH, Q1ACW3; HhSorDH, G0I050; HhMtlDH, G0I059 Besides sorbitol and mannitol dehydrogenases (Riveros-Rosas et al. 2003 ; Ceccaroli et al. 2007...”
  • “...M. musculus , Q64442; R. norvegicus , P27867; O. aries , P07846; H. sapiens , Q00796; H. gibbonsii , M0HN94; H. rarus , WP_256422950.1; H. marismortui , Q5V6U8; MtlDH: H. hispanica , G0I059; H. marismortui , Q5V6V7; T. borchii , Q1ACW3; L. mesenteroides , Q8KQG6; L....”
• Polymorphism Pro64His within galectin-3 has functional consequences at proteome level in thyroid cells.
  Silvestri, Frontiers in genetics 2024
  • “...564.65 0.3 1,131 P11766 ADH5 5 2 39,724 7.45 2.59E-04 5.1 84.44 64.88 1.3 1,134 Q00796 SORD 20 5 38,325 8.25 0.019 3.2 9.34 8.39 1.1 1,134 Q14103 HNRNPD 9 2 36,272 8.14 0.019 3.2 77.72 102.13 0.8 1,138 P07910 HNRNPC 7 2 32,338 4.94 0.002...”
• Plasma Proteomic Risk Markers of Incident Type 2 Diabetes Reflect Physiologically Distinct Components of Glucose-Insulin Homeostasis.
  Cronjé, Diabetes 2023
• Characterization of human oxidoreductases involved in aldehyde odorant metabolism.
  Boichot, Scientific reports 2023
  • “...0) Aldoketo reductase family 1 member C2 (AKR1C2) P52895 12 (23, 19, 0) Sorbitol dehydrogenase Q00796 10 (15, 21, 1) Aldoketo reductase family 1 member C3(AKR1C3) P42330 9 (17, 16, 0) Biliverdin reductase A P53004 11 (13, 15, 1) Alcohol dehydrogenase 1B (ADH1B) P00325 16 (17,...”
• Human amygdala involvement in Alzheimer's disease revealed by stereological and dia-PASEF analysis.
  Gonzalez-Rodriguez, Brain pathology (Zurich, Switzerland) 2023
  • “...1.62 0.0016 P20073 ANXA7_HUMAN ANXA7 Annexin A7 1.62 0.0309 O75223 GGCT_HUMAN GGCT Gammaglutamylcyclotransferase 1.62 0.0402 Q00796 DHSO_HUMAN SORD Sorbitol dehydrogenase 1.62 0.0153 P49189 AL9A1_HUMAN ALDH9A1 4trimethylaminobutyraldehyde dehydrogenase 1.62 0.0056 O14807 RASM_HUMAN MRAS Rasrelated protein MRas 1.61 0.0455 P30626 SORCN_HUMAN SRI Sorcin 1.61 0.0493 Q9BQA1 MEP50_HUMAN WDR77...”
• Global and Comparative Proteome Signatures in the Lens Capsule, Trabecular Meshwork, and Iris of Patients With Pseudoexfoliation Glaucoma
  Sahay, Frontiers in molecular biosciences 2022
  • “...2.7495566 6 Q15262 Receptor-type tyrosine-protein phosphatase kappa (PTPRK) 2.6854224 7 P01040 Cystatin-A (CSTA) 2.6790833 8 Q00796 Sorbitol dehydrogenase (SORD) 2.5792797 PXG, pseudoexfoliation glaucoma; PXF, pseudoexfoliation syndrome. The identified proteins described in Table 3 which were overexpressed/underexpressed were subjected to functional enrichment protein analysis through the FunRich...”
• Multi-Omics Analysis Revealed a Significant Alteration of Critical Metabolic Pathways Due to Sorafenib-Resistance in Hep3B Cell Lines
  Abushawish, International journal of molecular sciences 2022
  • “...1.74 10 6 1.015660763 Decreased P04179 7.79 10 5 1.049084345 Increased Q9P035 0.003254458 1.252471606 Increased Q00796 0.000258132 1.474272092 Increased O60701 4.02 10 13 2.068751653 Increased P09936 2.41 10 10 2.986876806 Increased...”
• Ellagic Acid Triggers the Necrosis of Differentiated Human Enterocytes Exposed to 3-Nitro-Tyrosine: An MS-Based Proteomic Study
  Díaz-Velasco, Antioxidants (Basel, Switzerland) 2022
  • “...reversible NAD + -dependent oxidation of sugar alcohols, a key enzyme in the polyol pathway Q00796 Proteasome subunit beta type 3 PSMB3 0.008 1.55 Non-catalytic component of proteasome complex involved in the proteolytic degradation of most intracellular proteins P49720 Proteasome subunit alpha type 6 PSMA6 9.00...”
• More
• Hereditary polyneuropathy with conduction block associated with SORD mutation in three siblings.
  Kabeloglu, Acta neurologica Belgica 2024 (PubMed)
  • GeneRIF: Hereditary polyneuropathy with conduction block associated with SORD mutation in three siblings.
• Expanding the genetic and clinical spectrum of SORD-related peripheral neuropathy by reporting a novel variant c.210T>G and evidence of subclinical muscle involvement.
  Li, Journal of the peripheral nervous system : JPNS 2023 (PubMed)
  • GeneRIF: Expanding the genetic and clinical spectrum of SORD-related peripheral neuropathy by reporting a novel variant c.210T>G and evidence of subclinical muscle involvement.
• Association of SORD mutation with autosomal recessive asymmetric distal hereditary motor neuropathy.
  Alluqmani, BMC medical genomics 2022
  • GeneRIF: Association of SORD mutation with autosomal recessive asymmetric distal hereditary motor neuropathy.
• Evaluation of SORD mutations as a novel cause of Charcot-Marie-Tooth disease.
  Yuan, Annals of clinical and translational neurology 2021
  • GeneRIF: Evaluation of SORD mutations as a novel cause of Charcot-Marie-Tooth disease.
• Biallelic variants in the SORD gene are one of the most common causes of hereditary neuropathy among Czech patients.
  Laššuthová, Scientific reports 2021
  • GeneRIF: Biallelic variants in the SORD gene are one of the most common causes of hereditary neuropathy among Czech patients.
• Polymorphisms in Sorbitol-Aldose Reductase (Polyol) Pathway Genes and Their Influence on Risk of Diabetic Retinopathy Among Han Chinese.
  Li, Medical science monitor : international medical journal of experimental and clinical research 2019
  • GeneRIF: ALR2 rs759853 and SDH rs2055858 polymorphisms were respectively associated with a higher and lower risk of diabetic retinopathy.
• Osmotic expression of aldose reductase in retinal pigment epithelial cells: involvement of NFAT5.
  Winges, Graefe's archive for clinical and experimental ophthalmology = Albrecht von Graefes Archiv fur klinische und experimentelle Ophthalmologie 2016 (PubMed)
  • GeneRIF: SDH gene expression was increased by hypoxia and oxidative stress, but not extracellular hyperosmolarity. Hyperosmolarity and hypoxia did not alter the SDH protein level.
• Sorbitol dehydrogenase overexpression and other aspects of dysregulated protein expression in human precancerous colorectal neoplasms: a quantitative proteomics study.
  Uzozie, Molecular & cellular proteomics : MCP 2014
  • GeneRIF: One of the most striking changes involved sorbitol dehydrogenase, a key enzyme in the polyol pathway. Validation studies revealed dramatically increased sorbitol dehydrogenase concentrations and activity in adenomas and cancer cell lines, along with important changes in the expression of other enzymes in the same (AKR1B1) and related (KHK) pathways.
• More

DHSO_CHICK / P0DMQ6 Sorbitol dehydrogenase; SDH; Polyol dehydrogenase; EC 1.1.1.- from Gallus gallus (Chicken) (see paper)
40% identity, 96% coverage

• function: Polyol dehydrogenase that catalyzes the reversible NAD(+)- dependent oxidation of various sugar alcohols. Is active with D- sorbitol (D-glucitol) as substrate, leading to the C2-oxidized product D-fructose (PubMed:15649778). Is a key enzyme in the polyol pathway that interconverts glucose and fructose via sorbitol, which constitutes an important alternate route for glucose metabolism (By similarity).
  catalytic activity: keto-D-fructose + NADH + H(+) = D-sorbitol + NAD(+) (RHEA:33031)
  cofactor: Zn(2+) (Binds 1 zinc ion per subunit.)
  subunit: Homotetramer.

W5QIT0 Sorbitol dehydrogenase from Ovis aries
40% identity, 95% coverage

• Comparative Proteomic Identification of Ram Sperm before and after In Vitro Capacitation
  Chen, Animals : an open access journal from MDPI 2024
  • “...13 1.74 10 5 3.02 W5PD71 CRP 25.27 251.4 33.5 7 3.57 10 5 2.83 W5QIT0 SORD 38.27 168.92 40.2 15 0.001724 2.56 W5PTV7 ACE 138.23 229.67 17 21 8.97 10 7 2.55 animals-14-02363-t004_Table 4 Table 4 Major differential proteins related to ram sperm capacitation in...”

XYL2_YEAST / Q07993 D-xylulose reductase; Xylitol dehydrogenase; XDH; EC 1.1.1.9 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see paper)
Q07993 D-xylulose reductase (EC 1.1.1.9) from Saccharomyces cerevisiae (see paper)
YLR070C Xyl2p from Saccharomyces cerevisiae
40% identity, 96% coverage

• catalytic activity: xylitol + NAD(+) = D-xylulose + NADH + H(+) (RHEA:20433)
  cofactor: Zn(2+) (Binds 1 zinc ion per subunit.)
• Molecular evolutionary insight of structural zinc atom in yeast xylitol dehydrogenases and its application in bioethanol production by lignocellulosic biomass
  Yoshiwara, Scientific reports 2023
  • “...the pentose-phosphate pathway. Although S. cerevisiae possesses the endogenous oxidoreductase pathway consisting of YHR104w (GRE3), YLR070c (XYL2), and YGR194c (XKS1; XK) as XR, XDH, and XK, respectively, the rate of D-xylose metabolism by strains overexpressing them has not yet reached industrially competitive levels 8 . Alternatively,...”
  • “...of four cysteine ligands for structural zinc in ScXDH As described in Introduction , the YLR070c protein from S. cerevisiae (45% sequence homology with PsXDH; Fig. 1 b) functions as XDH in the endogenous d -xylose pathway 8 , 25 , and possessed none of the...”
• Horizontal and vertical growth of S. cerevisiae metabolic network
  Grassi, BMC evolutionary biology 2011
  • “...0 N/A 0.68 2.2 -16 YDL080C YDR380W Y Y Y 0.67 0 0.08 0.033 YDL246C YLR070C Y Y Y N/A 0 N/A N/A YDR147W YLR133W Y Y N 0 0.5 0.09 0.02 YDR380W YGR087C Y Y Y 0.54 0 -0.07 0.065 YDR380W YLR044C Y Y Y...”
  • “...N/A 0.25 7.6 -11 YHR123W YNL130C Y Y Y 0 0 0.50 2.2 -16 YJR159W YLR070C Y Y Y N/A 0 0.38 2.2 -16 Only pairs identified as paralogs by at least by two paralogy definitions (Need: sequence identity above 30%; Ens: derived from the Ensembl...”
• On the formalization and reuse of scientific research
  King, Journal of the Royal Society, Interface 2011
  • “...0.038 0 n.a. YDL168W 0.018 0 0.024 0 n.a. YJL045W 0.016 0 0 0 n.a. YLR070C 0.012 0 0.019 0 Figure2. ( a ) The histogram shows the median observed differences in the growth rate of a knockout strain (k) and that of the wild-type (w)...”
• Saccharomyces cerevisiae signature genes for predicting nitrogen deficiency during alcoholic fermentation
  Mendes-Ferreira, Applied and environmental microbiology 2007
  • “...YMR175w YGL208w YGR248w YBL106c YLR178c YBR006w YIL101c YLR070c YCR061w YLR272c YDL218w YDR271c YGR043c YLR312c YMR090w YMR206w YNL115c YNL194c YNL195c ALP1...”
• The Ccr4-Not complex independently controls both Msn2-dependent transcriptional activation--via a newly identified Glc7/Bud14 type I protein phosphatase module--and TFIID promoter distribution
  Lenssen, Molecular and cellular biology 2005
  • “...Berkeley YOR135C YGR101W YEL070W YML087C YGR110W YLR116W YLR070C YER096W YHR211W YDR497C YML120C YKR052C YBR280C YBL075C YNL125C YJL225C YPR026W YDL078C YCLX05C...”
• A two-hybrid screen of the yeast proteome for Hsp90 interactors uncovers a novel Hsp90 chaperone requirement in the activity of a stress-activated mitogen-activated protein kinase, Slt2p (Mpk1p)
  Millson, Eukaryotic cell 2005
  • “...2 3 1 1 1 1 1 2 YOR332w YOR083w YLR070c YJL114w VMA4 WHI5 XYL2 YJL114w 2 2 2 1 Function of gene productb Histidyl-tRNA synthetase, mitochondrial and cytoplasmic...”
• Endogenous xylose pathway in Saccharomyces cerevisiae
  Toivari, Applied and environmental microbiology 2004
  • “...for a nonspecific aldose reductase, and XYL2 (YLR070c, ScXYL2), coding for a xylitol dehydrogenase (XDH), are overexpressed under endogenous promoters. In...”
  • “...encoding XDH, XYL2 of P. stipitis. Open reading frame YLR070c encodes an enzyme with XDH activity (referred to here as ScXYL2 and ScXDH, respectively) (32). The...”
• Molecular analysis of a Saccharomyces cerevisiae mutant with improved ability to utilize xylose shows enhanced expression of proteins involved in transport, initial xylose metabolism, and the pentose phosphate pathway
  Wahlbom, Applied and environmental microbiology 2003
  • “...encoding enzymes with XR (YHR104w) (9) and XDH (YLR070c) (19) activities was analyzed. These two genes showed slightly increased expression during growth on...”
  • “...3400 Xylose (TMB 3400) Xylose metabolism YHR104W YLR070C YGR194C Pentose phosphate pathway YNL241C YHR163W HXT4 HXT5 HXT7 GAL2 High-affinity glucose transporter...”
• More

DHSO_SHEEP / P07846 Sorbitol dehydrogenase; SDH; L-iditol 2-dehydrogenase; Polyol dehydrogenase; Xylitol dehydrogenase; XDH; EC 1.1.1.-; EC 1.1.1.14; EC 1.1.1.9 from Ovis aries (Sheep) (see 3 papers)
39% identity, 96% coverage

• function: Polyol dehydrogenase that catalyzes the reversible NAD(+)- dependent oxidation of various sugar alcohols. Is mostly active with xylitol, L-iditol and D-sorbitol (D-glucitol) as substrates, leading to the C2-oxidized products D-xylulose, L-sorbose and D-fructose, respectively (PubMed:1459146). Is a key enzyme in the polyol pathway that interconverts glucose and fructose via sorbitol, which constitutes an important alternate route for glucose metabolism (By similarity). May play a role in sperm motility by using sorbitol as an alternative energy source for sperm motility (By similarity).
  catalytic activity: xylitol + NAD(+) = D-xylulose + NADH + H(+) (RHEA:20433)
  catalytic activity: L-iditol + NAD(+) = keto-L-sorbose + NADH + H(+) (RHEA:10160)
  catalytic activity: keto-D-fructose + NADH + H(+) = D-sorbitol + NAD(+) (RHEA:33031)
  cofactor: Zn(2+) (Binds 1 zinc ion per subunit.)
  subunit: Homotetramer.
• Sugar alcohol degradation in Archaea: uptake and degradation of mannitol and sorbitol in Haloarcula hispanica
  Ortjohann, Extremophiles : life under extreme conditions 2024
  • “...binding of sorbitol in RnSorDH are conserved in HhSorDH (). UniProt accession: HsSorDH, Q00796; OaSorDH, P07846; RnSorDH, P27867; BsSorDH, Q06004; LrMtlDH, Q6ECH5; LpMtlDH, Q83VI5; TbMtlDH, Q1ACW3; HhSorDH, G0I050; HhMtlDH, G0I059 Besides sorbitol and mannitol dehydrogenases (Riveros-Rosas et al. 2003 ; Ceccaroli et al. 2007 ), the...”
  • “...B. argentifolii , O96496; M. musculus , Q64442; R. norvegicus , P27867; O. aries , P07846; H. sapiens , Q00796; H. gibbonsii , M0HN94; H. rarus , WP_256422950.1; H. marismortui , Q5V6U8; MtlDH: H. hispanica , G0I059; H. marismortui , Q5V6V7; T. borchii , Q1ACW3; L....”

A0A3S7PMC4 D-xylulose reductase (EC 1.1.1.9) from Torulaspora delbrueckii (see paper)
41% identity, 93% coverage

HAH_5138 NAD(P)-dependent alcohol dehydrogenase from Haloarcula hispanica ATCC 33960
G0I050 Zn-dependent oxidoreductase / NADPH2:quinone reductase from Haloarcula hispanica (strain ATCC 33960 / DSM 4426 / JCM 8911 / NBRC 102182 / NCIMB 2187 / VKM B-1755)
43% identity, 100% coverage

• Sugar alcohol degradation in Archaea: uptake and degradation of mannitol and sorbitol in Haloarcula hispanica
  Ortjohann, Extremophiles : life under extreme conditions 2024
  • “...which allows selection and counterselection in DF60. Deletion mutants of the following genes were generated: HAH_5138 ( mscS ), HAH_5147 ( mscM ), HAH_1078 ( khk ), HAH_1077 ( fruK ), HAH_1079 ( fbaB1 ), HAH_5148 ( mscR ), HAH_5146 ( mscE ), and HAH_1560 (...”
  • “...gfcR ). Overexpression and purification of enzymes Genes encoding putative sorbitol dehydrogenase ( mscS ; HAH_5138), mannitol dehydrogenase ( mscM ; HAH_5147), fructose-1-phosphate kinase ( fruK ; HAH_1077), and fructose-1,6-bisphosphate aldolase ( fbaB1 ; HAH_1079) from H. hispanica , and the ketohexokinase gene ( khk ;...”
• Sugar alcohol degradation in Archaea: uptake and degradation of mannitol and sorbitol in Haloarcula hispanica
  Ortjohann, Extremophiles : life under extreme conditions 2024
  • “...HsSorDH, Q00796; OaSorDH, P07846; RnSorDH, P27867; BsSorDH, Q06004; LrMtlDH, Q6ECH5; LpMtlDH, Q83VI5; TbMtlDH, Q1ACW3; HhSorDH, G0I050; HhMtlDH, G0I059 Besides sorbitol and mannitol dehydrogenases (Riveros-Rosas et al. 2003 ; Ceccaroli et al. 2007 ), the PDH family contains various different dehydrogenase subfamilies, such as archaeal glucose dehydrogenase...”
  • “...formaldehyde dehydrogenase. UniProtaccession: SorDH: B. subtilis , Q06004; S. cerevisiae , P35497; H. hispanica , G0I050; B. argentifolii , O96496; M. musculus , Q64442; R. norvegicus , P27867; O. aries , P07846; H. sapiens , Q00796; H. gibbonsii , M0HN94; H. rarus , WP_256422950.1; H. marismortui...”

Q5V6U8 NAD(P)-dependent alcohol dehydrogenase from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
43% identity, 100% coverage

• Sugar alcohol degradation in Archaea: uptake and degradation of mannitol and sorbitol in Haloarcula hispanica
  Ortjohann, Extremophiles : life under extreme conditions 2024
  • “...H. sapiens , Q00796; H. gibbonsii , M0HN94; H. rarus , WP_256422950.1; H. marismortui , Q5V6U8; MtlDH: H. hispanica , G0I059; H. marismortui , Q5V6V7; T. borchii , Q1ACW3; L. mesenteroides , Q8KQG6; L. pseudomesenteroides , Q83VI5; L. reuteri , Q6ECH5; H. gibbonsii , M0H624; H....”

LOC103960512 sorbitol dehydrogenase from Pyrus x bretschneideri
42% identity, 86% coverage

• QTL mapping and transcriptome analysis of sugar content during fruit ripening of Pyrus pyrifolia
  Jiang, Frontiers in plant science 2023
  • “...A weighted gene co-expression network analysis showed that two genes, sorbitol dehydrogenase ( PpSDH , LOC103960512 and LOC103960513), around the locus of qSugar-LG6-Chr7 were negatively co-expressed with the total sugar content, which was downregulated in the sweet cultivars. PpSDH and PpSUT may play important roles in...”
  • “...SAUR32 (LOC103951601) was also upregulated in sweet cultivars. Two genes, sorbitol dehydrogenase ( PpSDH , LOC103960512 and LOC103960513), were observed in the MEturquoise module. Their expression was negatively related to fructose content, which was downregulated in the sweet cultivars. The Dof zinc finger protein DOF3.7 (LOC103951625)...”

LOC103333266 sorbitol dehydrogenase from Prunus mume
42% identity, 89% coverage

• Analysis of Metabolites and Gene Expression Changes Relative to Apricot (Prunus armeniaca L.) Fruit Quality During Development and Ripening
  García-Gómez, Frontiers in plant science 2020
  • “...in the skin ( Xi etal., 2016 ; Zhang etal., 2019 ). Thus, SDH [ LOC103333266 ( PARG19420m03 )], described as a possible key factor during climacteric ripening in Japanese plum ( Fernandez i Marti etal., 2018 ), and SS [ LOC103340632 ( PARG27579m02 )] described...”

NAD-SDH / Q9ZR22 D-sorbitol dehydrogenase (EC 1.1.1.14) from Malus domestica (see paper)
41% identity, 88% coverage

Q9MBD7 NAD-dependent sorbitol dehydrogenase from Prunus persica
LOC18787602 sorbitol dehydrogenase from Prunus persica
41% identity, 89% coverage

• Transcriptomic and metabolite analyses of Cabernet Sauvignon grape berry development.
  Deluc, BMC genomics 2007
  • “...metabolism 16 11.07 1616255_at CF516475 TC57339 O82616 Fructokinase Carbohydrate metabolism 12 10.13 1612918_at CB972844 TC52651 Q9MBD7 NAD-dependent sorbitol dehydrogenase Carbohydrate metabolism 2 9.14 1608393_at CF403620 TC64860 O22658 ADP-glucose pyrophosphorylase Carbohydrate metabolism 7 8.79 1621067_at CF511425 TC51908 Q8W3C8 Glucose acyltransferase Carbohydrate metabolism 3 8.2 1612883_at CB911656 TC60606...”
• Effects of exogenous melatonin on sugar and organic acid metabolism in early-ripening peach fruits
  Zhou, PloS one 2023
  • “...ACCACAACTCACATTCCAGCA LOC18788228 PpNI NI F: TTCACCGCAGCCGAAATTG R: GTCGTCTTGCAAACCCTAGTC LOC18784736 PpAI AI F: TTGGAGACGTCCGCTAATGG R: CGGGTCATCAGGTATCCACG LOC18787602 PpSDH SDH F: GAAAACATGGCTGCTTGGCT R: CATCACTTCCGCATATCCCAAC LOC18779761 PpNADPME1 NADPME F: GCGTAGTGATGGAGAGCACA R: CTCGGTGGCAGTATCCTCAC LOC18788358 PpMDH1 MDH F: ACCAATGATCGCAAGGGGAGT R: GGAAAGCAGCATCGACCAACT LOC110755472 PpCS1 CS F: TTGTGAAGCAGCGTCTTGGC R: AAGCTCAATGTCGATCCAAGCC LOC18790559 PpPEPC1 PEPC...”

Q3C2L6 L-iditol 2-dehydrogenase (EC 1.1.1.14) from Solanum lycopersicum (see paper)
41% identity, 92% coverage

• Lignin metabolism involves Botrytis cinerea BcGs1- induced defense response in tomato
  Yang, BMC plant biology 2018
  • “...chain 1, chloroplastic 0.72863624 0.025037 P05349 Ribulose bisphosphate carboxylase small chain 3B, chloroplastic 0.701040127 0.005291 Q3C2L6 Sorbitol related enzyme 0.703582864 0.005221 K4CIE2 Peptidyl-prolyl cis-trans isomerase 0.76180139 0.019223 K4CAM3 Photosystem I reaction center subunit IV B, chloroplastic 0.766668988 0.008467 K4CJ02 Photosystem I reaction center subunit N, chloroplastic...”

LOC107448906 sorbitol dehydrogenase from Parasteatoda tepidariorum
35% identity, 96% coverage

• Microarray data on the comparison of transcript expression between normal and Pt-Delta RNAi embryos in the common house spider Parasteatoda tepidariorum
  Oda, Data in brief 2019
  • “...LOC107448180 0.598 eS7_SB_018_G10* end eS7_002_F12 5636 FY376729 g2859 LOC107449611 0.588 eS7_002_F12* eS7_006_B01 7269 FY377014 g15364 LOC107448906 0.598 eS7_SB_046_H04* end eS7_008_B09 6413 FY377193 g7446 LOC107444045 0.597 eS7_008_B09* end eS7_012_A12 11123 FY377551 g3860 LOC107451189 0.570 eS7_012_A12* end eS7_012_C04 6762 FY377567 g9240 LOC107445106 0.512 eS7_SB_007_G10* end eS7_012_F02 12018 FY377596...”

Q5I6M4 L-iditol 2-dehydrogenase (EC 1.1.1.14) from Malus domestica (see paper)
41% identity, 88% coverage

DHSO_ARATH / Q9FJ95 Sorbitol dehydrogenase; SDH; Polyol dehydrogenase; Ribitol dehydrogenase; RDH; Xylitol dehydrogenase; XDH; EC 1.1.1.-; EC 1.1.1.56; EC 1.1.1.9 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
AT5G51970 sorbitol dehydrogenase, putative / L-iditol 2-dehydrogenase, putative from Arabidopsis thaliana
NP_200010 GroES-like zinc-binding alcohol dehydrogenase family protein from Arabidopsis thaliana
42% identity, 88% coverage

• function: Polyol dehydrogenase that catalyzes the NAD(+)-dependent oxidation of various sugar alcohols. Is mostly active with D-sorbitol (D-glucitol), ribitol and xylitol as substrates, leading to the C2- oxidized products D-fructose, D-ribulose and D-xylulose, respectively. To a lesser extent, can also oxidize arabitol, mannitol, lactitol and maltitol in vitro. Is required for sorbitol metabolism. Cannot use NADP(+) as the electron acceptor.
  catalytic activity: keto-D-fructose + NADH + H(+) = D-sorbitol + NAD(+) (RHEA:33031)
  catalytic activity: ribitol + NAD(+) = D-ribulose + NADH + H(+) (RHEA:20053)
  catalytic activity: xylitol + NAD(+) = D-xylulose + NADH + H(+) (RHEA:20433)
  cofactor: Zn(2+) (Binds 1 zinc ion per subunit.)
  subunit: Homotetramer.
  disruption phenotype: Reduced dry weight and primary root length when grown in the presence of sorbitol. Increased resistance to dehydration under short-day conditions.
• Enhanced Resistance of atnigr1 against Pseudomonas syringae pv. tomato Suggests Negative Regulation of Plant Basal Defense and Systemic Acquired Resistance by AtNIGR1 Encoding NAD(P)-Binding Rossmann-Fold in Arabidopsis thaliana
  Al, Antioxidants (Basel, Switzerland) 2023
  • “...UDP glucose-hexose-1-1-phosphate uridylyltransferase 0.689 XK-2 Putative xylulose kinase 0.671 GAPA-2 Glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) 0.653 AT5G51970 GroES-like zinc-binding alcohol dehydrogenase family protein 0.649 GAPB Glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) 0.639 GAPA Glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) 0.630 antioxidants-12-00989-t002_Table 2 Table 2 Cysteine molecules predicted as potential targets for...”
• Comprehensive proteomic and metabolomic analysis uncover the response of okra to drought stress
  Wang, PeerJ 2022
  • “...0.03391341 118 TPI a 0.02928484 145 HEME2 0.02682115 124 HSC70-1 0.0264096 84 AT3G54470 0.02636206 102 AT5G51970 0.02472014 67 GS2 e 0.02222725 70 Notes: a Gene shared in all pairs. b Gene shared in P2 versus P1, P3 versus P1, P4 versus P1. c Gene shared in...”
• Molecular mechanisms of resistance to Myzus persicae conferred by the peach Rm2 gene: A multi-omics view
  Le, Frontiers in plant science 2022
  • “...Prupe_7G106600 AT3G12580 61.047 No 6.8 5.60E-06 HSP70-4; Heat shock 70 kDa protein 4 Polyols Prupe_2G288800 AT5G51970 81 yes 1.6 1.40E-02 Sorbitol dehydrogenase Prupe_8G101500 AT3G18830 65 No 2.3 3.30E-05 PLT5; Polyol transporter 5 Glyoxylate metabolism Prupe_4G258800 AT2G13360 86 Yes 2.2 5.60E-06 AGT1; Glyoxylate aminotransferase 1 Prupe_4G082600 AT3G14420...”
• Recent Findings Unravel Genes and Genetic Factors Underlying Leptosphaeria maculans Resistance in Brassica napus and Its Relatives
  Cantila, International journal of molecular sciences 2020
  • “...70 , 76 ] BnaA10g07410D RLK AT5G52510 SCL8 [ 70 , 76 ] BnaA10g07650D RLK AT5G51970 Sorbitol dehydrogenase [ 70 , 76 ] BnaA10g09120D RLK AT5G54850 Unknown protein [ 70 , 76 ] BnaA10g09500D RLK AT5G55280 Cell division protein FtsZ homolog 1, chloroplastic [ 70 ,...”
• Unveiling Kiwifruit Metabolite and Protein Changes in the Course of Postharvest Cold Storage
  Salzano, Frontiers in plant science 2019
  • “...hand, accumulation of Thr overtime was associated with the decreased representation of L -threonine 3-dehydrogenase (AT5G51970), which is involved in irreversible degradation of this amino acid. More complex was the tentative explanation of Asp, Ala, Glu, and GABA levels in the course of kiwifruit cold storage...”
• A Conserved Carbon Starvation Response Underlies Bud Dormancy in Woody and Herbaceous Species
  Tarancón, Frontiers in plant science 2017
  • “.../-Hydrolases superfamily protein I-IV At4g15530 PYRUVATE, PHOSPHATE DIKINASE 1 III At2g39400 /-Hydrolases superfamily protein I-III-IV At5g51970 SORBITOL DEHYDROGENASE IV At1g73920 /-Hydrolases superfamily protein II At4g02280 SUCROSE SYNTHASE 3 II At1g18460 /-Hydrolases superfamily protein II At5g16120 /-Hydrolases superfamily protein III At5g18630 /-Hydrolases superfamily protein IV At3g60340 /-Hydrolases...”
• New insights into the evolutionary history of plant sorbitol dehydrogenase
  Jia, BMC plant biology 2015
  • “...acid sequence similarity with SDH from tomato (Gene ID: 778312) and A. thaliana (Gene ID: AT5G51970) [ 48 ]. The 366 amino acid LIDH (UniProt ID: Q1PSI9) contains an N-terminal GroES-like fold and a C-terminal Rossmann fold [ 48 ], characteristics of the ADH family [...”
  • “...across species. SDH genes from the nine above-mentioned species were analysed. The single SDH gene (AT5G51970) from the model plant A. thaliana was also used as a reference for collinear block identification. As shown in Figure 4 , all target plant genomes contained at least one...”
• Polyol specificity of recombinant Arabidopsis thaliana sorbitol dehydrogenase studied by enzyme kinetics and in silico modeling
  Aguayo, Frontiers in plant science 2015
  • “...SDH in the non-sorbitol translocating species Arabidopsis thaliana (Brassicaceae) has been identified and characterized (AtSDH, At5g51970; Nosarzewski et al., 2012 ; Aguayo et al., 2013 ). The use of mutants is enabling the physiological role of SDH to be elucidated in these species. For example, atsdh-...”
• More
• Sorbitol dehydrogenase is a cytosolic protein required for sorbitol metabolism in Arabidopsis thaliana.
  Aguayo, Plant science : an international journal of experimental plant biology 2013 (PubMed)
  • GeneRIF: At5g51970 possesses the molecular characteristics of an SORBITOL DEHYDROGENASE (SDH). SDH is cytosolically localized. In the presence of NAD+, recombinant SDH exhibited greatest oxidative activity with sorbitol, ribitol and xylitol as substrates.
• Genome-wide identification and comparative evolutionary analysis of sorbitol metabolism pathway genes in four Rosaceae species and three model plants
  Li, BMC plant biology 2022
  • “...reviewed were retrieved from the Uniprot database ( http://www.uniprot.org/ ) with accession number of P28475, Q9FJ95, Q8RI1 (Table S 1 ). Fourth, each corresponding locus was queried against COG datasets constructed from the second step and the respective COGs were obtained. Fifth, each sequence in the...”
• Transcriptomic and metabolite analyses of Cabernet Sauvignon grape berry development
  Deluc, BMC genomics 2007
  • “...metabolism 10 3.69 1612870_s_at CF201540 TC66152 Q0DAH4 GDP-4-keto-6-deoxy-D-mannose-3,5-epimerase-4-reductase Carbohydrate metabolism 3 3.66 1608527_at CF515950 TC58983 Q9FJ95 Sorbitol dehydrogenase Carbohydrate metabolism 10 3.6 1619457_at CB969731 TC63406 P93653 Trehalose-6-phosphate synthase Carbohydrate metabolism 12 3.58 1611154_at CF204490 - Q42954 Pyruvate kinase Carbohydrate metabolism 3 3.54 1614552_at CB978862 TC54160 Q5SMZ1...”

Q0QWI2 Sorbitol dehydrogenase from Zea mays
42% identity, 90% coverage

• Integrated proteomics and metabolomics analysis of transgenic and gene-stacked maize line seeds
  Liu, GM crops & food 2021
  • “...Butanoate metabolism; Fructose and mannose metabolism; Metabolic pathways; Glycerolipid metabolism; Glycolysis/gluconeogenesis; Linoleic acid metabolism 2 Q0QWI2 Sorbitol dehydrogenase Up Metabolic pathways; Fructose and mannose metabolism 3 B6THG0 Peroxidase Up Metabolic pathways; Phenylalanine metabolism; Biosynthesis of secondary metabolites; Phenylpropanoid biosynthesis 4 B8A046 Phenylalanine ammonia-lyase Up Biosynthesis of...”

Q5I6M3 L-iditol 2-dehydrogenase (EC 1.1.1.14) from Malus domestica (see paper)
42% identity, 86% coverage

xdh1 / Q876R2 D-sorbitol dehydrogenase (EC 1.1.1.14; EC 1.1.1.9) from Hypocrea jecorina (see paper)
40% identity, 93% coverage

M0HN94 Zinc-binding dehydrogenase from Haloferax gibbonsii (strain ATCC 33959 / DSM 4427 / JCM 8863 / NBRC 102184 / NCIMB 2188 / Ma 2.38)
40% identity, 98% coverage

• Sugar alcohol degradation in Archaea: uptake and degradation of mannitol and sorbitol in Haloarcula hispanica
  Ortjohann, Extremophiles : life under extreme conditions 2024
  • “...R. norvegicus , P27867; O. aries , P07846; H. sapiens , Q00796; H. gibbonsii , M0HN94; H. rarus , WP_256422950.1; H. marismortui , Q5V6U8; MtlDH: H. hispanica , G0I059; H. marismortui , Q5V6V7; T. borchii , Q1ACW3; L. mesenteroides , Q8KQG6; L. pseudomesenteroides , Q83VI5; L....”

O96496 Sorbitol dehydrogenase from Bemisia argentifolii
39% identity, 96% coverage

• Sugar alcohol degradation in Archaea: uptake and degradation of mannitol and sorbitol in Haloarcula hispanica.
  Ortjohann, Extremophiles : life under extreme conditions 2024
  • “...B. subtilis , Q06004; S. cerevisiae , P35497; H. hispanica , G0I050; B. argentifolii , O96496; M. musculus , Q64442; R. norvegicus , P27867; O. aries , P07846; H. sapiens , Q00796; H. gibbonsii , M0HN94; H. rarus , WP_256422950.1; H. marismortui , Q5V6U8; MtlDH: H....”

F2CYT1 Predicted protein from Hordeum vulgare subsp. vulgare
41% identity, 90% coverage

• Na2CO3-responsive mechanisms in halophyte Puccinellia tenuiflora roots revealed by physiological and proteomic analyses
  Zhao, Scientific reports 2016
  • “...domain * (TA) O. sativa subsp . japonica 43,019 5.17 2.3090.739 2.1390.305 3.3911.210 * 3.1361.042 F2CYT1 Predicted protein, sorbitol dehydrogenase * (SDH) H. vulgare var . distichum 38,905 6.27 1.5170.138 1.7060.022 1.9150.062 * 1.9280.201 * F2CWQ6 ATP synthase gamma chain H. vulgare var . distichum 35,424...”

DQ124868 / Q1PSI9 L-idonate 5-dehydrogenase (EC 1.1.1.366) from Vitis vinifera (see paper)
IDND_VITVI / Q1PSI9 L-idonate 5-dehydrogenase; EC 1.1.1.366 from Vitis vinifera (Grape) (see paper)
Q1PSI9 L-idonate 5-dehydrogenase (EC 1.1.1.264); L-idonate 5-dehydrogenase (NAD+) (EC 1.1.1.366) from Vitis vinifera (see 3 papers)
40% identity, 89% coverage

• function: Involved in the catabolism of ascorbate to tartrate. The enzyme has no activity with NADP(+).
  catalytic activity: L-idonate + NAD(+) = 5-dehydro-D-gluconate + NADH + H(+) (RHEA:21172)
  cofactor: Zn(2+)
• Biochemical and Proteomic Changes in the Roots of M4 Grapevine Rootstock in Response to Nitrate Availability
  Prinsi, Plants (Basel, Switzerland) 2021
  • “...O, mitochondrial I a new * 14 F6HGZ9 14 160.9 Sucrose synthase new * 257 Q1PSI9 4 43.7 L-idonate 5-dehydrogenase 15.59 ** 323 A0A438D9B1 3 36.8 Glucose-6-phosphate 1-dehydrogenase new ** 169 A0A438HWY8 5 66.2 Probable 6-phosphogluconolactonase 0.29 * 64 F6HGH4 8 120.0 6-phosphogluconate dehydrogenase, decarboxylating 9.40...”
• Biosynthesis and Cellular Functions of Tartaric Acid in Grapevines
  Burbidge, Frontiers in plant science 2021
  • “...three L-IDH isoforms, which are co-located on chromosome 16 but only one ( VvLIDH3 ; Q1PSI9; VIT_16s0100g00290) has been shown definitively to oxidize L-idonate ( DeBolt et al., 2006 ; Sweetman et al., 2012 ; Higginson et al., 2016 ). VvLIDH1 (ABA01327) has a very high...”
• Tartaric acid pathways in Vitis vinifera L. (cv. Ugni blanc): a comparative study of two vintages with contrasted climatic conditions
  Cholet, BMC plant biology 2016
  • “...during 2011 ( e ) and 2013 ( f ); L-idonate dehydrogenase (L-IdnDH, uniprot ID: Q1PSI9) during 2011 ( g ) and 2013 ( h ). Error bars are standard errors of three biological replicates (LabelFree analysis). The developmental stage of veraison is indicated by a...”
• New insights into the evolutionary history of plant sorbitol dehydrogenase
  Jia, BMC plant biology 2015
  • “...A. thaliana (Gene ID: AT5G51970) [ 48 ]. The 366 amino acid LIDH (UniProt ID: Q1PSI9) contains an N-terminal GroES-like fold and a C-terminal Rossmann fold [ 48 ], characteristics of the ADH family [ 49 ], which has a distant homology to SDH [ 14...”
  • “...in the V. vinifera genome. One (GSVIVT01010646001) corresponded to the previously characterized LIDH (Uniprot No. Q1PSI9) [ 48 ] while the other two shared 99% (GSVIVT01010644001) and 77% (GSVIVT01010642001) amino acid sequence identity with V. vinifera LIDH (Additional file 2 : Table S4). Other important crops...”

1e3jA / O96496 Ketose reductase (sorbitol dehydrogenase) from silverleaf whitefly (see paper)
39% identity, 97% coverage

• Ligands: zinc ion; phosphate ion (1e3jA)

Q6ZBH2 Os08g0545200 protein from Oryza sativa subsp. japonica
41% identity, 89% coverage

• Three Diverse Granule Preparation Methods for Proteomic Analysis of Mature Rice (Oryza sativa L.) Starch Grain
  Provost, Molecules (Basel, Switzerland) 2022
  • “...2 * Q65XK0 Ketol-acid reductoisomerase Q75M03 Putative H+-pyrophosphatase Q6AVA8 Pyruvate, phosphate dikinase 1, chloroplastic * Q6ZBH2 Sorbitol dehydrogenase * B3VDJ4 Starch branching enzyme Q43009 Sucrose synthase 3 Q93X08 UTP-glucose-1-phosphate uridylyltransferase Miscellaneous Q6ZKC0 14-3-3-like protein GF14-C Q6Z782 Brittle1 (BT1) Q0DEP9 Early nodulin-93 A0A0P0WFP9 Fatty acid export 2,...”
• iTRAQ-based proteome profile analysis of superior and inferior Spikelets at early grain filling stage in japonica Rice
  You, BMC plant biology 2017
  • “...dehydrogenase 2 5.381.61 ns ns 104 Os06g0486800 Q0DC43 Formate dehydrogenase 3.250.54 2.410.74 ns 120 Os08g0545200 Q6ZBH2 Os08g0545200 protein/Sorbitol dehydrogenase 12.372.25 2.490.24 5.090.97 122 Os03g0293500 Q10MW3 Pyruvate decarboxylase 2 3.960.28 2.721.11 ns 125 Os06g0326400 Q69T78 Pyrophosphate-fructose 6-phosphate 1-phosphotransferase subunit alpha 2.050.21 ns 2.270.28 127 Os07g0187200 Q7XI14 Probable...”
• Proteome Profile of Starch Granules Purified from Rice (Oryza sativa) Endosperm
  Xing, PloS one 2016
  • “...involved in starch synthesis in the endosperm. Another possible starch granule associated protein included protein Q6ZBH2 with a peptide count of 153. This protein belongs to the alcohol dehydrogenase superfamily (zinc-type ) and maybe involved in fructose biosynthesis [ 56 ]. Its connection with starch synthesis...”
• A proteomic study on molecular mechanism of poor grain-filling of rice (Oryza sativa L.) inferior spikelets
  Zhang, PloS one 2014
  • “...Q10MW3 Similar to Pyruvate decarboxylase isozyme 3 497 65.8/5.53 5 DR DR 45 18 g Q6ZBH2 Alcohol dehydrogenase superfamily, zinc-containing protein 483 40.0/6.03 3 DR 1.11- Nitrogen 46 286 h Q338N8 Alanine aminotransferase 170 52.6/6.65 11 DR 47 157 g P14655 Glutamine synthetase,chloroplastic 265 49.8/6.18 2...”
  • “...62.9/5.60 22 UR 3 P 9 Q93X08 UDP-glucose pyrophosphorylase 134 51.7/5.60 2 DR 4 P26 Q6ZBH2 Putative sorbitol dehydrogenase 263 39.3/6.47 18 DR 5 P63 Q8S9Z2 Putative dTDP-glucose 4,6-dehydratase 39 44.3/6.25 5 DR 6 P61 Q9AUV8 Phosphorylase 352 106.2/5.94 17 UR DR P62 Q9AUV8 Phosphorylase 258...”

D7TMY3 Enoyl reductase (ER) domain-containing protein from Vitis vinifera
41% identity, 90% coverage

• New insights into the evolutionary history of plant sorbitol dehydrogenase
  Jia, BMC plant biology 2015
  • “...of plant SDHs, protein structure models of V. vinifera Class I SDH (Vv_SDH, UniProt No: D7TMY3) and Class II SDH (Vv_LIDH, UniProt No: Q1PSI9) were created based on human SDH (PDB: 1PL8; 46~47% identity with Vv_SDH and Vv_LIDH). Ligands including zinc, NAD + , D-sorbitol and...”
  • “...V. vinifera LIDH (Uniprot ID: Q1PSI9; accession no: GSVIVT01010646001) and V. vinifera SDH (Uniprot ID: D7TMY3; accession no: GSVIVT01010642001) structures were generated with the human SDH (PDB:1PL8) as a template. Given that no plant SDH structures exist in the protein data bank we chose the model...”

NCU00891 xylitol dehydrogenase from Neurospora crassa OR74A
39% identity, 86% coverage

• Collection and Curation of Transcriptional Regulatory Interactions in Aspergillus nidulans and Neurospora crassa Reveal Structural and Evolutionary Features of the Regulatory Networks
  Hu, Frontiers in microbiology 2018
  • “...xdh-1 Both Xanthine dehydrogenase XlnR xkiA P XLR-1 xyk-1 P D-xylulokinase XlnR xdhA P XLR-1 NCU00891 P Xylitol dehydrogenase XlnR xlnB P XLR-1 gh11-2 P Endo-1,4-beta-xylanase a B, binding experiments; P, TF-perturbation experiments; Both, both the above two types of experiments. Only low-throughput experiments were considered...”
• Direct target network of the Neurospora crassa plant cell wall deconstruction regulators CLR-1, CLR-2, and XLR-1
  Craig, mBio 2015
  • “...by XLR-1 NCU no. Locus Annotation or domain NCU00292 cea-3 Carboxy esterase NCU00709 gh3-8 -Xylosidase NCU00891 Xdh Xylitol dehydrogenase NCU01900 a gh43-2 Xylosidase/arabinosidase NCU02343 gh51-1 Alpha- l -arabinofuranosidase NCU03322 GDSL family lipase NCU04401 Fructose-bisphosphate aldolase NCU04537 Monosaccharide transporter NCU04870 a ce1 - 1 Acetyl xylan esterase...”
• Transcriptional comparison of the filamentous fungus Neurospora crassa growing on three major monosaccharides D-glucose, D-xylose and L-arabinose
  Li, Biotechnology for biofuels 2014
  • “...grown on D-xylose or L-arabinose. Genes tested included D-xylose reductase (XR, NCU08384), xylitol dehydrogenase (XDH, NCU00891), L-arabitol dehydrogenase (LAD NCU00643) and L-xylulose reductase (LXR NCU09041). The growth phenotypes showed that the deletion of xr or xdh significantly affected the growth on either D-xylose or L-arabinose. The...”
  • “...pathway on BDES plate plus 2%L-arabinose for 5days. XR, D-xylose reductase, NCU08384: XDH, xylitol dehydrogenase, NCU00891; LAD, L-arabitol dehydrogenase, NCU00643; LXR, L-xylulose reductase, NCU09041; NADH, nicotinamide adenine dinucleotide, reduced; NADPH, nicotinamide adenine dinucleotide phosphate, reduced; WT, wild-type. The length of the scale is about 0.5cm. Transcriptome...”
• A comparative systems analysis of polysaccharide-elicited responses in Neurospora crassa reveals carbon source-specific cellular adaptations
  Benz, Molecular microbiology 2014
  • “...to each other in the xylan-specific cluster 4: xylose reductase ( xyr-1 /NCU08384), xylitol dehydrogenase (NCU00891) and D-xylulose kinase ( xyk-1 /NCU11353) were only interrupted by a MFS transporter gene (NCU06384), with L-xylulose reductase (NCU09041) being located slightly more distant. Intriguingly, L-xylulose reductase is the only...”
• Deciphering transcriptional regulatory mechanisms associated with hemicellulose degradation in Neurospora crassa
  Sun, Eukaryotic cell 2012
  • “...including xylose reductase (NCU008384, xyr-1), xylitol dehydrogenase (NCU00891, xdh-1), and D-xylulose kinase (NCU11353, xyk-1), and 7 genes encoding the...”
  • “...endoxylanase (NCU08189, gh10-2), two xylose metabolism genes (NCU00891, xdh-1, and NCU08384, xyr-1), and two sugar transporter genes (NCU04963 and NCU05897). In...”
• Induction of lignocellulose-degrading enzymes in Neurospora crassa by cellodextrins
  Znameroski, Proceedings of the National Academy of Sciences of the United States of America 2012
  • “...acetyl xylan esterase; NCU01900, xylosidase/arabinosidase; NCU00891, xylitol dehydrogenase; NCU08384, xylose reductase). These results suggest that these...”
• Transcriptome analysis of Aspergillus niger grown on sugarcane bagasse
  de, Biotechnology for biofuels 2011
  • “...An01g10920 and An12g00030 (L-arabinitol 4-dehydrogenase ( N. crassa NCU00643) and xylitol dehydrogenase ( N. crassa NCU00891), respectively), also have increased mRNA accumulation in both substrates (Additional file 5 , Table S5). These data strongly suggest that although diverse biomasses could have a specific impact on gene...”
• Systems analysis of plant cell wall degradation by the model filamentous fungus Neurospora crassa
  Tian, Proceedings of the National Academy of Sciences of the United States of America 2009
  • “...the metabolism of pentose sugars (for example, NCU00891, xylitol dehydrogenase and NCU00643, a predicted arabinitol dehydrogenase), a predicted sugar...”
• More

B8B9C5 Enoyl reductase (ER) domain-containing protein from Oryza sativa subsp. indica
41% identity, 89% coverage

• Carbon and nitrogen partitioning of transgenic rice T2A-1 (Cry2A*) with different nitrogen treatments
  Ling, Scientific reports 2019
  • “...1 1 1.573 0.017 Os05g0301700 protein Q0DJC3 36.18 1 6 1.565 0.018 Putative uncharacterized protein B8B9C5 54.35 1 15 1.560 0.019 Beta-amylase A3ADZ2 2.52 1 1 1.545 0.022 Putative uncharacterized protein A2WV09 4.46 1 1 1.521 0.027 Putative uncharacterized protein B8B184 3.58 1 1 1.520 0.027...”

LOC126998993 sorbitol dehydrogenase-like from Eriocheir sinensis
39% identity, 89% coverage

• Transcriptome and metabolomics analysis of adaptive mechanism of Chinese mitten crab (Eriocheir sinensis) to aflatoxin B1
  Yang, PloS one 2023
  • “...m), showing a significant increase in the treated group compared with the untreated group. Gene LOC126998993 ( SORD ) encoded sorbitol dehydrogenase, and high expression of this protein indicated a signal of liver injury [ 26 ]. The expression level of LOC126998993 increased nearly fourfold before...”
  • “...]. The literature indicates that an increase in the expression levels of two DEGs ( LOC126998993 , novel . 4226 ) indicates liver injury, indicating that these two genes have an self-evident repair effect on liver tissue [ 26 ]. The abnormal expression of four hydrolytic...”

Q07786 L-iditol 2-dehydrogenase (EC 1.1.1.14) from Saccharomyces cerevisiae (see 2 papers)
YDL246C Protein of unknown function, computational analysis of large-scale protein-protein interaction data suggests a possible role in fructose or mannose metabolism from Saccharomyces cerevisiae
40% identity, 91% coverage

• Engineering cofactor supply and NADH-dependent D-galacturonic acid reductases for redox-balanced production of L-galactonate in Saccharomyces cerevisiae
  Harth, Scientific reports 2020
  • “...and strains The Saccharomyces cerevisiae endogenous open reading frames (ORFs) of HXT13 (YEL069C) and SOR2 (YDL246C) were PCR amplified using the primer pairs SiHP011-SiHP012 ( HXT13 ) and SiHP015-SiHP016 ( SOR2 ). The open reading frame encoding YlSdr 22 ; UniProtKBQ6CEE9) was amplified from Yarrowia lipolytica...”
• Horizontal and vertical growth of S. cerevisiae metabolic network
  Grassi, BMC evolutionary biology 2011
  • “...N 0 N/A 0.68 2.2 -16 YDL080C YDR380W Y Y Y 0.67 0 0.08 0.033 YDL246C YLR070C Y Y Y N/A 0 N/A N/A YDR147W YLR133W Y Y N 0 0.5 0.09 0.02 YDR380W YGR087C Y Y Y 0.54 0 -0.07 0.065 YDR380W YLR044C Y Y...”
• Translation initiation: a regulatory role for poly(A) tracts in front of the AUG codon in Saccharomyces cerevisiae
  Xia, Genetics 2011
  • “...YNL128W 265 12 6.9881 0.3633 YBR056W-A 47 11 7.5809 0.4077 YDL140C 519 11 10.1271 0.4864 YDL246C 321 11 7.1664 0.4695 YDR033W 555 11 12.1143 0.7725 YDR055W 82 11 9.3654 0.5406 YER115C 294 11 8.1442 0.3465 YER159C 180 11 8.5424 0.2948 YER165W 145 11 12.1955 0.7079 YGL037C...”
• Improvement of galactose uptake in Saccharomyces cerevisiae through overexpression of phosphoglucomutase: example of transcript analysis as a tool in inverse metabolic engineering
  Bro, Applied and environmental microbiology 2005
  • “...YFL011W YMR305C YKL216W YDR520C YGL035C YPL187W YMR199W YJR159W YDL246C YMR176W YOL058W YOR378W YGR249W URA3 GAL4 MAL31 GAL80 ZAP1 MLH2 PHO5 CEG1 RIB4 CTS1 GAL6...”
• A two-hybrid screen of the yeast proteome for Hsp90 interactors uncovers a novel Hsp90 chaperone requirement in the activity of a stress-activated mitogen-activated protein kinase, Slt2p (Mpk1p)
  Millson, Eukaryotic cell 2005
  • “...(2); YDL015c (TSC13) (2); YDL133w (1); YDL180w (1); YDL246c (SOR2) (1); YDL248c (COS7) (2); YDR051c (1); YDR281c (PHM6) (2); YDR319c (2); YDR412w (1); YER156c...”
• Endogenous xylose pathway in Saccharomyces cerevisiae
  Toivari, Applied and environmental microbiology 2004
  • “...encodes sorbitol dehydrogenase (SDH), and an open reading frame, YDL246c, that is almost identical to SOR1. The SDH enzyme also can use xylitol as a substrate...”
  • “...noncoding regions. The probe for SOR1 also detects YDL246c. The PCR products were cloned into pCR2.1-TOPO (Invitrogen), excised from the vector by digestion...”
• Predicting protein functions from redundancies in large-scale protein interaction networks
  Samanta, Proceedings of the National Academy of Sciences of the United States of America 2003
  • “...(MMS4) YHR105W (YPT35) YBL049W (MOH1), YCL039W (MOH2) YDL246C (SOR2) YMR322C (SNO4) YDR430C (CYM1) YJL199C (MBB1), YPL004C (LSP1), YGR086C (PIL1) YLR097C (HRT3)...”
• D-xylose metabolism in Hypocrea jecorina: loss of the xylitol dehydrogenase step can be partially compensated for by lad1-encoded L-arabinitol-4-dehydrogenase
  Seiboth, Eukaryotic cell 2003
  • “...(NP_013171.1), S. cerevisiae Sor1 (NP_012693.1), S. cerevisiae Ydl246c (NP_010035.1), Pichia stipitis Xdh1 (P22144), Candida sp. Xdh1 (AAC24597.1), N. crassa...”
• More

DHSO1_YEAST / P35497 Sorbitol dehydrogenase 1; SDH 1; Polyol dehydrogenase; Xylitol dehydrogenase; EC 1.1.1.-; EC 1.1.1.9 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see paper)
P35497 L-iditol 2-dehydrogenase (EC 1.1.1.14) from Saccharomyces cerevisiae (see 2 papers)
YJR159W Sor1p from Saccharomyces cerevisiae
40% identity, 91% coverage

• function: Polyol dehydrogenase that catalyzes the reversible NAD(+)- dependent oxidation of various sugar alcohols. Is active with D- sorbitol (D-glucitol) and xylitol as substrates, leading to the C2- oxidized product D-fructose and D-xylulose, respectively. Is likely involved in the utilization of D-sorbitol as a sole carbon source for growth. Has no activity on mannitol and primary alcohols such as ethanol.
  catalytic activity: keto-D-fructose + NADH + H(+) = D-sorbitol + NAD(+) (RHEA:33031)
  catalytic activity: xylitol + NAD(+) = D-xylulose + NADH + H(+) (RHEA:20433)
  cofactor: Zn(2+) (Binds 1 zinc ion per subunit.)
  subunit: Homotetramer.
• Sugar alcohol degradation in Archaea: uptake and degradation of mannitol and sorbitol in Haloarcula hispanica
  Ortjohann, Extremophiles : life under extreme conditions 2024
  • “...archaeal glucose dehydrogenase; FADH: formaldehyde dehydrogenase. UniProtaccession: SorDH: B. subtilis , Q06004; S. cerevisiae , P35497; H. hispanica , G0I050; B. argentifolii , O96496; M. musculus , Q64442; R. norvegicus , P27867; O. aries , P07846; H. sapiens , Q00796; H. gibbonsii , M0HN94; H. rarus...”
• Proteomics of Penicillium chrysogenum for a Deeper Understanding of Lead (Pb) Metal Bioremediation.
  Algahmadi, ACS omega 2024
  • “...and metabolism 1 probable aspartate-semialdehyde dehydrogenase P78780 DHAS_SCHPO nucleus 4.11 UP 2 sorbitol dehydrogenase 1e P35497 DHSO1_YEAST cytosol 4.65 UP 3 protein FMP27, mitochondrial Q06179 FMP27_YEAST mitochondria 3.72 DOWN 1.3 Proteins involved in carbohydrate transport and metabolism 1 sterol 3-beta-glucosyltransferase Q5B4C9 ATG26_EMENI cytoplasm 4.04 UP 1.4...”
• Horizontal and vertical growth of S. cerevisiae metabolic network
  Grassi, BMC evolutionary biology 2011
  • “...0 N/A 0.25 7.6 -11 YHR123W YNL130C Y Y Y 0 0 0.50 2.2 -16 YJR159W YLR070C Y Y Y N/A 0 0.38 2.2 -16 Only pairs identified as paralogs by at least by two paralogy definitions (Need: sequence identity above 30%; Ens: derived from the...”
• Mutational analysis of the C-terminal FATC domain of Saccharomyces cerevisiae Tra1
  Hoke, Current genetics 2010
  • “...2.3 Acid phosphatase YOL014W 2.3 Unknown YDR288W NSE3 2.3 Mms21-Smc5-Smc6 complex subunit YLR159C-A 2.2 unknown YJR159W SOR1 2.2 Sorbitol dehydrogenase YMR294W JNM1 2.2 Component of the dynactin complex YJL190C RPS22A 2.2 Ribosomal subunit YLR442C SIR3 2.2 Chromatin silencing YHR053C CUP1-1 2.2 Metallothionein YIR034C LYS1 2.1 Lysine...”
• The reacquisition of biotin prototrophy in Saccharomyces cerevisiae involved horizontal gene transfer, gene duplication and gene clustering
  Hall, Genetics 2007
  • “...(HXT16) YBR019C (GAL10) YBR298C (MAL31) YGR289C (MAL11) YJR159W (SOR1) Biotin synthesis Biotin synthesis Aryl-sulfate utilization Resistance to arsenic SAM...”
• Improvement of galactose uptake in Saccharomyces cerevisiae through overexpression of phosphoglucomutase: example of transcript analysis as a tool in inverse metabolic engineering
  Bro, Applied and environmental microbiology 2005
  • “...YOL126C YFL011W YMR305C YKL216W YDR520C YGL035C YPL187W YMR199W YJR159W YDL246C YMR176W YOL058W YOR378W YGR249W URA3 GAL4 MAL31 GAL80 ZAP1 MLH2 PHO5 CEG1 RIB4...”
• A two-hybrid screen of the yeast proteome for Hsp90 interactors uncovers a novel Hsp90 chaperone requirement in the activity of a stress-activated mitogen-activated protein kinase, Slt2p (Mpk1p)
  Millson, Eukaryotic cell 2005
  • “...1 1 2 2 1 1 2 YBR273c YKL035w YBR130c YER118c YML066c YJR159w YMR101c YIR011c YPL048w YNL131w UBX7 UGP1 SHE3 SHO1 SMA2 SOR1 SRT1 STS1 TEF3 TOM22 2 2 2 3 1 1 1 1...”
• Las21 participates in extracellular/cell surface phenomena in Saccharomyces cerevisiae
  Tohe, Genes & genetic systems 1999 (PubMed)
  • “...were obtained. They are ECM33 (YBR078W) and PIR2/HSP150 (YJR159W) both have some roles in an extracellular function. The common features of the suppressors,...”
• Complete nucleotide sequence of Saccharomyces cerevisiae chromosome X
  Galibert, The EMBO journal 1996
  • “...YJR151c YJR152w YJR153w YJR 154w YJR155w YJR156c YJR157w YJR158w YJR159w YJR160c YJR161c J2420 YJR162c J2251) J2255 J2261) 239 421 1442 1584 359 1648 347 342...”

XP_002318842 L-idonate 5-dehydrogenase from Populus trichocarpa
38% identity, 89% coverage

• Heterologous over-expression of ACC SYNTHASE8 (ACS8) in Populus tremula x P. alba clone 717-1B4 results in elevated levels of ethylene and induces stem dwarfism and reduced leaf size through separate genetic pathways
  Plett, Frontiers in plant science 2014
  • “...1-Aminocyclopropane-1-carboxylate 8 ( ACS8 ) PtpAffx.211163.1.S1_s_at XP_002319260 0.00E+00 2.8 GH3 family protein NUTRIENT TRANSPORT PtpAffx.79594.1.S1_s_at XP_002318842 8.00E164 3.2 Sorbitol dehydrogenase-like protein PtpAffx.15690.1.S1_at XP_002311043 0.00E+00 3.0 Proline transporter Ptp.3435.2.S1_s_at XP_002302223 0.00E+00 2.6 Amino acid permease Ptp.1552.1.S1_s_at XP_002302727 0.00E+00 2.1 SUS3 (sucrose synthase 3) Ptp.8110.1.S1_at XP_002313213 0.00E+00 3.5...”

NP_001149440 sorbitol dehydrogenase homolog 1 from Zea mays
42% identity, 90% coverage

• Identification and characterization of lysine-rich proteins and starch biosynthesis genes in the opaque2 mutant by transcriptional and proteomic analysis
  Jia, BMC plant biology 2013
  • “...Q43247 Glyceraldehyde-3-phosphate dehydrogenase 1.7 34 Q43247 Glyceraldehyde-3-phosphate dehydrogenase 1.8 35 AAA87580 Glyceroldehyde-3-phosphate dehydrogenase 1.6 36 NP_001149440 sorbitol dehydrogenase homolog1 2.7 37 ABA70761 sorbitol dehydrogenase 2.9 38 NP_001140424 triosephosphate isomerase, cytosolic 1.5 39 ACG35098 17.4kDa class I heat shock protein 3 1.2 40 NP_001140424 triosephosphate isomerase, cytosolic...”

LOC103933319 sorbitol dehydrogenase from Pyrus x bretschneideri
41% identity, 86% coverage

• Time-Series Transcriptome Analysis Reveals the Molecular Mechanism of Ethylene Reducing Cold Sensitivity of Postharvest 'Huangguan' Pear
  Wei, International journal of molecular sciences 2023
  • “...LOC103944529; LOC103928204; LOC103947597 Programmed cell death protein (2 genes) LOC103931100; LOC103940748 Sorbitol dehydrogenase (1 gene) LOC103933319 MLO-like protein (2 genes) LOC103948807; LOC103948871 Disease resistance protein RPP5 (1 gene) LOC103935452 alpha-amylase (3 genes) LOC103936498; LOC103936497; LOC103941903...”

NP_001188510 sorbitol dehydrogenase-2b from Bombyx mori
37% identity, 94% coverage

• Cloning of cDNAs encoding sorbitol dehydrogenase-2a and b, enzymatic characterization, and up-regulated expression of the genes in Bombyx mori diapause eggs exposed to 5 °C.
  Rubio, Insect biochemistry and molecular biology 2011 (PubMed)
  • GeneRIF: The sorbitol dehydrogenase (SDH2a and SDH2b) and SDH1 genes are located in tandem within about 40 kbp on chromosome 21.

gutB / Q06004 glucitol dehydrogenase monomer (EC 1.1.1.9; EC 1.1.1.14) from Bacillus subtilis (strain 168) (see paper)
DHSO_BACSU / Q06004 Sorbitol dehydrogenase; SDH; Glucitol dehydrogenase; L-iditol 2-dehydrogenase; Polyol dehydrogenase; Xylitol dehydrogenase; EC 1.1.1.-; EC 1.1.1.14; EC 1.1.1.9 from Bacillus subtilis (strain 168) (see paper)
gutB / GI|304153 L-iditol 2-dehydrogenase; EC 1.1.1.14 from Bacillus subtilis subsp. subtilis str. 168 (see 3 papers)
gutB / AAA22508.1 sorbitol dehydrogenase from Bacillus subtilis (see paper)
BSU06150 glucitol (sorbitol) dehydrogenase from Bacillus subtilis subsp. subtilis str. 168
35% identity, 97% coverage

• function: Polyol dehydrogenase that catalyzes the NAD(+)-dependent oxidation of various sugar alcohols. Is mostly active with D-sorbitol (D-glucitol), xylitol and L-iditol as substrates, leading to the C2- oxidized products D-fructose, D-xylulose and L-sorbose, respectively.
  catalytic activity: keto-D-fructose + NADH + H(+) = D-sorbitol + NAD(+) (RHEA:33031)
  catalytic activity: xylitol + NAD(+) = D-xylulose + NADH + H(+) (RHEA:20433)
  catalytic activity: L-iditol + NAD(+) = keto-L-sorbose + NADH + H(+) (RHEA:10160)
  cofactor: Zn(2+) (Binds 1 Zn(2+) ion per subunit.)
  subunit: Homotetramer.
• Sugar alcohol degradation in Archaea: uptake and degradation of mannitol and sorbitol in Haloarcula hispanica
  Ortjohann, Extremophiles : life under extreme conditions 2024
  • “...RnSorDH are conserved in HhSorDH (). UniProt accession: HsSorDH, Q00796; OaSorDH, P07846; RnSorDH, P27867; BsSorDH, Q06004; LrMtlDH, Q6ECH5; LpMtlDH, Q83VI5; TbMtlDH, Q1ACW3; HhSorDH, G0I050; HhMtlDH, G0I059 Besides sorbitol and mannitol dehydrogenases (Riveros-Rosas et al. 2003 ; Ceccaroli et al. 2007 ), the PDH family contains various...”
  • “...SORE: L-sorbose-1-phosphate reductase; GDH: archaeal glucose dehydrogenase; FADH: formaldehyde dehydrogenase. UniProtaccession: SorDH: B. subtilis , Q06004; S. cerevisiae , P35497; H. hispanica , G0I050; B. argentifolii , O96496; M. musculus , Q64442; R. norvegicus , P27867; O. aries , P07846; H. sapiens , Q00796; H. gibbonsii...”
• The nucleotide sequence of chromosome I from Saccharomyces cerevisiae
  Bussey, Proceedings of the National Academy of Sciences of the United States of America 1995
  • “...112 Acc sp P25621 sp X78160 gp X78160 sp P07262 sp Q06004 gp L35343 sp P27825 sp Q01574 sp P25611 sp P15298 sp P23884 sp Q01329 sp P11433 sp P13365 sp P06182...”
• Secondary structural entropy in RNA switch (Riboswitch) identification
  Manzourolajdad, BMC bioinformatics 2015
  • “...0.363 550 yeeG BSU06820 0.846 57 665425 665581 forward BSU06130 ydjC -677 0.3439 1963 gutB BSU06150 0.846 58 2106272 2106428 reverse BSU19360 odhB -1154 0.3949 79 yocR BSU19340 0.846 59 226409 226565 forward BSU02050 ybdO -82 0.3885 79 ybxG BSU02060 0.844 60 2106333 2106489 forward BSU19330...”
  • “...0.363 550 yeeG BSU06820 0.846 32 665425 665581 forward BSU06130 ydjC -677 0.3439 1963 gutB BSU06150 0.846 33 2106272 2106428 reverse BSU19360 odhB -1154 0.3949 79 yocR BSU19340 0.846 34 226409 226565 forward BSU02050 ybdO -82 0.3885 79 ybxG BSU02060 0.844 35 2106333 2106489 forward BSU19330...”

LOC105669158 sorbitol dehydrogenase from Linepithema humile
36% identity, 97% coverage

• Social environment affects the transcriptomic response to bacteria in ant queens
  Viljakainen, Ecology and evolution 2018
  • “...Protein tolllike (LOC105678648) 0.84 2.11E05 1.06E02 LOC105672608 Facilitated trehalose transporter Tret1like (LOC105672608) 0.84 4.20E04 8.24E02 LOC105669158 Sorbitol dehydrogenaselike (LOC105669158) 0.73 2.90E04 7.60E02 LOC105674664 Cytochrome P450 6a2like (LOC105674664) 0.71 2.59E04 7.42E02 LOC105670239 Uncharacterized LOC105670239 (LOC105670239) 0.67 2.52E04 7.42E02 LOC105671841 Pleckstrin homology domaincontaining family M member 2 (LOC105671841)...”
  • “...8.22E07 LOC105675436 Chymotrypsin inhibitorlike (LOC105675436) 1.69 1.42E10 9.16E08 LOC105669509 Arylsulfatase Blike (LOC105669509) 1.71 4.52E06 7.23E04 LOC105669158 Sorbitol dehydrogenaselike (LOC105669158) 1.71 8.01E09 3.21E06 LOC105675717 Defensing2 (LOC105675717) 1.80 1.05E08 3.93E06 LOC105679484 Sorbitol dehydrogenaselike (LOC105679484) 1.80 3.71E04 2.85E02 LOC105679620 Uncharacterized LOC105679620 (LOC105679620) 1.88 1.68E05 2.26E03 LOC105679945 Cytochrome P450 4C1like...”

LOC408871 sorbitol dehydrogenase from Apis mellifera
38% identity, 94% coverage

• Varroa destructor parasitism has a greater effect on proteome changes than the deformed wing virus and activates TGF-β signaling pathways
  Erban, Scientific reports 2019
  • “...2.61 1.19 1.61 LOC551927 >XP_006567931.1 alcohol dehydrogenase [NADP( + )]-like 0.72 1.07 2.12 1.40 1.05 LOC408871 >XP_392401.3 sorbitol dehydrogenase-like 1.08 0.62 2.48 1.41 3.10 LOC412231 >XP_623497.1 trans-1,2-dihydrobenzene-1,2-diol dehydrogenase-like 2.72 NaN 4.82 2.09 NaN LOC411188 >XP_006569462.1 L-lactate dehydrogenase-like 1.49 1.72 3.27 4.76 1.55 APD-3 >AER08515.1 apidermin 3-like...”

S6BFC0 D-xylulose reductase (EC 1.1.1.9) from Rhizomucor pusillus (see paper)
38% identity, 94% coverage

B6TEC1 Sorbitol dehydrogenase from Zea mays
42% identity, 90% coverage

• Proteomic comparison of basal endosperm in maize miniature1 mutant and its wild-type Mn1
  Silva-Sanchez, Frontiers in plant science 2013
  • “...Putative uncharacterized protein 0.58 0.01 0.81 0.01 B6TBZ8 Alanine aminotransferase 2 0.64 0.01 0.85 0.02 B6TEC1 Sorbitol dehydrogenase 0.67 0.00 0.80 0.05 Q43706 Sus1 protein 0.71 0.01 0.93 0.03 Q548K3 Farnesyl diphosphate synthase 0.74 0.02 1.01 0.02 Q5EUE1 b Protein disulfide isomerase 0.76 0.02 0.96 0.02...”

xdhA / Q5GN51 D-xylulose reductase (EC 1.1.1.9) from Aspergillus niger (see paper)
An12g00030 uncharacterized protein from Aspergillus niger
38% identity, 92% coverage

• The International Space Station Environment Triggers Molecular Responses in Aspergillus niger
  Blachowicz, Frontiers in microbiology 2022
  • “...B (An07g09330 and An01g11660), XlnA 1,4--xylanase (An03g00940), and D-xylose reductases XyrA and XdhA (An01g03740 and An12g00030) were regulated by XlnR. XlnR is a transcriptional regulator involved in degradation of polysaccharides, xylan, cellulose, and D-xylose ( Hasper et al., 2000 ). -glucanases An11g01540 and An02g00850, which are...”
  • “...1.10 1.77E-02 An07g09330 CbhA GH7 Cellobiohydrolase A 1.07 1.44E-03 An01g03740 XyrA D-xylose reductase 1.08 2.59E-02 An12g00030 XdhA D-xylulose reductase 1.10 1.72E-02 An07g08990 PkiA Pyruvate kinase 1.12 2.92E-03 An18g06500 Phosphomannomutase 1.14 6.84E-03 An12g03070 GlaB GH15 Glucoamylase 1.38 7.87E-03 An11g02550 Phosphoenolpyruvate carboxykinase 1.51 3.44E-03 An15g01920 McsA 2-Methylcitrate synthase...”
• The Cultivation Method Affects the Transcriptomic Response of Aspergillus niger to Growth on Sugar Beet Pulp
  Garrigues, Microbiology spectrum 2021
  • “...0.82 0.84 0.23 An01g03740 xyrA PCP 6,343.96 82.24 305.83 320.66 1,213.81 3,287.31 0.05 14.76 10.75 An12g00030 xdhA PCP 11,037.45 317.80 569.39 630.74 2,243.42 2,139.00 0.06 7.06 3.76 An07g03140 xkiA PCP 1,772.38 62.07 81.64 165.47 939.56 370.55 0.09 15.14 4.54 An13g00930 lraA l -Rhamnose pathway 1,059.12 23.84...”
• Updating genome annotation for the microbial cell factory Aspergillus niger using gene co-expression networks
  Schäpe, Nucleic acids research 2019
  • “...including those encoding an l-arabitol dehydrogenase (An01g10920), aldose 1-epimerase (An02g09090), glycoside hydrolase (An12g01850), xylitol dehydrogenase (An12g00030), sugar transporter (An03g01620) and short-chain dehydrogenase (An04g03530). We therefore conclude that sub-networks generated in our study can be used to define A. niger co-expression relationships and infer gene function across...”
• Trancriptional landscape of Aspergillus niger at breaking of conidial dormancy revealed by RNA-sequencing
  Novodvorska, BMC genomics 2013
  • “...involved in stress 6.84 6.95 0.92* An01g03400 transcription factor/amino acid metabolism 5.73 6.92 1.30 TID_203198 An12g00030 L-iditol 2-dehydrogenase 12.89 1.76 2.34 (B) ATCC 1015 ID CBS ID putative gene function T0-T1 fold change T0 AS/T1 AS AS/S at T0 TID_57297 An17g02080 hypothetical protein - metal ion...”
• Transcriptome analysis of Aspergillus niger grown on sugarcane bagasse
  de, Biotechnology for biofuels 2011
  • “...5 , Table S5). Genes involved in the metabolism of pentoses, such as An01g10920 and An12g00030 (L-arabinitol 4-dehydrogenase ( N. crassa NCU00643) and xylitol dehydrogenase ( N. crassa NCU00891), respectively), also have increased mRNA accumulation in both substrates (Additional file 5 , Table S5). These data...”
• Analysis of variance components reveals the contribution of sample processing to transcript variation
  van, Applied and environmental microbiology 2009
  • “...An03g00500 An15g01500 An11g01100 An03g01620 An06g00560 An01g10920 An01g03740 An12g00030 An07g03140 An02g03590 Signal sequence predicted Yes Yes Yes Yes Yes Yes...”

xdhA / Q86ZV0 NAD⁺-dependent xylitol dehydrogenase (EC 1.1.1.9) from Aspergillus oryzae (strain ATCC 42149 / RIB 40) (see paper)
XYL2_ASPOR / Q86ZV0 D-xylulose reductase A; Xylitol dehydrogenase A; EC 1.1.1.9 from Aspergillus oryzae (strain ATCC 42149 / RIB 40) (Yellow koji mold) (see paper)
Q86ZV0 D-xylulose reductase (EC 1.1.1.9) from Aspergillus oryzae (see 3 papers)
GI|83774265 xylitol dehydrogenase; EC 1.1.1.9 from Aspergillus oryzae (see paper)
xdhA / BAC75870.2 xylitol dehydrogenase from Aspergillus oryzae (see paper)
AO090038000631 No description from Aspergillus oryzae RIB40
38% identity, 92% coverage

• function: Xylitol dehydrogenase which catalyzes the conversion of xylitol to D-xylulose. Xylose is a major component of hemicelluloses such as xylan. Most fungi utilize D-xylose via three enzymatic reactions, xylose reductase (XR), xylitol dehydrogenase (XDH), and xylulokinase, to form xylulose 5-phosphate, which enters pentose phosphate pathway.
  catalytic activity: xylitol + NAD(+) = D-xylulose + NADH + H(+) (RHEA:20433)
  cofactor: Zn(2+) (Binds 1 zinc ion per subunit.)
• Translocated duplication of a targeted chromosomal segment enhances gene expression at the duplicated site and results in phenotypic changes in Aspergillus oryzae
  Takahashi, Fungal biology and biotechnology 2018
  • “...6.7 AbfB-alpha-L-arabinofuranosidase B AO090023000401 3.3 PglB-polygalacturonase B* AO090038000426 4.1 Dehydrogenases related to short-chain alcohol dehydrogenases* AO090038000631 3.5 xdhA1-Xylitol dehydrogenase* AO090103000087 3.0 Putative endoglucanase precursor* AO090103000268 6.2 Beta-xylosidase* AO090103000326 2.5 Beta-1,4-xylanase AO090103000423 2.8 XynF1, beta-1,4-xylanase* AO090103000426 4.0 Shikimate 5-dehydrogenase* AO090124000023 3.1 AbfA,;alpha-L-arabinofuranosidase AO090701000885 3.1 As Abf-alpha-L-arabinofuranosidase* AO090001000649...”
• Deciphering transcriptional regulatory mechanisms associated with hemicellulose degradation in Neurospora crassa
  Sun, Eukaryotic cell 2012
  • “...NCU09923 NCU09924 NCU10110 AO090012000445 AO090038000631 AO090005000698 AO090701000345 AO090001000207 AO090001000208 AO090001000069 AO090001000267...”
• A trispecies Aspergillus microarray: comparative transcriptomics of three Aspergillus species
  Andersen, Proceedings of the National Academy of Sciences of the United States of America 2008
  • “...AO090012000267 AO090010000684 AO090020000324 AO090020000603 AO090038000631 JGI55928 JGI48811 JGI212736 JGI199510 JGI209771 JGI203198 AN9173 AN9286...”

A0A3S7PMB5 D-xylulose reductase (EC 1.1.1.9) from Pichia kudriavzevii (see paper)
38% identity, 93% coverage

LOC105679484 sorbitol dehydrogenase-like from Linepithema humile
36% identity, 97% coverage

• Social environment affects the transcriptomic response to bacteria in ant queens
  Viljakainen, Ecology and evolution 2018
  • “...4.52E06 7.23E04 LOC105669158 Sorbitol dehydrogenaselike (LOC105669158) 1.71 8.01E09 3.21E06 LOC105675717 Defensing2 (LOC105675717) 1.80 1.05E08 3.93E06 LOC105679484 Sorbitol dehydrogenaselike (LOC105679484) 1.80 3.71E04 2.85E02 LOC105679620 Uncharacterized LOC105679620 (LOC105679620) 1.88 1.68E05 2.26E03 LOC105679945 Cytochrome P450 4C1like (LOC105679945) 1.95 1.30E03 7.71E02 LOC105679847 Probable phytanoylCoA dioxygenase (LOC105679847) 2.03 2.39E11 1.92E08 LOC105667920...”
  • “...1.32E08 LOC105676634 Carboxypeptidase Blike (LOC105676634) 1.39 1.55E06 4.88E04 LOC105668871 Phenoloxidase 2like (LOC105668871) 1.42 4.69E06 1.29E03 LOC105679484 Sorbitol dehydrogenaselike (LOC105679484) 1.45 1.09E04 1.70E02 LOC105675407 Inhibin beta E chain (LOC105675407) 1.57 1.85E15 2.47E12 LOC105670471 Trypsin epsilonlike (LOC105670471) 1.64 1.15E05 2.43E03 LOC105678258 Facilitated trehalose transporter Tret1like (LOC105678258) 1.87 6.36E06...”

YdjJ / b1774 putative zinc-binding dehydrogenase YdjJ from Escherichia coli K-12 substr. MG1655 (see 2 papers)
b1774 predicted oxidoreductase, Zn-dependent and NAD(P)-binding from Escherichia coli str. K-12 substr. MG1655
38% identity, 97% coverage

• 18th Congress of the European Hematology Association, Stockholm, Sweden, June 13–16, 2013
  , Haematologica 2013

B8B9C4 Enoyl reductase (ER) domain-containing protein from Oryza sativa subsp. indica
40% identity, 91% coverage

• Carbon and nitrogen partitioning of transgenic rice T2A-1 (Cry2A*) with different nitrogen treatments
  Ling, Scientific reports 2019
  • “...1 1 1.787 0.002 Amine oxidase B8B7J8 2.84 1 1 1.755 0.003 Putative uncharacterized protein B8B9C4 55.4 1 15 1.719 0.004 Hexokinase-7 Q1WM16 8.42 2 3 1.660 0.007 Os08g0501132 protein (Fragment) A0A0P0XHL9 8.6 1 1 1.636 0.009 Putative uncharacterized protein B8A7D9 7.14 1 1 1.627 0.010...”
  • “...1.290 0.004 Pyruvate kinase 2, cytosolic Q2QXR8 37 1 17 1.282 0.006 Putative uncharacterized protein B8B9C4 55.4 1 15 1.268 0.008 Lipoxygenase 7, chloroplastic P38419 32.14 12 23 1.265 0.009 Cytochrome c A2Y4S9 20.54 2 2 1.257 0.011 OSIGBa0106G07.1 protein Q01IX2 15.81 6 7 1.253 0.012...”

5vm2A / P77280 Crystal structure of eck1772, an oxidoreductase/dehydrogenase of unknown specificity involved in membrane biogenesis from escherichia coli
38% identity, 97% coverage

• Ligands: magnesium ion; zinc ion (5vm2A)

Cthe_2445 Alcohol dehydrogenase GroES-like protein from Clostridium thermocellum ATCC 27405
Clo1313_0076 NAD(P)-dependent alcohol dehydrogenase from Acetivibrio thermocellus DSM 1313
34% identity, 99% coverage

• Clostridium thermocellum transcriptomic profiles after exposure to furfural or heat stress
  Wilson, Biotechnology for biofuels 2013
  • “...after all stress treatments. These included the genes encoding DnaK (Cthe_1322), the GroES domain protein (Cthe_2445), and genes in the dnaK operon (Cthe_1321-Cthe_1324). The dnaK operon in C. thermocellum has a similar architecture to that in B. subtilis [ 43 ] and includes the genes encoding...”
• Proteomic analysis of Clostridium thermocellum core metabolism: relative protein expression profiles and growth phase-dependent changes in protein expression
  Rydzak, BMC microbiology 2012
  • “...acetaldehyde, albeit at lower levels. Two other zinc-containing ADH GroES-like heat shock proteins, Cthe_0388 and Cthe_2445, were also detected, the former being more highly expressed ( Additional file 4 ). While crude cell-free extract enzyme activities have shown the presence of both NADH and NADPH-dependent ADH...”
• The role of AdhE on ethanol tolerance and production in Clostridium thermocellum
  Pech-Canul, The Journal of biological chemistry 2024
  • “...cytoplasm ( Fig.S6 ). Several genes in C.thermocellum have been annotated as putative ADHs, including Clo1313_0076, Clo1313_0166, Clo1313_1798 ( adhE ), Clo1313_1827, Clo1313_1833, and Clo1313_2130 that may be responsible for this activity. Thus, in the mutants with reduced ADH activity, acetaldehyde to ethanol conversion could be...”
• Ethanol tolerance in engineered strains of Clostridium thermocellum
  Olson, Biotechnology for biofuels and bioproducts 2023
  • “...any of the adapted strains. C. thermocellum has five other genes annotated as alcohol dehydrogenases (Clo1313_0076, Clo1313_0166, Clo1313_1827, Clo1313_1833, and Clo1313_2130). In this set of genes, there was only a single mutation, A151V in Clo1313_1827. This mutation only appeared in a single lineage (LL1732 population and...”
• Ethanol tolerance of Clostridium thermocellum: the role of chaotropicity, temperature and pathway thermodynamics on growth and fermentative capacity
  Kuil, Microbial cell factories 2022
  • “...encodes for several alcohol dehydrogenases ( clo1313_2130 , clo1313_1827 , clo1313_0166 , clo1313_1833 , and clo1313_0076 ) and one aldehyde dehydrogenase ( clo1313_2911 ), potentially allowing for indirect conversion of acetyl-CoA into ethanol. However, all these genes are low or moderately expressed in transcriptomic and proteomic...”

Afu1g11020 L-arabinitol 4-dehydrogenase from Aspergillus fumigatus Af293
35% identity, 93% coverage

• Evolutionary Analysis of Sequence Divergence and Diversity of Duplicate Genes in Aspergillus fumigatus
  Yang, Evolutionary bioinformatics online 2012
  • “...< 1). However, there were several cases, in which these negatively selected genes, such as Afu1g11020 and Afu6g11810, were found to be under positive selection using MKPRF. On the other hand, several genes, such as Afu4g02720 and Afu1g00810, with a greater 2 than their duplicated copies...”
  • “...4.31 [1.93, 1.24] Afu4g10000 1.48 [0.52, 2.33] Afu2g03090 0.37 [1.29, 2.02] Afu5g03930 1.46 [0.76, 2.61] Afu1g11020 3.52 [1.66, 0.93] Afu5g01230 1.45 [0.62, 2.40] Afu3g01030 2.26 [2.16, 1.11] Afu7g08510 1.42 [0.17, 1.73] Afu1g00650 4.47 [1.85, 1.48] Afu4g14510 1.37 [0.63, 2.37] Afu2g11120 0.81 [1.51, 1.17] Afu3g10960 1.37 [0.76,...”

NP_524311 sorbitol dehydrogenase 2 from Drosophila melanogaster
37% identity, 94% coverage

• Global transcriptome analysis of orange wheat blossom midge, Sitodiplosis mosellana (Gehin) (Diptera: Cecidomyiidae) to identify candidate transcripts regulating diapause
  Gong, PloS one 2013
  • “...Apis mellifera , AmSDH1 (XP_003251602) and AmSDH2 (XP-392401), Drosophila melanogaster , DmSDH1 (NP_477348) and DmSDH2 (NP_524311), Glossina morsitans morsitans , GmSDH (ADD19424), Bombyx mori , BmSDH1 (D13371), BmSDH2a (AB164059) and BmSDH2b (AB604175). Juvenile hormone epoxide hydrolase (JHEHs) and juvenile hormone esterase (JHE) which were down-regulated in...”

NP_477348 sorbitol dehydrogenase 1, isoform A from Drosophila melanogaster
36% identity, 94% coverage

• Global transcriptome analysis of orange wheat blossom midge, Sitodiplosis mosellana (Gehin) (Diptera: Cecidomyiidae) to identify candidate transcripts regulating diapause
  Gong, PloS one 2013
  • “...the sequences are: Apis mellifera , AmSDH1 (XP_003251602) and AmSDH2 (XP-392401), Drosophila melanogaster , DmSDH1 (NP_477348) and DmSDH2 (NP_524311), Glossina morsitans morsitans , GmSDH (ADD19424), Bombyx mori , BmSDH1 (D13371), BmSDH2a (AB164059) and BmSDH2b (AB604175). Juvenile hormone epoxide hydrolase (JHEHs) and juvenile hormone esterase (JHE) which...”

An08g09380 uncharacterized protein from Aspergillus niger
36% identity, 88% coverage

• Transcriptome analysis of Aspergillus niger grown on sugarcane bagasse
  de, Biotechnology for biofuels 2011
  • “...increase in mRNA accumulation of the genes encoding these enzymes (xylose reductase (An01g03740), xylitol dehydrogenase (An08g09380) and D-xylulokinase (An07g03140)) during growth of A. niger on SEB. These data are supported by promoter analysis of the genes with putative binding sites for XlnR (reported herein and by...”

KLMA_70044 sorbitol dehydrogenase 1 from Kluyveromyces marxianus DMKU3-1042
39% identity, 92% coverage

• Genetic basis of the highly efficient yeast Kluyveromyces marxianus: complete genome sequence and transcriptome analyses
  Lertwattanasakul, Biotechnology for biofuels 2015
  • “...GAL1 Galactose KLMA_20331 Galactose-1-phosphate uridylyltransferase GAL7 KLMA_30099 Phosphoglucomutase GAL5 (PGM2) KLMA_10683 Xylose reductase XYL1 Xylose KLMA_70044 Xylitol dehydrogenase XYL2 KLMA_80066 Xylulokinase XKS1 KLMA_30577 Arabinose dehydrogenase [NADP + dependent] ARA1 Arabinose KLMA_40310 Arabinose dehydrogenase [NAD dependent] ARA2 KLMA_80176 Xylose/arabinose reductase YJR096W KLMA_10558 D-Arabitol-2-dehydrogenase ARD2 KLMA_10157 Probable ribokinase...”

G3AIP8 D-xylulose reductase (EC 1.1.1.9) from Spathaspora passalidarum (see paper)
37% identity, 91% coverage

LAD_ASPOZ / Q763T4 L-arabinitol 4-dehydrogenase; LAD; EC 1.1.1.12 from Aspergillus oryzae (Yellow koji mold) (see paper)
Q763T4 L-arabinitol 4-dehydrogenase (EC 1.1.1.12) from Aspergillus oryzae (see 3 papers)
AO090005001078 No description from Aspergillus oryzae RIB40
34% identity, 86% coverage

• function: Catalyzes the NAD-dependent oxidation of L-arabinitol to L- xylulose in the fungal L-arabinose catabolic pathway. L-arabinose catabolism is important for using plant material as a carbon source. Also active on ribitol and xylitol. Not active with NADP as cosubstrate.
  catalytic activity: L-arabinitol + NAD(+) = L-xylulose + NADH + H(+) (RHEA:16381)
  cofactor: Zn(2+) (Binds 2 Zn(2+) ions per subunit.)
  subunit: Homotetramer.
• Comprehensive annotation of secondary metabolite biosynthetic genes and gene clusters of Aspergillus nidulans, A. fumigatus, A. niger and A. oryzae
  Inglis, BMC microbiology 2013
  • “...AO090005000993 AO090005000990 - AO090005001001 AO090005000986 - AO090005001002 AO090005000990 - AO090005000993 ECS ECS AO090005001079 cluster AO090005001079 AO090005001078 - AO090005001087 AO090005001075 - AO090005001081 - n/a n/a AO090005001551 cluster AO090005001551 - AO090005001668 - AO090005001555 - n/a n/a AO090009000052 cluster AO090009000052 - AO090009000046 - AO090009000717 AO090009000051 - AO090009000717 IGD IGD...”
• A trispecies Aspergillus microarray: comparative transcriptomics of three Aspergillus species
  Andersen, Proceedings of the National Academy of Sciences of the United States of America 2008
  • “...AN0423 AN0942 AO090001000069 AO090005000767 AO090003000859 AO090005001078 JGI55668 JGI55419 JGI51997 JGI46405 AN10124 AN10169 AO090003000497 AO090038000426...”

ladB / A2R6Z2 D-galactitol dehydrogenase from Aspergillus niger (strain ATCC MYA-4892 / CBS 513.88 / FGSC A1513) (see paper)
An16g01710 uncharacterized protein from Aspergillus niger
A2R6Z2 D-xylulose reductase from Aspergillus niger (strain ATCC MYA-4892 / CBS 513.88 / FGSC A1513)
33% identity, 96% coverage

• Genetic Interaction of Aspergillus nidulans galR, xlnR and araR in Regulating D-Galactose and L-Arabinose Release and Catabolism Gene Expression
  Kowalczyk, PloS one 2015
  • “...XxkA = AN7459. Gene numbers of A . niger enzymes: XyrA = An01g03740, LadB = An16g01710, XhrA = An16g01650, SdhA = An07g01290, HxkA = An02g14380. Filamentous fungi use several pathways for D-galactose catabolism. The best studied pathway is the Leloir pathway, which is present in prokaryotic...”
• Integration of enzyme constraints in a genome-scale metabolic model of Aspergillus niger improves phenotype predictions
  Zhou, Microbial cell factories 2021
  • “...A2QMS4, A2Q8B5, A2QG25, A2QVE5, and A2QB6 are involved in the xylose metabolism pathway, and A2QB7, A2R6Z2, A2Q8B5, and A2QG25 are enzymes related to arabinose-related enzyme synthesis and metabolism (Fig. 11 A). It could be seen from the metabolic pathway diagram of A. niger that the xylose...”

PPTG_17182 chlorophyll synthesis pathway protein BchC from Phytophthora nicotianae INRA-310
38% identity, 92% coverage

• Transcriptomic and Ultrastructural Signatures of K⁺-Induced Aggregation in Phytophthora parasitica Zoospores
  Bassani, Microorganisms 2020
  • “...most expressed genes presented respectively 2 alcohol dehydrogenase domains, containing a Zn 2+ binding site (PPTG_17182; 6359 FPKM) and a ribonucleotide reductase domain (PPTG_16020; 6171 FPKM), possibly being involved in carbohydrate and nucleotide metabolism. Because of its role in DNA synthesis, ribonucleotide reductase could be involved...”

SS1G_05959 hypothetical protein from Sclerotinia sclerotiorum 1980 UF-70
37% identity, 93% coverage

• The Coupling Between Cell Wall Integrity Mediated by MAPK Kinases and SsFkh1 Is Involved in Sclerotia Formation and Pathogenicity of Sclerotinia sclerotiorum
  Cong, Frontiers in microbiology 2022
  • “...obtained from RNA-seq were selected for qRT-PCR analysis including SS1G_12143, SS1G_06394, SS1G_13636, SS1G_04353, SS1G_00601, SS1G_09402, SS1G_05959, SS1G_10880, SS1G_14424, and SS1G_12905. In general, the findings of qRT-PCR were consistent with those of transcriptome analysis, thereby demonstrating that RNA-Seq data was valid and accurate ( Figure 3A )....”

LAD_NEUCR / Q7SI09 L-arabinitol 4-dehydrogenase; LAD; EC 1.1.1.12 from Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) (see 2 papers)
Q7SI09 L-arabinitol 4-dehydrogenase (EC 1.1.1.12) from Neurospora crassa (see paper)
NCU00643 L-arabinitol 4-dehydrogenase from Neurospora crassa OR74A
33% identity, 91% coverage

• function: Catalyzes the NAD-dependent oxidation of L-arabinitol to L- xylulose in the fungal L-arabinose catabolic pathway. L-arabinose catabolism is important for using plant material as a carbon source. Not active on D-arabinitol, D-sorbitol and D-mannitol.
  catalytic activity: L-arabinitol + NAD(+) = L-xylulose + NADH + H(+) (RHEA:16381)
  cofactor: Zn(2+) (Binds 2 Zn(2+) ions per subunit.)
  subunit: Homotetramer.
• The regulatory and transcriptional landscape associated with carbon utilization in a filamentous fungus
  Wu, Proceedings of the National Academy of Sciences of the United States of America 2020
  • “...two -xylosidases (NCU00709, NCU09923), the l -arabinose transporter lat-1 (NCU02188), and l -arabinitol dehydrogenase ard-1 (NCU00643) ( Fig. 2 E and Dataset S4 ), suggesting that the NCU05414 mutant would be defective for utilization of arabinan, arabinose, and galactose. As predicted, the NCU05414 strain showed dramatically...”
• The transcription factor PDR-1 is a multi-functional regulator and key component of pectin deconstruction and catabolism in Neurospora crassa
  Thieme, Biotechnology for biofuels 2017
  • “...homolog NCU09034, the -galactosidases GH35-1 (NCU00642) and GH35-2 (NCU04623), and the l -arabinitol 4-dehydrogenase ARD-1 (NCU00643). Fig.3 Scatterplots and clustering of RNA-seq data from WT and pdr - 1 . Scatterplot diagram ( A , B ) axes are log 10 -scaled. A Full-genome expression profile...”
  • “...and rha1 homologs (NCU09034 and NCU09035, respectively), the putative gaaB/lgd1 homolog (NCU07064), ard - 1 (NCU00643), and the GCY protein-coding gene NCU01906. In particular, the failed induction of the endo-PG-encoding gh28 - 1 and NCU07064, probably being responsible for the second step in d -GalA catabolism,...”
• Transcriptional comparison of the filamentous fungus Neurospora crassa growing on three major monosaccharides D-glucose, D-xylose and L-arabinose
  Li, Biotechnology for biofuels 2014
  • “...L-arabinose. Genes tested included D-xylose reductase (XR, NCU08384), xylitol dehydrogenase (XDH, NCU00891), L-arabitol dehydrogenase (LAD NCU00643) and L-xylulose reductase (LXR NCU09041). The growth phenotypes showed that the deletion of xr or xdh significantly affected the growth on either D-xylose or L-arabinose. The mutants of xr ,...”
  • “...plus 2%L-arabinose for 5days. XR, D-xylose reductase, NCU08384: XDH, xylitol dehydrogenase, NCU00891; LAD, L-arabitol dehydrogenase, NCU00643; LXR, L-xylulose reductase, NCU09041; NADH, nicotinamide adenine dinucleotide, reduced; NADPH, nicotinamide adenine dinucleotide phosphate, reduced; WT, wild-type. The length of the scale is about 0.5cm. Transcriptome analysis of N. crassa...”
• A comparative systems analysis of polysaccharide-elicited responses in Neurospora crassa reveals carbon source-specific cellular adaptations
  Benz, Molecular microbiology 2014
  • “...cultures. (E) The absence of LAT-1 specifically affects L-Ara signaling. The expression strength of ard-1 (NCU00643), xyr-1 (NCU08384) and gh28-2 (NCU06961) in WT vs . lat-1 was assessed by qPCR after a 4h transfer to either no carbon or 2 M of the indicated monosaccharides. The...”
• Deciphering transcriptional regulatory mechanisms associated with hemicellulose degradation in Neurospora crassa
  Sun, Eukaryotic cell 2012
  • “...and NCU04623), NCU09041 (L-xylulose reductase), NCU00643 (L-arabinitol 4dehydrogenase), two D-arabinitol 2-dehydrogenase genes (NCU02097 and NCU20791), NCU03188...”
• Transcriptome analysis of Aspergillus niger grown on sugarcane bagasse
  de, Biotechnology for biofuels 2011
  • “...in the metabolism of pentoses, such as An01g10920 and An12g00030 (L-arabinitol 4-dehydrogenase ( N. crassa NCU00643) and xylitol dehydrogenase ( N. crassa NCU00891), respectively), also have increased mRNA accumulation in both substrates (Additional file 5 , Table S5). These data strongly suggest that although diverse biomasses...”
• Systems analysis of plant cell wall degradation by the model filamentous fungus Neurospora crassa
  Tian, Proceedings of the National Academy of Sciences of the United States of America 2009
  • “...sugars (for example, NCU00891, xylitol dehydrogenase and NCU00643, a predicted arabinitol dehydrogenase), a predicted sugar transporter (NCU01132), and 48...”
• Understanding Functional Roles of Native Pentose-Specific Transporters for Activating Dormant Pentose Metabolism in Yarrowia lipolytica
  Ryu, Applied and environmental microbiology 2018
  • “...ADHNcr (from N. crassa; UniProt accession no. Q7SI09 [34]), NADPH-dependent XLRAni (UniProt accession no. G3YG17 [35]), NADPH-dependent XLRTre (from Trichoderma...”

3m6iA / Q7SI09 L-arabinitol 4-dehydrogenase (see paper)
33% identity, 92% coverage

• Ligands: zinc ion; nicotinamide-adenine-dinucleotide (3m6iA)

PITG_04121 sorbitol dehydrogenase, putative from Phytophthora infestans T30-4
38% identity, 92% coverage

• Niche-specific metabolic adaptation in biotrophic and necrotrophic oomycetes is manifested in differential use of nutrients, variation in gene content, and enzyme evolution
  Ah-Fong, PLoS pathogens 2019
  • “...( e . g . PITG_03721; EC 2.7.9.1), sorbitol/iditol dehydrogenase ( e . g . PITG_04121; EC 1.1.1.14), salicylate dehydrogenase (PITG_17117; EC 1.14.13.1), and formate dehydrogenase (PITG_13448; EC 1.2.1.2). Based on searching the Fungidb.org and Eumicrobedb.org web sites [ 22 , 23 ], orthologs of these...”

PICST_86924, XP_001386982 D-xylulose reductase (Xylitol dehydrogenase) (XDH) from Scheffersomyces stipitis CBS 6054
P22144 D-xylulose reductase from Scheffersomyces stipitis (strain ATCC 58785 / CBS 6054 / NBRC 10063 / NRRL Y-11545)
35% identity, 91% coverage

• Development of a Vector Set for High or Inducible Gene Expression and Protein Secretion in the Yeast Genus Blastobotrys
  Boisramé, Journal of fungi (Basel, Switzerland) 2022
  • “...was performed using the S. stipitis coding sequences for xylose-reductase XR (PICST_89614), xylitol dehydrogenase XDH (PICST_86924) and xylulose kinase XK (PICST_68734) as queries to identify LS3 homologues. Results presented in Table 3 clearly indicate that LS3 contains in its genome the set of enzymes required to...”
  • “...ARAD1C28094g cd19115 T. ciferrii KAA8897533.1 (79%) Su. lignohabitans XP_018737989.1 (74%) XDH (Xylitol dehydrogenase) S. stipitis PICST_86924 (XP_001386982.1) ARAD1D37840g (CAG34729.1) - T. ciferrii KAA8903833.1 (64%) Su. lignohabitans XP_018736469.1 (60%) XK (Xylulo kinase) S. stipitis PICST_68734 (XP_001387325.2) ARAD1C08800g cd07776 T. ciferrii KAA8897400.1 (59%) Su. lignohabitans XP_018737264.1 (59%)...”
• Engineering xylose utilization in Yarrowia lipolytica by understanding its cryptic xylose pathway
  Rodriguez, Biotechnology for biofuels 2016
  • “...metabolic pathway for xylose utilization. Well-characterized xylose metabolism enzymes from S. stipitis (XYR: XP_001385181, XDH: XP_001386982, and XKS: XP_001387325) were used as the query to BLAST against the Y. lipolytica CLIB 122 protein database. The results of the top hits for each of the hypothetical enzymes,...”
  • “...lipolytica were identified using S. stipitis genes for xylose reductase (NCBI: XP_001385181), xylitol dehydrogenase (NCBI: XP_001386982), and xylulose kinase (NCBI: XP_001387325) as the query. The BLAST search [ 36 ] was targeted to the Y. lipolytica CLIB 122 genome and individual gene DNA sequences were compared...”
• A constraint-based model of Scheffersomyces stipitis for improved ethanol production
  Liu, Biotechnology for biofuels 2012
  • “...the xylose medium. The four genes exclusively belonged to xylose metabolism were XYL1 (PICST_89614), XYL2 (PICST_86924), PGI1 (PICST_84923), and TAL1 (PICST_74289). Of them, XYL1 (xylose reductase) and XYL2 (xylitol dehydrogenase) encode the two initial enzymes of xylose metabolic pathway, which has been introduced to S. cerevisiae...”
  • “...is a well characterized pathway including three reactions encoded by three genes XYL1 (PICST_89614), XYL2 (PICST_86924), and XKS (PICST_68734), respectively [ 39 ]. Based on our simulation, this pathway is thought to be the only route redirecting carbon flux from xylose to PPP in the wild-type...”
• Comparison of SHF and SSF processes from steam-exploded wheat straw for ethanol production by xylose-fermenting and robust glucose-fermenting Saccharomyces cerevisiae strains.
  Tomás-Pejó, Biotechnology and bioengineering 2008 (PubMed)
  • GeneRIF: Introduced in S.cerevisiae F12, succesfully enable it to metabolize xylose from cereal straw
• Thermostabilization of Pichia stipitis xylitol dehydrogenase by mutation of structural zinc-binding loop.
  Annaluru, Journal of biotechnology 2007 (PubMed)
  • GeneRIF: A high thermostability of this enzyme was obtained by subsequent site-directed mutagenesis of the structural zinc-binding loop.
• Molecular Modification Enhances Xylose Uptake by the Sugar Transporter KM_SUT5 of Kluyveromyces marxianus
  Luo, International journal of molecular sciences 2024
  • “...inserting D-xylose reductase gene XYL1 (UniprotKB number: P31867) and D-xylitol dehydrogenase gene XYL2 (UniprotKB number: P22144) from Scheffersomyces stipitis into linearized YEplac195 using the DNA assembler method [ 34 , 35 ]. All plasmids were chemically transformed into Escherichia coli DH5 competent cells to construct the...”
• Functional survey for heterologous sugar transport proteins, using Saccharomyces cerevisiae as a host
  Young, Applied and environmental microbiology 2011
  • “...Q2MEV7 GXS1 DEHA0D02167 Q2MDH1 Q6AWX0 At5g17010 GXF1 Q0WWW9 P22144 At5g59250 P31867 XYL2 UniProt accession no. XYL1 Gene/locus tag E. coli D. hansenii C....”

G3AIB3 D-xylulose reductase (EC 1.1.1.9) from Spathaspora passalidarum (see paper)
37% identity, 91% coverage

7y9pA / P22144 Xylitol dehydrogenase s96c/s99c/y102c mutant(thermostabilized form) from pichia stipitis (see paper)
35% identity, 93% coverage

• Ligand: zinc ion (7y9pA)

XYL2 D-xylulose reductase from Candida albicans (see 2 papers)
XP_719434 L-iditol 2-dehydrogenase from Candida albicans SC5314
35% identity, 92% coverage

• CharProtDB CGD description: Protein described as similar to D-xylulose reductase; immunogenic in mouse; soluble protein in hyphae; Hog1p-induced; induced during cell wall regeneration; caspofungin or fluconazole-induced; Mnl1p-induced in weak acid stress
• Xylose metabolism in the fungus Rhizopus oryzae: effect of growth and respiration on L+-lactic acid production
  Maas, Journal of industrial microbiology & biotechnology 2008
  • “...numbers of XDH were: Pichia stipitis (A16166), Neurospora crassa (XP_325071), Aspergillus oryzae (AB109101), Candida albicans (XP_719434). Accession numbers of XK were: Piromyces sp. (AJ249910), Pichia stipitis (AAF72328), Aspergillus niger (AJ305311), Neurospora crassa (EAA33587), Candida sp. (DQ087275). Since no fungal genes other than the Piromyces sp. gene...”

LAD_PENRW / B6HI95 L-arabinitol 4-dehydrogenase; LAD; EC 1.1.1.12 from Penicillium rubens (strain ATCC 28089 / DSM 1075 / NRRL 1951 / Wisconsin 54-1255) (Penicillium chrysogenum) (see paper)
B6HI95 L-arabinitol 4-dehydrogenase (EC 1.1.1.12) from Penicillium chrysogenum (see paper)
33% identity, 85% coverage

• function: Catalyzes the NAD-dependent oxidation of L-arabinitol to L- xylulose in the fungal L-arabinose catabolic pathway. L-arabinose catabolism is important for using plant material as a carbon source. NADP cannot act as a cosubstrate.
  catalytic activity: L-arabinitol + NAD(+) = L-xylulose + NADH + H(+) (RHEA:16381)
  cofactor: Zn(2+) (Binds 2 Zn(2+) ions per subunit.)
  subunit: Homotetramer.

ladA putative L-arabinitol 4-dehydrogenase from Emericella nidulans (see paper)
33% identity, 85% coverage

• CharProtDB Description: Putative L-arabinitol 4-dehydrogenase with a predicted role in L-arabinose/arabitol and D-xylose/D,L-xylulose/xylitol metabolism; Source:AspGD

Q6KAV2 D-xylulose reductase (EC 1.1.1.9) from Blastobotrys adeninivorans (see paper)
39% identity, 90% coverage

lad1 / Q96V44 D-galactitol dehydrogenase (EC 1.1.1.12) from Hypocrea jecorina (see paper)
LAD_HYPJE / Q96V44 L-arabinitol 4-dehydrogenase; LAD; EC 1.1.1.12 from Hypocrea jecorina (Trichoderma reesei) (see 4 papers)
Q96V44 L-arabinitol 4-dehydrogenase (EC 1.1.1.12) from Trichoderma reesei (see 5 papers)
34% identity, 84% coverage

• function: Catalyzes the NAD-dependent oxidation of L-arabinitol to L- xylulose in the fungal L-arabinose catabolic pathway. L-arabinose catabolism is important for using plant material as a carbon source. Can partially compensate for xylitol dehydrogenase in xdh1 mutants. Also oxidizes galactitol to L-xylo-3-hexulose as an alternative to the standard Leloir pathway for D-galactose metabolism. NADP cannot act as a cosubstrate.
  catalytic activity: L-arabinitol + NAD(+) = L-xylulose + NADH + H(+) (RHEA:16381)
  cofactor: Zn(2+) (Binds 2 Zn(2+) ions per subunit.)
  subunit: Homotetramer.

H6WCP4 L-arabinitol 4-dehydrogenase (EC 1.1.1.12) from Aspergillus tubingensis (see paper)
33% identity, 85% coverage

ladA / A2QAC0 L-arabinitol 4-dehydrogenase (EC 1.1.1.9; EC 1.1.1.12) from Aspergillus niger (strain ATCC MYA-4892 / CBS 513.88 / FGSC A1513) (see 2 papers)
LAD_ASPNC / A2QAC0 L-arabinitol 4-dehydrogenase; LAD; EC 1.1.1.12 from Aspergillus niger (strain ATCC MYA-4892 / CBS 513.88 / FGSC A1513) (see 3 papers)
A2QAC0 L-arabinitol 4-dehydrogenase (EC 1.1.1.12) from Aspergillus niger (see 2 papers)
An01g10920 uncharacterized protein from Aspergillus niger
33% identity, 85% coverage

• function: Catalyzes the NAD-dependent oxidation of L-arabinitol to L- xylulose in the fungal L-arabinose catabolic pathway. L-arabinose catabolism is important for using plant material as a carbon source. Not active with NADP as cosubstrate.
  catalytic activity: L-arabinitol + NAD(+) = L-xylulose + NADH + H(+) (RHEA:16381)
  cofactor: Zn(2+) (Binds 2 Zn(2+) ions per subunit.)
  subunit: Homotetramer.
• The Cultivation Method Affects the Transcriptomic Response of Aspergillus niger to Growth on Sugar Beet Pulp
  Garrigues, Microbiology spectrum 2021
  • “...0.09 1.25 0.14 An08g01740 xyrB PCP 1,661.46 100.20 118.87 152.42 590.32 391.79 0.09 5.89 3.30 An01g10920 ladA PCP 5,723.10 77.96 111.08 611.80 2,149.41 247.24 0.11 27.57 2.23 An08g01930 lxrA PCP 4,773.27 39.21 163.31 407.68 1,199.78 86.13 0.09 30.60 0.53 An07g03570 lxrB PCP 1,711.10 619.79 418.27 1,399.26...”
• Mutations in AraR leading to constitutive expression of arabinolytic genes in Aspergillus niger under derepressing conditions [corrected]
  Reijngoud, Applied microbiology and biotechnology 2019
  • “...used for RNA extraction and subsequent Northern blot analysis. Probes used include ladA (L-arabitol dehydrogenase; An01g10920), abnA (endo-1,5-alpha-arabinanase; An09g01190), and the arabinofuranosidases encoded by abfA (An01g00330), abfB (An15g02300), and abfC (An08g01710). 18S RNA probe was used as loading control The expression of arabinofuranosidases abfA , abfB...”
• Updating genome annotation for the microbial cell factory Aspergillus niger using gene co-expression networks
  Schäpe, Nucleic acids research 2019
  • “...response genes reported by Andersen etal. ( 51 ), including those encoding an l-arabitol dehydrogenase (An01g10920), aldose 1-epimerase (An02g09090), glycoside hydrolase (An12g01850), xylitol dehydrogenase (An12g00030), sugar transporter (An03g01620) and short-chain dehydrogenase (An04g03530). We therefore conclude that sub-networks generated in our study can be used to define...”
• Transcriptome analysis of Aspergillus niger grown on sugarcane bagasse
  de, Biotechnology for biofuels 2011
  • “...(Additional file 5 , Table S5). Genes involved in the metabolism of pentoses, such as An01g10920 and An12g00030 (L-arabinitol 4-dehydrogenase ( N. crassa NCU00643) and xylitol dehydrogenase ( N. crassa NCU00891), respectively), also have increased mRNA accumulation in both substrates (Additional file 5 , Table S5)....”
• Analysis of variance components reveals the contribution of sample processing to transcript variation
  van, Applied and environmental microbiology 2009
  • “...An09g03300 An03g00500 An15g01500 An11g01100 An03g01620 An06g00560 An01g10920 An01g03740 An12g00030 An07g03140 An02g03590 Signal sequence predicted Yes Yes Yes...”

Afu8g02000 sorbitol/xylitol dehydrogenase, putative from Aspergillus fumigatus Af293
34% identity, 90% coverage

• The Transcriptome Response to Azole Compounds in Aspergillus fumigatus Shows Differential Gene Expression across Pathways Essential for Azole Resistance and Cell Survival
  Hokken, Journal of fungi (Basel, Switzerland) 2023
  • “...-2,70 Afu6g11840 Sodium bile acid symporter family protein N/A -2,70 Afu6g00430 IgE-binding protein N/A -2,76 Afu8g02000 Sorbitol/xylitol dehydrogenase; putative N/A V162(R)-ISA) Up-Regulated 2logFC gene Description 8,95 Afu3g12910 O-methyltransferase GliM-like; putative hasC 6,59 Afu3g01960 Putative uncharacterized protein N/A 6,58 Afu6g11850 Putative uncharacterized protein N/A 6,25 Afu4g02720 GPI...”

LAD_TALEM / C5J3R8 L-arabinitol 4-dehydrogenase; LAD; EC 1.1.1.12 from Talaromyces emersonii (Thermophilic fungus) (Rasamsonia emersonii) (see paper)
C5J3R8 L-arabinitol 4-dehydrogenase (EC 1.1.1.12) from Rasamsonia emersonii (see paper)
34% identity, 85% coverage

• function: Catalyzes the NAD-dependent oxidation of L-arabinitol to L- xylulose in the fungal L-arabinose catabolic pathway. L-arabinose catabolism is important for using plant material as a carbon source. NADP cannot act as a cosubstrate.
  catalytic activity: L-arabinitol + NAD(+) = L-xylulose + NADH + H(+) (RHEA:16381)
  cofactor: Zn(2+) (Binds 2 Zn(2+) ions per subunit.)
  subunit: Homotetramer.

CNAG_00115 chlorophyll synthesis pathway protein BchC from Cryptococcus neoformans var. grubii H99
35% identity, 89% coverage

• Brain inositol is a novel stimulator for promoting Cryptococcus penetration of the blood-brain barrier
  Liu, PLoS pathogens 2013
  • “...CNAG_06628 Aldehyde dehydrogenase 4.31 CNC02480 CNAG_01745 sn-Glycerol-3-phosphate dehydrogenase 3.52 CNF04450 CNAG_07660 Pyruvate dehydrogenase 3.51 CNA01050 CNAG_00115 Sorbitol dehydrogenase 3.33 CNJ00950 CNAG_04659 Pyruvate decarboxylase 3.23 CNG00600 CNAG_07745 Mannitol-1-phosphate dehydrogenase 3.00 CNC06440 CNAG_01539 Inositol-1-phosphate synthase (Ino1) 2.79 CNE01560 CNAG_02399 Glutathione reductase 2.72 CND00180 CNAG_00879 Glutamate dehydrogenase 2.63 CNA04610...”

CNJ01090 xylitol dehydrogenase from Cryptococcus neoformans var. neoformans JEC21
35% identity, 89% coverage

• Transcription factor Nrg1 mediates capsule formation, stress response, and pathogenesis in Cryptococcus neoformans
  Cramer, Eukaryotic cell 2006
  • “...protein Formate dehydrogenase CNI02800 CNL04840 CNN00660 CNA08060 CNA02580 CNJ01090 CNM00600 CNF03470 4.4 3.7 3.5 3 2.8 2.7 0.29 0.22 CNC00480 3.4 CNK01630...”

sdhA / A2QM95 L-arabinitol dehydrogenase (EC 1.1.1.12; EC 1.1.1.9; EC 1.1.1.14) from Aspergillus niger (strain ATCC MYA-4892 / CBS 513.88 / FGSC A1513) (see 3 papers)
An07g01290 uncharacterized protein from Aspergillus niger
34% identity, 92% coverage

• Genetic Interaction of Aspergillus nidulans galR, xlnR and araR in Regulating D-Galactose and L-Arabinose Release and Catabolism Gene Expression
  Kowalczyk, PloS one 2015
  • “...A . niger enzymes: XyrA = An01g03740, LadB = An16g01710, XhrA = An16g01650, SdhA = An07g01290, HxkA = An02g14380. Filamentous fungi use several pathways for D-galactose catabolism. The best studied pathway is the Leloir pathway, which is present in prokaryotic and eukaryotic organisms [ 14 ]....”

CNA01050 sorbitol dehydrogenase from Cryptococcus neoformans var. neoformans JEC21
35% identity, 89% coverage

• Brain inositol is a novel stimulator for promoting Cryptococcus penetration of the blood-brain barrier
  Liu, PLoS pathogens 2013
  • “...CNF03900 CNAG_06628 Aldehyde dehydrogenase 4.31 CNC02480 CNAG_01745 sn-Glycerol-3-phosphate dehydrogenase 3.52 CNF04450 CNAG_07660 Pyruvate dehydrogenase 3.51 CNA01050 CNAG_00115 Sorbitol dehydrogenase 3.33 CNJ00950 CNAG_04659 Pyruvate decarboxylase 3.23 CNG00600 CNAG_07745 Mannitol-1-phosphate dehydrogenase 3.00 CNC06440 CNAG_01539 Inositol-1-phosphate synthase (Ino1) 2.79 CNE01560 CNAG_02399 Glutathione reductase 2.72 CND00180 CNAG_00879 Glutamate dehydrogenase 2.63...”

Atu1408 sorbitol dehydrogenase from Agrobacterium tumefaciens str. C58 (Cereon)
35% identity, 99% coverage

• Coordinated Regulation of Species-Specific Hydroxycinnamic Acid Degradation and Siderophore Biosynthesis Pathways in Agrobacterium fabrum
  Baude, Applied and environmental microbiology 2016
  • “...regions, i.e., the SpG8-1a subregion, spanning atu1398 to atu1408, and the SpG8-1b subregion, spanning atu1409 to atu1423. Genes atu1415, atu1416, atu1417, and...”
  • “...of SpG8-1b in the SpG8-1a region spanning atu1398 to atu1408 (3), was significantly downregulated. This gene encodes a putative GntR family regulator and may be...”

RHTO_01629 L-iditol 2-dehydrogenase from Rhodotorula toruloides NP11
36% identity, 80% coverage

• Genome-scale metabolic modeling reveals metabolic trade-offs associated with lipid production in Rhodotorula toruloides
  Reķēna, PLoS computational biology 2023
  • “...mentioned: However, protein levels of L-xylulose reductase (EC 1.1.1.10, RHTO_00373) and L-arabinitol dehydrogenase (EC 1.1.1.12, RHTO_01629) were also 10-fold upregulated during growth on xylose versus other substrates. 17. Page 22, line 459-461, the authors mentioned: In support of this mechanism, the metabolic model could only predict...”
• Xylose Metabolism and the Effect of Oxidative Stress on Lipid and Carotenoid Production in Rhodotorula toruloides: Insights for Future Biorefinery
  Pinheiro, Frontiers in bioengineering and biotechnology 2020
  • “...(DAD, RHTO_07844), and L-iditol 2-dehydrogenase, identified by Bommareddy et al. (2015) as L-arabitol dehydrogenase (LAD, RHTO_01629) were all down-regulated under nitrogen- limiting conditions. Approximately four-fold increased transketolase (TKT, RHTO_03248) abundance compared to phosphoketolase (PK, RHTO_04463) was consistent with the simulated increased flux through the transketolase reaction....”

AO090020000635 No description from Aspergillus oryzae RIB40
35% identity, 89% coverage

• Proteomic analysis of the secretory response of Aspergillus niger to D-maltose and D-xylose
  de, PloS one 2011
  • “...Hnt1 (4.1/7.5) Sc Adk1 (4.7), Sc Aat2 (4.6), Hs PYCR1 (4.5), Sc Gph1 (4.2) Ao AO090020000635 (5.2), Sp SPAC19G12.04 (4.3), Sc Cys4 (4.1) ROS defence An02g12940 (5.1/4.0) Nuclear Sc Nic96 (6.5), An09g00500 (4.6), Sc Nup170 (4.0) Unknown and others Hs CIRBP (5.5/9.4) Nc NCU03370 (10.7), Sp...”

B4DKI2 Sorbitol dehydrogenase from Homo sapiens
37% identity, 73% coverage

• Analysis of proteomic differences between liquefied after-cataracts and normal lenses using two-dimensional gel electrophoresis and mass spectrometry.
  Ge, International journal of ophthalmology 2017

BCAM1704 2,3-butanediol dehydrogenase from Burkholderia cenocepacia J2315
33% identity, 93% coverage

• Burkholderia cenocepacia differential gene expression during host-pathogen interactions and adaptation to the host environment
  O'Grady, Frontiers in cellular and infection microbiology 2011
  • “...Putative lyase 1.74 BCAM1602 Conserved hypothetical protein 1.59 BCAM1623 Thiolase 2.75 BCAM1643 AMP-binding protein 1.76 BCAM1704 2,3-Butanediol dehydrogenase 1.79 BCAM1710 Putative enoyl-CoA hydratase/isomerase 1.58 BCAM1711 Phenylacetate-coenzyme A ligase 1.57 BCAM1733 Putative membrane protein 2.36 BCAM1734 Putative cytochrome c 1.73 BCAM1735 Putative oxidoreductase 1.89 BCAM1736 Conserved hypothetical...”

CCM_06561 sorbitol dehydrogenase from Cordyceps militaris CM01
33% identity, 91% coverage

• Transcriptome-wide analysis reveals the progress of Cordyceps militaris subculture degeneration
  Yin, PloS one 2017
  • “...of C . militaris polysaccharide, including1,4--glucan branching enzyme(CCM_03369), -N-acetylglucosaminidase (CCM_04090), mannan endo-1,6--mannosidase (CCM_05709), sorbitol dehydrogenase (CCM_06561), mannosidase MsdS (CCM_08733), and sorbitol utilization protein (CCM_09007)[ 39 ]. Toxic substances such as mycotoxins, active oxygen and other nonnutritional xenobiotic compounds, naturally exist in the environment and can be...”

WP_039351048 2,3-butanediol dehydrogenase from Burkholderia contaminans
32% identity, 97% coverage

• Employing Genomic Tools to Explore the Molecular Mechanisms behind the Enhancement of Plant Growth and Stress Resilience Facilitated by a Burkholderia Rhizobacterial Strain
  Chang, International journal of molecular sciences 2024
  • “...cellulase VOCs -Terpenoid synthesis WP_039342858 ispF WP_011352390 ispD WP_039342723 Dxr WP_039360848 terpene synthase -Acetoin biosynthesis WP_039351048 Bdh1 WP_039344544 Bdh1 Lipopolysaccharide synthesis WP_039360609 waaF WP_039360073 LptD Spermidine synthesis WP_039360784 speD WP_039370372 SpdS WP_039353965 speB WP_039360775 SPMS WP_039339273 SPMS Osmolytes synthesis -Proline WP_039361374 proC WP_039353092 proB WP_039361497 proA...”

DHSO_SCHPO / P36624 Sorbitol dehydrogenase; SDH; Polyol dehydrogenase; Protein tms1; EC 1.1.1.- from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) (see paper)
tms1 / RF|NP_595120.1 hexitol dehydrogenase (predicted); EC 1.1.1.- from Schizosaccharomyces pombe (see 2 papers)
SPBC1773.05c hexitol dehydrogenase (predicted) from Schizosaccharomyces pombe
32% identity, 94% coverage

• function: Polyol dehydrogenase that catalyzes the reversible NAD(+)- dependent oxidation of various sugar alcohols. Is active with D- sorbitol (D-glucitol) as substrate, leading to the C2-oxidized product D-fructose (By similarity). Suppresses growth arrest induced by a p53 tumor mutant in fission yeast (PubMed:8223615).
  catalytic activity: keto-D-fructose + NADH + H(+) = D-sorbitol + NAD(+) (RHEA:33031)
  cofactor: Zn(2+) (Binds 1 zinc ion per subunit.)
  subunit: Homotetramer.
• CharProtDB Source (per GeneDB): GeneDB_Spombe
• D-xylose metabolism in Hypocrea jecorina: loss of the xylitol dehydrogenase step can be partially compensated for by lad1-encoded L-arabinitol-4-dehydrogenase
  Seiboth, Eukaryotic cell 2003
  • “...tree were as follows: S. pombe Sdh1 (P36624), S. pombe putative dehydrogenase (put. DH) (S38345), Saccharomyces cerevisiae Ylr070c (NP_013171.1), S. cerevisiae...”
  • “...P. stipitis Xdh1 (P22144); and SpSdh1, S. pombe Sdh1 (P36624). Diamonds indicate the first zinc binding site (C50, H75, and E161), and asterisks indicate the...”
• Molecular evolutionary insight of structural zinc atom in yeast xylitol dehydrogenases and its application in bioethanol production by lignocellulosic biomass
  Yoshiwara, Scientific reports 2023
  • “...enzyme. Serine mutants of four cysteine ligands for structural zinc in SpXDH The hypothetical protein SPBC1773.05c from S. pombe (40% sequence homology with PsXDH; Fig. 1 b) had four cysteine ligands at positions 97, 100, 103, and 111 (Fig. 2 ); therefore, we selected it as...”
  • “...XDH gene of P. stipitis (encoded by PICST_86924 gene), S. cerevisiae (YLR070c), and S. pombe (SPBC1773.05c) was introduced into pQE-81L (Qiagen), a plasmid vector for conferring an N-terminal (His) 6 -tag on expressed proteins, to yield pQE-PsXDH WT , pQE-ScXDH WT , and pQE-SpXDH WT ,...”
• A defect in protein farnesylation suppresses a loss of Schizosaccharomyces pombe tsc2+, a homolog of the human gene predisposing to tuberous sclerosis complex
  Nakase, Genetics 2006
  • “...SPCC1450.13c SPAC3C7.02c SPCC70.10 SPAC25B8.09 SPCC70.08c SPAC16E8.03 SPBC1773.05c SPBC16A3.17c SPBC839.06 SPCC191.11 Tf2-2 tf2-3 tf2-4 tf2-10 Tf2-3 tf2-8 Tf2-9...”

A0A1B4XTS0 L-arabinitol 4-dehydrogenase (EC 1.1.1.12); D-xylulose reductase (EC 1.1.1.9) from Meyerozyma caribbica (see paper)
34% identity, 95% coverage

PGUG_01218 uncharacterized protein from Meyerozyma guilliermondii ATCC 6260
32% identity, 91% coverage

• Identification of genes involved in xylose metabolism of Meyerozyma guilliermondii and their genetic engineering for increased xylitol production
  Atzmüller, AMB Express 2020
  • “...XYL1 (PGUG_00922) in M. guilliermondii (=[pU-XR]) This study pU-XDH-XR-KO Plasmid for genomic replacement of XDH1 (PGUG_01218) by XYL1 (PGUG_00922) This study In order to overexpress the putative XR-gene, XYL1 (PGUG_00922), it was amplified by PCR from the genome of M. guilliermondii ATCC6260 (primer P5 and P6)...”

PGUG_05726 uncharacterized protein from Meyerozyma guilliermondii ATCC 6260
34% identity, 78% coverage

• Identification of genes involved in xylose metabolism of Meyerozyma guilliermondii and their genetic engineering for increased xylitol production
  Atzmüller, AMB Express 2020
  • “...S1, plasmids in Table 2 . For the knockout of the putative XDH gene, XDH1 (PGUG_05726), 1000bp upstream (primer P1 and P2) and 1000bp downstream (primer P3 and P4) of XDH1 were amplified by PCR and cloned up- and down-stream of the URA5-selection cassette of pGRU5R...”
  • “...vector control [pU-EV]) (Defosse et al. 2014 ) pU-XDH-KO Plasmid for genomic knockout of XDH1 (PGUG_05726) with URA5 This study pU-XR Plasmid for the expression of XYL1 (PGUG_00922) in M. guilliermondii (=[pU-XR]) This study pU-XDH-XR-KO Plasmid for genomic replacement of XDH1 (PGUG_01218) by XYL1 (PGUG_00922) This...”

CTK_RS07810 2,3-butanediol dehydrogenase from Clostridium tyrobutyricum
30% identity, 96% coverage

• Transcriptome analysis reveals reasons for the low tolerance of Clostridium tyrobutyricum to furan derivatives
  Suo, Applied microbiology and biotechnology 2023 (PubMed)
  • “...only the ad gene CTK_RS02625 and the bud gene CTK_RS07810 showed a significant increase of ~ 1.05-fold. Then, the enzyme activity assays indicated that BUD...”
  • “...Tables S2-S4). In addition, the gene CTK_RS07810, encoding 2,3-butanediol dehydrogenase (BUD), was also significantly upregulated by 1.05-fold under...”

CIBE_1696 2,3-butanediol dehydrogenase from Clostridium beijerinckii
Cbei_1464 alcohol dehydrogenase from Clostridium beijerincki NCIMB 8052
30% identity, 95% coverage

• σ⁵⁴ (σ^L) plays a central role in carbon metabolism in the industrially relevant Clostridium beijerinckii
  Hocq, Scientific reports 2019
  • “...not detected in our culture conditions, the only gene predicted to encode a 2,3-butanediol dehydrogenase (CIBE_1696, similar to the one described by Raedts et al .) 20 was identified as being part of the regulon. Unlike other sigma factors, 54 -bound RNA polymerase requires the ATPase...”
  • “...Importantly, genes encoding 54 EBPs were found in the direct vicinity of CIBE_2622, CIBE_3470 and CIBE_1696, which strengthens the hypothesis of a 54 -driven transcriptional control of their expression. In order to investigate the functionality of the 54 -regulon, we used the synteny tool from MaGe...”
• A rapid and sensitive enzymatic assay for 2,3-butanediol
  Lee, 3 Biotech 2019
  • “...with the alcohol dehydrogenase from C. beijerinckii NCIMB 8052 (Cbei_1464), which exhibits high activity at pH 8 and 45 C with (R,R)- and (R,S)-2,3-BDO (Raedts...”
• Molecular characterization of an NADPH-dependent acetoin reductase/2,3-butanediol dehydrogenase from Clostridium beijerinckii NCIMB 8052
  Raedts, Applied and environmental microbiology 2014
  • “...eight potential acetoin reductases. One of them (CBEI_1464) showed substantial acetoin reductase activity after expression in Escherichia coli. The purified...”
  • “...The putative acetoin reductase genes, CBEI_0223, CBEI_0685, CBEI_1464 (C. beijerinckii ACR [Cb-ACR]), CBEI_2243, CBEI_3864, and CBEI_3890, were amplified by PCR...”
• Transcriptional analysis of Clostridium beijerinckii NCIMB 8052 to elucidate role of furfural stress during acetone butanol ethanol fermentation
  Zhang, Biotechnology for biofuels 2013
  • “...dehydrogenase/reductase (SDR) (Cbei_3904), DSBA oxidoreductase (Cbei_2058), FAD linked oxidase domain-containing protein (Cbei_0312), and alcohol dehydrogenase (Cbei_1464) (Figure 1 A and Additional file 1 : Table S4A). The transcriptome of C. beijerinckii 8052 after furfural challenge at the solventogenic phase shows some similarities in terms of redox...”
  • “...enzymes. All the above genes, except FAD linked oxidase domain-containing protein (Cbei_0312), and alcohol dehydrogenase (Cbei_1464), were also induced by furfural challenge at the solventogenic phase (Figure 1 A and Additional file 1 : Table S4C). Figure 1 Comparison of gene expression after furfural challenge at...”

BC0668, NP_830481 (R,R)-butanediol dehydrogenase from Bacillus cereus ATCC 14579
32% identity, 97% coverage

• Proteomic evidences for rex regulation of metabolism in toxin-producing Bacillus cereus ATCC 14579
  Laouami, PloS one 2014
  • “...0,03 Hpr BC_4049 NP_833767 Phosphocarrier protein HPr N N 2,4 0,03 1,18 0,079 Bdh BC_0868 NP_830481 (R,R)-butanediol dehydrogenase N N 3,32 0,06 3,6 0,02 PtsA BC_4048 NP_833766 Phosphotransferase N N 2,12 0,058 3,2 0,00 SfcA BC_4604 NP_834310 NAD-dependent malic enzyme N N 0,86 0,187 1,6 0,04...”
• Global gene expression profile for swarming Bacillus cereus bacteria
  Salvetti, Applied and environmental microbiology 2011
  • “...BC0406 BC0407 BC0408 BC0409 BC0410 BC0491 BC0492 BC2220 BC0668 BC2134 BC2128 Virulence Other a BC3526 BC3698 BC3101 BC0753 BC0754 BC0755 BC0756 BC1435 BC1436...”
• Low concentrations of bile salts induce stress responses and reduce motility in Bacillus cereus ATCC 14579 [corrected]
  Kristoffersen, Journal of bacteriology 2007
  • “...Metabolism; glycolysis, fermentation, and electron transport BC5320 BC0668 BC4599 BC4600 BC4962 BC3721 BC1376 Protein synthesis BC0135 BC5075 BC0154 BC3864...”
  • “...the cell density at the time of harvest. F, BC0668 butanediol dhg; f, BC4599 pyruvate kinase; }, BC1376 flavodoxin; OE, BC5320 PTS, glucose specific. VOL. 189,...”

WP_039344544 2,3-butanediol dehydrogenase from Burkholderia contaminans
33% identity, 92% coverage

• Employing Genomic Tools to Explore the Molecular Mechanisms behind the Enhancement of Plant Growth and Stress Resilience Facilitated by a Burkholderia Rhizobacterial Strain
  Chang, International journal of molecular sciences 2024
  • “...-Terpenoid synthesis WP_039342858 ispF WP_011352390 ispD WP_039342723 Dxr WP_039360848 terpene synthase -Acetoin biosynthesis WP_039351048 Bdh1 WP_039344544 Bdh1 Lipopolysaccharide synthesis WP_039360609 waaF WP_039360073 LptD Spermidine synthesis WP_039360784 speD WP_039370372 SpdS WP_039353965 speB WP_039360775 SPMS WP_039339273 SPMS Osmolytes synthesis -Proline WP_039361374 proC WP_039353092 proB WP_039361497 proA -Trehalose WP_039348314...”

Q93R65 Acetylacetoin reductase from Bacillus cereus
32% identity, 97% coverage

• Propane monooxygenase and NAD+-dependent secondary alcohol dehydrogenase in propane metabolism by Gordonia sp. strain TY-5
  Kotani, Journal of bacteriology 2003
  • “...Pseudomonas putida Bacillus cereus Trichoderma reesei P14940 P47734 L35343 Q93R65 AAO42466 25 55 22 20 Adh3 THCA HDALD ACOD ALD1 ALDB 506 506 506 506 503 506...”

BCV53_03685 2,3-butanediol dehydrogenase from Parageobacillus thermoglucosidasius
31% identity, 98% coverage

• Metabolic engineering for the production of acetoin and 2,3-butanediol at elevated temperature in Parageobacillus thermoglucosidasius NCIMB 11955
  Sheng, Frontiers in bioengineering and biotechnology 2023
  • “...The P. thermoglucosidasius NICMB 11955 genome possesses genes encoding homologues of ALS (BCV53_05415) and BDH (BCV53_03685) but not ALD. Although it may still be able to produce 2,3-BDO via the oxygen-dependent, spontaneous oxidation of acetolactate to di-acetyl, no trace was evident in culture supernatants following growth...”

SGO_0440 L-iditol 2-dehydrogenase BH3949 from Streptococcus gordonii str. Challis substr. CH1
31% identity, 99% coverage

• Streptococcus gordonii Poised for Glycan Feeding through a MUC5B-Discriminating, Lipoteichoic Acid-Mediated Outside-In Signaling Circuit
  Lima, Journal of bacteriology 2022 (secret)
• Transcriptome analysis of Streptococcus gordonii Challis DL1 indicates a role for the biofilm-associated fruRBA operon in response to Candida albicans
  Jesionowski, Molecular oral microbiology 2016
  • “...into three predicted functional categories ( Tanenbaum et al. , 2010 ): energy metabolism (SGO_0184, SGO_0440, SGO_0631, SGO_1283, SGO_1300, SGO_1592, SGO_1593, SGO_0384), central intermediary metabolism (SGO_0278, SGO_1720, SGO_1757), and transport and binding proteins (SGO_0383, SGO_0630, SGO_0982, SGO_0985, SGO_1216). The shifts in expression generally relate to genes...”
  • “...and binding proteins/Amino acids, peptides and amines 2.0 0.002 SGO_1301 hypothetical protein Hypothetical 2.0 0.003 SGO_0440 L-iditol 2-dehydrogenase Energy metabolism/Sugars 2.0 0.019 SGO_1593 arginine deiminase arcA Energy metabolism/Amino acids and amines 1.9 0.009 SGO_1757 glucosamine-fructose-6-phosphate aminotransferase glmS Central intermediary metabolism/Amino sugars 1.9 0.008 SGO_1300 NADPH-dependent reductase...”
• Multiple alcohol dehydrogenases but no functional acetaldehyde dehydrogenase causing excessive acetaldehyde production from ethanol by oral streptococci
  Pavlova, Microbiology (Reading, England) 2013
  • “...mutant GGAACAATGATCAGTGACCCTGG GTACTAGCGTTCCAATAGCTGTGC of SGO_0440 insertion mutant AGTTGGCGATCGGGTAACAG GAACAGCAGCCAAAGCTTGC of SGO_0841 insertion mutant...”
  • “...Additionally, three more genes, SGO_0273 (1005 bp), SGO_0440 (1047 bp) and SGO_0841 (993 bp), which encode putative Zn-binding dehydrogenases, were mutated...”

DMR38_12050 2,3-butanediol dehydrogenase from Clostridium sp. AWRP
29% identity, 96% coverage

• Domestication of the novel alcohologenic acetogen Clostridium sp. AWRP: from isolation to characterization for syngas fermentation
  Lee, Biotechnology for biofuels 2019
  • “...2,3-butanediol synthesis, including acetolactate synthase (DMR38_10440-DMR38_10445, DMR38_19400, and DMR38_12130), acetolactate decarboxylase (DMR38_03970), and 2,3-butanediol dehydrogenase (DMR38_12050). The AWRP genome harbors the genes for nitrogen assimilation, including nitrogenase (DMR38_02115-DMR38_02120 and DMR38_11920-DMR38_11925) and an ammonium transporter (DMR38_01655), respectively. Also, the strain AWRP may assimilate nitrate or nitrite using...”

AXG94_01200 2,3-butanediol dehydrogenase from Pseudomonas corrugata
31% identity, 96% coverage

• Complete genome sequence of Pseudomonas corrugata strain RM1-1-4, a stress protecting agent from the rhizosphere of an oilseed rape bait plant
  Zachow, Standards in genomic sciences 2017
  • “...and orthologues of genes required for the biosynthesis of other volatile components such as 2,3-butanediol (AXG94_01200) and its precursor acetoin (AXG94_01195) were annotated too. Beside the presence of specific genes and the noticeable ability of RM1-1-4 to expose stress protection, the function of particular genes needs...”

Q9HWM8 (R,R)-butanediol dehydrogenase (EC 1.1.1.4) from Pseudomonas aeruginosa (see paper)
PA4153 2,3-butanediol dehydrogenase from Pseudomonas aeruginosa PAO1
31% identity, 93% coverage

• Trophic cooperation promotes bacterial survival of Staphylococcus aureus and Pseudomonas aeruginosa
  Camus, The ISME journal 2020
  • “...liuA dguA PA5099 mmsA edd bauD gltF zwf gntK PA4153 acoB acoR PA4148 -800 Membrane and virulence factors Up-regulation Fig. 1 Alteration of the P. aeruginosa...”
  • “...(57.2%, 12/21), PA4148 (66.7%, 14/21), acoB (57.1%, 8/14) and PA4153 (64.3%, 9/14), 3098 L. Camus et al. Fold change (co-culture/monoculture) A B 400 200 50 4...”
• GcsR, a TyrR-Like Enhancer-Binding Protein, Regulates Expression of the Glycine Cleavage System in Pseudomonas aeruginosa PAO1
  Sarwar, mSphere 2016
  • “...PA3875 narG 2.8 Nitrogen metabolism PA3876 narK2 2.85 Nitrogen metabolism PA3877 narK1 2.53 Nitrogen metabolism PA4153 2.58 Butanediol catabolic process PA4280.3 7.5 tRNA-Ala PA4704.1 prrF1 2.2 Iron homeostasis PA4704.3 prrF2 3.22 Iron homeostasis PA4746.1 2.04 tRNA-Met PA4937.1 2.49 tRNA-Leu The five glycine metabolism genes gcvH2 ,...”
• Pseudomonas aeruginosa PAO1 virulence factors and poplar tree response in the rhizosphere
  Attila, Microbial biotechnology 2008
  • “...promoter region of PA3278 gene, hence, PA3278 function may not be completely disrupted), PA4150, PA4151, PA4153, PA4295 and PA4549. Two of the most induced genes (PA2461 and PA2459) are part of a putative haemolysin operon; hence, we investigated pathogenesis with isogenic mutations in PA2462 (putative haemolysin)...”
  • “...almost the same ability to compete with the wild type in the rhizosphere whereas the PA4153 mutant was 100fold less competitive ( Table1 ); hence, PA4153 encodes a protein that is very important for competition in the rhizosphere. As a control, the wildtype strain ( P....”
• Host and invader impact of transfer of the clc genomic island into Pseudomonas aeruginosa PAO1
  Gaillard, Proceedings of the National Academy of Sciences of the United States of America 2008
  • “...the two others are implicated in acetoin (PA4148 to PA4153, or aco genes) and in glycolate catabolism (PA5351 to PA5355, or glcDEF) (Table S1). None of these...”
  • “...to PAO1-rif. PA4152 PA4149 PA4148 acetoin catabolism PA4153 PA4151 PA5353 PA5352 PA5355 glycolate catabolism PAO1-clc1 stationary phase PAO1-rif PAO1-clc1...”

CAETHG_0385, CLJU_c23220 2,3-butanediol dehydrogenase from Clostridium autoethanogenum DSM 10061
29% identity, 96% coverage

• Recent progress in engineering Clostridium autoethanogenum to synthesize the biochemicals and biocommodities
  Wan, Synthetic and systems biotechnology 2024
  • “...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 the genome ( Fig. 3 ). When reconstructing the complete pathway through expressing those enzymes in the E.coli ,...”
• 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_0406 Acetolactate synthase 0.006 0.30 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...”
• Metabolic Engineering Interventions for Sustainable 2,3-Butanediol Production in Gas-Fermenting Clostridium autoethanogenum
  Ghadermazi, mSystems 2022
  • “...be finally reduced to 2,3-BDO by a butanol dehydrogenase (here BTDDx), which is encoded by CAETHG_0385 in C. autoethanogenum , or by a primary-secondary alcohol dehydrogenase (here BTDDy), which is encoded by CAETHG_0553 in C. autoethanogenum ( 16 , 17 ). It has been hypothesized that...”
  • “...1. The reduction of acetoin to 2,3-BDO can be carried out by a butanediol dehydrogenase (CAETHG_0385), whose activity has been shown to be favored by NADH ( 5 ). Therefore, it is plausible that the reducing equivalents generated by the NAD- and ferredoxin-dependent [FeFe]-hydrogenase, which was...”
• Acetogenic production of 3-Hydroxybutyrate using a native 3-Hydroxybutyryl-CoA Dehydrogenase
  Lo, Frontiers in microbiology 2022
  • “...and a codon optimized version), one from Rhodobacter sphaeroides (Rsph17025_1507), and one from C. ljungdahlii (CLJU_c23220) ( Jones et al., 2016 ; Flchter et al., 2019 ). We also note that the native C. ljungdahlii gene we overexpressed is not the gene responsible for 3HBDH activity...”
  • “...in a recently published paper ( Jia et al., 2021 ). Nevertheless, the overexpression of CLJU_c23220 serves as a non- 3hbdh overexpression control. We also wanted to compare the hbd1 pathway to our ctfAB/3hbdh pathway due to a report of high 3HB titers in C. autoethanogenum...”
• Control of solvent production by sigma-54 factor and the transcriptional activator AdhR in Clostridium beijerinckii
  Yang, Microbial biotechnology 2020
  • “...from C.saccharobutylicum , Cspa_c27830 gene from C.saccharoperbutylacetonicum , CLJU_c24880 and CLJU_c39950 genes from C.ljungdahlii and CAETHG_0385 gene from C.autoethanogenum were chemically synthesized by GenScript. The DNA fragment containing the three UAS sites in the promoter region of adhA1 or adhA2 genes was PCRamplified from C.beijerinckii genome...”
• Genome editing of Clostridium autoethanogenum using CRISPR/Cas9
  Nagaraju, Biotechnology for biofuels 2016
  • “...alcohol dehydrogenase ( adh ; CAETHG_0553) and a 2,3-butanediol dehydrogenase ( 2,3 - bdh ; CAETHG_0385), were chosen. The rationale for targeting these genes is centered on their involvement in ethanol and 2,3-butanediol metabolism [ 20 , 21 ] and the fact that both genes had...”
• Industrial Acetogenic Biocatalysts: A Comparative Metabolic and Genomic Analysis
  Bengelsdorf, Frontiers in microbiology 2016
  • “...). Kpke et al. (2014) showed that C. autoethanogenum possesses two alcohol dehydrogenases (encoded by CAETHG_0385 and CAETHG_0553) that reduce acetoin to 2,3-butanediol. First, the 2,3-butanediol dehydrogenase (2,3-Bdh; CAETHG_0385) is reducing stereospecifically R- acetoin to 2 R ,3 R -butanediol. Second, a strictly NADPH-dependent primary-secondary alcohol...”
• Characterization of an acetoin reductase/2,3-butanediol dehydrogenase from Clostridium ljungdahlii DSM 13528
  Tan, Enzyme and microbial technology 2015 (PubMed)
  • “...In Clostridium ljungdahlii DSM 13528, the gene CLJU_c23220 encoding the putative Zn2+-dependent alcohol dehydrogenase was cloned and expressed in Escherichia...”
  • “...with NADPH as the cofactor. Furthermore, the gene CLJU_c23220 was introduced into Clostridium acetobutylicum ATCC 824 and the transformant was conferred the...”
• More

ELZ14_17085 2,3-butanediol dehydrogenase from Pseudomonas brassicacearum
31% identity, 96% coverage

• Genetic Potential of the Biocontrol Agent Pseudomonas brassicacearum (Formerly P. trivialis) 3Re2-7 Unraveled by Genome Sequencing and Mining, Comparative Genomics and Transcriptomics
  Nelkner, Genes 2019
  • “...root exudates and low pH [ 61 ]. The translated protein sequence of the gene ELZ14_17085 shows 100% identity to the Pseudomonas multispecies protein sequence of butanediol dehydrogenase. This enzyme is involved in the production of the volatile 2,3-butanediol [ 61 ]. Genetic determinants possibly involved...”
  • “...of acetoin dehydrogenase were reported to be transcribed in an operon including a 2,3-butanediol dehydrogenase (ELZ14_17085) and an ATP-NAD kinase gene (ELZ14_17105). NAD and NADH are cofactors of 2,3-butanediol dehydrogenase [ 91 ]. 2,3-Butanediol dehydrogenase was shown to be able to catalyze the irreversible reduction of...”

F8TEL7 (R,R)-butanediol dehydrogenase (EC 1.1.1.4) from Clostridium autoethanogenum (see 2 papers)
29% identity, 96% coverage

BAS0641 alcohol dehydrogenase, zinc-containing from Bacillus anthracis str. Sterne
32% identity, 97% coverage

• Ser/Thr protein kinase PrkC-mediated regulation of GroEL is critical for biofilm formation in Bacillus anthracis
  Arora, NPJ biofilms and microbiomes 2017
  • “...reductase, alpha subunit Bas1977 160 33% Phosphoglucomutase/Phosphomannomutase family protein Bas4790 213 58% Zinc-containing alcohol dehydrogenase Bas0641 118 34% Hypoxanthine-guanine phosphoribosyltransferase Bas0063 85 45% Hypothetical protein, HTH arsenical resistance operon repressor domain Bas4146 125 50% Three substrates identified in screening were independently validated by in vitro phosphorylation...”

A0U95_29290 2,3-butanediol dehydrogenase from Pseudomonas brassicacearum
31% identity, 96% coverage

• Complete genome sequence of Pseudomonas brassicacearum strain L13-6-12, a biological control agent from the rhizosphere of potato
  Zachow, Standards in genomic sciences 2017
  • “...et al. [ 25 ]. Genes predicting biosynthesis of other volatile components such as 2,3-butanediol (A0U95_29290) and acetoin (A0U95_29285) were found as well. We further identified genes most probably involved in the direct promotion of plant growth, such as biosynthesis or carrier gene clusters for spermidine...”

CH_000557 (R,R)-butanediol dehydrogenase; EC 1.1.1.4 from Pseudomonas putida (see paper)
adh / AAB58982.1 2,3-butanediol dehydrogenase from Pseudomonas putida (see paper)
30% identity, 94% coverage

PP0552, PP_0552 2,3-butanediol dehydrogenase from Pseudomonas putida KT2440
30% identity, 94% coverage

• UEG Week 2024 Poster Presentations
  , United European gastroenterology journal 2024
• UEG Week 2023 Poster Presentations
  , United European gastroenterology journal 2023
• Dehydrogenation Mechanism of Three Stereoisomers of Butane-2,3-Diol in Pseudomonas putida KT2440
  Liu, Frontiers in bioengineering and biotechnology 2021
  • “...channeled to central mechanism via acetoin dehydrogenase enzyme system. (2 R ,3 R )-2,3-BDO dehydrogenase (PP0552) was detailedly characterized and identified to participate in (2 R ,3 R )-2,3-BDO and meso -2,3-BDO dehydrogenation. Two quinoprotein alcohol dehydrogenases, PedE (PP2674) and PedH (PP2679), were confirmed to be...”
  • “...R , R -BDH was amplified from genomic DNA of P. putida KT2440 using primers pp0552 -F/ pp0552 -R ( Supplementary Table S2 ). The PCR product was cloned into the pETDuet-1 plasmid to obtain plasmid pETDuet- pp0552 . E. coli BL21(DE3) containing pETDuet- pp0552 was...”
• Light Response of Pseudomonas putida KT2440 Mediated by Class II LitR, a Photosensor Homolog
  Sumi, Journal of bacteriology 2020 (secret)
• Genome editing and transcriptional repression in Pseudomonas putida KT2440 via the type II CRISPR system
  Sun, Microbial cell factories 2018
  • “...21 7/7 ND KT2440 harboring pCAS-RK2K pSEVA-NicA21 A20 20 5/5 ND KT2440 harboring pCAS-RK2K pSEVA-gR0552T PP_0552 1089 8/10 ND KT2440 harboring pCAS-RK2K pSEVA-gR3361T PP_3361 3048 11/13 ND KT2440 harboring pCAS-RK2K pSEVA-gR3733T PP_3733 1059 18/18 ND KT2440 harboring pCAS-RK2K pSEVA-gR3889T PP_3889 1299 11/12 ND KT2440 harboring pCAS-RK2T...”
  • “...mutation was retained Aside from these versatile mutations of nicC gene, nine other target sites, PP_0552, PP_3361, PP_3733, PP_3889, PP_3939PP_3940, PP_3947PP_3948, PP_1706, PP_3846 and PP_5301, were used to further examine the mutation rate of the CRISPR/Cas9 system. PP_0552, PP_3361, PP_3733 and PP_3889 were selected as genome...”
• Transcriptome dynamics of Pseudomonas putida KT2440 under water stress
  Gülez, Applied and environmental microbiology 2012
  • “...PP_4011 PP_4034 PP_0103 PP_0104 PP_0105 PP_0106 PP_0490 PP_0552 PP_0553 PP_0554 PP_0555 PP_0556 PP_0557 PP_0596 PP_0989 PP_0999 PP_1000 PP_1001 PP_1157 PP_2351...”

PPE_03421 2,3-butanediol dehydrogenase from Paenibacillus polymyxa E681
31% identity, 97% coverage

• Occurrence of phenotypic variation in Paenibacillus polymyxa E681 associated with sporulation and carbohydrate metabolism
  Lee, Biotechnology reports (Amsterdam, Netherlands) 2022
  • “.../277/180 /163/297 /309 56.0/37.0 /56.3/56.2 56.2/33.1 /56.0 5.3/4.9 /5.0/5.1 /5.2/5.3 /5.3 19.6/2.9 /90.6/3205.5 /10.0/2.5 /5.8 PPE_03421 ER 1.13 0.000 12 6802 succinate dehydrogenase flavoprotein subunit SDH gi|308,070,598 40 212 83.8 5.6 2.8 PPE_03868 C 1.14 0.000 13 307/6306 Flagellin HAG gi|308,071,102 39/41 132/236 37.8/39.8 4.2/5.8 0.2/1.4...”

SSA_0572 Dehydrogenase, putative from Streptococcus sanguinis SK36
30% identity, 99% coverage

• Glucose Phosphotransferase System Modulates Pyruvate Metabolism, Bacterial Fitness, and Microbial Ecology in Oral Streptococci
  Zeng, Journal of bacteriology 2023 (secret)

MLD56_18150 2,3-butanediol dehydrogenase from Paenibacillus peoriae
31% identity, 97% coverage

• Comparative genomic and functional analyses of Paenibacillus peoriae ZBSF16 with biocontrol potential against grapevine diseases, provide insights into its genes related to plant growth-promoting and biocontrol mechanisms
  Yuan, Frontiers in microbiology 2022
  • “...Acetolactate decarboxlase MLD56_10750 UMY56882.1 WP_000215036.1 68.25 WP_016821069.1 97.18 NA 97.58 bdh 2,3-Butanediol ISR 23-Butanediol dehydrogenase MLD56_18150 UMY53485.1 WP_019688213.1 98.29 WP_013311373.1 99.43 NA 96.00 ilvN 2,3-Butanediol ISR Acetolactate synthase small subunit MLD56_07545 UMY56280.1 WP_007429525.1 98.76 WP_013309386.1 99.38 NA 99.38 metH Methanethio ISR Methionine synthase MLD56_13735 UMY52659.1 WP_010345928.1...”

A0A3Q8GZQ4 (R,R)-butanediol dehydrogenase (EC 1.1.1.4) from Paenibacillus brasilensis (see paper)
31% identity, 97% coverage

Atu4740 zinc-binding dehydrogenase from Agrobacterium tumefaciens str. C58 (Cereon)
30% identity, 90% coverage

• Transcriptome profiling and functional analysis of Agrobacterium tumefaciens reveals a general conserved response to acidic conditions (pH 5.5) and a complex acid-mediated signaling involved in Agrobacterium-plant interactions
  Yuan, Journal of bacteriology 2008
  • “...Atu0035 Atu0607 Atu0811 Atu0881 Atu0944 Atu2224 Atu4020 Atu4130 Atu4740 0.95 2.06 1.05 1.59 1.43 1.81 1.89 1.24 1.47 Amino acid synthesis and degradation gene...”

E7EKB8 (R,R)-butanediol dehydrogenase (EC 1.1.1.4) from Paenibacillus polymyxa (see paper)
31% identity, 97% coverage

• Mechanism of microbial production of acetoin and 2,3-butanediol optical isomers and substrate specificity of butanediol dehydrogenase
  Li, Microbial cell factories 2023
  • “...F1T242; B. aurantiacum, UniProt ID A0A2A3YZ33; S. cerevisiae, UniProt ID P39714; P. polymyxa, UniProt ID E7EKB8; B. subtilis, UniProt ID O34788; M. dioxanotrophicus, KEGG ID BTO20_28760; S. profundus, UniProt ID A0A1U7D589; E. ludwigii, KEGG ID EcWSU1_01150; K. pneumoniae, GenBank ID AFB82681.1; Bacillus sp., GenBank ID QIS93452.1;...”

An09g03900 uncharacterized protein from Aspergillus niger
32% identity, 84% coverage

• A single amino acid change (Y318F) in the L-arabitol dehydrogenase (LadA) from Aspergillus niger results in a significant increase in affinity for D-sorbitol
  Rutten, BMC microbiology 2009
  • “...niger . Two of these corresponded to ladA and xdhA , while a third was An09g03900. In addition, two homologues of A. nidulans ladA , ladB and ladC , have been described [ 7 ] although no biochemical function has been reported for these proteins. Putative...”
  • “...candidate sorbitol dehydrogenase might be the enzyme encoded by the uncharacterised gene from A. niger (An09g03900) that is in the groups that splits of the XDH branch in the tree. As orthologues for this gene were found in all tested fungi, it appears to encode a...”

CNA02580 sorbitol dehydrogenase from Cryptococcus neoformans var. neoformans JEC21
30% identity, 81% coverage

• Transcription factor Nrg1 mediates capsule formation, stress response, and pathogenesis in Cryptococcus neoformans
  Cramer, Eukaryotic cell 2006
  • “...protein Formate dehydrogenase CNI02800 CNL04840 CNN00660 CNA08060 CNA02580 CNJ01090 CNM00600 CNF03470 4.4 3.7 3.5 3 2.8 2.7 0.29 0.22 CNC00480 3.4...”

CNAG_00269 sorbitol dehydrogenase from Cryptococcus neoformans var. grubii H99
30% identity, 76% coverage

• Pleiotropic effects of deubiquitinating enzyme Ubp5 on growth and pathogenesis of Cryptococcus neoformans
  Fang, PloS one 2012
  • “...Category Gene ID * Fold change ubp5?/WT P value Functional annotation * Carbohydrate/amino acid metabolism CNAG_00269 1.80 8.30E-09 Sorbitol dehydrogenase CNC05840 1.50 4.60E-07 Glycosyl hydrolase CNAG_06035 1.49 2.00E-08 Alcohol dehydrogenase CNC01140 1.38 3.00E-10 Lipase CNB00370 1.29 1.80E-07 Fatty acid beta-oxidation-related protein CNE01100 0.71 1.50E-09 long-chain-fatty-acid-CoA ligase...”

jpw_02880 2,3-butanediol dehydrogenase from Pseudomonas asiatica
30% identity, 96% coverage

• Genomic Analysis of Pseudomonas asiatica JP233: An Efficient Phosphate-Solubilizing Bacterium
  Wang, Genes 2022
  • “...large subunit jpw_22100 ilvH acetolactate synthase small subunit jpw_22105 ilvB acetolactate synthase 3 large subunit jpw_02880 butB 2,3-butanediol dehydrogenase Tolerance against metal toxicity jpw_11350 arsH arsenical resistance protein ArsH jpw_05755 arsC arsenate reductase ArsC jpw_03420 arsB arsenic transporter jpw_11360 arsR metalloregulator ArsR/SmtB family transcription factor jpw_08360...”

NCU01905 sorbitol dehydrogenase from Neurospora crassa OR74A
30% identity, 79% coverage

• The SEB-1 Transcription Factor Binds to the STRE Motif in Neurospora crassa and Regulates a Variety of Cellular Processes Including the Stress Response and Reserve Carbohydrate Metabolism
  Freitas, G3 (Bethesda, Md.) 2016
  • “...system protein, NCU04615 ) and repressed os-2 (osmotic sensitive-2, NCU07024 ), sdh-1 (sorbitol dehydrogenase 1, NCU01905 ), and sou-2 (sorbitol utilization protein 2, NCU03803 ) genes ( Figure 10A , see osmotic stress panel). As expected, all genes identified by RNA-seq ( P < 0.05) within...”

SMb20445 putative alcohol dehydrogenase protein from Sinorhizobium meliloti 1021
34% identity, 95% coverage

• Mapping the Sinorhizobium meliloti 1021 solute-binding protein-dependent transportome
  Mauchline, Proceedings of the National Academy of Sciences of the United States of America 2006
  • “...SMb20443 (small permease), SMb20444 (large permease), SMb20445 (putative alcohol dehydrogenase), and SMb02446 (D-mannonate dehydratase), because the intergenic...”

Pc16g12970 uncharacterized protein from Penicillium rubens
30% identity, 83% coverage

• Studying the Gene Expression of Penicillium rubens Under the Effect of Eight Essential Oils
  Kisová, Antibiotics (Basel, Switzerland) 2020
  • “...and Pc12g16040); the pentose phosphate pathway (Pc12g02790, Pc13g14570, Pc12g13500 and Pc20g04410); fructose and mannose metabolisms (Pc16g12970, Pc22g09390, Pc21g05470, Pc20g01550, Pc13g12020, Pc12g09190, Pc12g13500, Pc21g04410, Pc21g04400 and Pc16g10970) and galactose metabolism (Pc12g13500, Pc14g00310, Pc12g07810 and Pc20g04410). The dominant gene in each group is 6-phosphofructokinase (Pc12g13500). It is responsible...”

CD0490 putative sugar-phosphate dehydrogenase from Clostridium difficile 630
28% identity, 94% coverage

• Genome-Wide Transcription Start Site Mapping and Promoter Assignments to a Sigma Factor in the Human Enteropathogen Clostridioides difficile
  Soutourina, Frontiers in microbiology 2020
  • “...ATGCTT T CD0402/LeuR CD0442/ord # ord-ortAB-oraSEF-orr-nhaC Ornithine degradation NR T TGGCA CGATTT ATGCTT T CD0441/OrdR CD0490 # CD0490-CD0494 Sugar-P-dehydrogenase, PTS mannose/fructose/sorbose family 0.24* T TGGCAT GAAAG TTGCTT T CD0516? LevR-type CD0800/crt1 # crt1 - CD0801-catB-bcd-etfBA2 Crotonase, permease, CoA transferase, acyl-CoA dehydrogenase, EtfBA NR T TGGCA TAGTAC...”
  • “...upstream of 7 operons encoding phosphotransferase systems (PTS) belonging to the mannose ( CD0284 , CD0490 , CD3279 ), cellobiose ( CD0860 ) or mannitol/galactitol ( CD0040 , CD2283 , CD2327 ) sub-families ( Table 4 and Supplementary Figure S9 ). These PTS operons are associated...”

DDGAH_PSEA6 / Q15SS1 2-dehydro-3-deoxy-L-galactonate 5-dehydrogenase; 2-keto-3-deoxy-L-galactonate 5-dehydrogenase; EC 1.1.1.389 from Pseudoalteromonas atlantica (strain T6c / ATCC BAA-1087)
34% identity, 92% coverage

• function: Involved in the degradation of 3,6-anhydro-L-galactose, which is the major monomeric sugar of red macroalgae. Catalyzes the third step of the pathway, the NAD(+)-dependent oxidation of 2-dehydro-3- deoxy-L-galactonate (L-KDGal) to 3-deoxy-D-glycero-2,5-hexodiulosonate (L-DDGal).
  catalytic activity: 2-dehydro-3-deoxy-L-galactonate + NAD(+) = 3-deoxy-D-glycero- 2,5-hexodiulosonate + NADH + H(+) (RHEA:47988)
  cofactor: Zn(2+) (Binds 2 Zn(2+) ions per subunit.)

Pcar_0330 2,3-butanediol dehydrogenase from Pelobacter carbinolicus str. DSM 2380
30% identity, 96% coverage

• The genome of Pelobacter carbinolicus reveals surprising metabolic capabilities and physiological features
  Aklujkar, BMC genomics 2012
  • “...( R )-acetoin. Genome sequencing of P . carbinolicus revealed three 2,3-butanediol dehydrogenases (MDR budX Pcar_0330, SDR budY Pcar_0903, SDR budZ Pcar_2068), but the published studies have either noted only one [ 11 ] or assigned them to only two stereoisomers [ 10 ]. The correct...”
  • “...in the same direction [ 9 ]. The third gene of this cluster is budX (Pcar_0330) and the seventh gene (Pcar_3424) encodes a small protein similar to the C-termini of BudY and BudZ (Figure 2 ), which might function as a modulator of 2,3-butanediol metabolism. The...”
• Evolution from a respiratory ancestor to fill syntrophic and fermentative niches: comparative fenomics of six Geobacteraceae species
  Butler, BMC genomics 2009
  • “...). Both Pelobacter species catabolize butanediol and acetoin [ 12 ]. The butanediol dehydrogenase (Bdh, Pcar_0330) and acetoin dehydrogenase (AcoABCL, Pcar_0343Pcar0346), which catalyze the initial steps in the metabolism of these compounds, have been characterized in P. carbinolicus [ 32 ]. P. propionicus has genes with...”

BH3949 L-iditol 2-dehydrogenase from Bacillus halodurans C-125
30% identity, 91% coverage

• Identification and distribution of new insertion sequences in the genome of alkaliphilic Bacillus halodurans C-125
  Takami, Journal of bacteriology 2001
  • “...5B. Six CDSs (BH0175, BH1413, BH2525, BH2697, BH3502, and BH3949) likely occurred by truncation of the original CDS by IS insertion. Two CDSs, BH2697 and...”

SEN1433 putative hexonate dehydrogenase from Salmonella enterica subsp. enterica serovar Enteritidis str. P125109
33% identity, 92% coverage

• Molecular study of the mechanisms controlling the induction of the hexonate/hexuronate-utilization genes of Salmonella enterica (serotype Enteritidis) upon exposure to egg white
  Ghareeb, 2018
• Global Gene-expression Analysis of the Response of Salmonella Enteritidis to Egg White Exposure Reveals Multiple Egg White-imposed Stress Responses
  Baron, Frontiers in microbiology 2017
  • “...isomerase ( uxaC ) n.s. 8.81 10.68 HEXONATE UTILIZATION eda Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase 2.09 2.01 1.94 SEN1433 L-idonate 5-dehydrogenase IdnD 3.05 3.21 5.17 SEN1434 Hexonate sugar transporter n.s. 2.70 5.68 SEN1435 Gluconate 5-dehydrogenase n.s. 3.07 .40 SEN1436 D-galactonate dehydratase family member SEN1436 n.s. 10.30 33.38 Highlighted fold...”

L2164_19520 L-idonate 5-dehydrogenase from Pectobacterium brasiliense
31% identity, 91% coverage

• A data catalogue of alcohol dehydrogenases in the genome of a tissue macerating Pectobacterium brasiliense isolated from potato in South Africa
  Otun, Data in brief 2024
  • “...MCG5049632.1 NAD(P)-dependent alcohol dehydrogenase L2164_17495 MCG5050486.1 Iron-containing alcohol dehydrogenase family protein L2164_19300 MCG5050844.1 Alcohol dehydrogenase L2164_19520 MCG5050887.1 Alcohol dehydrogenase catalytic domain-containing protein When compared with other bacteria, it was discovered that similarly, the 5111,375bp genome of strain PCC1 of P. brasiliense (GenBank CP128509.1) deposited on www.ncbi.nlm.nih.gov...”

Ppro_1043 Alcohol dehydrogenase GroES domain protein from Pelobacter propionicus DSM 2379
31% identity, 96% coverage

• Evolution from a respiratory ancestor to fill syntrophic and fermentative niches: comparative fenomics of six Geobacteraceae species
  Butler, BMC genomics 2009
  • “...of the putative acetoin dehydrogenase included a duplication of the A and B subunits (Bdh, Ppro_1043 and AcoABCABL, Ppro_1024Ppro1029, see Additional file 1 ). Phylogenetic analysis showed that the most closely related enzymes are not from Geobacter or Desulfuromonas , nor any other delta - Proteobacteria...”

BMMGA3_RS07345 zinc-binding dehydrogenase from Bacillus methanolicus MGA3
31% identity, 97% coverage

• Characterization of D-Arabitol as Newly Discovered Carbon Source of Bacillus methanolicus
  López, Frontiers in microbiology 2019
  • “...uptake (BMMGA3_RS07330, BMMGA3_RS07335, and BMMGA3_RS07340 renamed to atlABC ) and a putative arabitol phosphate dehydrogenase (BMMGA3_RS07345 renamed to atlD ). C. glutamicum is a natural D -arabitol utilizer that requires arabitol dehydrogenase MtlD for arabitol catabolism. The C. glutamicum mtlD deletion mutant was chosen for complementation...”
  • “...et al., 2001 pVWEx1- atlABCD pVWEx1 derivative for IPTG-inducible expression of BMMGA3_RS07330, BMMGA3_RS07335, BMMGA3_RS07340 and BMMGA3_RS07345 ( atlABCD ) from B. methanolicus MGA3 This study pVWEx1- atlD pVWEx1 derivative for IPTG-inducible expression of BMMGA3_RS07345 ( atlD ) from B. methanolicus MGA3 This study pVWEx1- atlABCDEF pVWEx1...”

Swol_1727 zinc-binding dehydrogenase from Syntrophomonas wolfei subsp. wolfei str. Goettingen
30% identity, 93% coverage

• Proteomic analysis reveals metabolic and regulatory systems involved in the syntrophic and axenic lifestyle of Syntrophomonas wolfei
  Sieber, Frontiers in microbiology 2015
  • “...0.001 0.011 0.003 0.007 0.001 Swol_1244 Polyhydroxyalkanoate synthesis regulator 0.001 0.001 0.027 0.003 0.023 0.002 Swol_1727 Zn-dependent dehydrogenase ND 0.019 0.004 0.028 0.005 Swol_1855 60 kDa chaperonin GROEL 0.042 0.001 0.027 0.004 0.014 0.001 Swol_1856 10 kDa chaperonin GROES 0.049 0.004 0.031 0.007 0.022 0.003 Swol_2030...”
  • “...the chromosome and are not co-localized or within a genomic island. A putative zinc-dependent dehydrogenase (Swol_1727 gene product) was among the most abundant proteins detected (NSAF > 0.02) when S . wolfei was grown with M. hungatei on either crotonate or butyrate (Table 1 ; Figure...”

PA14_10900 putative Zn-dependent alcohol dehydrogenase from Pseudomonas aeruginosa UCBPP-PA14
30% identity, 97% coverage

• Evolution of biofilm-adapted gene expression profiles in lasR-deficient clinical Pseudomonas aeruginosa isolates
  Jeske, NPJ biofilms and microbiomes 2022
  • “...PA14_34420 mtlE 1.01 PA14_20030 hasD 1.13 PA14_10650 hpaG1 1.23 PA14_42080 fadB 1.00 PA14_20040 hasE 1.29 PA14_10900 ydjL 1.55 PA14_43420 1.18 PA14_32740 optS 1.20 PA14_10990 hpaC 0.92 PA14_45000 gcl 1.45 PA14_33270 pvdG 1.32 PA14_11000 hpaA 0.96 PA14_45010 hyi 1.37 PA14_33690 pvdE 2.51 PA14_11020 fabG 1.40 PA14_45020 glxR...”

BSQ49_10255 2,3-butanediol dehydrogenase from Liquorilactobacillus hordei
29% identity, 97% coverage

• Living the Sweet Life: How Liquorilactobacillus hordei TMW 1.1822 Changes Its Behavior in the Presence of Sucrose in Comparison to Glucose
  Bechtner, Foods (Basel, Switzerland) 2020
  • “...fructose-specific IIC/D component fig|468911.3.peg.2001 BSQ49_10175 41 0.35 3.41 Butanediol dehydrogenase Amino Acids and Derivatives fig|468911.3.peg.2017 BSQ49_10255 42 1.42 9.64 ABC-transporter substrate-binding protein, glycerol-3-phosphate specific Carbohydrates fig|468911.3.peg.2080 BSQ49_10570 43 1.12 7.83 ABC-transporter ATP-binding protein Carbohydrates fig|468911.3.peg.2084 BSQ49_10590 44 0.74 5.81 PTS system, fructose-specific IID component fig|468911.3.peg.2194 BSQ49_11155...”

LMRG_02209 alcohol dehydrogenase, zinc-dependent from Listeria monocytogenes 10403S
29% identity, 97% coverage

• Alternative σ Factors Regulate Overlapping as Well as Distinct Stress Response and Metabolic Functions in Listeria monocytogenes under Stationary Phase Stress Condition
  Orsi, Pathogens (Basel, Switzerland) 2021
  • “...to ribose 5-phosphate epimerase LMRG_02208 lmo2663 94.76 68.20 22.11 3.04 24.13 similar to polyol dehydrogenase LMRG_02209 lmo2664 59.73 44.42 16.19 2.36 24.58 similar to sorbitol dehydrogenase LMRG_02210 lmo2665 43.67 33.93 15.14 2.60 18.64 similar to PTS system galactitol-specific enzyme IIC component LMRG_02211 lmo2666 34.02 29.44 19.08...”

lmo0506 similar to polyol (sorbitol) dehydrogenase from Listeria monocytogenes EGD-e
31% identity, 94% coverage

• Cis-encoded non-coding antisense RNAs in streptococci and other low GC Gram (+) bacterial pathogens
  Cho, Frontiers in genetics 2015
  • “...(Transposase) 97 rli25 lmo0330 (Transposase) 102 rli29 Antisense to the 5UTR of lmo0471 193 rli30 lmo0506 115 rli35 lmo0828 (Transposase) 102 rli45 Antisense to rli46 (small non-coding RNA) 77 rli46 Antisense to rli45 294 Anti2095-8 RNA1 RNA2 lmo2095 lmo2095-8 255 2149 Anti2325-7 RNA1 RNA2 lmo2325 lmo2325-7...”
• Small regulatory RNAs from low-GC Gram-positive bacteria
  Brantl, RNA biology 2014
  • “...Rli23, 25, 35 lmo0172 # transposases Rli45 rli46 # ? Rli29 lmo9471 # ? Rli30 lmo0506 # ? Only sRNAs are listed for which target genes have been identified or #proposed. a In analogy to S. aureus RsaE, which interacts via C-rich loops with SD sequences,...”
• An overview of RNAs with regulatory functions in gram-positive bacteria
  Romby, Cellular and molecular life sciences : CMLS 2010
  • “...aa ND ND ND ND rli31, rli32 rli34, rli36 lmo0506 ND rli30 Antisense sRNA complementary to the 5'UTR Homologous sRNAs rli37 lmo0471 ND Antisense homologous sRNAs...”
• Glycerol metabolism and PrfA activity in Listeria monocytogenes
  Joseph, Journal of bacteriology 2008
  • “...of California, Berkeley lmo0500 lmo0502a,b lmo0503 lmo0505 lmo0506 lmo0507a,b lmo0508 lmo0521a lmo0524 lmo0536b lmo0539 lmo0546 lmo0554 lmo0555 lmo0560 lmo0610b...”

lmo2664 / Q8Y413 pentitolphosphate dehydrogenase Lmo2664 (EC 1.1.1.301) from Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) (see 2 papers)
lmo2664 similar to sorbitol dehydrogenase from Listeria monocytogenes EGD-e
29% identity, 97% coverage

• Bacterial Microcompartments Coupled with Extracellular Electron Transfer Drive the Anaerobic Utilization of Ethanolamine in Listeria monocytogenes
  Zeng, mSystems 2021
  • “..., rpmG1 , and lmo0111 ) ( TableS5 ), and zinc-containing dehydrogenases ( lmo2663 , lmo2664 , and lmo2097 ). To summarize, the significant upregulation of the eut operon at the proteomic level, including structural shell proteins, strongly supports that BMC-dependent EA utilization is processed by...”
• Alternative σ Factors Regulate Overlapping as Well as Distinct Stress Response and Metabolic Functions in Listeria monocytogenes under Stationary Phase Stress Condition
  Orsi, Pathogens (Basel, Switzerland) 2021
  • “...ribose 5-phosphate epimerase LMRG_02208 lmo2663 94.76 68.20 22.11 3.04 24.13 similar to polyol dehydrogenase LMRG_02209 lmo2664 59.73 44.42 16.19 2.36 24.58 similar to sorbitol dehydrogenase LMRG_02210 lmo2665 43.67 33.93 15.14 2.60 18.64 similar to PTS system galactitol-specific enzyme IIC component LMRG_02211 lmo2666 34.02 29.44 19.08 1.95...”
• Protein level identification of the Listeria monocytogenes sigma H, sigma L, and sigma C regulons
  Mujahid, BMC microbiology 2013
  • “...ATP-proton motive force interconversion Lmo2648 2.50 hypothetical protein lmo2648 Unclassified Role category not yet assigned Lmo2664 1.72 L-iditol 2-dehydrogenase lmo2664 Central intermediary metabolism Other Energy metabolism Glycolysis/gluconeogenesis Energy metabolism Electron transport Energy metabolism TCA cycle Energy metabolism Fermentation Lmo2696 2.68 dihydroxyacetone kinase L subunit lmo2696 Energy...”
• Utilization of D-ribitol by Lactobacillus casei BL23 requires a mannose-type phosphotransferase system and three catabolic enzymes
  Bourand, Journal of bacteriology 2013
  • “...University of California, Berkeley listerial D-arabinitol-phosphate dehydrogenases (Lmo2664) and 31% identity to the enzyme encoded by the neighboring gene. In...”
• Listeria monocytogenes {sigma}B has a small core regulon and a conserved role in virulence but makes differential contributions to stress tolerance across a diverse collection of strains
  Oliver, Applied and environmental microbiology 2010
  • “...lmo2397 lmo2415 lmo2507 lmo2547 lmo2633 lmo2660 lmo2664 lmo2665 lmo2666 lmo2667 lmo2668 lmo2758 lmo2791 lmoh7858_0080.5 Ser/Thr protein phosphatase family...”
• Microarray-based characterization of the Listeria monocytogenes cold regulon in log- and stationary-phase cells
  Chan, Applied and environmental microbiology 2007
  • “...6490 CHAN ET AL. ons (i.e., those consisting of lmo2664 and lmo2663 and lmo2661 to lmo2659; see above) also showed higher transcript levels in stationary-phase...”
  • “...to lmo2665), including the operon consisting of lmo2664 and lmo2663 (encoding sorbitol dehydrogenase and polyol dehydrogenase, respectively) and that consisting...”

PA4097 probable alcohol dehydrogenase (Zn-dependent) from Pseudomonas aeruginosa PAO1
31% identity, 92% coverage

• Transcriptional profiling of Pseudomonas aeruginosa mature single- and dual-species biofilms in response to meropenem
  Alam, Microbiology (Reading, England) 2023
  • “...on the transcription profile of P. aeruginosa . The most significantly differentially regulated genes were PA4097 (a lipolytic protein) and PA5384 (an alcohol dehydrogenase), which were both twofold upregulated in the presence of C. albicans . GO term enrichment analysis ( Fig. 4a ) and KEGG...”
  • “...biofilms Gene ID log 2 fold change P -value Padj Upregulated PA5384 1.136608573 4.28E-06 0.0002779376198 PA4097 1.000660434 3.17E-05 0.001214321657 cdhB 0.9811955186 5.21E-06 0.0003198899691 PA2161 0.9810583138 0.0003525619038 0.008808371695 cdhC 0.936864827 9.18E-07 7.92E-05 cdhA 0.9176339588 1.17E-09 4.57E-07 ssrS 0.9064141369 8.59E-13 6.76E-10 PA0698 0.9014266847 1.42E-05 0.0006654679167 PA2349 0.8950640392 2.59E-05...”
• Bactericidal potential of silver nanoparticles synthesized using cell-free extract of Comamonas acidovorans: in vitro and in silico approaches
  Rudakiya, 3 Biotech 2017
  • “...decreased after incubating with AgNPs. Alcohol dehydrogenase (PA4097) and oxidoreductase (PA1648) were inhibited because of interacting Ag? ions in P....”

Afu3g01490 alcohol dehydrogenase, putative from Aspergillus fumigatus Af293
38% identity, 66% coverage

• Distinct transcriptional responses to fludioxonil in Aspergillus fumigatus and its ΔtcsC and Δskn7 mutants reveal a crucial role for Skn7 in the cell wall reorganizations triggered by this antifungal
  Schruefer, BMC genomics 2023
  • “...18 ]. Four other genes that belong to this putative gene cluster, namely Afu3g01450, Afu3g01480, Afu3g01490 and Afu3g01500, were also up-regulated, but only in the wild type and the skn 7 mutant. Fig. 5 Heat maps of genes that were differentially regulated in all three strains....”
• SreA-mediated iron regulation in Aspergillus fumigatus
  Schrettl, Molecular microbiology 2008
  • “...( Lan et al ., 2004 ). SreA control of glycogen phosphorylase (Afu1g12920), alcohol dehydrogenase (Afu3g01490), isoamyl alcohol oxidase (Afu3g07410) and NAD-dependent formate dehydrogenase (Afu6g04920) links iron and carbon metabolism. Selected genes displayed the same mode of regulation in Northern blot analysis ( Fig. 4 )...”

SEN4237 l-idonate 5-dehydrogenase (ec 1.1.1.264) from Salmonella enterica subsp. enterica serovar Enteritidis str. P125109
29% identity, 99% coverage

• Salmonella enterica Serovars Dublin and Enteritidis Comparative Proteomics Reveals Differential Expression of Proteins Involved in Stress Resistance, Virulence, and Anaerobic Metabolism
  Martinez-Sanguiné, Infection and immunity 2021 (secret)

PGA1_c34320 L-threonine 3-dehydrogenase (EC 1.1.1.103) from Phaeobacter inhibens DSM 17395
30% identity, 99% coverage

• mutant phenotype: Specifically important for utilizing L-Threonine. Automated validation from mutant phenotype: the predicted function (1.1.1.103) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

Clo1313_1833 zinc-binding dehydrogenase from Acetivibrio thermocellus DSM 1313
Cthe_0388 Alcohol dehydrogenase GroES-like protein from Clostridium thermocellum ATCC 27405
28% identity, 97% coverage

• The role of AdhE on ethanol tolerance and production in Clostridium thermocellum
  Pech-Canul, The Journal of biological chemistry 2024
  • “...C.thermocellum have been annotated as putative ADHs, including Clo1313_0076, Clo1313_0166, Clo1313_1798 ( adhE ), Clo1313_1827, Clo1313_1833, and Clo1313_2130 that may be responsible for this activity. Thus, in the mutants with reduced ADH activity, acetaldehyde to ethanol conversion could be due to either thelow levels of residual...”
• Ethanol tolerance in engineered strains of Clostridium thermocellum
  Olson, Biotechnology for biofuels and bioproducts 2023
  • “...adapted strains. C. thermocellum has five other genes annotated as alcohol dehydrogenases (Clo1313_0076, Clo1313_0166, Clo1313_1827, Clo1313_1833, and Clo1313_2130). In this set of genes, there was only a single mutation, A151V in Clo1313_1827. This mutation only appeared in a single lineage (LL1732 population and LL1806 isolate). Phospholipase...”
• Ethanol tolerance of Clostridium thermocellum: the role of chaotropicity, temperature and pathway thermodynamics on growth and fermentative capacity
  Kuil, Microbial cell factories 2022
  • “..., C. thermocellum encodes for several alcohol dehydrogenases ( clo1313_2130 , clo1313_1827 , clo1313_0166 , clo1313_1833 , and clo1313_0076 ) and one aldehyde dehydrogenase ( clo1313_2911 ), potentially allowing for indirect conversion of acetyl-CoA into ethanol. However, all these genes are low or moderately expressed in...”
• Integrated omics analyses reveal the details of metabolic adaptation of Clostridium thermocellum to lignocellulose-derived growth inhibitors released during the deconstruction of switchgrass
  Poudel, Biotechnology for biofuels 2017
  • “...C5 sugar-related enzymes, we also detected a very high abundance of alcohol dehydrogenase GroES-like protein (Cthe_0388; cluster 2). This enzyme converts D-xylulose (hemicellulose-derived sugar) into xylitol, which accumulated almost ninefold in late-stationary phase (Additional file 2 : Table S1). Even though the abundance of this protein...”
  • “...only way xylitol can be formed biologically is by the reduction of xylulose, potentially by Cthe_0388 enzyme mentioned above. Further work is needed to confirm this additional functionality. Compared to xylitol, xylulose increased only ~2-fold by stationary phase. There are two possibilities for this accumulation; xylulose...”
• Proteomic analysis of Clostridium thermocellum core metabolism: relative protein expression profiles and growth phase-dependent changes in protein expression
  Rydzak, BMC microbiology 2012
  • “...ethanol from acetaldehyde, albeit at lower levels. Two other zinc-containing ADH GroES-like heat shock proteins, Cthe_0388 and Cthe_2445, were also detected, the former being more highly expressed ( Additional file 4 ). While crude cell-free extract enzyme activities have shown the presence of both NADH and...”

ECs4494 threonine dehydrogenase from Escherichia coli O157:H7 str. Sakai
29% identity, 98% coverage

• Canonical Single Nucleotide Polymorphisms (SNPs) for High-Resolution Subtyping of Shiga-Toxin Producing Escherichia coli (STEC) O157:H7
  Griffing, PloS one 2015
  • “...[ 19 ] Reported in Humans ECs3076 3015872 No [ 19 ] Reported in Humans ECs4494 4538018 No [ 19 ] Reported in Humans ECs1017 1124089 Cluster 1 [ 19 ] Reported in Humans ECs2000 1976735 Cluster 1 [ 19 ] Reported in Humans ECs5049 5137547...”

PMI3178 L-threonine 3-dehydrogenase from Proteus mirabilis HI4320
29% identity, 98% coverage

• Transcriptome of Proteus mirabilis in the murine urinary tract: virulence and nitrogen assimilation gene expression
  Pearson, Infection and immunity 2011
  • “...PMI1469 PMI0022 PMI1595 PMI1622 PMI0291 PMI0596 PMI1656 PMI3178 PMI1943 PMI1620 PMI1666 PMI1645 PMI0044 PMI1621 PMI3211 PMI1506 PMI1879 PMI1489 PMI1617 PMI1061...”
• Transcriptome of swarming Proteus mirabilis
  Pearson, Infection and immunity 2010
  • “...PMI1075 PMI0968 PMI3559 PMI3556 PMI0564 PMI0971 PMI1451 PMI3178 PMI2256 PMI1471 PMI1473 PMI1171 PMI1472 PMI1616 PMI0360 PMI1730 PMI2268 PMI0047 PMI2036 PMI1737...”

Tdh / b3616 threonine dehydrogenase (EC 1.1.1.103) from Escherichia coli K-12 substr. MG1655 (see 5 papers)
tdh / P07913 threonine dehydrogenase (EC 1.1.1.103) from Escherichia coli (strain K12) (see 10 papers)
TDH_ECOLI / P07913 L-threonine 3-dehydrogenase; TDH; L-threonine dehydrogenase; EC 1.1.1.103 from Escherichia coli (strain K12) (see 2 papers)
P07913 L-threonine 3-dehydrogenase (EC 1.1.1.103) from Escherichia coli (see paper)
NP_418073 threonine dehydrogenase from Escherichia coli str. K-12 substr. MG1655
b3616 L-threonine 3-dehydrogenase from Escherichia coli str. K-12 substr. MG1655
WP_000646007 L-threonine 3-dehydrogenase from Escherichia coli
29% identity, 98% coverage

• function: Catalyzes the NAD(+)-dependent oxidation of L-threonine to 2- amino-3-ketobutyrate. To a lesser extent, also catalyzes the oxidation of D-allo-threonine and L-threonine amide, but not that of D-threonine and L-allothreonine. Cannot utilize NADP(+) instead of NAD(+).
  catalytic activity: L-threonine + NAD(+) = (2S)-2-amino-3-oxobutanoate + NADH + H(+) (RHEA:13161)
  cofactor: Zn(2+) Co(2+) Cd(2+) (Binds 2 Zn(2+) ions per subunit. Co(2+) and Cd(2+) can exchange for Zn(2+) (PubMed:2007567). Probably contains one structural ion and one catalytic ion that seems to be less tightly bound at the site (PubMed:9784233).)
  subunit: Homotetramer.
• Mononuclear iron enzymes are primary targets of hydrogen peroxide stress.
  Anjem, The Journal of biological chemistry 2012
  • GeneRIF: Data show that peptide deformylase, threonine dehydrogenase, and cytosine deaminase are very sensitve to hydrogen peroxide.
• The primary structure of Escherichia coli L-threonine dehydrogenase.
  Aronson, The Journal of biological chemistry 1989 (PubMed)
  • GeneRIF: N-terminus verified by Edman degradation on complete protein
• Sugar alcohol degradation in Archaea: uptake and degradation of mannitol and sorbitol in Haloarcula hispanica
  Ortjohann, Extremophiles : life under extreme conditions 2024
  • “...reuteri , Q6ECH5; H. gibbonsii , M0H624; H. marisrubri , A0A2P4NQW5; TDH: E. coli , P07913; P. furiosus , Q8U259; T. kodakarensis , Q5JI69; P. horikoshii , O58389; secADH: C. beijerinckii , P25984; E. histolytica , P35630; T. brockii , P14941; M. pneumoniae , P75214; SORE:...”
• The Thioredoxin Fold Protein (TFP2) from Extreme Acidophilic Leptospirillum sp. CF-1 Is a Chaperedoxin-like Protein That Prevents the Aggregation of Proteins under Oxidative Stress
  Muñoz-Villagrán, International journal of molecular sciences 2024
  • “...4.92 0.040 P16095 L-serine deaminase I sdaA 7.14 0.003 P0A9S3 galactitol-1-phosphate 5-dehydrogenase gatD 5.87 0.026 P07913 threonine dehydrogenase tdh 7.38 0.004 P08142 acetohydroxy acid synthase I subunit IlvB ilvB 5.96 0.004 P00963 asparagine synthetase A asnA 7.40 0.026 P0AB80 branched-chain-amino-acid aminotransferase ilvE 3.91 0.043 F. Nucleotide...”
• Biodistribution of ⁸⁹Zr-DFO-labeled avian pathogenic Escherichia coli outer membrane vesicles by PET imaging in chickens
  Li, Poultry science 2023
  • “...Cytoplasm 78 P0DTT0 BIPA Signal transduction mechanisms Cytoplasm 79 Q46868 UBIK Function unknown Cytoplasm 80 P07913 TDH Function unknown Cytoplasm 81 P0A717 KPRS Function unknown Cytoplasm 82 P0A7G2 RBFA Translation, ribosomal structure and biogenesis Cytoplasm 83 P26646 ACUI Function unknown Cytoplasm 84 P0A9H9 CHEZ Function unknown...”
• The Escherichia coli proteome: past, present, and future prospects
  Han, Microbiology and molecular biology reviews : MMBR 2006
  • “...5.73/9,663.98 TatB P69425 5.13/18,420.87 Tdh P07913 Sec-independent protein translocase protein L-Threonine 3-dehydrogenase 5.94/37,239.04 TehB P25397 Tellurite...”
• Proteomic response analysis of a threonine-overproducing mutant of Escherichia coli
  Kim, The Biochemical journal 2004
  • “...31.37 43.21 48.06 50.73 49.91 39.36 35.24 29.99 P04422 P07913 P27250 P06999 P05640 P06721 P00891 P14178 P30127 P25437 P30867 P06994 58.8 76.9 57.1 66.7 64.3...”
• The human L-threonine 3-dehydrogenase gene is an expressed pseudogene
  Edgar, BMC genetics 2002
  • “...and ESTs; Caenorhabditis elegans , Ce, genomic DNA (U64847) and ESTs; Escherichia coli , EcTDH (P07913) and EcGALE (AAC73846). The locations of the exon/exon boundaries are shown on the translated protein as underlined residues. Conserved residues are indicated by a (*), strongly similar residues by a...”
• Functional genomics analysis of free fatty acid production under continuous phosphate limiting conditions
  Youngquist, Journal of industrial microbiology & biotechnology 2017
  • “...b2903 gcvP 4.63 3.6 10 6 glycine decarboxylase b2905 gcvT 4.3 3.1 10 5 aminomethyltransferase b3616 tdh 2.2 2.4 10 2 threonine dehydrogenase b2965 speC 3.9 1.0 10 2 ornitine decarboxylase Fatty acid metabolism b0954 fabA 3.0 4.8 10 2 beta-hydroxydecanoyl thioester dehydrase b2323 fabB 2.1...”
• Analysis of pleiotropic transcriptional profiles: a case study of DNA gyrase inhibition
  Jeong, PLoS genetics 2006
  • “...iron transport proteins, domain 33. Domain 15 spanned across 32 genes, in a region from b3616 to b3650 . This region contains two operons of the lipopolysaccharide synthesis genes (rfa genes: b3619 ~ b3632) along with some functionally unrelated open reading frames (ORFs). Differential and coherent...”
• Interfering with different steps of protein synthesis explored by transcriptional profiling of Escherichia coli K-12
  Sabina, Journal of bacteriology 2003
  • “...b2600 b1260 b1973 b1262 b3340 b1779 b3321 b3308 b3304 b3616 b3339 b2155 b3829 b3317 b3296 b2913 b0631 b2416 b3305 b3303 b1043 b3509 0.03 0.11 0.13 0.16 0.17...”
• Combined, functional genomic-biochemical approach to intermediary metabolism: interaction of acivicin, a glutamine amidotransferase inhibitor, with Escherichia coli K-12
  Smulski, Journal of bacteriology 2001
  • “...b3461 b1814 b3506 b1642 b3349 b3129 b4062 b2521 b4148 b3616 b3706 b0004 b0001 b0738 b0998 b3519 b1421 b1610 b3453 b1183 b3495 b1521 b0422 b4031 b2605 b3073...”
• Construction of an Alternative NAD⁺ De Novo Biosynthesis Pathway
  Ding, Advanced science (Weinheim, Baden-Wurttemberg, Germany) 2021
  • “...Cell Factory A 2.4 kb DNA fragment containing the 1.0 kb EcTdh (EcTDH, Accession No. WP_000646007) and the 1.4 kb SpaNox (SpaNox, Accession No. WP_002989788) genes was synthesized and inserted into the Nco I /Xho I sites of pRSFDuet1 to afford plasmid pRSF EcTdh SpaNox ....”

NMC0547 putative zinc-binding alcohol dehydrogenase from Neisseria meningitidis FAM18
A1KSL2 Zinc-binding alcohol dehydrogenase from Neisseria meningitidis serogroup C / serotype 2a (strain ATCC 700532 / DSM 15464 / FAM18)
29% identity, 92% coverage

• Neisseria meningitidis rifampicin resistant strains: analysis of protein differentially expressed
  Neri, BMC microbiology 2010
  • “...Sequence (5'3') Protein encoded (Locus tag) ADZ-f 576170 GCGTTTCAGACGGCATTTGT 576189 * putative zinc-binding alcohol dehydrogenase (NMC0547) ADZ-r 577320 GCCAGATTCAGACGGTATTCC 577300 * ICD-f 893762 ACGACGAATGTTCAGACGG 893780 * isocitrate dehydrogenase (NMC0897) ICD-r 896097 TGCCATAATAGCCACGCAC 896079 * PTA-f 607259 AAGCCGTTTGTCAGCCTT 607276 * putative phosphate acyltransferase Pta (NMC0575) PTA-r 608401...”
  • “...NMC1625 54 221 48731/5.80 up Energy metabolism: amino acid metabolism 15 Putative zinc-binding alcohol dehydrogenase (NMC0547) A1KSL2 NMC0547 38 235 38283/5.32 down* Carbohydrate metabolism: butanoate metabolism 16 Succinyl-CoA ligase [ADP-forming] subunit beta ( suc C) A1KTM6 NMC0935 26 125 41567/5.01 up Carbohydrate metabolism: TCA cycle 17...”
• Neisseria meningitidis rifampicin resistant strains: analysis of protein differentially expressed
  Neri, BMC microbiology 2010
  • “...54 221 48731/5.80 up Energy metabolism: amino acid metabolism 15 Putative zinc-binding alcohol dehydrogenase (NMC0547) A1KSL2 NMC0547 38 235 38283/5.32 down* Carbohydrate metabolism: butanoate metabolism 16 Succinyl-CoA ligase [ADP-forming] subunit beta ( suc C) A1KTM6 NMC0935 26 125 41567/5.01 up Carbohydrate metabolism: TCA cycle 17 DNA-directed...”

NMB0604 alcohol dehydrogenase, zinc-containing from Neisseria meningitidis MC58
29% identity, 92% coverage

• Transcriptional profiling of Neisseria meningitidis interacting with human epithelial cells in a long-term in vitro colonization model
  Hey, Infection and immunity 2013
  • “...days NMB0018 NMB0128 NMB0143 NMB0345 NMB0382 NMB0546 NMB0554 NMB0604 NMB0634 NMB1313 NMB1429 NMB1533 NMB1710 NMB1972 NMB2039 NMB2159 pilE rplA rplD 1.8 2.2 1.6...”
• Proteomic analysis of outer membranes and vesicles from wild-type serogroup B Neisseria meningitidis and a lipopolysaccharide-deficient mutant
  Williams, Infection and immunity 2007
  • “...molecular mass, 105 kDa) and zinc-containing alcohol dehydrogenase (NMB0604; molecular mass, 38 kDa) (Table 2). Detection of Opa proteins. The OM preparation...”
• Analysis of the heat shock response of Neisseria meningitidis with cDNA- and oligonucleotide-based DNA microarrays
  Guckenberger, Journal of bacteriology 2002
  • “...NMB0164 NMB0165 NMB0214 NMB0294 NMB0370 NMB0557 NMB0561 NMB0604 NMB0906 NMB0907 NMB0946 NMB0947 NMB1056 NMB1231 NMB1334 NMB1377 NMB1468 NMB1469 NMB1472 NMB1563...”

Z5043 threonine dehydrogenase from Escherichia coli O157:H7 EDL933
29% identity, 98% coverage

• Validation of a Bioinformatics Workflow for Routine Analysis of Whole-Genome Sequencing Data and Related Challenges for Pathogen Typing in a European National Reference Center: Neisseria meningitidis as a Proof-of-Concept
  Bogaerts, Frontiers in microbiology 2019
  • “...The oxa gene was found in five more samples (Z4690 run C, Z4707 run B, Z5043 run C, Z6414 run B, and Z6430 run B) with over 99% identity and covering around 65% of the reference sequence. As this results in a total of 12 between-run...”
• Evaluation of a fluorescence-based PCR method for identification of serogroup a meningococci
  Diggle, Journal of clinical microbiology 2003
  • “...41 42 43 Z1466 Z1506 Z4186 Z1269 Z4099 Z5043 Z5035 Z3906 Z1534 Z3771 97-250767 96-254609 01-240815 97-252274 96-254609 00-242137 97-252274 02-240706 01-240815...”

BDH_NEIG1 / Q5FA46 (R,R)-butanediol dehydrogenase; BDH; (2R,3R)-2,3-butanediol dehydrogenase; (2R,3R)-BDH; NgBDH; Acetoin/diacetyl reductase; EC 1.1.1.4 from Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090) (see paper)
NGFG_00324, NGO_0186 2,3-butanediol dehydrogenase from Neisseria gonorrhoeae MS11
NGO0186 putative zinc-binding alcohol dehydrogenas from Neisseria gonorrhoeae FA 1090
29% identity, 92% coverage

• function: NAD-dependent butanediol dehydrogenase which catalyzes the oxidation of (R,R)-butane-2,3-diol to (3R)-acetoin and of meso-butane- 2,3-diol to (3S)-acetoin (PubMed:33763825). Preferentially oxidizes (R,R)-butane-2,3-diol, with a catalytic efficiency approximately fourfold higher than with meso-butane-2,3-diol (PubMed:33763825). Shows a very low activity with (S,S)-butane-2,3-diol (PubMed:33763825). Can also catalyze the reduction of (3R/3S)-acetoin and diacetyl in the presence of NADH (PubMed:33763825).
  catalytic activity: (R,R)-butane-2,3-diol + NAD(+) = (R)-acetoin + NADH + H(+) (RHEA:24340)
  catalytic activity: (S)-acetoin + NAD(+) = diacetyl + NADH + H(+) (RHEA:27286)
  cofactor: Zn(2+) (Binds 1 Zn(2+) per subunit.)
• Iron-regulated small RNA expression as Neisseria gonorrhoeae FA 1090 transitions into stationary phase growth
  Jackson, BMC genomics 2017
  • “...ORF Fe Regulation NrfA NGO_0007 cis NGO_0010 a NGO_0011 Induced NrfB NGO_0184 cis NGO_0185 a NGO_0186 Induced NrfC NGO_0198 trans NGO_0199 Induced NrfD NGO_0274 cis NGO_0275 NGO_0276 Repressed NrfE NGO_0646 cis NGO_03400 a NGO_0647 Induced NrfF NGO_0773 cis NGO_0775 NGO_0777 Induced NrfG NGO_1347 trans NGO_1349 Induced...”
• Transcriptional landscape and essential genes of Neisseria gonorrhoeae
  Remmele, Nucleic acids research 2014
  • “...primary and secondary TSS are a lipoprotein coding gene (NGFG_00049) and a zinc-binding alcohol dehydrogenase (NGFG_00324). For genes with primary as well as internal TSS, cytochrome c biogenesis protein (NGFG_00240) and disulfide bond formation protein B (NGFG_02168) are exemplary. Only gene NGFG_04218 encoding for a hypothetical...”
• Manganese regulation of virulence factors and oxidative stress resistance in Neisseria gonorrhoeae
  Wu, Journal of proteomics 2010
  • “...3.62.33 NGO1046 endopeptidase Clp ATP-binding chain B / heat shock protein F84.1 clpB Q 4.23.67 NGO0186 zinc binding alcohol dehydrogenase aid M 2.91.83 Membrane fractions: NGO0346 pilus retraction, twitching motility protein pilT O 1.911.30 NGO0562 pyruvate E3 component, lipoamide dehydrogenase / glycine cleavage L protein (OMP...”

YPO0060 threonine 3-dehydrogenase from Yersinia pestis CO92
29% identity, 96% coverage

• Tn-Seq Analysis Identifies Genes Important for Yersinia pestis Adherence during Primary Pneumonic Plague
  Eichelberger, mSphere 2020
  • “...(2.32) 3.26 (2.59) YPOs02 ssrS Noncoding RNA 4.12 (4.68) 4.02 (4.35) 3.41 (2.67) 3.56 (2.85) YPO0060 tdh l -Threonine 3-dehydrogenase 2.84 (3.46) 2.74 (3.09) 3.59 (2.60) 3.98 (3.23) YPO2905 ail Attachment invasion locus 3.96 (4.28) 4.02 (4.35) 3.93 (3.10) 4.34 (3.57) YPO2235 rnb Exoribonuclease II 4.57...”
• Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
  Rosso, BMC microbiology 2008
  • “...1.531 (0.042) YPTB0024 (glnA) YPO0024 glutamine synthetase 0.49 (< 0.001) 0.448 (< 0.001) YPTB0057 (tdh) YPO0060 threonine 3-dehydrogenase 0.663 (0.041) YPTB0066 (cysE) YPO0070 serine acetyltransferase 1.669 (0.016) YPTB0106 (metL) YPO0116 bifunctional aspartokinase/homoserine dehydrogenase II 1.565 (0.045) YPTB0111 (argB) YPO3925 acetylglutamate kinase 1.495 (0.016) YPTB0112 (argH) YPO3924...”
  • “...0.001) R: general function prediction only YPTB0026 YPO0027 conserved hypothetical protein 0.616 (0.018) YPTB0057 (tdh) YPO0060 threonine 3-dehydrogenase 0.663 (0.041) YPTB0063 (secB) YPO0067 protein-export protein 0.683 (0.012) YPTB0071 (cpxP) YPO0075 putative exported protein 0.337 (< 0.001) YPTB0156 YPO3881 putative chaperone protein 0.657 (0.01) YPTB0158 YPO3879 putative...”

UTI89_C4162 threonine 3-dehydrogenase from Escherichia coli UTI89
29% identity, 98% coverage

• High-throughput sequencing of sorted expression libraries reveals inhibitors of bacterial cell division
  Mediati, BMC genomics 2018
  • “...S 4,049,5154,052,967 UTI89_C4158 yibP (envC) D 3453 51.7 12,724.5 UTI89_C4159 yibQ S UTI89_C4160 yibD M UTI89_C4162 tdh ER 4,997,0734,999,597 UTI89_C5098 S 2525 14.8 584.6 UTI89_C5099 S UTI89_C5100 S UTI89_C5101 yfdN2 S UTI89_C5102 S a Coordinates were determined from Genbank accession NC_007946.1 as the minimal region identified...”

Q83F39 L-threonine 3-dehydrogenase from Coxiella burnetii (strain RSA 493 / Nine Mile phase I)
30% identity, 92% coverage

• Quantitative proteome profiling of C. burnetii under tetracycline stress conditions
  Vranakis, PloS one 2012
  • “...including protein folding and stabilization-heat response (Q83CE9), aspartate biosynthesis (P24703), detoxification (Q83AQ8), threonine catabolic process (Q83F39), purine ribonucleoside salvage (Q83FC4), transport and binding (Q83BF9, Q82OW5, Q83DI7 and Q83AW2) and unknown function (B5QSC3, B5QSC0, Q83A96, Q83EA1, Q83EJ9, Q83A79, Q83D04, Q83DR4, Q83B41 and Q83CL9). One example of the...”

STM3708 threonine 3-dehydrogenase from Salmonella typhimurium LT2
29% identity, 96% coverage

• Hydrogen-stimulated carbon acquisition and conservation in Salmonella enterica serovar Typhimurium
  Lamichhane-Khadka, Journal of bacteriology 2011
  • “...2.2 2.1/2.1 Amino acids STM0791 STM3106 STM3709 STM0890 STM3708 STM0828-30 STM2071-78 STM4007 STM2555 STM4477 STM0002 hutH ansB kbl artI tdh glnQ/P/H hisA-I...”

YPTB0057 threonine 3-dehydrogenase from Yersinia pseudotuberculosis IP 32953
29% identity, 96% coverage

• Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
  Rosso, BMC microbiology 2008
  • “...aspartate-ammonia ligase 1.531 (0.042) YPTB0024 (glnA) YPO0024 glutamine synthetase 0.49 (< 0.001) 0.448 (< 0.001) YPTB0057 (tdh) YPO0060 threonine 3-dehydrogenase 0.663 (0.041) YPTB0066 (cysE) YPO0070 serine acetyltransferase 1.669 (0.016) YPTB0106 (metL) YPO0116 bifunctional aspartokinase/homoserine dehydrogenase II 1.565 (0.045) YPTB0111 (argB) YPO3925 acetylglutamate kinase 1.495 (0.016) YPTB0112...”
  • “...2.142 (< 0.001) R: general function prediction only YPTB0026 YPO0027 conserved hypothetical protein 0.616 (0.018) YPTB0057 (tdh) YPO0060 threonine 3-dehydrogenase 0.663 (0.041) YPTB0063 (secB) YPO0067 protein-export protein 0.683 (0.012) YPTB0071 (cpxP) YPO0075 putative exported protein 0.337 (< 0.001) YPTB0156 YPO3881 putative chaperone protein 0.657 (0.01) YPTB0158...”

A6TFL2 L-threonine 3-dehydrogenase from Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)
29% identity, 96% coverage

• Disruption of KPC-producing Klebsiella pneumoniae membrane via induction of oxidative stress by cinnamon bark (Cinnamomum verum J. Presl) essential oil
  Yang, PloS one 2019
  • “...B5XNC0 Transport Control 99 L-lactate dehydrogenase lldD A6TFK0 Energy synthesis Control 100 L-threonine 3-dehydrogenase tdh A6TFL2 Protein biosynthesis Control Of the overlapping 232 proteins identified in both treatment groups, only 41 proteins showed significant differences, in terms of fold change between the groups. The majority of...”

SACOL0235 hexitol dehydrogenase from Staphylococcus aureus subsp. aureus COL
SAOUHSC_00219 hypothetical protein from Staphylococcus aureus subsp. aureus NCTC 8325
SAUSA300_0244 oxidoreductase, zinc-binding dehydrogenase family from Staphylococcus aureus subsp. aureus USA300_FPR3757
Newbould305_0793 galactitol-1-phosphate 5-dehydrogenase from Staphylococcus aureus subsp. aureus str. Newbould 305
30% identity, 98% coverage

• Importance of bacillithiol in the oxidative stress response of Staphylococcus aureus
  Posada, Infection and immunity 2014
  • “...ldh1 manA pckA pflA pflB SACOL0235 Sorbitol dehydrogenase 6-Phospho-beta-galactosidase L-Lactate dehydrogenase Mannose-6-phosphate isomerase Phosphoenolpyruvate...”
• Predictive characterization of hypothetical proteins in Staphylococcus aureus NCTC 8325
  School, Bioinformation 2016
  • “...classified as hypothetical. The protein loci were SAOUHSC_00010, SAOUHSC_00077, SAOUHSC_00082, SAOUHSC_00085, SAOUHSC_00091, SAOUHSC_00136, SAOUHSC_00145, SAOUHSC_00156, SAOUHSC_00219, SAOUHSC_00238, SAOUHSC_00303, SAOUHSC_00307, SAOUHSC_00308, SAOUHSC_00328, SAOUHSC_00423, SAOUHSC_00455, SAOUHSC_00548, SAOUHSC_00751, SAOUHSC_00766, SAOUHSC_00837, SAOUHSC_00972, SAOUHSC_01024, SAOUHSC_01291, SAOUHSC_01306, SAOUHSC_01402, SAOUHSC_01851, SAOUHSC_01931, SAOUHSC_01937, SAOUHSC_02471, SAOUHSC_02570, SAOUHSC_02770, SAOUHSC_02889, SAOUHSC_02901, SAOUHSC_02911, and SAOUHSC_02934. Several algorithms characterized...”
  • “...ATP-binding protein 99% 6.00E-179 SAOUHSC_00145 4'-phosphopantetheinyl transferase 99% 8.00E-157 SAOUHSC_00156 outer surface protein 99% 0 SAOUHSC_00219 galactitol-1-phosphate 5-dehydrogenase 99% 0 SAOUHSC_00238 hypothetical protein 98% 3.00E-20 SAOUHSC_00303 hypothetical protein 97% 6.00E-25 SAOUHSC_00307 deacetylase SIR2 99% 0 SAOUHSC_00308 lipoate-protein ligase A 99% 0 SAOUHSC_00328 twin arginine-targeting protein translocase...”
• Identification of Methicillin-Resistant Staphylococcus aureus (MRSA) Genetic Factors Involved in Human Endothelial Cells Damage, an Important Phenotype Correlated with Persistent Endovascular Infection
  Xiao, Antibiotics (Basel, Switzerland) 2022
  • “...SAUSA300_2284 hypothetical hypothetical protein 12.20 10.36 SAUSA300_2225 moaC molybdenum cofactor biosynthesis protein MoaC 12.08 9.05 SAUSA300_0244 hypothetical zinc-binding dehydrogenase family oxidoreductase 12.05 9.79 SAUSA300_2022 rpoF RNA polymerase sigma factor SigB 12.05 6.83 SAUSA300_1089 lspA lipoprotein signal peptidase 11.97 6.81 SAUSA300_1618 hemX hemA concentration negative effector hemX...”
• Recombination-mediated remodelling of host-pathogen interactions during Staphylococcus aureus niche adaptation
  Spoor, Microbial genomics 2015
  • “...domain sulfur transferase Newbould305_0534 Acetyltransferase Newbould305_0564 Pyrrolidone carboxylate peptidase Newbould305_0641 Amidohydrolase cysG Newbould305_0486 Precorrin-2 dehydrogenase Newbould305_0793 Hexitol dehydrogenase Newbould305_0736 RND transporter Newbould305_0757 NADH-dependent dehydrogenase Newbould305_0815 Ribose transporter RbsU Newbould305_0748 -Glutamyltransferase Newbould305_0719 4-Phosphopantetheinyl transferase * Locus tags according to annotations in strain MW2 (GenBank accession number NC_003923...”

SAR0245 putative zinc-binding dehydrogenase from Staphylococcus aureus subsp. aureus MRSA252
30% identity, 98% coverage

• A functional menadione biosynthesis pathway is required for capsule production by Staphylococcus aureus
  Altwiley, Microbiology (Reading, England) 2021
  • “...protein 0.031847864 SAR1995 putative lipoprotein 0.031847864 SAR0463 putative lipoprotein 0.031847864 SAR0010 putative membrane protein 0.033712843 SAR0245 putative zinc-binding dehydrogenase 0.035487178 ureE urease accessory protein UreE 0.035624064 odhA 2-oxoglutarate dehydrogenase E1 component 0.036566931 SAR2186 conserved hypothetical protein 0.037233673 hisB putative imidazoleglycerol-phosphate dehydratase 0.037571061 SAR0291 putative membrane protein...”

4cpdA / B2ZRE3 Alcohol dehydrogenase tadh from thermus sp. Atn1
32% identity, 95% coverage

• Ligands: zinc ion; nicotinamide-adenine-dinucleotide (4cpdA)

B2ZRE3 alcohol dehydrogenase (EC 1.1.1.1) from Thermus sp. (see paper)
32% identity, 94% coverage

• Light-driven biocatalytic oxidation
  Yun, Chemical science 2022
  • “...30 C for 24 h 24 and 25 ADH from Thermus sp. ATN1 (TADH) EU681191 (B2ZRE3) TADH was produced by transforming pASZ2 (PET) into E. coli BL21 (DE3) pLysS cells and cultivation of the recombinant E. coli using the autoinduction system 26 ADH from horse liver...”
• Structure and Dynamics of a Thermostable Alcohol Dehydrogenase from the Antarctic Psychrophile Moraxella sp. TAE123
  Petratos, ACS omega 2020
  • “...Gs ADH, UniProtKB ID P42328), 13 and Thermus sp. ATN1 ( Th ADH, UniProtKB ID B2ZRE3). 14 Moreover, circular dichroism (CD) spectropolarimetry and enzyme kinetics of Mo ADH have been carried out at varying temperatures. Finally, molecular dynamics (MD) simulation results for a single subunit of...”
  • “...(1347) (1176) Th ADH:NAD + 1.56 1.60 1.59 (PDB ID 4CPD) (264) (271) (271) (UniProtKB: B2ZRE3) 1.78 1.94 1.76 (913) (715) (915) a The right diagonal half of the table shows the per cent sequence identity of the respective enzymes. In the left diagonal half, each...”

YjgV / b4267 L-idonate 5-dehydrogenase (EC 1.1.1.264) from Escherichia coli K-12 substr. MG1655 (see 5 papers)
idnD / P39346 L-idonate 5-dehydrogenase (EC 1.1.1.264) from Escherichia coli (strain K12) (see 3 papers)
IDND_ECOLI / P39346 L-idonate 5-dehydrogenase (NAD(P)(+)); EC 1.1.1.264 from Escherichia coli (strain K12) (see paper)
idnD / GB|AAC77224.1 L-idonate 5-dehydrogenase; EC 1.1.1.264 from Escherichia coli K12 (see 4 papers)
b4267 L-idonate 5-dehydrogenase, NAD-binding from Escherichia coli str. K-12 substr. MG1655
31% identity, 90% coverage

• function: Catalyzes the NADH/NADPH-dependent oxidation of L-idonate to 5-ketogluconate (5KG).
  catalytic activity: L-idonate + NADP(+) = 5-dehydro-D-gluconate + NADPH + H(+) (RHEA:21176)
  catalytic activity: L-idonate + NAD(+) = 5-dehydro-D-gluconate + NADH + H(+) (RHEA:21172)
  cofactor: Zn(2+) (Binds 2 Zn(2+) ions per subunit.)
• Human body temperature (37degrees C) increases the expression of iron, carbohydrate, and amino acid utilization genes in Escherichia coli K-12
  White-Ziegler, Journal of bacteriology 2007
  • “...transport system (ABC superfamily, membrane) idnD b4267 L-idonate 5-dehydrogenase, NAD binding livG b3455 ATP-binding component of high-affinity branched-chain...”
• Functional Prediction of Biological Profile During Eutrophication in Marine Environment
  Sbaoui, Bioinformatics and biology insights 2022
  • “...at high temperature HybF P0A703 Hydrogenase maturation protein IbpA P0C054 Small heat shock protein IdnD P39346 l -idonate 5-dehydrogenase KorB P07674 Transcriptional repressor protein LtxA P16462 Leukotoxin LtxB A0A2G8ZPA1 RTX toxin hemolysin A MaeA P26616 NAD-dependent malic enzyme Mdh P61889 Malate dehydrogenase Mfd P30958 Transcription-repair ATP-dependent...”
• L-tartaric acid synthesis from vitamin C in higher plants
  DeBolt, Proceedings of the National Academy of Sciences of the United States of America 2006
  • “...proteins that includes an Escherichia coli protein (P39346), which catalyses the reversible oxidation of L-idonate to 5-keto D-gluconic acid within the...”
• Sequence analysis of the GntII (subsidiary) system for gluconate metabolism reveals a novel pathway for L-idonic acid catabolism in Escherichia coli
  Bausch, Journal of bacteriology 1998
  • “...New (accession no.) gntV yjgV idnK (P39208) idnD (P39346) yjgU idnO (P39345) gntW yjgS idnT (P39344) idnR (P39343) Gene product D-Gluconate L-Idonate kinase...”

SA0240 hypothetical protein from Staphylococcus aureus subsp. aureus N315
30% identity, 98% coverage

• Identification of Staphylococcus aureus proteins recognized by the antibody-mediated immune response to a biofilm infection
  Brady, Infection and immunity 2006
  • “...SA2415 SA0452 SA1329 SA0688 SA2694 SA0594 SA1377 SA0829 SA2105 SA1614 SA1462 SA0240 SA2296 SA0660 SA0833 SA2656 \ \ \ \ \ \ \ \ \ a Symbols: and , up-regulated...”

CH51_RS01175 zinc-binding dehydrogenase from Staphylococcus aureus
30% identity, 95% coverage

• Staphylococcus aureus PhoU Homologs Regulate Persister Formation and Virulence
  Shang, Frontiers in microbiology 2020
  • “...expressed genes of phoU1 and USA500 2395. Gene Description Fold change RNA-seq qRT-PCR Carbon metabolism CH51_RS01175 Sorbitol dehydrogenase 2.04 ND CH51_RS14180 Gluconate permease 2.17 ND CH51_RS14185 Gluconokinase 2.52 ND CH51_RS14680 Acyl esterase 2.26 ND CH51_RS14690 Pantoate-beta-alanine ligase 2.14 ND CH51_RS14700 2-Dehydropantoate 2-reductase 2.63 ND CH51_RS11580 Carbohydrate...”

6dkhC / P39346 The crystal structure of l-idonate 5-dehydrogenase from escherichia coli str. K-12 substr. Mg1655
31% identity, 90% coverage

• Ligand: zinc ion (6dkhC)

STM4484 L-idonate 5-dehydrogenase from Salmonella typhimurium LT2
28% identity, 99% coverage

• Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits
  Seif, Nature communications 2018
  • “...fitness score Locus tag Encoded reactions Nutrient conditions STM1002 2,3-diaminopropionate ammonia lyase (N-O2+/, C-O2+) 2,3-diaminopropionate STM4484 ( idnD ) l -idonate 5-dehydrogenase (C-O2+/) l -Idonate STM0042 ( xylP ) d -xylose transport in via proton symport (C-O2+/) d -Xylose STM3354 l (+)-tartrate dehydratase (C-O2+/) l -tartrate...”
• Salmonella serovar identification using PCR-based detection of gene presence and absence
  Arrach, Journal of clinical microbiology 2008
  • “...STM4319, STM4373, STM4413, STM4420, STM4426, STM4445, STM4484, STM4486, STM4493, STM4499, STM4524, STM4527, STM4537, STM4573, STM4574, STM4589, STM4590,...”

SA0239 sorbitol dehydrogenase from Staphylococcus aureus subsp. aureus N315
30% identity, 95% coverage

• Insights Into the Impact of Small RNA SprC on the Metabolism and Virulence of Staphylococcus aureus
  Zhou, Frontiers in cellular and infection microbiology 2022
  • “...Fructose and mannose metabolism Mannitol-1-phosphate 5-dehydrogenase SAOUHSC_02811 SA2297 1.22 Purine metabolism Putative GTP pyrophosphokinase SAOUHSC_00217 SA0239 -1.37 Sorbitol dehydrogenase; alcohol dehydrogenase L-iditol 2-dehydrogenase SAOUHSC_01954 lukD -5.15 Leukocidin D Leukotoxin LukD SAOUHSC_01955 lukE -4.98 Leukocidin E Leukotoxin LukE SAOUHSC_02411 -2.03 Hypothetical protein SAOUHSC_02412 -1.87 Hypothetical protein SAOUHSC_02721...”
  • “...modA -81.5 SAOUHSC_00204 SA0231 -90.1 SAOUHSC_00712 SA0658 -80.7 SAOUHSC_01012 purQ -88.8 SAOUHSC_02299 rsbW -80 SAOUHSC_00217 SA0239 -88.5 SAOUHSC_02381 dps -78.2 SAOUHSC_02862 clpl -87.9 SAOUHSC_01646 glcK -75.8 SAOUHSC_01017 purH -86.5 SAOUHSC_01010 purC -73.9 SAOUHSC_02571 ssaa2 -85.7 SAOUHSC_02811 SA2297 -73.8 SAOUHSC_01807 pfk -85.6 SAOUHSC_02882 SA2352 -72.1 SAOUHSC_02403 mtlD...”
• Transcriptome and functional analysis of the eukaryotic-type serine/threonine kinase PknB in Staphylococcus aureus
  Donat, Journal of bacteriology 2009
  • “...protein, similar to indole-3-pyruvate decarboxylase SA0239 Sorbitol dehydrogenase SA0258 rbsK Ribokinase SA0304 nanA N-Acetylneuraminate lyase subunit...”
• Factors contributing to the biofilm-deficient phenotype of Staphylococcus aureus sarA mutants
  Tsang, PloS one 2008
  • “...reductase, which is required to convert acetoin to 2,3-butanediol, and expression of the corresponding gene (SA0239 in the N315 genome) was also reduced in a sarA mutant [33] . Thus, restoration of acetoin production in a sarA mutant may not fully restore the ability to convert...”

Q8KQG6 mannitol 2-dehydrogenase (EC 1.1.1.67) from Leuconostoc mesenteroides (see paper)
31% identity, 93% coverage

• Sugar alcohol degradation in Archaea: uptake and degradation of mannitol and sorbitol in Haloarcula hispanica
  Ortjohann, Extremophiles : life under extreme conditions 2024
  • “...H. hispanica , G0I059; H. marismortui , Q5V6V7; T. borchii , Q1ACW3; L. mesenteroides , Q8KQG6; L. pseudomesenteroides , Q83VI5; L. reuteri , Q6ECH5; H. gibbonsii , M0H624; H. marisrubri , A0A2P4NQW5; TDH: E. coli , P07913; P. furiosus , Q8U259; T. kodakarensis , Q5JI69; P....”

TDH_THET8 / Q5SKS4 L-threonine 3-dehydrogenase; TDH; EC 1.1.1.103 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
2dq4A / Q5SKS4 Crystal structure of threonine 3-dehydrogenase
31% identity, 99% coverage

• function: Catalyzes the NAD(+)-dependent oxidation of L-threonine to 2- amino-3-ketobutyrate.
  catalytic activity: L-threonine + NAD(+) = (2S)-2-amino-3-oxobutanoate + NADH + H(+) (RHEA:13161)
  cofactor: Zn(2+) (Binds 2 Zn(2+) ions per subunit. Contains one structural ion and one catalytic ion that may be less tightly bound at the site. {ECO:0000255|HAMAP-Rule:MF_00627, ECO:0000269|Ref.)2}
  subunit: Homotetramer.
• Ligand: zinc ion (2dq4A)

SAOUHSC_00217 sorbitol dehydrogenase, putative from Staphylococcus aureus subsp. aureus NCTC 8325
30% identity, 95% coverage

• Insights Into the Impact of Small RNA SprC on the Metabolism and Virulence of Staphylococcus aureus
  Zhou, Frontiers in cellular and infection microbiology 2022
  • “...1.05 Fructose and mannose metabolism Mannitol-1-phosphate 5-dehydrogenase SAOUHSC_02811 SA2297 1.22 Purine metabolism Putative GTP pyrophosphokinase SAOUHSC_00217 SA0239 -1.37 Sorbitol dehydrogenase; alcohol dehydrogenase L-iditol 2-dehydrogenase SAOUHSC_01954 lukD -5.15 Leukocidin D Leukotoxin LukD SAOUHSC_01955 lukE -4.98 Leukocidin E Leukotoxin LukE SAOUHSC_02411 -2.03 Hypothetical protein SAOUHSC_02412 -1.87 Hypothetical protein...”
  • “...SAOUHSC_02549 modA -81.5 SAOUHSC_00204 SA0231 -90.1 SAOUHSC_00712 SA0658 -80.7 SAOUHSC_01012 purQ -88.8 SAOUHSC_02299 rsbW -80 SAOUHSC_00217 SA0239 -88.5 SAOUHSC_02381 dps -78.2 SAOUHSC_02862 clpl -87.9 SAOUHSC_01646 glcK -75.8 SAOUHSC_01017 purH -86.5 SAOUHSC_01010 purC -73.9 SAOUHSC_02571 ssaa2 -85.7 SAOUHSC_02811 SA2297 -73.8 SAOUHSC_01807 pfk -85.6 SAOUHSC_02882 SA2352 -72.1 SAOUHSC_02403...”

DJ41_566 2,3-butanediol dehydrogenase from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
30% identity, 93% coverage

• Role of EmaSR in Ethanol Metabolism by Acinetobacter baumannii
  Shu, International journal of molecular sciences 2022
  • “...gene cluster that demonstrated elevated expression levels from 2.9~6.42 of log 2 ratio, DJ41_571 ~ DJ41_566 , was discovered to be involved in acetoin catabolism ( Figure 5 D). TCS regulate gene expression in response to different stimuli, and have also been reported to self-regulate expression...”
• Light Modulates Metabolic Pathways and Other Novel Physiological Traits in the Human Pathogen Acinetobacter baumannii
  Müller, Journal of bacteriology 2017 (secret)

lgnH / BAM68211.1 L-gluconate dehydrogenase lgnH from Paracoccus laeviglucosivorans (see 2 papers)
K7ZKU8 2-desacetyl-2-hydroxyethyl bacteriochlorophyllide A dehydrogenase from Paracoccus laeviglucosivorans
33% identity, 99% coverage

• l-Galactose metabolism in Bacteroides vulgatus from the human gut microbiota
  Hobbs, Biochemistry 2014
  • “...sorbitol dehydrogenase. The closest homologue with an experimentally determined catalytic function is LgnH (gi|425703034, UniProt K7ZKU8) from Paracoccus sp. 43P , with a sequence identity of 46%. The gene for LgnH is contained in an operon for the catabolism of the rare sugar l -glucose. LgnH...”

D4GPB2 2-dehydro-3-deoxy-L-rhamnonate dehydrogenase (NAD+) (EC 1.1.1.401) from Haloferax volcanii (see paper)
30% identity, 95% coverage

apdH / Q8KQL2 D-arabitol-phosphate dehydrogenase monomer (EC 1.1.1.301) from Enterococcus avium (see paper)
ARPD_ENTAV / Q8KQL2 D-arabitol-phosphate dehydrogenase; APDH; EC 1.1.1.301 from Enterococcus avium (Streptococcus avium) (see paper)
Q8KQL2 D-arabitol-phosphate dehydrogenase (EC 1.1.1.301) from Enterococcus avium (see paper)
32% identity, 93% coverage

• function: Involved in the arabitol catabolism via the arabitol phosphate route. Catalyzes only the transformation of D-arabitol 1- phosphate (Arb1P) and D-arabitol 5-phosphate (Arb5P) into D-xylulose 5- phosphate (Xlu5P) and ribulose 5-phosphate, respectively. It can use both NAD and NADP.
  catalytic activity: D-arabinitol 1-phosphate + NAD(+) = D-xylulose 5-phosphate + NADH + H(+) (RHEA:26002)
  cofactor: Mn(2+) (Binds 2 manganese ions per subunit.)
  subunit: Homotetramer.

Q83VI5 mannitol 2-dehydrogenase (EC 1.1.1.67) from Leuconostoc pseudomesenteroides (see 3 papers)
31% identity, 94% coverage

• Sugar alcohol degradation in Archaea: uptake and degradation of mannitol and sorbitol in Haloarcula hispanica
  Ortjohann, Extremophiles : life under extreme conditions 2024
  • “...HhSorDH (). UniProt accession: HsSorDH, Q00796; OaSorDH, P07846; RnSorDH, P27867; BsSorDH, Q06004; LrMtlDH, Q6ECH5; LpMtlDH, Q83VI5; TbMtlDH, Q1ACW3; HhSorDH, G0I050; HhMtlDH, G0I059 Besides sorbitol and mannitol dehydrogenases (Riveros-Rosas et al. 2003 ; Ceccaroli et al. 2007 ), the PDH family contains various different dehydrogenase subfamilies, such...”
  • “...H. marismortui , Q5V6V7; T. borchii , Q1ACW3; L. mesenteroides , Q8KQG6; L. pseudomesenteroides , Q83VI5; L. reuteri , Q6ECH5; H. gibbonsii , M0H624; H. marisrubri , A0A2P4NQW5; TDH: E. coli , P07913; P. furiosus , Q8U259; T. kodakarensis , Q5JI69; P. horikoshii , O58389; secADH:...”

MTCOM_21580 zinc-dependent dehydrogenase from Moorella thermoacetica
31% identity, 96% coverage

• Isolation and characterization of novel acetogenic Moorella strains for employment as potential thermophilic biocatalysts
  Böer, FEMS microbiology ecology 2024
  • “...and MOTHA_10720), AdhC (MTKAM_23920, MTMBA_25190, and MOTHA_24090), and a putative zinc-type alcohol dehydrogenase-like protein YdjJ (MTCOM_21580). Nevertheless, all five M. thermoacetica strains also encoded at least three copies of an aldehyde ferredoxin oxidoreductase (AOR). This enzyme has originally been described from M. thermoacetica (White et al....”

RSAU_000193 zinc-binding dehydrogenase from Staphylococcus aureus subsp. aureus 6850
30% identity, 95% coverage

• Identification of a Novel LysR-Type Transcriptional Regulator in Staphylococcus aureus That Is Crucial for Secondary Tissue Colonization during Metastatic Bloodstream Infection
  Groma, mBio 2020
  • “...5.00 7.83E04 pgcA RSAU_000006 5.04 1.76E06 gyrA RSAU_000735 5.04 8.10E04 hprK RSAU_000187 5.08 2.36E04 ptsG RSAU_000193 5.10 2.36E04 gutB RSAU_001351 5.14 1.24E04 ebpS RSAU_002484 5.15 5.55E04 manP RSAU_002525 5.16 3.05E04 hisZ RSAU_000259 5.17 9.20E04 nupC RSAU_000009 5.19 1.24E04 serS RSAU_000666 5.22 1.50E04 Transporter anion-sodium symporter family...”

Pden_4931 Alcohol dehydrogenase, zinc-binding domain protein from Paracoccus denitrificans PD1222
32% identity, 99% coverage

• An L-glucose catabolic pathway in Paracoccus species 43P
  Shimizu, The Journal of biological chemistry 2012
  • “...which has 100% identity with strain PD1222 Pden_4931, a putative oxidoreductase that is a member of the zinc-containing alcohol dehydrogenase family....”

WP_000642458 2,3-butanediol dehydrogenase from Bacillus pacificus
27% identity, 100% coverage

• Exploring the Biologically Active Metabolites Produced by Bacillus cereus for Plant Growth Promotion, Heat Stress Tolerance, and Resistance to Bacterial Soft Rot in Arabidopsis
  Tsai, Metabolites 2023
  • “...large subunit 5010240-5008525 WP_000822944 acetolactate synthase small subunit 247570-247061 WP_000095846 acetolactate synthase large subunit 249267-247567 WP_000642458 2,3-butanediol dehydrogenase 3763547-3764614 AAS39887 acetolactate synthase 723478-721781 -dimethyl disulfide WP_000460299 methionine gamma-lyase 3328355-3329626 WP_000726591 methionine gamma-lyase 2387529-2388707 WP_001201908 cystathionine gamma-lyase 2694257-2695390 WP_000122291 cystathionine beta-lyase 2797135-2795972 -terpenoids WP_000251030 IPP isomerase 153587-152538...”

Q57517 Uncharacterized zinc-type alcohol dehydrogenase-like protein HI_0053 from Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
HI0053 zinc-type alcohol dehydrogenase from Haemophilus influenzae Rd KW20
29% identity, 97% coverage

• Prediction of enzymatic pathways by integrative pathway mapping
  Calhoun, eLife 2018
  • “...Cloning, expression, and purification of Hi GulD and Hi UxuA The genes HiGulD (Uniprot ID Q57517) and HiUxuA (Uniprot ID P44488) were amplified from H. influenzae strain Rd KW20 (ATCC 51907) genomic DNA. PCR was performed using KOD Extreme DNA Polymerase (Novagen) according to the manufacturers...”
• Sporangium-specific gene expression in the oomycete phytopathogen Phytophthora infestans
  Kim, Eukaryotic cell 2003
  • “...Bacillus subtilis (AAA22508), Haemophilus influenzae (Q57517), Pseudomonas putida (AAB58982), Agrobacterium tumefaciens (NP357437), Gluconobacter suboxydans...”
• Prediction of enzymatic pathways by integrative pathway mapping
  Calhoun, eLife 2018
  • “...The same approach was used to create a genetic deletion of the putative L-gulonate dehydrogenase (HI0053). To generate the triple overlap extension product for deletion of HI0053, primers Del_HI0053_arm1fwd and Del_HI0053_arm1rev and primers Del_HI0053_arm2fwd and Del_HI0053_arm2rev were used to amplify the regions~1000 bps upstream and downstream...”
  • “...and Del_HI0053_arm2rev to generate a~3 kb fragment with arms homologous to the genomic regions flanking HI0053, with an intervening kanamycin resistance cassette. Primer sequences are provided in Supplementary file 9 . Each of the triple overlap PCR products was gel-purified and 100 ng was transformed into...”
• Comparative genomic analysis reveals distinct genotypic features of the emerging pathogen Haemophilus influenzae type f
  Su, BMC genomics 2014
  • “...ZitB HI0291 Periplasmic mercury transport-like protein HI0661 Hemoglobin-binding protein OapA HI0712 Hemoglobin-binding protein Other metabolism HI0053 Zinc-type alcohol dehydrogenase (fructose and mannose metabolism) HI0692 Xanthine-guanine phosphoribosyltransferase (purine metabolism) HI1649 D-lactate dehydrogenase (pyruvate metabolism) Others HI0584 Peptidase, aminobenzoyl-glutamate utilization protein HI0947 Virulence-associated protein C HI1251 Virulence-associated protein...”
• Codon usage comparison of novel genes in clinical isolates of Haemophilus influenzae
  Gladitz, Nucleic acids research 2005
  • “...to translation initiation factor) UU 28.5 HI0054 31 266 22.52 Uxuoperon regulator (uxuR) PF 32 HI0053 35 343 25.14 Zinc-type alcohol dehydrogenase CB 37.8 HI0051 31 166 28.76 Conserved hypothetical transmembrane protein (homol. to transport protein) BB 40.5 HI1647 44 291 25.32 Conserved hypothetical protein (homol....”

CD630_23230 zinc-binding dehydrogenase from Clostridioides difficile 630
32% identity, 90% coverage

• [Transcriptomic analysis of the ΔPaLoc mutant of Clostridioides difficile and verification of its toxicity]
  Cui, Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine] 2022 (PubMed)
  • “...17.92,11.40,8.93 and 7.55 fold, respectively. Whereas the hom2 (high serine dehydrogenase), the CD630_15810 (spore-forming protein), CD630_23230 (zinc-binding dehydrogenase) and CD630_23240 (galactitol 1-phosphate 5-dehydrogenase) genes were down-regulated by 0.06, 0.075, 0.133 and 0.183 fold, respectively. The GO and KEGG enrichment analyses showed that the differentially transcribed genes...”

WP_135197409 2,3-butanediol dehydrogenase from Leuconostoc sp.
28% identity, 98% coverage

• The Metabolism of Leuconostoc Genus Decoded by Comparative Genomics
  Candeliere, Microorganisms 2024
  • “...(AFT82058) of L. carnosum , diacetyl reductase (SPJ42929) of L. carnosum , and 2,3-butanediol dehydrogenase (WP_135197409) of L. carnosum . BLASTp searches were also conducted for mannitol dehydrogenase (ACM66886.1) of L. mesenteroides , malic enzyme (BAX72645.1) of L. mesenteroides , malolactic enzyme (KGB50834.1) of L. mesenteroides...”
• Comparative Genomics of Leuconostoc carnosum
  Candeliere, Frontiers in microbiology 2020
  • “...(AFT82058) of L. carnosum , diacetyl reductase (SPJ42929) of L. carnosum , and 2,3-butanediol dehydrogenase (WP_135197409) of L. carnosum . The genes encoding the carboxylases yielding biogenic amines were searched ( Li et al., 2018 ; Rodrigo-Torres et al., 2019 ): tyrosine decarboxylase (AAN77279) and agmatine...”

ACIAD1021 putative (R,R)-butanediol dehydrogenase from Acinetobacter sp. ADP1
29% identity, 88% coverage

• A complete collection of single-gene deletion mutants of Acinetobacter baylyi ADP1
  de, Molecular systems biology 2008
  • “...isofunctional enzyme involved in the pyruvate/oxoglutarate dehydrogenase complex. The deletion of the putative butanediol dehydrogenase (ACIAD1021) results in severe growth impairment of the mutant, indicating that another dehydrogenase may perform this function, albeit weakly. The data clearly show that the putative acetaldehyde dehydrogenase (ACIAD2018) is also...”
  • “...ACIAD1018 Acetoin:2,6-dichlorophenolindophenol oxidoreductase subunit ( acoB ) + ACIAD1019 Dihydrolipoamide acetyltransferase ( acoC ) + ACIAD1021 Putative (R,R)-butanediol dehydrogenase Growth defect + ACIAD1052 Putative membrane-bound protein in GNT I transport system + ACIAD1550 Putative oxidoreductase, short-chain dehydrogenase/reductase family + ACIAD2018 Aldehyde dehydrogenase ( ald1 ) +...”
• Iterative reconstruction of a global metabolic model of Acinetobacter baylyi ADP1 using high-throughput growth phenotype and gene essentiality data
  Durot, BMC systems biology 2008
  • “...ACIAD3365 (murE) E step 2 ACIAD0556 (ndk) D step 3 ACIAD3371 (gltX) E step 2 ACIAD1021 D step 3 ACIAD1710 (pcaC) E step 3 ACIAD1707 (pcaB) E step 3 ACIAD2018 (ald1) E step 3 ACIAD1711 (pcaH) E step 3 ACIAD2088 (aspQ) E step 3 ACIAD1712 (pcaG)...”
• Unique features revealed by the genome sequence of Acinetobacter sp. ADP1, a versatile and naturally transformation competent bacterium
  Barbe, Nucleic acids research 2004
  • “...a gene coding for a putative butanediol dehydrogenase (ACIAD1021), are adjacent and transcribed in the same direction. Although the genes for acetolactate...”

Cbei_0544 alcohol dehydrogenase from Clostridium beijerincki NCIMB 8052
30% identity, 92% coverage

• Molecular characterization of an NADPH-dependent acetoin reductase/2,3-butanediol dehydrogenase from Clostridium beijerinckii NCIMB 8052
  Raedts, Applied and environmental microbiology 2014
  • “...predicted acetoin reductases encoded by CBEI_0223, CBEI_0528, CBEI_0544, CBEI_0685, CBEI_1464, CBEI_2243, CBEI_3864, and CBEI_3890 are all annotated in NCBI...”
  • “...in E. coli; the gene constructs of CBEI_0528 and CBEI_0544 failed to produce transformants in E. coli and were therefore no longer considered here. The initial...”

eltD / A0QXD8 erythritol/L-threitol dehydrogenase (EC 1.1.1.56; EC 1.1.1.12; EC 1.1.1.9) from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (see paper)
ELTD_MYCS2 / A0QXD8 Erythritol/L-threitol dehydrogenase; EC 1.1.1.- from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (Mycobacterium smegmatis) (see paper)
MSMEG_3265 arabitol-phosphate dehydrogenase from Mycobacterium smegmatis str. MC2 155
28% identity, 94% coverage

• function: Catalyzes the NAD-dependent reversible oxidation of erythritol and L-threitol. Involved in the degradation pathways of erythritol and L-threitol, that allow M.smegmatis to grow on these compounds as the sole carbon source.
  catalytic activity: erythritol + NAD(+) = D-erythrulose + NADH + H(+) (RHEA:48756)
  catalytic activity: L-threitol + NAD(+) = L-erythrulose + NADH + H(+) (RHEA:48760)
  cofactor: Zn(2+) (Binds 2 Zn(2+) ions per subunit.)
  disruption phenotype: Complete loss of the ability to grow on erythritol or on L-threitol.
• MnoSR removal in Mycobacterium smegmatis triggers broad transcriptional response to 1,3-propanediol and glucose as sole carbon sources
  Płocińska, Frontiers in cellular and infection microbiology 2024
  • “...msmeg_3938 were identified. Other important up-regulated genes grouped in operons included genes from the operon msmeg_3265 to msmeg_3273 , regulating carbohydrate metabolism. The largest cluster of upregulated genes ranged from msmeg_1766 to msmeg_1806 , with the exclusion of msmeg_1776 and msmeg_1795-1799 . However, most of the...”
  • “...various sugars as the sole source of carbon. Since genes related to carbohydrate metabolism ( msmeg_3265 to msmeg_3273 ) were upregulated in the mutant comparing to wild-type, when both grown on 2% glucose; and were down-regulated in the mutant comparing to wild-type, when both strains were...”
• A VapBC toxin-antitoxin module is a posttranscriptional regulator of metabolic flux in mycobacteria
  McKenzie, Journal of bacteriology 2012
  • “...protein D-Ribose-binding periplasmic protein Unknown MSMEG_3264 MSMEG_3265 MSMEG_3266 MSMEG_3267 MSMEG_3268 MSMEG_3269 MSMEG_3270 MSMEG_3271 abcR sugK abcE abcF...”

llmg_1642 2,3-butanediol dehydrogenase from Lactococcus lactis subsp. cremoris MG1363
30% identity, 90% coverage

• Task Distribution between Acetate and Acetoin Pathways To Prolong Growth in Lactococcus lactis under Respiration Conditions
  Cesselin, Applied and environmental microbiology 2018
  • “...(llmg_1309) M_als_For M_als_Rev als_Ext-For pta (llmg_1642) deletion M_pta_For M_pta_intRev M_pta_intFor M_pta_Rev pta_For_ext pta_Rev_ext als complementation...”
• Fermentation-induced variation in heat and oxidative stress phenotypes of Lactococcus lactis MG1363 reveals transcriptome signatures for robustness
  Dijkstra, Microbial cell factories 2014
  • “...stress protein E Negative llmg_0556 Hypothetical protein Positive llmg_0909 kinA Sensor protein kinase kinA Negative llmg_1642 butB 2,3-butanediol dehydrogenase Positive llmg_0870 Transporter Negative llmg_1181 ilvE Branched-chain amino acid aminotransferase Negative llmg_1830 menX Menaquinone biosynthesis related protein Positive llmg_0487 Putative trehalose/maltose hydrolase Positive llmg_0066 araT Aromatic amino...”

GulDH / E1V4Y1 L-gulonate 5-dehydrogenase (EC 1.1.1.380) from Halomonas elongata (strain ATCC 33173 / DSM 2581 / NBRC 15536 / NCIMB 2198 / 1H9) (see paper)
E1V4Y1 L-gulonate 5-dehydrogenase (EC 1.1.1.380) from Halomonas elongata (see paper)
30% identity, 99% coverage

• Investigating the physiological roles of low-efficiency D-mannonate and D-gluconate dehydratases in the enolase superfamily: pathways for the catabolism of L-gulonate and L-idonate
  Wichelecki, Biochemistry 2014
  • “...encoding the l -gulonate 5-dehydrogenase from Halomonas elongata DSM 2581 ( He GulDH, Uniprot entry E1V4Y1, an orthologue of the l -gulonate 5-dehydrogenase from C. salexigens DSM3043, Cs GulDH), the l -idonate dehydrogenase from Salmonella enteriditis ( Se IdoDH, Uniprot entry B5R538), and the d -gluconate...”
  • “...alcohol dehydrogenase from the closely related H. elongata DSM 2581 ( He GulDH, Uniprot entry E1V4Y1) is 76% identical and 86% similar to Cs GulDH. Additionally, the genome neighborhood of He GulDH is identical to the Cs GulDH neighborhood. The purified He GulDH was screened for...”

AFUA_2G15930 alcohol dehydrogenase, zinc-containing from Aspergillus fumigatus Af293
31% identity, 97% coverage

• RNAseq analysis of Aspergillus fumigatus in blood reveals a just wait and see resting stage behavior
  Irmer, BMC genomics 2015
  • “...in the utilization of ethanol as a carbon source AFUA_2G11250 aryl-alcohol dehydrogenase Aad14, unknown function AFUA_2G15930 alcohol dehydrogenase, ortholog in S. pombe role in detoxifying alcohols and related compounds, protecting against environmental stresses AFUA_4G12990 trr1 thioredoxin reductase Trr1/Trr2, orthologs play a role in detoxification Iron homeostasis...”
  • “...up-regulated at B180s like three alcohol hydrogenases AFUA_2G10960 (alcohol dehydrogenase Adh2), AFUA_2G11250 (aryl-alcohol dehydrogenase Aad14), AFUA_2G15930 (alcohol dehydrogenase, zinc-containing) and the putative thioredoxin reductase encoding gene AFUA_4G12990 (Aspf29, an allergen and putative thioredoxin TrxA). Iron starvation Under less stringent evaluation, siderophore-iron transport is significantly enriched for...”

NTHI0063 conserved hypothetical zinc-type alcohol dehydrogenase-like protein from Haemophilus influenzae 86-028NP
29% identity, 97% coverage

• The OxyR regulon in nontypeable Haemophilus influenzae
  Harrison, Journal of bacteriology 2007
  • “...0.4 ND ND ND ND 1 ND ND ND NTHI1588 NTHI1801 NTHI1802 NTHI0371 NTHI0063 impA pntB pntA hxuA 3 3 2 2 2 0.3 4 5 0.7 1 ND ND ND ND ND NTHI0729 NTHI0496 NTHI0684...”

ECA0168 L-threonine 3-dehydrogenase from Erwinia carotovora subsp. atroseptica SCRI1043
28% identity, 90% coverage

• Enterobacterial small mobile sequences carry open reading frames and are found intragenically--evolutionary implications for formation of new peptides
  Delihas, Gene regulation and systems biology 2007
  • “...Gene loci shown represent large proteins that have conserved domains ( ECA3499 , amidase and ECA0168 , L-threonine 3-dehydrogenase), unique open reading frames displaying sequence similarities to conserved motifs ( YPO3245 hypothetical protein with PapB motif and PLU3667 hypothetical protein, HlyD motif), and a hypothetical protein...”
  • “...its comparable downstream sequence displays a long stable stem loop (data not shown). E. carotovora, ECA0168 (L-threonine 3-dehydrogenase) ECA0168 is predicted to encode a 361 amino acid L-threonine 3-dehydrogenase enzyme in E. carotovora . L-threonine 3-dehydrogenase is a highly conserved protein in Gram-negative bacteria and displays...”

ETAE_0085 L-threonine 3-dehydrogenase from Edwardsiella tarda EIB202
29% identity, 98% coverage

• Genome sequence of the versatile fish pathogen Edwardsiella tarda provides insights into its adaptation to broad host ranges and intracellular niches
  Wang, PloS one 2009
  • “...facultative anaerobic lifestyle in intracellular niches. 10.1371/journal.pone.0007646.t004 Table 4 Dehydrogenases in EIB202. CDS Gene Annotation ETAE_0085 tdh L-threonine 3-dehydrogenase ETAE_0104 wecC UDP-N-acetyl-D-mannosaminuronate dehydrogenase ETAE_0240 Putative iron-containing alcohol dehydrogenase ETAE_0386 mdh Malate/lactate dehydrogenases ETAE_0565 thrA Bifunctional aspartokinase I/homeserine dehydrogenase I ETAE_0571 gabD Succinate-semialdehyde dehydrogenase I ETAE_0587 xdhC...”

STM1542 putative zinc-binding dehydrogenase from Salmonella typhimurium LT2
29% identity, 95% coverage

• Phylogenetic diversity of the enteric pathogen Salmonella enterica subsp. enterica inferred from genome-wide reference-free SNP characters
  Timme, Genome biology and evolution 2013
  • “...632030 Coding A_A_A GCA_GCC_GCT 502 132233 leuA STM0113 2-isopropylmalate synthase 647650 Intergenic 1528293 Upstream of STM1542, putative POT family peptide transport protein 78823 Coding L_L TTA_TTG 41 1832990 cls STM1739 + Cardiolipin synthase Clade A SNPs 135358 Intergenic 2449145 + Upsteam of STM2338, phosphotransacetylase 267325 Coding...”

F1T242 (R,R)-butanediol dehydrogenase (EC 1.1.1.4) from Mycobacterium sp. (see paper)
32% identity, 87% coverage

• Mechanism of microbial production of acetoin and 2,3-butanediol optical isomers and substrate specificity of butanediol dehydrogenase
  Li, Microbial cell factories 2023
  • “...follows: R. erythropolis, UniProt ID A0A0E4A9D6; G. arilaitensis, UniProt ID E1W0D5; Mycobacterium sp., UniProt ID F1T242; B. aurantiacum, UniProt ID A0A2A3YZ33; S. cerevisiae, UniProt ID P39714; P. polymyxa, UniProt ID E7EKB8; B. subtilis, UniProt ID O34788; M. dioxanotrophicus, KEGG ID BTO20_28760; S. profundus, UniProt ID A0A1U7D589;...”

O35045 Uncharacterized zinc-type alcohol dehydrogenase-like protein YjmD from Bacillus subtilis (strain 168)
BSU12330 putative oxidoreductase from Bacillus subtilis subsp. subtilis str. 168
29% identity, 95% coverage

• Enterocloster alcoholdehydrogenati sp. nov., a Novel Bacterial Species Isolated from the Feces of a Patient with Alcoholism
  Oikawa, Current microbiology 2023
  • “...P0A9Q7), a putative zinc-type alcohol dehydrogenase with similarity to YjmD of Bacillus subtilis (UniProt code, O35045), and a putative catalase with similarity to a catalase of Lactiplantibacillus plantarum (basonym: Lactobacillus plantarum ; UniProt code, P60355). These genes might be related to the observed phenotypic characteristics of...”
• rocF affects the production of tetramethylpyrazine in fermented soybeans with Bacillus subtilis BJ3-2
  Liu, BMC biotechnology 2022
  • “...Up BSU12340 11.731 114.535 3.28 8.88E-08 1.47E-05 Up BSU11760 8.632 81.025 3.22 2.99E-06 3.11E-04 Up BSU12330 10.765 97.552 3.17 2.41E-07 3.25E-05 Up BSU13520 4.768 33.11 2.77 1.24E-05 1.01E-03 Up BSU10710 12.019 81.937 2.76 7.47E-04 2.78E-02 Up BSU36960 49.193 320.369 2.7 1.70E-06 1.94E-04 Up BSU12360 7.415 48.837...”
• The program of gene transcription for a single differentiating cell type during sporulation in Bacillus subtilis
  Eichenberger, PLoS biology 2004
  • “...yitD (BSU10950), yitE (BSU10960), yjcA (BSU11790), yjcM (BSU11910), yjcN (BSU11920), yjcO (BSU11930), yjmC (BSU12320), yjmD (BSU12330), yjmF (BSU12350), yknT (BSU14250), yknU (BSU14320), yknV (BSU14330), ykuD (BSU14040), ykvI (BSU13710), ykvU (BSU13830), ylbJ (BSU15030), ylbO/gerR (BSU15090), yngE (BSU18210), yngF (BSU18220), yngG (BSU18230), yngH (BSU18240), yngI (BSU18250), yngJ (BSU18260),...”

CLJU_c25840 zinc-binding dehydrogenase from Clostridium ljungdahlii DSM 13528
28% identity, 94% coverage

• Industrial Acetogenic Biocatalysts: A Comparative Metabolic and Genomic Analysis
  Bengelsdorf, Frontiers in microbiology 2016
  • “...16 respective genes. In the genome of C. ragsdalei , the OGs for CLJU_c19540, CLJU_c11560, CLJU_c25840, and CLJU_c16150 of C. ljungdahlii are missing. Different alcohol dehydrogenases were previously assigned into c lusters of o rthologous g roups of proteins (COGs). Analyzed genomes contained alcohol dehydrogenases classified...”

RBAM_006650 YdjL from Bacillus amyloliquefaciens FZB42
29% identity, 99% coverage

• Differential proteomics analysis of Bacillus amyloliquefaciens and its genome-shuffled mutant for improving surfactin production
  Zhao, International journal of molecular sciences 2014
  • “...+4.0 1178 Unnamed protein product gi|311069921 YP_003974844 35,900/5.10 35,212/5.82 93 33 +164.7 1212 Hypothetical protein RBAM_006650 gi|154685120 YP_001420281 ydjL 37,552/5.09 35,242/4.57 91 29 +3.5, +4.9 1213, 1220 YdjL gi|363726006 EHM06144 37,580/5.04 36,899/4.59 86 31 +14.6 1223 Multifunctional SOS repair factor gi|308173657 YP_003920362 recA 37,938/5.05 37,432/5.21 148...”
  • “...CHOH group of donors, NAD or NADP as acceptor, pyrroline-5-carboxylate reductase activity 1212 Hypothetical protein RBAM_006650 ER Cytoplasmic Unknown Nucleotide binding, oxidoreductase activity, zinc ion binding 1213, 1220 YdjL ER Cytoplasmic Unknown Nucleotide binding, oxidoreductase activity, zinc ion binding Nucleotide Transport and Metabolism 1067 Hypothetical protein...”

A0A0E4A9D6 (R,R)-butanediol dehydrogenase (EC 1.1.1.4) from Rhodococcus erythropolis (see paper)
29% identity, 92% coverage

MS6_A0925 L-threonine 3-dehydrogenase from Vibrio cholerae MS6
VCA0885 threonine 3-dehydrogenase from Vibrio cholerae O1 biovar eltor str. N16961
27% identity, 95% coverage

• Exception to the Rule: Genomic Characterization of Naturally Occurring Unusual Vibrio cholerae Strains with a Single Chromosome
  Xie, International journal of genomics 2017
  • “...NSCV2 A closer examination of the insertion junctions indicates that an NSCV2-like intermediate probably possessed MS6_A0925- and MS6_A0924-like Chr2 CDS on Chr1 flanked by 2 prophages ( Figure 5 (top panel)). In that intermediate strain, Chr2 was inserted via recombination of the homologous segments (VAB027_307 versus...”
  • “...2,643,208bp or between MS6_2336 and MS6_2335 on MS6 Chr1 backbone and inserted between MS6_A0924 and MS6_A0925 break points (852,904852,973) on MS6 Chr2 backbone ( Figure 5 (bottom panel)). The insertion boundary is flanked by 245bp repeats located at 337,552 to 337,796bp and 1,351,093 to 1,351,337bps with...”
• CRISPR-Cas systems are present predominantly on mobile genetic elements in Vibrio species
  McDonald, BMC genomics 2019
  • “...all 8 strains was associated with a 62-kb region inserted within chromosome 2 at ORF VCA0885 relative to the El Tor reference genome N16961, which lacked the region (Fig. 5 a). Analysis of this 62-kb region using Phaster [ 54 ], a phage identification tool, showed...”
  • “...The hybrid system is at the 3 region of a prophage located between VCA0884 and VCA0885 relative to the reference strain N16961, which lacks the region. A homologous phage was found in V. metoecus RC341 and was inserted at the same genomic location. b The conserved...”
• A Vibrio cholerae autoinducer-receptor pair that controls biofilm formation
  Papenfort, Nature chemical biology 2017
  • “...significantly (~4-fold) reduced fluorescence compared to the wild-type. Both insertions resided in the tdh ( vca0885 ) gene ( Fig. 2A ). To verify this result, we generated an in-frame deletion of tdh in V. cholerae carrying the chromosomal PvqmR::mkate2 reporter. The tdh mutant also produced...”
  • “...DNA polymerase (Bio-Rad) was used for all PCR reactions. For plasmids pKP-426 and pKP-427, the vca0885 and vc0886 genes were PCR-amplified using V. cholerae genomic DNA with oligonucleotide pairs KPO-886x887 and KPO-0900x0901, respectively. The PCR products were ligated into plasmid pKP-418 24 using KpnI restriction sites....”

SO_4673 threonine 3-dehydrogenase from Shewanella oneidensis MR-1
28% identity, 98% coverage

• Activation of an Otherwise Silent Xylose Metabolic Pathway in Shewanella oneidensis
  Sekar, Applied and environmental microbiology 2016
  • “...SO_0900 gene JM109 complemented with pQE80L harboring SO_4673 gene JM109 complemented with pQE80L harboring SO_4230 gene JM109 complemented with pQE80L...”
  • “...E. coli. The primers used for cloning genes SO_0900, SO_4673, SO_4230, and SO_2452 are listed in Table 3. These primers were used to PCR amplify the full-length...”

AO090023000523 No description from Aspergillus oryzae RIB40
29% identity, 97% coverage

• Comprehensive annotation of secondary metabolite biosynthetic genes and gene clusters of Aspergillus nidulans, A. fumigatus, A. niger and A. oryzae
  Inglis, BMC microbiology 2013
  • “...- AO090023000444 AO090023000450 - AO090023000436 AO090023000447 - AO090023000443 FA ECS AO090023000528 cluster AO090023000528 AO090023000528 - AO090023000523 AO090023000536 - AO090023000521 AO090023000529 - AO090023000523 ECS, IGD ECS AO090023000877 cluster AO090023000877 AO090023000881 - AO090023000875 AO090023000884 - AO090023000869 - n/a n/a AO090026000009 (afl) cluster* AO090026000009 AO090026000004 - AO090026000029 AO090026000001 -...”

WP_029946299 (R,R)-butanediol dehydrogenase from Bacillus sp. SN32
31% identity, 92% coverage

• Examining the Transcriptomic and Biochemical Signatures of Bacillus subtilis Strains: Impacts on Plant Growth and Abiotic Stress Tolerance
  Chang, International journal of molecular sciences 2023
  • “...IspD 0.0 AGA24047 Dxr 1.1 WP_032722383 fni 3.8 WP_003235520 IspD 0.3 2,3-BD 6IE0-A R-BDH 2.3 WP_029946299 bdhA 2.1 Serine protease WP_014479598 Isp 4.8 WP_024572446 AprX 5.6 WP_032721588 AprX 1.0 WP_014479598 Isp 4.0 WP_015250812 HtrC 1.5 WP_015250812 HtrC 1.3 WP_032722717 Vpr 3.1 WP_134982250 Vpr 4.9 WP_015382840 TLS...”

6ie0B / O34788 X-ray crystal structure of 2r,3r-butanediol dehydrogenase from bacillus subtilis
31% identity, 91% coverage

• Ligand: zinc ion (6ie0B)

BDHA_BACSU / O34788 (R,R)-butanediol dehydrogenase; Acetoin reductase/2,3-butanediol dehydrogenase; AR/BDH; EC 1.1.1.4 from Bacillus subtilis (strain 168) (see 3 papers)
O34788 (R,R)-butanediol dehydrogenase (EC 1.1.1.4) from Bacillus subtilis (see paper)
BSU06240, NP_388505 acetoin reductase/2,3-butanediol dehydrogenase from Bacillus subtilis subsp. subtilis str. 168
NP_388505 acetoin reductase/2,3-butanediol dehydrogenase from Bacillus subtilis subsp. subtilis str. 168
31% identity, 92% coverage

• catalytic activity: (R,R)-butane-2,3-diol + NAD(+) = (R)-acetoin + NADH + H(+) (RHEA:24340)
  cofactor: Zn(2+) (Binds 1 Zn(2+) per subunit.)
  subunit: Homotetramer (Ref.6). Interacts with BrxC (PubMed:33722570).
  disruption phenotype: Cells lacking this gene have no acetoin reductase/2,3-butanediol dehydrogenase activity.
• Metabolic engineering design to enhance (R,R)-2,3-butanediol production from glycerol in Bacillus subtilis based on flux balance analysis
  Vikromvarasiri, Microbial cell factories 2021
  • “...found that the L-lactate dehydrogenase (BSU03050, lctE ) reaction might compete with the (R,R)-butanediol dehydrogenase (BSU06240; bdhA ) reaction for NADH, which is mainly produced by glycerol-3-phosphate dehydrogenase (BSU22830; glpD ) and glyceraldehyde-3-phosphate dehydrogenase (BSU33940; gapA ). Hence, the deletion of lctE eliminates the NADH competitive...”
• Comparison of Bacillus subtilis transcriptome profiles from two separate missions to the International Space Station
  Morrison, NPJ microgravity 2019
  • “...NsrR, ResD, SigA, TnrA BSU05720 ydhE 1.32 1.33 1.23 1.27 Similar to macrolide glycosyltransferase LiaR BSU06240 bdhA 1.45 1.46 1.19 1.32 Acetoin reductase/butanediol dehydrogenase AbrB BSU10230 yhfH 1.19 1.29 1.59 1.74 Unknown Unknown BSU17710 tatAC 1.30 1.33 1.28 1.33 Component of the twin-arginine translocation pathway Unknown...”
• Effect of deletion of 2,3-butanediol dehydrogenase gene (bdhA) on acetoin production of Bacillus subtilis.
  Zhang, Preparative biochemistry & biotechnology 2017 (PubMed)
  • GeneRIF: Constructed was a recombinant strain BS168D by deleting the 2,3-butanediol dehydrogenase gene bdhA of the B. subtilis168, and there was almost no 2,3-butanediol production in 20 g/L of glucose media. The acetoin yield of BS168D reached 6.61 g/L, which was about 1.5 times higher than that of the control B. subtilis168 (4.47 g/L).
• The rebalanced pathway significantly enhances acetoin production by disruption of acetoin reductase gene and moderate-expression of a new water-forming NADH oxidase in Bacillus subtilis.
  Zhang, Metabolic engineering 2014 (PubMed)
  • GeneRIF: Moderate-expression of YODC in the bdhA disrupted B. subtilis weakened the NADH-linked pathways to by-product pools of acetoin.
• Double-blind characterization of non-genome-sequenced bacteria by mass spectrometry-based proteomics
  Jabbour, Applied and environmental microbiology 2010
  • “...Hypothetical protein BSU03830 Hypothetical protein BSU06240 Hypothetical protein BSU06240 Hypothetical protein BSU06240 Hypothetical protein BSU06240...”
• The Bacillus subtilis ydjL (bdhA) gene encodes acetoin reductase/2,3-butanediol dehydrogenase.
  Nicholson, Applied and environmental microbiology 2008
  • GeneRIF: Bacillus subtilis ydjL (bdhA) Gene Encodes Acetoin Reductase/2,3-Butanediol Dehydrogenase
• Mechanism of microbial production of acetoin and 2,3-butanediol optical isomers and substrate specificity of butanediol dehydrogenase
  Li, Microbial cell factories 2023
  • “...A0A2A3YZ33; S. cerevisiae, UniProt ID P39714; P. polymyxa, UniProt ID E7EKB8; B. subtilis, UniProt ID O34788; M. dioxanotrophicus, KEGG ID BTO20_28760; S. profundus, UniProt ID A0A1U7D589; E. ludwigii, KEGG ID EcWSU1_01150; K. pneumoniae, GenBank ID AFB82681.1; Bacillus sp., GenBank ID QIS93452.1; B. licheniformis, KEGG ID BLi02066;Microbacterium...”
• Glycerol dehydrogenase plays a dual role in glycerol metabolism and 2,3-butanediol formation in Klebsiella pneumoniae
  Wang, The Journal of biological chemistry 2014
  • “...(2R,3R)-BDHs from B. subtilis (Bs(2R,3R)-BDH, NP_388505); P. polymyxa (Pp(2R,3R)-BDH, ADV15558); Thermoanaerobacter brockii (Tb(2R,3R)-BDH, CAA46053); and...”

ZP_02432273 hypothetical protein from Clostridium scindens ATCC 35704
28% identity, 99% coverage

• Clostridium scindens: a human gut microbe with a high potential to convert glucocorticoids into androgens
  Ridlon, Journal of lipid research 2013
  • “...present in this subtree are distant from C. scindens DesC, including another C. scindens sequence (ZP_02432273, also from strain ATCC 35704). This sequence presents a much stronger match (E-value of 0) to the threonine dehydrogenase-like domain cd08234 than DesC (E-value 7e-63), and it is also placed...”

Q1QT88 Alcohol dehydrogenase GroES-like protein from Chromohalobacter salexigens (strain ATCC BAA-138 / DSM 3043 / CIP 106854 / NCIMB 13768 / 1H11)
29% identity, 93% coverage

• Investigating the physiological roles of low-efficiency D-mannonate and D-gluconate dehydratases in the enolase superfamily: pathways for the catabolism of L-gulonate and L-idonate
  Wichelecki, Biochemistry 2014
  • “...the Cs ManD Genome Neighborhood: Cs GulDH The alcohol dehydrogenase ( Cs GulDH, Uniprot entry Q1QT88) in the Cs ManD genome neighborhood was not amenable to purification, despite several cloning strategies. A presumably orthologous alcohol dehydrogenase from the closely related H. elongata DSM 2581 ( He...”
  • “...deposited as UniProt entries E1V4Y1, Q1QT83, and Q8FHD0. Proteins deposited as UniProt entries Q1QT84 and Q1QT88 are also characterized by homology and conserved genome context. This research was supported by a program project grant and three cooperative agreements from the National Institutes of Health (P01GM071790, U54GM093342,...”

AS588_RS00220 2,3-butanediol dehydrogenase from Bacillus amyloliquefaciens
29% identity, 92% coverage

• Key Impact of an Uncommon Plasmid on Bacillus amyloliquefaciens subsp. plantarum S499 Developmental Traits and Lipopeptide Production
  Molinatto, Frontiers in microbiology 2017
  • “...98 alsS AS588_RS16690 RBAM_RS16555 Acetolactate synthase 99 alsR AS588_RS16695 RBAM_RS16560 LysR transcriptional regulator 98 bdhA AS588_RS00220 RBAM_RS03320 2,3-butanediol dehydrogenase 99 dhaS AS588_RS05800 RBAM_RS09505 Putative indole-3-acet-aldehyde dehydrogenase 98 Phy S588_RS05510 RBAM_RS09795 Phytase 98 yhcX AS588_RS10830 RBAM_RS04750 Nitrilase 98 ysnE AS588_RS17725 RBAM_RS17660 Putative IAA acetyl-transferase 96 ywkB AS588_RS17210...”

A0A075BZ18 (R,R)-butanediol dehydrogenase (EC 1.1.1.4) from Bacillus sp. (in: Bacteria) (see paper)
S6FPW0 (R,R)-butanediol dehydrogenase (EC 1.1.1.4) from Bacillus amyloliquefaciens (see paper)
BVY13_17360 2,3-butanediol dehydrogenase from Bacillus amyloliquefaciens
29% identity, 92% coverage

• Draft genome sequence of Bacillus amyloliquefaciens subsp. plantarum strain Fito_F321, an endophyte microorganism from Vitis vinifera with biocontrol potential
  Pinto, Standards in genomic sciences 2018
  • “...a set of genes that catalyse the 2,3-butanediol pathway, such as butanediol dehydrogenase bdhA gene (BVY13_17360), acetolactate synthase als and alsD (BVY13_14285, BVY13_09195) and acetolactate decarboxylase alsD (BVY13_14290) were identified. Regarding nitrogen fixation, several nif genes were not identified among Fito_F321 genome, though other genes involved...”

CD2279 putative sugar dehydrogenase from Clostridium difficile 630
30% identity, 91% coverage

• Genome-Wide Transcription Start Site Mapping and Promoter Assignments to a Sigma Factor in the Human Enteropathogen Clostridioides difficile
  Soutourina, Frontiers in microbiology 2020
  • “...CD2091-CD2089 Putative Xanthine/uracile permease (PbuX), adenosine derivate deaminase NR T TGGCA TTATAA TTGCTT C CD2092-DioR1 CD2279 CD2279 Sugar-P dehydrogenase A TGGCA TAGATA TTGCTA T CD2283? CD2283 CD2283-CD2280 Activator, PTS fructose/mannitol family NR A TGGCA TGATAG TTGCTT A CD2283 LevR-type CD2327# CD2327-CD2323 Arabitol/xylitol PTS, sugar-P dehydrogenases 0.03*...”

MS141 putative dehydrogenase from Microscilla sp. PRE1
30% identity, 88% coverage

• Sequence analysis of a 101-kilobase plasmid required for agar degradation by a Microscilla isolate
  Zhong, Applied and environmental microbiology 2001
  • “...MS132 MS133 MS134 MS135 MS136 MS137 MS138 MS139 MS140 MS141 MS142 MS143 MS144 MS145 MS146 MS147 MS148 MS149 MS150 MS151 40616 41809 42170 44151 45397 47228...”
  • “...dehydrogenase genes were found. MS123, MS137, MS138, and MS141 appear to be alcohol dehydrogenases, MS142 putatively is a gluconate dehydrogenase, and MS143...”

O31776 L-threonine 3-dehydrogenase (EC 1.1.1.103) from Bacillus subtilis (see paper)
30% identity, 92% coverage

• Proteomic Analysis of the Characteristic Flavor Components in Bacillus subtilis BSNK-5-Fermented Soymilk
  Hu, Foods (Basel, Switzerland) 2024
  • “...serine, and threonine metabolism Q04797 asd Aspartate-semialdehyde dehydrogenase 0.45 A0A1B2B4F9 kbl 8-amino-7-ketopelargonate synthase 0.47 0.34 O31776 tdh L-threonine 3-dehydrogenase 0.20 0.20 A0A6H2K6M6 yvcT Glyoxylate reductase YvcT 0.44 P08495 lysC Aspartokinase 2 0.26 0.41 A0A199WF35 gbsA Betaine aldehyde dehydrogenase 2.46 P71017 gbsB Choline dehydrogenase 2.70 2.64 A3F3S8...”

BMMGA3_RS07355 galactitol-1-phosphate 5-dehydrogenase from Bacillus methanolicus MGA3
29% identity, 94% coverage

• Characterization of D-Arabitol as Newly Discovered Carbon Source of Bacillus methanolicus
  López, Frontiers in microbiology 2019
  • “...study pVWEx1- atlABCDEF pVWEx1 derivative for IPTG-inducible expression of BMMGA3_RS07330, BMMGA3_RS07335, BMMGA3_RS07340, BMMGA3_RS07345, BMMGA3_RS07350, and BMMGA3_RS07355 ( atlABCDEF ) from B. methanolicus MGA3 This study Km R , kanamycin resistance. Recombinant DNA Work The description of all plasmids constructed in this study is presented in Table...”
  • “...component c 2.73 BMMGA3_RS07345 atlD c Arabitol phosphate dehydrogenase c 2.90 BMMGA3_RS07350 Hypothetical protein 3.00 BMMGA3_RS07355 Galactitol-1-phosphate 5-dehydrogenase 2.97 BMMGA3_RS07360 S -methyl-5-thioribose-1-phosphate isomerase 2.15 a Cut-off values set to a change in expression level higher than 30; P 0.01, determined by Students t -test. b Annotation...”

WP_013350835 zinc-binding dehydrogenase from Bacillus amyloliquefaciens
31% identity, 70% coverage

• Glucosidase Inhibitors Screening in Microalgae and Cyanobacteria Isolated from the Amazon and Proteomic Analysis of Inhibitor Producing Synechococcus sp. GFB01
  Gradíssimo, Microorganisms 2021
  • “...in Bacillus nojirimycin biosynthesis, GutB, the following sequences were used as query: WP_003156784; WP_007408027; WP_011996208; WP_013350835 and WP_020955232. 2.6. Protein Extraction and Peptide Digestion To the cell concentrate, 5 mL of lysis solution containing -mercaptoethanol and 10 L of protease inhibitor cocktail (Sigma-Aldrich, St. Louis, MO,...”

MTKAM_23920, MTMBA_25190 zinc-binding dehydrogenase from Moorella thermoacetica
29% identity, 96% coverage

• Isolation and characterization of novel acetogenic Moorella strains for employment as potential thermophilic biocatalysts
  Böer, FEMS microbiology ecology 2024
  • “...were detected. Other alcohol dehydrogenases detected were AdhB (MTKAM_10310, MTBGP_12010, MTCOM_9650, MTMBA_12080, and MOTHA_10720), AdhC (MTKAM_23920, MTMBA_25190, and MOTHA_24090), and a putative zinc-type alcohol dehydrogenase-like protein YdjJ (MTCOM_21580). Nevertheless, all five M. thermoacetica strains also encoded at least three copies of an aldehyde ferredoxin oxidoreductase (AOR)....”
  • “...detected. Other alcohol dehydrogenases detected were AdhB (MTKAM_10310, MTBGP_12010, MTCOM_9650, MTMBA_12080, and MOTHA_10720), AdhC (MTKAM_23920, MTMBA_25190, and MOTHA_24090), and a putative zinc-type alcohol dehydrogenase-like protein YdjJ (MTCOM_21580). Nevertheless, all five M. thermoacetica strains also encoded at least three copies of an aldehyde ferredoxin oxidoreductase (AOR). This...”

gutB1 / A7Z0T4 2-amino-2-deoxy-D-mannitol dehydrogenase from Bacillus velezensis (strain DSM 23117 / BGSC 10A6 / LMG 26770 / FZB42) (see 4 papers)
RBAM_002060 GutB1 from Bacillus amyloliquefaciens FZB42
WP_011996208 zinc-binding dehydrogenase from Bacillus velezensis
30% identity, 70% coverage

• Comparative genomic analysis of azasugar biosynthesis
  Beal, AMB Express 2021
  • “...to be part of the azasugar synthetic machinery. However, we hypothesize that the MFS transporter (RBAM_002060) may be involved in azasugar transport, as it is commonly found associated with 3GCs. Given that known azasugar producers feature the aforementioned three gene cluster (3GC), we suggest that this...”
• Glucosidase Inhibitors Screening in Microalgae and Cyanobacteria Isolated from the Amazon and Proteomic Analysis of Inhibitor Producing Synechococcus sp. GFB01
  Gradíssimo, Microorganisms 2021
  • “...step in Bacillus nojirimycin biosynthesis, GutB, the following sequences were used as query: WP_003156784; WP_007408027; WP_011996208; WP_013350835 and WP_020955232. 2.6. Protein Extraction and Peptide Digestion To the cell concentrate, 5 mL of lysis solution containing -mercaptoethanol and 10 L of protease inhibitor cocktail (Sigma-Aldrich, St. Louis,...”

WP_003156784 zinc-binding dehydrogenase from Bacillus velezensis
30% identity, 70% coverage

• Glucosidase Inhibitors Screening in Microalgae and Cyanobacteria Isolated from the Amazon and Proteomic Analysis of Inhibitor Producing Synechococcus sp. GFB01
  Gradíssimo, Microorganisms 2021
  • “...For last step in Bacillus nojirimycin biosynthesis, GutB, the following sequences were used as query: WP_003156784; WP_007408027; WP_011996208; WP_013350835 and WP_020955232. 2.6. Protein Extraction and Peptide Digestion To the cell concentrate, 5 mL of lysis solution containing -mercaptoethanol and 10 L of protease inhibitor cocktail (Sigma-Aldrich,...”

CD2324 putative galactitol-1-phosphate 5-dehydrogenase from Clostridium difficile 630
CD630_23240 galactitol-1-phosphate 5-dehydrogenase from Clostridioides difficile 630
26% identity, 97% coverage

• Comparative transcriptional analysis of clinically relevant heat stress response in Clostridium difficile strain 630
  Ternan, PloS one 2012
  • “...introduction of phosphorylated sorbitol and glucose to the fructose and mannose metabolism pathways (CD0768, CD3064, CD2324). These perturbations could be a means of adaptation to different carbon sources for energy generation, or for biosyntheses of amino sugars or recycling of nucleotides. A de novo purine biosynthesis...”
• [Transcriptomic analysis of the ΔPaLoc mutant of Clostridioides difficile and verification of its toxicity]
  Cui, Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine] 2022 (PubMed)
  • “...respectively. Whereas the hom2 (high serine dehydrogenase), the CD630_15810 (spore-forming protein), CD630_23230 (zinc-binding dehydrogenase) and CD630_23240 (galactitol 1-phosphate 5-dehydrogenase) genes were down-regulated by 0.06, 0.075, 0.133 and 0.183 fold, respectively. The GO and KEGG enrichment analyses showed that the differentially transcribed genes in PaLoc were enriched...”

ZP_02081557 hypothetical protein from Clostridium leptum DSM 753
29% identity, 93% coverage

• Clostridium scindens: a human gut microbe with a high potential to convert glucocorticoids into androgens
  Ridlon, Journal of lipid research 2013
  • “...hand, desC grouped with a group that, besides the clostridia ( Clostridium leptum DSM 753 ZP_02081557, Clostridium ljungdahlii DSM 13528 YP_003780744 and YP_003780741, Clostridium sp . MSTE9 EJF39056, and Clostridium carboxidivorans P7 ZP_05390048), also contained a sequence from the Spirochaetes Treponema primitia ZAS-1 (ZP_09717055) and the...”

swp_5068 Zinc-containing alcohol dehydrogenase superfamily from Shewanella piezotolerans WP3
27% identity, 94% coverage

• Condition-Specific Molecular Network Analysis Revealed That Flagellar Proteins Are Involved in Electron Transfer Processes of Shewanella piezotolerans WP3
  Ding, Genetics research 2021
  • “...10 6 0.53 4.29 E 02 Microbial metabolism in diverse environments swp_1907, swp_2623, swp_1982, swp_4429, swp_5068, swp_1640 Note: the bold enrichment term indicates that there was no KEGG enrichment, and InterPro enrichment was used alternatively; indicate that the enrichment analysis returned no results. Table 5 The...”

LMOf2365_2643 alcohol dehydrogenase, zinc-dependent from Listeria monocytogenes str. 4b F2365
30% identity, 96% coverage

• Transcriptomic Analysis of Listeria monocytogenes in Response to Bile Under Aerobic and Anaerobic Conditions
  Chakravarty, Frontiers in microbiology 2021
  • “...Galactitol PTS system EIIA component 8.5 tkt-3 LMOf2365_2640 Transketolase 6.2 arcA LMOf2365_0052 Arginine deiminase 6.1 LMOf2365_2643 Alcohol dehydrogenase, zinc-dependent 5.7 qoxA LMOf2365_0016 Cytochrome aa3-600 menaquinol oxidase subunit II, Oxidative phosphorylation 5.5 gabD LMOf2365_0935 Succinate-semialdehyde dehydrogenase 5.4 LMOf2365_2364 Ferredoxin/flavodoxinNADP+ reductase 5.3 LMOf2365_0209 UDP-N-acetylglucosamine pyrophosphorylase 4.9 guaB LMOf2365_2746...”

CH1034_300308 Zn-dependent oxidoreductase from Klebsiella pneumoniae
28% identity, 99% coverage

• Transcriptional profiling of Klebsiella pneumoniae defines signatures for planktonic, sessile and biofilm-dispersed cells
  Guilhen, BMC genomics 2016
  • “...13h-old biofilm CH1034_220106 yidP Transcriptional regulator, GntR family protein 109.08 208.43 197.27 3617.98 125.67 3 CH1034_300308 rspB putative oxidoreductase, Zn-dependent and NAD(P)-binding 180.70 248.45 122.42 1590.79 106.96 3 CH1034_10036 ibpA heat shock chaperone 3204.61 4686.30 2252.81 29872.19 4924.76 3 CH1034_270020 bglK Beta-glucoside kinase 177.63 350.06 423.50...”

WP_020955232 zinc-binding dehydrogenase from Bacillus velezensis
30% identity, 70% coverage

• Glucosidase Inhibitors Screening in Microalgae and Cyanobacteria Isolated from the Amazon and Proteomic Analysis of Inhibitor Producing Synechococcus sp. GFB01
  Gradíssimo, Microorganisms 2021
  • “...nojirimycin biosynthesis, GutB, the following sequences were used as query: WP_003156784; WP_007408027; WP_011996208; WP_013350835 and WP_020955232. 2.6. Protein Extraction and Peptide Digestion To the cell concentrate, 5 mL of lysis solution containing -mercaptoethanol and 10 L of protease inhibitor cocktail (Sigma-Aldrich, St. Louis, MO, USA) were...”

WP_007408027 zinc-binding dehydrogenase from Bacillus sp. 916
30% identity, 70% coverage

• Glucosidase Inhibitors Screening in Microalgae and Cyanobacteria Isolated from the Amazon and Proteomic Analysis of Inhibitor Producing Synechococcus sp. GFB01
  Gradíssimo, Microorganisms 2021
  • “...last step in Bacillus nojirimycin biosynthesis, GutB, the following sequences were used as query: WP_003156784; WP_007408027; WP_011996208; WP_013350835 and WP_020955232. 2.6. Protein Extraction and Peptide Digestion To the cell concentrate, 5 mL of lysis solution containing -mercaptoethanol and 10 L of protease inhibitor cocktail (Sigma-Aldrich, St....”

VV21485 Threonine dehydrogenase from Vibrio vulnificus CMCP6
27% identity, 98% coverage

• Global gene expression as a function of the iron status of the bacterial cell: influence of differentially expressed genes in the virulence of the human pathogen Vibrio vulnificus
  Alice, Infection and immunity 2008
  • “...3.83 (0.00026) Amino acid metabolic process VV21485 Threonine dehydrogenase 2.74 (0.00016) Biosynthesis and degradation of polysaccharides VV12131...”

Q91_0877 2,3-butanediol dehydrogenase from Cycloclasticus sp. P1
26% identity, 99% coverage

• An Intracellular Sensing and Signal Transduction System That Regulates the Metabolism of Polycyclic Aromatic Hydrocarbons in Bacteria
  Wang, mSystems 2021
  • “...permease gene perT 2 (gene Q91_0869) and the promoters of various operons (genes Q91_0870 to Q91_0877, pyrene-degrading; genes Q91_2218 to Q91_2220, genes Q91_2224 to Q91_2227, and genes Q91_2242 to Q91_2244/PQ91_2242 to Q91_2244). A DNA fragment of the Q91_1174 promoter was used as a negative control. His6-tagged...”

VPA1509 threonine 3-dehydrogenase from Vibrio parahaemolyticus RIMD 2210633
FORC22_4519, WP_005478141 L-threonine 3-dehydrogenase from Vibrio parahaemolyticus
27% identity, 98% coverage

• QseC Inhibition as a Novel Antivirulence Strategy for the Prevention of Acute Hepatopancreatic Necrosis Disease (AHPND)-Causing Vibrio parahaemolyticus
  Yang, Frontiers in cellular and infection microbiology 2020
  • “...Sigma-fimbriae usher protein VPA1507 -1.80196 6.91E-10 Sigma-fimbriae usher protein VPA1508 -1.66659 2.43E-09 Sigma-fimbriae usher protein VPA1509 -1.76698 1.29E-09 Sigma-fimbriae chaperone protein 2 VPA0636 -1.55671 1.22E-07 Arginine ABC transporter VPA0637 -1.69805 1.73E-09 Arginine ABC transporter VPA0638 -1.5677 3.61E-08 Arginine ABC transporter 3 VPA1099 -1.95092 7.45E-08 Predicted redox...”
• Transcriptomic Analysis of Vibrio parahaemolyticus Reveals Different Virulence Gene Expression in Response to Benzyl Isothiocyanate
  Song, Molecules (Basel, Switzerland) 2019
  • “...(Q_BITC vs. C_BITC) Pval (Q_BITC vs. C_BITC) Padj (Q_BITC vs. C_BITC) Significant (Q_BITC vs. C_BITC) VPA1509 tdh 0.32858 0.04469 0.62131 DOWN VPA0318 - 0.95983 8.44E10 7.18E07 DOWN VP2246 fliI 0.3946 0.029624 0.57503 DOWN VP1057 - 0.38624 0.049817 0.63785 DOWN VPA0243 - 0.49488 0.0045398 0.19316 DOWN VPA0202...”
• Surface sensing in Vibrio parahaemolyticus triggers a programme of gene expression that promotes colonization and virulence
  Gode-Potratz, Molecular microbiology 2011
  • “...18 4 2 * 76 42 VPA0288 leukocidin 88 38 3 1 * 10 4 VPA1509 threonine 3-dehydrogenase 6 6 5 4 13 11 VPA1510 f 2-amino-3-ketobutyrate coenzyme A ligase 8 5 11 7 18 11 a Core induced genes were regulated in all surface to...”
• Potential Survival and Pathogenesis of a Novel Strain, Vibrio parahaemolyticus FORC_022, Isolated From a Soy Sauce Marinated Crab by Genome and Transcriptome Analyses
  Chung, Frontiers in microbiology 2018
  • “...0 FORC22_3982 Formate efflux transporter 81.91 0 FORC22_4639 Putrescine/proton symporter, putrescine/ornithine antiporter PotE 45.65 0 FORC22_4519 L -threonine 3-dehydrogenase 27.89 0 FORC22_4520 2-amino-3-ketobutyrate coenzyme A ligase 21.07 0 FORC22_2890 Aspartate ammonia-lyase 19.15 0 FORC22_3230 Multidrug resistance protein D 15.24 0 FORC22_2891 C4-dicarboxylate transporter DcuA 13.31 0...”
• Regulation of Thermostable Direct Hemolysin and Biofilm Formation of Vibrio parahaemolyticus by Quorum-Sensing Genes luxM and luxS.
  Guo, Current microbiology 2018 (PubMed)
  • GeneRIF: The expression of Vibrio parahaemolyticus virulence factor, thermostable direct hemolysin gene (tdh), is negatively regulated by Quorum-Sensing Gene luxM and positively regulated by luxS.

A1S_1705 putative (RR)-butanediol dehydrogenase from Acinetobacter baumannii ATCC 17978
29% identity, 82% coverage

• Colistin Resistant A. baumannii: Genomic and Transcriptomic Traits Acquired Under Colistin Therapy
  Cafiso, Frontiers in microbiology 2018
  • “...showed 3 affected KEGG pathways including the Butanoate metabolism (5 genes: A1S_1729, A1S_1699, A1S_1341, A1S_2102, A1S_1705), Tryptophan metabolism (4 genes: A1S_1729, A1S_1341, A1S_2102, A1S_2450), Lysine degradation (3 genes: A1S_1729, A1S_1341, A1S_2102), Fatty acid metabolism, Limonene and pinene degradation (3 genes: A1S_1344, A1S_1341, A1S_2102), Benzoate degradation via...”

PAAG_04541 alcohol dehydrogenase from Paracoccidioides lutzii Pb01
27% identity, 82% coverage

• Proteomics of Paracoccidioides lutzii: Overview of Changes Triggered by Nitrogen Catabolite Repression
  Cruz-Leite, Journal of fungi (Basel, Switzerland) 2023
  • “...identified in the cell wall proteome of P. lutzii , along with another alcohol dehydrogenase (PAAG_04541) [ 108 ], which is also secreted by P. restrepiensis [ 109 ]. Additionally, thioredoxin, an enzyme involved in detoxification and predicted to be an adhesin, binds to plasminogen in...”
• Predicting copper-, iron-, and zinc-binding proteins in pathogenic species of the Paracoccidioides genus
  Tristão, Frontiers in microbiology 2014
  • “...Pancholi and Chhatwal, 2003 Zn PAAG_05227 PABG_07631 PADG_05031 alcohol dehydrogenase Pancholi and Chhatwal, 2003 Zn PAAG_04541 PABG_04316 PADG_04701 alcohol dehydrogenase GroES domain-containing protein Pancholi and Chhatwal, 2003 Zn PAAG_06104 PABG_06552 PADG_08012 fructose-biphosphate aldolase Pancholi and Chhatwal, 2003 Zn PAAG_01995 PABG_02260 PADG_00668 fructose-biphosphate aldolase Pancholi and Chhatwal,...”

lmo2663 / Q8Y414 pentitolphosphate dehydrogenase Lmo2663 (EC 1.1.1.301) from Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) (see 2 papers)
lmo2663 similar to polyol dehydrogenase from Listeria monocytogenes EGD-e
30% identity, 96% coverage

• Bacterial Microcompartments Coupled with Extracellular Electron Transfer Drive the Anaerobic Utilization of Ethanolamine in Listeria monocytogenes
  Zeng, mSystems 2021
  • “...( dilvB , rpmG1 , and lmo0111 ) ( TableS5 ), and zinc-containing dehydrogenases ( lmo2663 , lmo2664 , and lmo2097 ). To summarize, the significant upregulation of the eut operon at the proteomic level, including structural shell proteins, strongly supports that BMC-dependent EA utilization is...”
• Alternative σ Factors Regulate Overlapping as Well as Distinct Stress Response and Metabolic Functions in Listeria monocytogenes under Stationary Phase Stress Condition
  Orsi, Pathogens (Basel, Switzerland) 2021
  • “...13.46 unknown LMRG_02207 lmo2662 40.53 32.08 11.56 2.18 14.62 similar to ribose 5-phosphate epimerase LMRG_02208 lmo2663 94.76 68.20 22.11 3.04 24.13 similar to polyol dehydrogenase LMRG_02209 lmo2664 59.73 44.42 16.19 2.36 24.58 similar to sorbitol dehydrogenase LMRG_02210 lmo2665 43.67 33.93 15.14 2.60 18.64 similar to PTS...”
• Microarray-based characterization of the Listeria monocytogenes cold regulon in log- and stationary-phase cells
  Chan, Applied and environmental microbiology 2007
  • “...ET AL. ons (i.e., those consisting of lmo2664 and lmo2663 and lmo2661 to lmo2659; see above) also showed higher transcript levels in stationary-phase cells at...”
  • “...including the operon consisting of lmo2664 and lmo2663 (encoding sorbitol dehydrogenase and polyol dehydrogenase, respectively) and that consisting of lmo2661,...”

LMRG_02208 alcohol dehydrogenase, zinc-dependent from Listeria monocytogenes 10403S
30% identity, 95% coverage

• Alternative σ Factors Regulate Overlapping as Well as Distinct Stress Response and Metabolic Functions in Listeria monocytogenes under Stationary Phase Stress Condition
  Orsi, Pathogens (Basel, Switzerland) 2021
  • “...11.18 13.46 unknown LMRG_02207 lmo2662 40.53 32.08 11.56 2.18 14.62 similar to ribose 5-phosphate epimerase LMRG_02208 lmo2663 94.76 68.20 22.11 3.04 24.13 similar to polyol dehydrogenase LMRG_02209 lmo2664 59.73 44.42 16.19 2.36 24.58 similar to sorbitol dehydrogenase LMRG_02210 lmo2665 43.67 33.93 15.14 2.60 18.64 similar to...”

4ej6A / Q92PZ3 Crystal structure of a putative zinc-binding dehydrogenase (target psi-012003) from sinorhizobium meliloti 1021
30% identity, 93% coverage

• Ligand: zinc ion (4ej6A)

DSB67_20895 L-threonine 3-dehydrogenase from Vibrio campbellii
26% identity, 98% coverage

• The quorum-sensing systems of Vibrio campbellii DS40M4 and BB120 are genetically and functionally distinct
  Simpson, Environmental microbiology 2021
  • “...Locus tag vqmA 64.5% 92% VIBHAR_07094 64.5% 92% DSB67_18870 tdh 91.84% 100% VIBHAR_05001 91.55% 100% DSB67_20895 cqsR 54.76% 98% VIBHAR_01620 55.03% 98% DSB67_05165 vpsS 50.35% 98% VIBHAR_02306 65% 39.37% DSB67_09490 69% 36.50% DSB67_07055 70% 39.49% DSB67_07080 72% 31.11% DSB67_12445 69% 37.06% DSB67_12965 67% 36.16% LuxQ 65%...”

SCO1682 zinc-binding alcohol dehydrogenase from Streptomyces coelicolor A3(2)
31% identity, 92% coverage

• Multi-level regulation of coelimycin synthesis in Streptomyces coelicolor A3(2)
  Bednarz, Applied microbiology and biotechnology 2019
  • “...inhibitor. GntR GntR (SCO1678) is a FadR subfamily gluconate-binding repressor of the gluconate operon SCO1679 SCO1682 . ACT synthesis was shown to be decreased in gluconate-supplemented in comparison with the glucose-supplemented SMM medium in S. coelicolor A3(2). What is more, in gntR mutant, gluconate induced the...”
• Role of GntR Family Regulatory Gene SCO1678 in Gluconate Metabolism in Streptomyces coelicolor M145
  Tsypik, BioMed research international 2017
  • “...gluconate permease that transports the molecule into a cell. The next two genes, SCO1681 - SCO1682 (gntZ - gntZ2) , overlap by 4 nucleotides and encode gluconate dehydrogenase and zinc-binding alcohol dehydrogenase, respectively. RT-PCR confirmed transcriptional coupling of genes SCO1679-1680-1681 ( Figure 1(b) ). Another carbohydrate...”

VIBHAR_05001 threonine 3-dehydrogenase from Vibrio harveyi ATCC BAA-1116
26% identity, 94% coverage

• The quorum-sensing systems of Vibrio campbellii DS40M4 and BB120 are genetically and functionally distinct
  Simpson, Environmental microbiology 2021
  • “...cholerae Query Cover Locus tag vqmA 64.5% 92% VIBHAR_07094 64.5% 92% DSB67_18870 tdh 91.84% 100% VIBHAR_05001 91.55% 100% DSB67_20895 cqsR 54.76% 98% VIBHAR_01620 55.03% 98% DSB67_05165 vpsS 50.35% 98% VIBHAR_02306 65% 39.37% DSB67_09490 69% 36.50% DSB67_07055 70% 39.49% DSB67_07080 72% 31.11% DSB67_12445 69% 37.06% DSB67_12965 67%...”

BPSS0006 threonine 3-dehydrogenase from Burkholderia pseudomallei K96243
27% identity, 98% coverage

• GvmR - A Novel LysR-Type Transcriptional Regulator Involved in Virulence and Primary and Secondary Metabolism of Burkholderia pseudomallei
  Duong, Frontiers in microbiology 2018
  • “...metZ ), BPSL0197 ( metX ) (cysteine and methionine metabolism), BPSS0005 ( kbl ) and BPSS0006 ( tdh ) (glycine, serine, and threonine metabolism) were found to be downregulated in the mutant while others were upregulated, e.g., BPSL2545 ( metE ) (cysteine and methionine metabolism), BPSL2738...”
• Characterization and analysis of the Burkholderia pseudomallei BsaN virulence regulon
  Chen, BMC microbiology 2014
  • “...metX homoserine O-acetyltransferase 3.4 BPSS1691 metZ O-succinylhomoserine sulfhydrylase 3.2 BPSS0005 kbl 2-amino-3-ketobutyrate CoA ligase 6.3 BPSS0006 tdh L-threonine dehydrogenase 5.5 BPSL1793 Periplasmic binding protein (ribose binding) 3.4 Regulatory BPSS1494 virG T6SS-1 response regulator 22.4 BPSS1495 virA T6SS-1 His kinase 15.8 BPSS1520 bprC T3SS-3 AraC-type regulator 24.5...”

BDP_0423 Putative dehydrogenase from Bifidobacterium dentium Bd1
29% identity, 93% coverage

• Genomic insights into bifidobacteria
  Lee, Microbiology and molecular biology reviews : MMBR 2010
  • “...BAD_0316 BAD_0314 BAD_0316 BAD_0317 BAD_0318 BDP_0423 BDP_0424 BIFBRE_00261 BIFBRE_00262 BIFBRE_00263 BIFBRE_00266 BIFBRE_00267 BIFBRE_00268 BIFCAT_01546...”

CNBG_3919 xylitol dehydrogenase from Cryptococcus deuterogattii R265
36% identity, 39% coverage

• Zap1 regulates zinc homeostasis and modulates virulence in Cryptococcus gattii
  Schneider, PloS one 2012
  • “...quinone oxidoreductase Alcohol dehydrogenase GroES-like domain 2.00 CNBG_3878 zinc-binding dehydrogenase Alcohol dehydrogenase GroES-like domain 2.73 CNBG_3919 xylitol dehydrogenase Alcohol dehydrogenase GroES-like domain 2.48 CNBG_4844 conserved hypothetical protein Fungal Zn(2)-Cys(6) binuclear cluster domain 1.59 CNBG_4875 R,R-butanediol dehydrogenase Alcohol dehydrogenase GroES-like domain; 2.67 CNBG_5308 conserved hypothetical protein Zinc...”

gutB1 / E3EJK4 2-amino-2-deoxy-D-mannitol dehydrogenase from Paenibacillus polymyxa (strain SC2) (see 4 papers)
28% identity, 99% coverage

New Search

Statistics

How It Works

PaperBLAST builds a database of protein sequences that are linked to scientific articles. These links come from automated text searches against the articles in EuropePMC and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot, BRENDA, CAZy (as made available by dbCAN), BioLiP, CharProtDB, MetaCyc, EcoCyc, TCDB, REBASE, the Fitness Browser, and a subset of the European Nucleotide Archive with the /experiment tag. Given this database and a protein sequence query, PaperBLAST uses protein-protein BLAST to find similar sequences with E < 0.001.

To build the database, we query EuropePMC with locus tags, with RefSeq protein identifiers, and with UniProt accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use queries of the form "locus_tag AND genus_name" to try to ensure that the paper is actually discussing that gene. Because EuropePMC indexes most recent biomedical papers, even if they are not open access, some of the links may be to papers that you cannot read or that our computers cannot read. We query each of these identifiers that appears in the open access part of EuropePMC, as well as every locus tag that appears in the 500 most-referenced genomes, so that a gene may appear in the PaperBLAST results even though none of the papers that mention it are open access. We also incorporate text-mined links from EuropePMC that link open access articles to UniProt or RefSeq identifiers. (This yields some additional links because EuropePMC uses different heuristics for their text mining than we do.)

For every article that mentions a locus tag, a RefSeq protein identifier, or a UniProt accession, we try to select one or two snippets of text that refer to the protein. If we cannot get access to the full text, we try to select a snippet from the abstract, but unfortunately, unique identifiers such as locus tags are rarely provided in abstracts.

PaperBLAST also incorporates manually-curated protein functions:

• Proteins from NCBI's RefSeq are included if a GeneRIF entry links the gene to an article in PubMed^®. GeneRIF also provides a short summary of the article's claim about the protein, which is shown instead of a snippet.
• Proteins from Swiss-Prot (the curated part of UniProt) are included if the curators identified experimental evidence for the protein's function (evidence code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that describe the protein's function are shown (with bold headings).
• Proteins from BRENDA, a curated database of enzymes, are included if they are linked to a paper in PubMed and their full sequence is known.
• Every protein from the non-redundant subset of BioLiP, a database of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself does not include descriptions of the proteins, those are taken from the Protein Data Bank. Descriptions from PDB rely on the original submitter of the structure and cannot be updated by others, so they may be less reliable. (For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every ligand is represented among a group of structures with similar sequences, but for PaperBLAST, we use the non-redundant set provided by BioLiP.)
• Every protein from EcoCyc, a curated database of the proteins in Escherichia coli K-12, is included, regardless of whether they are characterized or not.
• Proteins from the MetaCyc metabolic pathway database are included if they are linked to a paper in PubMed and their full sequence is known.
• Proteins from the Transport Classification Database (TCDB) are included if they have known substrate(s), have reference(s), and are not described as uncharacterized or putative. (Some of the references are not visible on the PaperBLAST web site.)
• Every protein from CharProtDB, a database of experimentally characterized protein annotations, is included.
• Proteins from the CAZy database of carbohydrate-active enzymes are included if they are associated with an Enzyme Classification number. Even though CAZy does not provide links from individual protein sequences to papers, these should all be experimentally-characterized proteins.
• Proteins from the REBASE database of restriction enzymes are included if they have known specificity.
• Every protein with an evidence-based reannotation (based on mutant phenotypes) in the Fitness Browser is included.
• Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators) with experimentally-determined DNA binding sites from the PRODORIC database of gene regulation in prokaryotes.
• Putative transcription factors from RegPrecise that have manually-curated predictions for their binding sites. These predictions are based on conserved putative regulatory sites across genomes that contain similar transcription factors, so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
• Coding sequence (CDS) features from the European Nucleotide Archive (ENA) are included if the /experiment tag is set (implying that there is experimental evidence for the annotation), the nucleotide entry links to paper(s) in PubMed, and the nucleotide entry is from the STD data class (implying that these are targeted annotated sequences, not from shotgun sequencing). Also, to filter out genes whose transcription or translation was detected, but whose function was not studied, nucleotide entries or papers with more than 25 such proteins are excluded. Descriptions from ENA rely on the original submitter of the sequence and cannot be updated by others, so they may be less reliable.

Except for GeneRIF and ENA, the curated entries include a short curated description of the protein's function. For entries from BioLiP, the protein's function may not be known beyond binding to the ligand. Many of these entries also link to articles in PubMed.

For more information see the PaperBLAST paper (mSystems 2017) or the code. You can download PaperBLAST's database here.

Changes to PaperBLAST since the paper was written:

• November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
• February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
• June 2022: incorporated some coding sequences from ENA with the /experiment tag.
• March 2022: incorporated BioLiP.
• April 2020: incorporated TCDB.
• April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
• February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
• January 2018: incorporated BRENDA.
• December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
• September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.

Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.

Secrets

PaperBLAST cannot provide snippets for many of the papers that are published in non-open-access journals. This limitation applies even if the paper is marked as "free" on the publisher's web site and is available in PubmedCentral or EuropePMC. If a journal that you publish in is marked as "secret," please consider publishing elsewhere.

Omissions from the PaperBLAST Database

Many important articles are missing from PaperBLAST, either because the article's full text is not in EuropePMC (as for many older articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an article that characterizes a protein's function but is missing from PaperBLAST, please notify the curators at UniProt or add an entry to GeneRIF. Entries in either of these databases will eventually be incorporated into PaperBLAST. Note that to add an entry to UniProt, you will need to find the UniProt identifier for the protein. If the protein is not already in UniProt, you can ask them to create an entry. To add an entry to GeneRIF, you will need an NCBI Gene identifier, but unfortunately many prokaryotic proteins in RefSeq do not have corresponding Gene identifers.

References

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.