PaperBLAST

PaperBLAST Hits for tr|Q9I5T1|Q9I5T1_PSEAE Ribulose-phosphate 3-epimerase OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=rpe PE=1 SV=1 (224 a.a., MQPFAIAPSI...)

Show query sequence

>tr|Q9I5T1|Q9I5T1_PSEAE Ribulose-phosphate 3-epimerase OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=rpe PE=1 SV=1
MQPFAIAPSILSADFARLGEDVDKVLAAGADIVHFDVMDNHYVPNLTIGPMVCSALRKYG
VSAPIDVHLMVSPVDRIIGDFIEAGATYITFHPEASQHIDRSLQLIRDGGCKAGLVFNPA
TPLEVLKYVMDKVDMVLLMSVNPGFGGQKFIPGTLDKLREARALIDASGREIRLEIDGGV
NVKNIREIAAAGADTFVAGSAIFNAPDYAEVIRAMHAELAQAHQ

Running BLASTp...

Found 173 similar proteins in the literature:

PA0607 ribulose-phosphate 3-epimerase from Pseudomonas aeruginosa PAO1
Q9I5T1 Ribulose-phosphate 3-epimerase from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
100% identity, 100% coverage

• Distinct transcriptome and traits of freshly dispersed Pseudomonas aeruginosa cells
  Kalia, mSphere 2024
  • “...isomerase 0.77 0.28 0.302 PA0548 Transketolase 0.96 0.432 0.152 PA0555 Fructose-1,6-bisphosphate aldolase 0.72 0.389 0.07 PA0607 Ribulose-phosphate-3-epimerase 0.86 0.346 0.54 PA1499 Conserved hypothetical protein 1.91 2.11 3.99 PA2261 Probable 2-ketogluconate kinase 1.21 2.65 3 PA3182 6-Phosphogluconolactonase 1.92 2.68 1.196 PA3183 Glucose-6-phosphate-1-dehydrogenase 1.26 1.46 1.03 PA3194 Phosphogluconate...”
• A theoretical and experimental proteome map of Pseudomonas aeruginosa PAO1
  Lecoutere, MicrobiologyOpen 2012
  • “...15 PA0555 fda Fructose bisphosphate aldolase G C 38.6 41 5.34 5.39 0.804 0.201 16 PA0607 rpe Ribulose phosphate epimerase G C 24.1 23 5.16 5.08 0.745 0.208 17 PA0655 Hypothetical protein H C 23.6 26 5.39 5.55 0.697 0.266 18 PA0664 hypothetical protein M C...”
• Proteome-wide identification of druggable targets and inhibitors for multidrug-resistant <i>Pseudomonas aeruginosa</i> using an integrative subtractive proteomics and virtual screening approach
  Vemula, Heliyon 2025
  • “...2044 Q9I4R5 3126 Q9HX63 4208 Q9I221 963 Q9I5R7 2045 Q9I4R6 3127 Q9HX64 4209 Q9I223 964 Q9I5T1 2046 Q9I4R7 3128 Q9HX65 4210 Q9I224 965 Q9I5U2 2047 Q9I4R8 3129 Q9HX67 4211 Q9I225 966 Q9I5U3 2048 Q9I4R9 3130 Q9HX68 4212 Q9I226 967 Q9I5U5 2049 Q9I4U3 3131 Q9HX71 4213 Q9I227...”

7u5yA / Q9I5T1 Crystal structure of ribulose-phosphate 3-epimerase from pseudomonas aeruginosa
99% identity, 99% coverage

• Ligand: zinc ion (7u5yA)

PP0415 ribulose-phosphate 3-epimerase from Pseudomonas putida KT2440
92% identity, 87% coverage

• UEG Week 2024 Poster Presentations
  , United European gastroenterology journal 2024
• UEG Week 2023 Poster Presentations
  , United European gastroenterology journal 2023
• Integrated analysis of gene expression and metabolic fluxes in PHA-producing Pseudomonas putida grown on glycerol
  Beckers, Microbial cell factories 2016
  • “...reductase 0.15 0.17 0.10 0.2 rpiA PP5150 Ribose-5-phosphate isomerase A 0.09 0.06 0.10 0.06 rpe PP0415 Ribulose-phosphate 3-epimerase 0.04 0.20 0.74 0.5 tktA PP4965 Transketolase 0.28 0.29 0.10 0.46 tal PP2168 Transaldolase B 0.6 0.07 0.10 0.70 Entner-Doudoroff pathway edd PP1010 6-Phosphogluconate dehydratase 0.9 0.22 0.03...”
• Production of medium chain length polyhydroxyalkanoate in metabolic flux optimized Pseudomonas putida
  Borrero-de, Microbial cell factories 2014
  • “...kguD PP3376 2-Ketogluconate 6-phosphate reductase -0.7 -0.5 rpiA PP5150 Ribose-5-phosphate isomerase A 0.3 0.0 rpe PP0415 Ribulose-phosphate 3-epimerase -0.5 -0.1 tktA PP4965 Transketolase 0.3 0.7 tal PP2168 Transaldolase B 0.4 0.3 Entner-Doudoroff pathway edd PP1010 6-Phosphogluconate dehydratase -0.3 -0.3 eda PP1024 KDPG aldolase 0.0 -0.5 Pyruvate...”
  • “...kguD PP3376 2-Ketogluconate 6-phosphate reductase 0.1 -0.1 rpiA PP5150 Ribose-5-phosphate isomerase A 0.3 -0.4 rpe PP0415 Ribulose-phosphate 3-epimerase 0.2 -0.1 tktA PP4965 Transketolase 0.7 0.3 tal PP2168 Transaldolase B 0.2 0.1 Entner-Doudoroff pathway edd PP1010 6-Phosphogluconate dehydratase 0.2 0.1 eda PP1024 KDPG aldolase 0.4 -0.2 Pyruvate...”

PP_0415 ribulose-phosphate 3-epimerase from Pseudomonas putida KT2440
92% identity, 100% coverage

• Addressing genome scale design tradeoffs in Pseudomonas putida for bioconversion of an aromatic carbon source
  Banerjee, NPJ systems biology and applications 2025
  • “...either a low activity pJ23109 promoter from the Anderson collection 31 or the low abundance PP_0415 promoter sequence identified in Eng et al. 21 (Fig. 1D ). PP_0897 abundance was strongly reduced ~8 fold as expected in both PP_0897 promoter titration strains (Supplementary Fig. 4B )....”
  • “...and similarly, only 19 metabolic and 37 non-metabolic proteins had different abundances in the P PP_0415 strain (Supplementary Fig. 4A ). As both strains down-titrated PP_0897 expression and had similar impacts on growth and production, we reasoned that biologically relevant changes would be common between both...”
• Computational analysis into the potential of azo dyes as a feedstock for actinorhodin biosynthesis in Pseudomonas putida
  Nayyara, PloS one 2024
  • “...SUCDi, GLYOX, NACODA, ACACt2pp, RPE PP_0356, PP_2492, PP_2265, PP_1945, PP_2589, PP_0545, PP_2694, PP_4190, PP_4144, PP_5186, PP_0415, PP_3124 4 1 1 SUCOAS, HIBDkt, PUTA3, ALDD2y, GLYOX, ACS2, PPS, ACONTb, GLYO1, PGL, ACACt2pp, MDH, ALDD2x, NTD11, FTHFD, PC, GARFT, ICL, IMPD, P5CD PP_4186, PP_4666, PP_4947, PP_2492, PP_4144, PP_2351,...”

PFLU5563 ribulose-phosphate 3-epimerase from Pseudomonas fluorescens SBW25
89% identity, 100% coverage

• Role of the Transporter-Like Sensor Kinase CbrA in Histidine Uptake and Signal Transduction
  Zhang, Journal of bacteriology 2015
  • “...5746559 5746001 pgk (pflu5705) ptsP (pflu5819) rpe (pflu5563) apaH (pflu5580) pflu3160 sucC (pflu1823) ilvE (pflu3968) pyrC (pflu5759) rpe (pflu5563) carB...”

y3938 D-ribulose-5-phosphate 3-epimerase from Yersinia pestis KIM
79% identity, 97% coverage

• Deletion of Yersinia pestis ail Causes Temperature-Sensitive Pleiotropic Effects, Including Cell Lysis, That Are Suppressed by Carbon Source, Cations, or Loss of Phospholipase A Activity
  Kolodziejek, Journal of bacteriology 2021
  • “...and modification 1 2.0 y3977 fkpA FKBP-type peptidyl-prolyl cis-trans isomerase Proteinstranslation and modification 1 4.7 y3938 rpe Ribulose-phosphate 3-epimerase Central intermediary metabolism: nonoxidative branch, pentose pathway 1 6.1 y3855 prlC Oligopeptidase A Degradation of proteins, peptides 1 1.5 y3712 talB Transaldolase B Central intermediary metabolism: nonoxidative...”

ABUW_3231 ribulose-phosphate 3-epimerase from Acinetobacter baumannii
80% identity, 96% coverage

• Insights into the Periplasmic Proteins of Acinetobacter baumannii AB5075 and the Impact of Imipenem Exposure: A Proteomic Approach
  Scribano, International journal of molecular sciences 2019
  • “...0.538 0.181 CYT score = 0.200913 Fatty acid and phospholipid metabolism 0.677 V5VGJ7 Ribulose-phosphate 3-epimerase ABUW_3231 rpe Sec SP MLCS: 120 [RLG-ED]. Rs: 0.731 0.076 0.207 CYT score = 0.200913 Energy metabolism 0.205 V5VGP5 Pantothenate synthetase ABUW_3295 panC Sec SP MLCS: 119 [ARA-AR]. Rs: 0.991 0.120...”

PmVP161_1767 ribulose-phosphate 3-epimerase from Pasteurella multocida
75% identity, 98% coverage

• Genome-Wide Investigation of Pasteurella multocida Identifies the Stringent Response as a Negative Regulator of Hyaluronic Acid Capsule Production
  Smallman, Microbiology spectrum 2022
  • “...PmVP161_1635 ATP synthase subunit beta 7.7 1.86E80 2.2 pgl PmVP161_1693 6-Phosphogluconolactonase 5.6 1.24E30 1.0 rpe PmVP161_1767 Ribulose-phosphate 3-epimerase 3.8 4.88E45 1.2 thiE PmVP161_1798 Thiamine-phosphate synthase 4.0 0.000551 0.9 thiM PmVP161_1800 Hydroxyethylthiazole kinase 6.6 6.31E05 2.2 ssuB PmVP161_1804 Aliphatic sulfonates import ATP-binding protein SsuB 6.6 5.96E26 2.5...”

M.Sen6759Dam orphan methyltransferase recognizing GATC with methylation at 2(m6A) from Salmonella enterica subsp. enterica NCTC6759
75% identity, 43% coverage

D4I319 Ribulose-phosphate 3-epimerase from Erwinia amylovora (strain CFBP1430)
74% identity, 98% coverage

• Paramixta manurensis gen. nov., sp. nov., a novel member of the family Erwiniaceae producing indole-3-acetic acid isolated from mushroom compost
  Kim, Scientific reports 2024
  • “...PMPD1_2270 UPI0003456E87 WP_017800006.1 83.4 0 d -xylulokinase PMPD1_2271 UPI0005526436 WP_034914917.1 81.2 0 Ribulose-phosphate 3-epimerase PMPD1_0329 D4I319 WP_004160688.1 91.2 2.99E152 Utilization of l -fucose 40 l -fucose dehydrogenase PMPD1_3766 A0A085G0Q3 WP_034796198.1 76.7 1.03E131 l -fuconolactonase PMPD1_3767 K8A015 WP_007671895.1 64.0 4.22E115 l -fuconate dehydratase PMPD1_3768 A0A0H3FNB4 WP_015703671.1 85.4...”

SO0292 ribulose-phosphate 3-epimerase from Shewanella oneidensis MR-1
76% identity, 98% coverage

• Transcriptional analysis of Shewanella oneidensis MR-1 with an electrode compared to Fe(III)citrate or oxygen as terminal electron acceptor
  Rosenbaum, PloS one 2012
  • “...protein CcmE 0.0000 Cytochrome c biosynthesis 3.736397 SO0264 ScyA 0.0000 ScyA, monoheme cytochrome c5 1.329064 SO0292 ribulose-phosphate 3-epimerase 0.0329 2.049366 SO0401 alcohol dehydrogenase 0.0001 2.91455 SO0406 thioredoxin 1 0.0000 1.351289 SO0432 aconitate hydratase 2 0.0307 1.187912 SO0476 CcmG-2 0.0009 1.197626 SO0478 CcmF-2 0.0088 1.783812 SO0716 hypothetical...”

Dod / b3386 ribulose-phosphate 3-epimerase (EC 5.1.3.1) from Escherichia coli K-12 substr. MG1655 (see 7 papers)
rpe / P0AG07 ribulose-phosphate 3-epimerase (EC 5.1.3.1) from Escherichia coli (strain K12) (see 5 papers)
RPE_ECOLI / P0AG07 Ribulose-phosphate 3-epimerase; Pentose-5-phosphate 3-epimerase; PPE; R5P3E; EC 5.1.3.1 from Escherichia coli (strain K12) (see paper)
rpe / RF|NP_417845 pentose-5-phosphate 3-epimerase from Escherichia coli K12 (see 2 papers)
NP_417845 ribulose-phosphate 3-epimerase from Escherichia coli str. K-12 substr. MG1655
UTI89_C3884 D-ribulose-5-phosphate 3-epimerase from Escherichia coli UTI89
b3386 ribulose-phosphate 3-epimerase from Escherichia coli str. K-12 substr. MG1655
Z4739 D-ribulose-5-phosphate 3-epimerase from Escherichia coli O157:H7 EDL933
ECRM13514_RS21640 ribulose-phosphate 3-epimerase from Escherichia coli O145:H28 str. RM13514
75% identity, 98% coverage

• function: Catalyzes the reversible epimerization of D-ribulose 5- phosphate to D-xylulose 5-phosphate.
  catalytic activity: D-ribulose 5-phosphate = D-xylulose 5-phosphate (RHEA:13677)
  cofactor: Co(2+) Fe(2+) Mn(2+) Zn(2+) (Binds 1 divalent metal cation per subunit. Active with Co(2+), Fe(2+), Mn(2+) and Zn(2+).)
• Iron enzyme ribulose-5-phosphate 3-epimerase in Escherichia coli is rapidly damaged by hydrogen peroxide but can be protected by manganese.
  Sobota, Proceedings of the National Academy of Sciences of the United States of America 2011
  • GeneRIF: These data indicate that mononuclear iron enzymes such as ribulose-5-phosphate 3-epimerase can be primary targets of H(2)O(2) stress and that cells adapt by shifting from iron- to manganese-centered metabolism.
• Functional Prediction of Biological Profile During Eutrophication in Marine Environment
  Sbaoui, Bioinformatics and biology insights 2022
  • “...P0A8V0 Ribonuclease BN RbsR P0ACQ0 DNA-binding transcriptional dual regulator RfbD P37760 TDP-rhamnose synthetase, NAD(P)-binding Rpe P0AG07 Ribulose-5-phosphate 3-epimerase RpiA P0A7Z0 Ribose 5-phosphate isomerase RpmJ P0A7Q6 50S ribosomal subunit protein L36 RpoN P24255 RNA polymerase, sigma 54 (sigma N) factor RseP P0AEH1 Intramembrane zinc metalloprotease RtxA A0A3L0W7I6...”
• The Escherichia coli proteome: past, present, and future prospects
  Han, Microbiology and molecular biology reviews : MMBR 2006
  • “...Rnt P30014 RNase T 5.19/23,522.7 Rpe P0AG07 5.13/24,554.25 RpiA P0A7Z0 Ribulose-phosphate 3-epimerase Ribose-5-phosphate isomerase A 5.20/22,860.40 5.06/25,943...”
• High-throughput sequencing of sorted expression libraries reveals inhibitors of bacterial cell division
  Mediati, BMC genomics 2018
  • “...M 3,723,7553,724,973 UTI89_C3832 rpoB K 1219 42.4 7961.0 UTI89_C3834 rplL J UTI89_C3835 rplJ J 3,767,2413,770,673 UTI89_C3884 rpe G 3433 61.3 5157.4 UTI89_C3885 dam L UTI89_C3886 damX D UTI89_C3887 aroB E 3,921,2313,922,700 UTI89_C4038 hmuV P 1470 19.0 1402.3 UTI89_C4039 yhiD S 4,049,5154,052,967 UTI89_C4158 yibP (envC) D 3453...”
• Automated characterization and analysis of expression compatibility between regulatory sequences and metabolic genes in Escherichia coli
  Wen, Synthetic and systems biotechnology 2024
  • “...tpiA Triose-phosphate isomerase b4025 pgi Glucose-6-phosphate isomerase b3956 ppc Phosphoenolpyruvate carboxylase b4090 rpiB Ribose-5-phosphate isomerase b3386 rpe Ribulose 5-phosphate 3-epimerase b3403 pck Phosphoenolpyruvate carboxykinase b3612 gpmM Phosphoglycerate mutase b3952 pflC Pyruvate formate lyase b3951 pflD Pyruvate formate lyase b3236 mdh Malate dehydrogenase b4014 aceB Malate synthase...”
• Understanding flux switching in metabolic networks through an analysis of synthetic lethals
  Narasimha, NPJ systems biology and applications 2024
  • “...same extent. Specifically, genes coding for the reactions RPI ( b2914, b4090 ), RPE ( b3386 ), TKT1 ( b2935, b2465 ), and TKT2 ( b2935, b2465 ) co-expressed together as these form synthetic lethals with each other. Conversely, PSL genes (Supplementary Table 1 ) exhibited...”
• The genome sequence of E. coli W (ATCC 9637): comparative genome analysis and an improved genome-scale reconstruction of E. coli
  Archer, BMC genomics 2011
  • “...W genome. e.g. reaction "RPE" from iAF1260 can be catalyzed by the enzyme encoded by b3386 or b4301. However, in W, an ortholog for b4301 is not present while an ortholog for b3386 is present so the reaction still occurs within the cell. Click here for...”
• Role of SeqA and Dam in Escherichia coli gene expression: a global/microarray analysis
  Løbner-Olesen, Proceedings of the National Academy of Sciences of the United States of America 2003
  • “...aroB damX dam rpe gph trpS b0687 b0688 b3390 b3389 b3388 b3387 b3386 b3385 b3384 0.06* 0.36 1.1 1.1 1.1 1.1 1.0 1.2 0.99 48 1.3 0.90 0.98 0.83 0.93 1.4 1.0 1.3...”
• Microarray analysis of orthologous genes: conservation of the translational machinery across species at the sequence and expression level
  Jiménez, Genome biology 2003
  • “...Yes* COG0180 J2 Tryptophanyl-tRNA synthetase Dam superoperon b3385 Yes COG0546 R 2-phosphoglycolate phosphatase Dam superoperon b3386 Yes COG0036 G3 D-ribulose-5-phosphate epimerase Dam superoperon b3387 No COG0338 L Adenine methylase Dam superoperon b3388 No COG3266 S Putative membrane protein; interferes with cell division Dam superoperon b3389 Yes...”
• Characterizing the Escherichia coli O157:H7 proteome including protein associations with higher order assemblies
  Pieper, PloS one 2011
  • “...yieF 20375 CY, Ho-2 6.99E-07 0 13599 5096 flavoprotein containing FMN cofactor C3 ribulose-phosphate 3-epimerase Z4739 rpe 24553 CY 2.13E-06 233 4390 68 carbohydrate metabolism C3 nucleoid-associated protein YejK Z3445 yejK 37822 CY 1.63E-05 338 1890 21 unknown function C3 glyoxylate/hydroxypyruvate reductase Z1666 ghrA 36853 CY...”
• Clonal and antigenic analysis of serogroup A Neisseria meningitidis with particular reference to epidemiological features of epidemic meningitis in the People's Republic of China
  Wang, Infection and immunity 1992
  • “...Z4081, Z4097, Z4104, Z4109, Z4115, Z4736, Z4737, Z4738, Z4739, Z4740, Z4744, Z4745, Z4747, Z4748, Z4749, Z4750 Z4752, Z4061 Z4755 Z4049, Z4741 Z4068 Z4072 Z4022...”
• Epigenetic regulation of gene expression in Shiga toxin-producing Escherichia coli: Transcriptomic data
  Carter, Data in brief 2021
  • “...the genes encoding the protein DamX (locus ID, ECRM13514_RS21650) and the ribulose-phosphate 3-epimerase (locus ID, ECRM13514_RS21640). The detailed information about the wild-type (WT) strain RM13514 and the two isogenic mutant strains are described in Table1 . When grown in LB broth at 37C, strains RM13514 and...”

IL2324 D-ribulose-5-phosphate 3-epimerase from Idiomarina loihiensis L2TR
77% identity, 98% coverage

• Genome sequence of the deep-sea gamma-proteobacterium Idiomarina loihiensis reveals amino acid fermentation as a source of carbon and energy
  Hou, Proceedings of the National Academy of Sciences of the United States of America 2004
  • “...(IL2214), ribose 5-phosphate isomerase (IL2103), and ribulose5-phosphate-3-epimerase (IL2324), which are encoded by I. loihiensis, appear to be sufficient to...”

APL_1820 ribulose-phosphate 3-epimerase from Actinobacillus pleuropneumoniae L20
75% identity, 98% coverage

• Host-pathogen interactions of Actinobacillus pleuropneumoniae with porcine lung and tracheal epithelial cells
  Auger, Infection and immunity 2009
  • “...2-phosphate synthase 2.913 Energy metabolism APL_1849 APL_1820 APL_1191 APL_1331 APL_1685 APL_1689 APL_1684 APL_1333 APL_1019 APL_0896 lldD rpe namA...”

PMPD1_0329 ribulose-phosphate 3-epimerase from Paramixta manurensis
71% identity, 98% coverage

• Paramixta manurensis gen. nov., sp. nov., a novel member of the family Erwiniaceae producing indole-3-acetic acid isolated from mushroom compost
  Kim, Scientific reports 2024
  • “...4-dehydrogenase PMPD1_2270 UPI0003456E87 WP_017800006.1 83.4 0 d -xylulokinase PMPD1_2271 UPI0005526436 WP_034914917.1 81.2 0 Ribulose-phosphate 3-epimerase PMPD1_0329 D4I319 WP_004160688.1 91.2 2.99E152 Utilization of l -fucose 40 l -fucose dehydrogenase PMPD1_3766 A0A085G0Q3 WP_034796198.1 76.7 1.03E131 l -fuconolactonase PMPD1_3767 K8A015 WP_007671895.1 64.0 4.22E115 l -fuconate dehydratase PMPD1_3768 A0A0H3FNB4 WP_015703671.1...”

B7FRG3 Ribulose-phosphate 3-epimerase from Phaeodactylum tricornutum (strain CCAP 1055/1)
PHATRDRAFT_53935 plastidic ribulose-phosphate 3-epimerase from Phaeodactylum tricornutum CCAP 1055/1
72% identity, 85% coverage

• Metabolomic, proteomic and lactylated proteomic analyses indicate lactate plays important roles in maintaining energy and C:N homeostasis in Phaeodactylum tricornutum
  Huang, Biotechnology for biofuels and bioproducts 2022
  • “...2.78 0.06 3.32 0.02 Calvin cycle, OPPP 29 B7FUU0 Transketolase 0.60 0.18 0.34 0.02 31 B7FRG3 Ribulose-phosphate 3-epimerase 1.16 0.44 0.49 0.03 Calvin cycle, TCA cycle 30 B7GEG9 Malate dehydrogenase 1.05 0.82 1.50 0.01 Glycolysis 9 B7GD69 Probable phosphoglycerate mutase 1.85 0.07 2.51 0.01 11 B7G9G7...”
• A Metabolic Probe-Enabled Strategy Reveals Uptake and Protein Targets of Polyunsaturated Aldehydes in the Diatom Phaeodactylum tricornutum
  Wolfram, PloS one 2015
  • “...B7FRW2 21328.5 OO O X 2) Molecular function Catalytic activity, isomerase activity Ribulose-phosphate 3-epimerase Rpe B7FRG3 27812.0 OO O O Catalytic activity, ligase activity Predicted protein, family: Aspartate-ammonia ligase PHATRDRAFT_44902 a B7FW24 43206.1 X OO O Catalytic activity, oxidoreductase activity Predicted protein, domains: Thioredoxin-like fold, Thioredoxin...”
• Proteomics to reveal metabolic network shifts towards lipid accumulation following nitrogen deprivation in the diatom Phaeodactylum tricornutum.
  Yang, Journal of applied phycology 2014
  • “...categorized as being involved in biological process of carbon and energy metabolism. Plastidic ribulose-phosphate 3-epimerase (PHATRDRAFT_53935), which catalyzes the reversible epimerization of d -ribulose 5-phosphate to d -xylulose 5-phosphate, showed a large increase in expression under N. The enzyme is located in the thylakoid membrane and...”

BCAL0401 putative ribulose-phosphate 3-epimerase from Burkholderia cenocepacia J2315
72% identity, 98% coverage

• Identification of Burkholderia cenocepacia non-coding RNAs expressed during Caenorhabditis elegans infection
  Pita, Applied microbiology and biotechnology 2023
  • “...- 64|49* - BCAL1995 AHL, quorum sensing - - 0|21*** BCAL0739 Phosphoglyceromutase - - 55|32* BCAL0401 Pentose-phosphate shunt - - 60|7** RIT55 (ncS11) 153.25x Bcc B. pseudomallei BCAL2830 Two-component system - - 47|78* BCAL2211 Two-component system - - 153|129** BCAL1369 Sigma factor 70 EcfC - -...”
• Genetic Determinants Associated With in Vivo Survival of Burkholderia cenocepacia in the Caenorhabditis elegans Model
  Wong, Frontiers in microbiology 2018
  • “...cenocepacia infection. Genes involved in the biosynthesis of amino acids (i.e., argB, talB, gpmA , BCAL0401 and BCAL2231) were also identified suggesting that B. cenocepacia responds to nutritional cues within the host environment by adjusting its metabolic pathways to sustain growth. Several studies have shown that...”

BP3266 ribulose-phosphate 3-epimerase from Bordetella pertussis Tohama I
73% identity, 88% coverage

• Immuno-proteomics analysis between OMV of vaccine and dominant wild type strains of Bordetella pertussis in Iran
  Badamchi, Iranian journal of microbiology 2020
  • “...OMV of the vaccine strain tested and OMV of Bp IP91 including (BP2759), (BP2377), (BP2818), (BP3266) (BP0965), (BP0205) and BP0558. ( Figs. 4A and B ). Fig. 3. Functional classes of proteins identified from OMV of Bp. Fig. 4. Protein fingerprint of OMV from Bp both...”
  • “...7.7 265 cytoplasm 4 BP0182 6.135 Iron-sulfur cluster carrier protein 38.2 6.2 163 cytoplasm 5 BP3266 4.898 Ribulose-phosphate 3-epimerase 26.426 5.8 245 cytoplasm 6 BP0965 28.64 Antioxidant protein 23.777 5.6 213 cytoplasm 7 BP0205 34.04 Putative exported protein 11.77 8.4 114 Extracellular 8 ahpC 23.08 Alkyl...”

NGO0758 putative ribulose-phosphate 3-epimerase from Neisseria gonorrhoeae FA 1090
69% identity, 97% coverage

• Deep sequencing-based analysis of the anaerobic stimulon in Neisseria gonorrhoeae
  Isabella, BMC genomics 2011
  • “...Lrp lldD NGO0639 -7.1 -11.1 L-lactate dehydrogenase eda NGO0713 -3.0 -5.6 KHG-KDPG bifunctional aldolase rpeC NGO0758 -4.8 -3.8 Ribulose-phosphate 3-epimerase fdx NGO0825 -5.3 -5.3 Ferredoxin cisY NGO0918 -3.6 -3.8 Type II citrate synthase Lrp sdhB NGO0920 -2.9 -4.2 Succinate dehydrogenase, iron-sulfur protein Lrp sdhA NGO0921 -3.7...”

5umfC / B4RLV9 Crystal structure of a ribulose-phosphate 3-epimerase from neisseria gonorrhoeae with bound phosphate
69% identity, 98% coverage

• Ligand: zinc ion (5umfC)

H16_A3317 ribulose-phosphate 3-epimerase from Cupriavidus necator H16
H16_A3317 Ribulose-phosphate 3-epimerase from Ralstonia eutropha H16
69% identity, 95% coverage

• Detection of phase-dependent transcriptomic changes and Rubisco-mediated CO2 fixation into poly (3-hydroxybutyrate) under heterotrophic condition in Ralstonia eutropha H16 based on RNA-seq and gene deletion analyses
  Shimizu, BMC microbiology 2013
  • “...would have a role in establishing the non-oxidative branch of pentose-phosphate cycle, along with rpe (H16_A3317), rpiA (H16_A2345), tal (H16_A2346), tktA (H16_A3147) located in loci other than the cbb operons, thereby providing essential precursors for nucleotides and aromatic amino acids. The expression of cbb genes has...”

7sbjA / B2FKL8 Crystal structure of ribulose-phosphate 3-epimerase from stenotrophomonas maltophilia k279a
75% identity, 97% coverage

• Ligand: zinc ion (7sbjA)

V6E02_08935 ribulose-phosphate 3-epimerase from Thiobacter aerophilum
69% identity, 96% coverage

• Thiobacter aerophilum sp. nov., a Thermophilic, Obligately Chemolithoautotrophic, Sulfur-Oxidizing Bacterium from a Hot Spring and Proposal of Thiobacteraceae fam. nov
  Dukat, Microorganisms 2024
  • “...bifunctional fructose-/sedoheptulose-bisphosphate aldolase class II (V6E02_11045), bifunctional fructose-/sedoheptulose-bisphosphatase type I (V6E02_08490), transketolase (V6E02_11025), ribulose-phosphate 3-epimerase (V6E02_08935), ribose-5-phosphate isomerase A (V6E02_08820), and phosphoribulokinase (V6E02_04755). Assimilation of carbon dioxide via the Calvin cycle has previously been shown for both sulfur-oxidizing ( Thiomonas arsenitoxydans [ 35 ], Thiomonas intermedia...”

NMA1413 putative ribulose-phosphate 3-epimerase from Neisseria meningitidis Z2491
68% identity, 92% coverage

• Comprehensive Identification of Meningococcal Genes and Small Noncoding RNAs Required for Host Cell Colonization
  Capel, mBio 2016
  • “..., edd , and eda . Moreover, 5 other enzymes of the PP pathway (NMA0412, NMA1413, rpiA , tal , and pgi2 ) were growth defective. The use of these alternative routes to catabolize glucose is consistent with the fact that N.meningitidis lacks the phosphofructokinase enzyme,...”

cbbE / RF|NP_943058.1 ribulose-phosphate 3-epimerase; EC 5.1.3.1 from Ralstonia eutropha H16 (see paper)
PHG423 ribulose-phosphate 3-epimerase from Cupriavidus necator H16
PHG423 ribulose-5-phosphate 3-epimerase from Ralstonia eutropha H16
67% identity, 90% coverage

• Engineering Cupriavidus necator H16 for enhanced lithoautotrophic poly(3-hydroxybutyrate) production from CO₂
  Kim, Microbial cell factories 2022
  • “...cbbY2 (H16_B1392) HAD family hydrolase, unknown function 2.7 cbbE2 (H16_B1391) ribulose-phosphate 3-epimerase; rpe 1.6* cbbEp (PHG423) ribulose-phosphate 3-epimerase; rpe 2.3* cbbTp (PHG420) Transketolase; tkt 1.3 cbbT2 (H16_B1388) Transketolase; tkt 1.7 TCA cycle H16_B0357 Citrate synthase 58.3 H16_B0414 Citrate synthase 22 ED pathway pyk3 (H16_B0961) Pyruvate kinase,...”

cbbE / GI|304019 ribulose-phosphate 3-epimerase; EC 5.1.3.1 from Ralstonia eutropha H16 (see paper)
H16_B1391 Ribulose-phosphate 3-epimerase from Ralstonia eutropha H16
H16_B1391 ribulose-phosphate 3-epimerase from Cupriavidus necator H16
70% identity, 84% coverage

• Engineering Cupriavidus necator H16 for enhanced lithoautotrophic poly(3-hydroxybutyrate) production from CO₂
  Kim, Microbial cell factories 2022
  • “...accessory protein CbbX, AAA ATPase 3.6 cbbY2 (H16_B1392) HAD family hydrolase, unknown function 2.7 cbbE2 (H16_B1391) ribulose-phosphate 3-epimerase; rpe 1.6* cbbEp (PHG423) ribulose-phosphate 3-epimerase; rpe 2.3* cbbTp (PHG420) Transketolase; tkt 1.3 cbbT2 (H16_B1388) Transketolase; tkt 1.7 TCA cycle H16_B0357 Citrate synthase 58.3 H16_B0414 Citrate synthase 22...”

FTL_1432 D-ribulose-phosphate 3-epimerase from Francisella tularensis subsp. holarctica
FTN_1221 D-ribulose-phosphate 3-epimerase from Francisella tularensis subsp. novicida U112
64% identity, 99% coverage

• The Francisella tularensis Polysaccharides: What Is the Real Capsule?
  Freudenberger, Microbiology and molecular biology reviews : MMBR 2020 (secret)
• Glycosylation of a Capsule-Like Complex (CLC) by Francisella novicida Is Required for Virulence and Partial Protective Immunity in Mice
  Freudenberger, Frontiers in microbiology 2017
  • “...tularensis subsp. tularensis schuS4 ORF % Sequence Identity to type A FTN_1221 669 D-ribulose-phosphate 3-epimerase FTL_1432 FTT_0789 98 FTN_1220 1395 Glycosyltransferase FTL_1431 FTT_0790 97 FTN_1219 1020 UDP-glucose 4-epimerase FTL_1430 FTT_0791 97 FTN_1218 1230 Glycosyltransferase FTL_1429 FTT_0792 97 FTN_1217 1689 ATP-binding membrane transporter FTL_1428 FTT_0793 98 Not...”
• Isolation and mutagenesis of a capsule-like complex (CLC) from Francisella tularensis, and contribution of the CLC to F. tularensis virulence in mice
  Bandara, PloS one 2011
  • “...PCR showed that expression of genes in a putative polysaccharide locus in the LVS genome (FTL_1432 through FTL_1421) was upregulated when CLC expression was enhanced. Open reading frames FTL_1423 and FLT_1422, which have homology to genes encoding for glycosyl transferases, were deleted by allelic exchange, and...”
  • “...strain SCHU S4 [32] (NC_006570). This locus contains 12 putative genes in the LVS genome: FTL_1432 through FTL_1421. We sought to purify and analyze the electron dense CLC that appears to be upregulated under specific growth conditions, with emphasis on the carbohydrate component. Furthermore, to determine...”
• The pentose phosphate pathway constitutes a major metabolic hub in pathogenic Francisella
  Rytter, PLoS pathogens 2021
  • “...( FTN_1333 , encoding transketolase), rpiA ( FTN_1185 , encoding ribose 5-phosphate isomerase), rpe ( FTN_1221 , encoding ribulose phosphate 3-epimerase) and talA ( FTN_0781 , encoding transaldolase) ( S1 Fig ). These four genes are scattered along the F . novicida chromosome and each of...”
  • “...transposon insertion mutants of F . novicida ( rpiA : FTN_1185 , tnfn1_pw060328p07q169; rpe : FTN_1221 , tnfn1_pw060419p02q104; talA : FTN_0781 , tnfn1_pw060323p07q189 ), were designated here rpiA , rpe and talA for simplicity. Bacteria were grown at 37C on PolyViteX agar plates (BioMerieux), TSB, Schaedler...”
• Glycosylation of a Capsule-Like Complex (CLC) by Francisella novicida Is Required for Virulence and Partial Protective Immunity in Mice
  Freudenberger, Frontiers in microbiology 2017
  • “...(Invitrogen) following the manufacturer's instructions. The primers used to amplify cDNA of genes FTN_1211 to FTN_1221 for RT-PCR are listed in Table S1 . Purification of the putative CLC F. novicida was grown in CDMB to just past mid-log phase, subcultured consecutively in fresh medium 10...”
  • “...holarctica LVS ORF F. tularensis subsp. tularensis schuS4 ORF % Sequence Identity to type A FTN_1221 669 D-ribulose-phosphate 3-epimerase FTL_1432 FTT_0789 98 FTN_1220 1395 Glycosyltransferase FTL_1431 FTT_0790 97 FTN_1219 1020 UDP-glucose 4-epimerase FTL_1430 FTT_0791 97 FTN_1218 1230 Glycosyltransferase FTL_1429 FTT_0792 97 FTN_1217 1689 ATP-binding membrane transporter...”

FTT_0789 D-ribulose-phosphate 3-epimerase from Francisella tularensis subsp. tularensis SCHU S4
64% identity, 99% coverage

• The Francisella tularensis Polysaccharides: What Is the Real Capsule?
  Freudenberger, Microbiology and molecular biology reviews : MMBR 2020 (secret)
• Role of Glycosylation/Deglycolysation Processes in Francisella tularensis Pathogenesis
  Barel, Frontiers in cellular and infection microbiology 2017
  • “...Balonova et al., 2010 pglA PglA Oligosaccharyltransferase Pilin and Protein glycosylation Egge-Jacobsen et al., 2011 FTT_0789 Ribulose-phosphate 3-epimerase Glycan Biosynthesis Thomas et al., 2011 FTT_0798 Glycosyl transferase family protein Putative glycosyltransferase Thomas et al., 2011 FTH_0069 FTT_1676 Hypothetical protein Glycosylated lipoprotein Virulence Factor Balonova et al.,...”
• Glycosylation of a Capsule-Like Complex (CLC) by Francisella novicida Is Required for Virulence and Partial Protective Immunity in Mice
  Freudenberger, Frontiers in microbiology 2017
  • “...BLAST (Altschul et al., 1990 ) using the F. tularensis Type A SchuS4 glycosylation locus (FTT_0789 to FTT_0800) for comparison. Mutagenesis of F. novicida Suicide plasmid pSC-1423/1422K, which was used for mutagenesis of LVS, was also used for mutagenesis of F. novicida by allelic exchange, targeting...”
  • “...subsp. tularensis schuS4 ORF % Sequence Identity to type A FTN_1221 669 D-ribulose-phosphate 3-epimerase FTL_1432 FTT_0789 98 FTN_1220 1395 Glycosyltransferase FTL_1431 FTT_0790 97 FTN_1219 1020 UDP-glucose 4-epimerase FTL_1430 FTT_0791 97 FTN_1218 1230 Glycosyltransferase FTL_1429 FTT_0792 97 FTN_1217 1689 ATP-binding membrane transporter FTL_1428 FTT_0793 98 Not present...”
• Isolation and mutagenesis of a capsule-like complex (CLC) from Francisella tularensis, and contribution of the CLC to F. tularensis virulence in mice
  Bandara, PloS one 2011
  • “...tularensis CLC biosynthesis. ORF in LVS ORF in Schu S4 Size (bp) Product a FTL_1432 FTT_0789 669 D-ribulose-phosphate 3-epimerase FTL_1431 FTT_0790 1395 Sugar transferase family protein (Glycosyl transferase) FTL_1430 FTT_0791 1020 UDP-glucose 4-epimerase FTL_1429 FTT_0792 1230 Glycosyl transferase group 1 family protein FTL_1428 FTT_0793 1683 ATP-binding...”

AFE_3247 ribulose-phosphate 3-epimerase from Acidithiobacillus ferrooxidans ATCC 23270
61% identity, 98% coverage

• Effect of CO₂ Concentration on Uptake and Assimilation of Inorganic Carbon in the Extreme Acidophile Acidithiobacillus ferrooxidans
  Esparza, Frontiers in microbiology 2019
  • “...pykA Pyruvate kinase II [2.7.1.40] AFE_3249 cbbA Fructose-biphosphate aldolase [4.1.2.13] AFE_3248 cbbE Ribulose-5-phosphate 3-epimerase [5.1.3.1] AFE_3247 cbbZ Phosphoglycolate phosphatase [3.1.3.18] AFE_3246 trpE Anthranilate synthase component I [4.1.3.27] AFE_3245 trpG Anthranilate synthase component II [4.1.3.27] AFE_3244 trpD Anthranilate phosphoribosyltransferase [2.4.2.18] AFE_3243 trpC Indole-3-glycerol phosphate synthase [4.1.1.48] AFE_3242...”
• Anaerobic sulfur metabolism coupled to dissimilatory iron reduction in the extremophile Acidithiobacillus ferrooxidans
  Osorio, Applied and environmental microbiology 2013
  • “...AFE_1813 AFE_0424 2.4 7.1 2.2 AFE_2155 AFE_2924 AFE_3247 AFE_0419 AFE_1843 AFE_1667b AFE_1667b AFE_2836 AFE_2024 AFE_2025 AFE_1823 AFE_2053 2.9 10.9 2.5 2.2...”
  • “...[AFE_2025]), and several nonoxidative branch proteins (AFE_1843, AFE_3247, and AFE_0419), possibly to produce reducing power and ribulose-5phosphate for carbon...”

Rru_A2402 Ribulose-phosphate 3-epimerase from Rhodospirillum rubrum ATCC 11170
60% identity, 92% coverage

• The poor growth of Rhodospirillum rubrum mutants lacking RubisCO is due to the accumulation of ribulose-1,5-bisphosphate
  Wang, Journal of bacteriology 2011
  • “...and cbbP (Rru_A2404) single mutants but not a cbbE (Rru_A2402) mutant. As shown in Fig. 3A, unlike the cbbM mutant, the cbbF (UR2564), cbbP (UR2565), and cbbT...”
  • “...conditions. We were unable to obtain a cbbE (Rru_A2402) mutant under any growth condition tested, including photoheterotrophic growth in MG or SMN rich medium...”

D9S318 Ribulose-phosphate 3-epimerase from Thermosediminibacter oceani (strain ATCC BAA-1034 / DSM 16646 / JW/IW-1228P)
54% identity, 94% coverage

• Activation of PPARγ in bladder cancer via introduction of the long arm of human chromosome 9.
  Shimizu, Oncology letters 2022
  • “...9p12; UT801, 9p11.2; SHGC-141463, 9q12; SHGC-146514, 9q13; D9S15, 9q21.12; D9S1122, 9q21.2; D9S153, 9q21.31; D9S777, 9q22.1; D9S318, 9q22.2; D9S287, 9q22.32; D9S277, 9q31.1; D9S177, 9q33.1; D9S290, 9q34.11; D9S66, 9q34.2; and D9S158, 9q34.3). Primer sequences were obtained from the National Center for Biotechnology Information ( https://www.ncbi.nlm.nih.gov ). PCR was...”

Clocl_2564 ribulose-phosphate 3-epimerase from Acetivibrio clariflavus DSM 19732
53% identity, 94% coverage

• Complete Genome Sequence of Clostridium clariflavum DSM 19732
  Izquierdo, Standards in genomic sciences 2012
  • “...that produces D-ribulose-5P used in the pentose phosphate pathway is present elsewhere in the genome (Clocl_2564). It therefore seems that C. clariflavum DSM 19732 has much of the capabilities to grow on xylan and xylose, but seems to have lost that ability due to the absence...”

alr0782 ribulose-phosphate 3-epimerase from Nostoc sp. PCC 7120
51% identity, 90% coverage

• The Anabaena sp. PCC 7120 Exoproteome: Taking a Peek outside the Box
  Oliveira, Life (Basel, Switzerland) 2015
  • “...protein NrtA N 2 , NO 3 , NH 4 + Amino acid biosynthesis Anabaena Alr0782 Ribulose-phosphate 3-epimerase NH 4 + Central intermediary metabolism N. commune , Anabaena Alr0834 Porin major outer membrane protein N 2 , NO 3 Cell envelope - Alr0880 Oligopeptidase A NH...”
• ChIP analysis unravels an exceptionally wide distribution of DNA binding sites for the NtcA transcription factor in a heterocyst-forming cyanobacterium
  Picossi, BMC genomics 2014
  • “...are also found ascribed to target regions. These include the pentose-phosphate pathway genes gnd , alr0782 , alr4670 and all2563 , the Calvin cycle rbcLXS operon and all4021 , and many others (see Additional file 2 : Table S1), such as the cmpR gene, whose product...”

BA3998 ribulose-phosphate 3-epimerase from Bacillus anthracis str. Ames
50% identity, 95% coverage

• Application of high-throughput technologies to a structural proteomics-type analysis of Bacillus anthracis
  Au, Acta crystallographica. Section D, Biological crystallography 2006 (PubMed)
  • “...important protein structures, BA4899, BA1655 and BA3998, involved in tRNA modification, sporulation control and carbohydrate metabolism, respectively, are...”
  • “...determination of B. anthracis d-ribulose5-phosphate epimerase (BA3998) showed several interesting features (Carter et al., in preparation). The protein...”

ZCP4_RS05995 ribulose-phosphate 3-epimerase from Zymomonas mobilis subsp. mobilis str. CP4 = NRRL B-14023
57% identity, 94% coverage

• Limited Diversity of Thermal Adaptation to a Critical Temperature in <i>Zymomonas mobilis</i>: Evidence from Multiple-Parallel Laboratory Evolution Experiments
  Pattanakittivorakul, International journal of molecular sciences 2025
  • “...). Of these, the genes for fundamental metabolism, ZCP4_RS01475 , ZCP4_RS03815 , ZCP4_RS03820 , and ZCP4_RS05995 , can be excluded because their upregulation should be observed in other thermoadapted mutants if they are needed for growth at the CHT. Genes for transcriptional regulators can also be...”

I3DZ65 ribulose-phosphate 3-epimerase (EC 5.1.3.1) from Bacillus methanolicus (see paper)
BMMGA3_05905 ribulose-phosphate 3-epimerase from Bacillus methanolicus MGA3
49% identity, 94% coverage

• Transcriptome analysis of thermophilic methylotrophic Bacillus methanolicus MGA3 using RNA-sequencing provides detailed insights into its previously uncharted transcriptional landscape
  Irla, BMC genomics 2015
  • “...] BMMGA3_00415 - BMMGA3_00450 8 + Folic acid biosynthesis [7/9] [ 38 ] BMMGA3_05870 - BMMGA3_05905 8 + Various, mainly translation, ribosomal structure, signal transduction [3 + 3/7] +2, [ 39 , 40 ] BMMGA3_14725 - BMMGA3_14760 8 - Histidine biosynthesis Similar, [ 41 ] 1...”

SYNPCC7002_A0324 ribulose-phosphate 3-epimerase from Synechococcus sp. PCC 7002
48% identity, 93% coverage

• Transcription Profiling of the Model Cyanobacterium Synechococcus sp. Strain PCC 7002 by Next-Gen (SOLiD™) Sequencing of cDNA
  Ludwig, Frontiers in microbiology 2011
  • “...6-Phosphogluconate DH, decarboxylating SYNPCC7002_A1269 $ 2.45 0.09 0.06 0.66 1.39 rpiA Ribose 5-phosphate isomerase A SYNPCC7002_A0324 $ 2.99 0.47 0.22 0.47 0.99 rpe Ribulose-phosphate 3-epimerase SYNPCC7002_A1022 $ 1.31 0.40 0.55 1.36 0.90 tkt Transketolase SYNPCC7002_A0010* 0.85 4.41 1.05 0.24 0.71 fbaB Fructose-bisphosphate aldolase class I SYNPCC7002_A0329*...”
  • “...tpiA Triosephosphate isomerase SYNPCC7002_A1269 $ 2.45 0.09 0.06 0.66 1.39 rpiA Ribose 5-phosphate isomerase A SYNPCC7002_A0324 $ 2.99 0.47 0.22 0.47 0.99 rpe Ribulose-phosphate 3-epimerase SYNPCC7002_A2857 2.34 0.39 0.03 0.09 1.15 prk Phosphoribulokinase SYNPCC7002_A2665 1.36 1.10 0.40 0.36 1.05 prk Phosphoribulokinase CO 2 CONCENTRATION SYNPCC7002_A1805 0.63...”

BMEI1116 RIBULOSE-PHOSPHATE 3-EPIMERASE from Brucella melitensis 16M
55% identity, 75% coverage

• Analyses of Brucella pathogenesis, host immunity, and vaccine targets using systems biology and bioinformatics
  He, Frontiers in cellular and infection microbiology 2012
  • “...12761078 G: CARBOHYDRATE TRANSPORT AND METABOLISM** 42 BMEII1045 BMEII1045 Mice, macrophages, HeLa 14979322 43 cbbE BMEI1116 Macrophages, HeLa 14979322 44 dbsA BMEII0300 HeLa 14979322 45 eryC BMEII0428 Mice, macrophages 16177356 46 galcD BMEII0485 Mice, macrophages, HeLa 14979322 47 gluP BMEII1053 Mice 12414147 48 gnd BMEII1124 Mice...”
• The Brucella abortus S19 DeltavjbR live vaccine candidate is safer than S19 and confers protection against wild-type challenge in BALB/c mice when delivered in a sustained-release vehicle
  Arenas-Gamboa, Infection and immunity 2009
  • “...transposon mutagenesis (2, 13). Among these, vjbR (BMEI1116), encoding the luxR-like quorum sensing-related transcriptional regulator is required for virB...”
• Mutations of the quorum sensing-dependent regulator VjbR lead to drastic surface modifications in Brucella melitensis
  Uzureau, Journal of bacteriology 2007
  • “...genome (16), the previously described VjbR regulator (BMEI1116) (14) and a second regulator, currently undergoing characterization, called BabR (BMEI1758)....”

RL2598 putative ribulose-phosphate 3-epimerase from Rhizobium leguminosarum bv. viciae 3841
54% identity, 99% coverage

• The Use of Transposon Insertion Sequencing to Interrogate the Core Functional Genome of the Legume Symbiont Rhizobium leguminosarum
  Perry, Frontiers in microbiology 2016
  • “...isomerase B PVGI 0.83 5.2 GD 0.83 21.8 NE 3.3.9 Putative ribose-5-phosphate isomerase B 4.3 RL2598 rpe Ribulose-phosphate 3-epimerase VGI 0.38 2.33 GD 0.63 9.2 NE 3.3.9 Putative ribulose phosphate 3-epimerase 4.3 pRL120033 D-allulose-6-phosphate 3-epimerase PGN 1 20.6 NE 1 21 NE 3.3.9 Putative D-allulose-6-phosphate 3-epimerase...”

RTCIAT899_RS09635 ribulose-phosphate 3-epimerase from Rhizobium tropici CIAT 899
55% identity, 89% coverage

• Dissecting the Acid Stress Response of Rhizobium tropici CIAT 899
  Guerrero-Castro, Frontiers in microbiology 2018
  • “...product AR vs. BR AR vs. CR JG241 RTCIAT899_RS09205 MAS 0.082820403 0.358090297 Triose-phosphate isomerase JG1042 RTCIAT899_RS09635 MAS 0.562135533 0.019664157 Ribulose phosphate 3-epimerase. JG4882 RTCIAT899_RS05920 MAS 1.127623534 0.775841137 prolyl aminopeptidase JG6187 RTCIAT899_RS18500 MAS 0.2711116 0.62190933 Acs acetyl-coenzyme A synthetase JG5373 RTCIAT899_RS15005 MAS 0.19186143 0.374167234 Glutathione-dependent formaldehyde-activating GFA...”
  • “...in genes related to anabolic and energy generation process like ribulose phosphate 3-epimerase (locus tag RTCIAT899_RS09635), prolyl aminopeptidase (RTCIAT899_RS05920) and acetyl-coenzyme A synthetase (Acs) (RTCIAT899_RS18500). Another mutant (JG283) presented an insertion in a gene encoding a polysaccharide biosynthesis protein. Polysaccharide and exopolysaccharide biosynthesis has been reported...”

cce_0798 ribulose-phosphate 3-epimerase from Cyanothece sp. ATCC 51142
49% identity, 91% coverage

• Analysis of Protein Complexes in the Unicellular Cyanobacterium Cyanothece ATCC 51142
  Aryal, Journal of proteome research 2018
  • “...glucose 6-phosphate dehydrogenase; Zwf (cce_2536), 6-phosphogluconate dehydrogenase; Gnd (cce_3746), 6-phosphogluconolactonase; Pgl (cce_4743), ribulose-phosphate 3-epimerase; Rpe (cce_0798), and transaldolases; TalC (cce_4208) and TalA (cce_4687) were identified as complexes. For example, Zwf, a branching enzyme of the PP pathway was identified with R app > 6. In contrast,...”
  • “...phosphoenolpyruvate carboxylase (cce_3822), Gnd; 6-phosphogluconate dehydrogenase (cce_3746), RpiA; ribose 5-phosphate isomerase (cce_0103), Rpe; ribulose-phosphate 3-epimerase (cce_0798), TalA; transaldolase (cce_4687), TktA; transketolase (cce_4627), Pkt; phosphoketolase (cce_2225), GltA; citrate synthase (cce_1900), AcnB; aconitate hydratase 2 (cce_3280), Icd; isocitrate dehydrogenase (cce_3202), GabD; succinate-semialdehyde dehydrogenase (cce_4228), SucC; succi nyl-CoA synthetase...”

Cthe_0576 ribulose-5-phosphate 3-epimerase from Clostridium thermocellum ATCC 27405
49% identity, 94% coverage

• 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
  • “...2. Transketolase subunit A Cthe_2443, 2704; 3. Ribulose - 5 - phosphate 3 - epimerase Cthe_0576; 4. Ribose - 5 - phosphate 3 - isomerase Cthe_2597; 5. Ribose - phosphate pyrophosphokinase Cthe_2630; 6. Phosphopentomutase Cthe_0677; Phosphoglucomutase Cthe_1265; 7. 6 - Phosphofructokinase Cthe_0347; 8. Fructose - bisphosphate...”

APA386B_2378 ribulose-phosphate 3-epimerase from Acetobacter pasteurianus 386B
50% identity, 98% coverage

• Complete genome sequence and comparative analysis of Acetobacter pasteurianus 386B, a strain well-adapted to the cocoa bean fermentation ecosystem
  Illeghems, BMC genomics 2013
  • “...APA386B_2134); (15) gluconolactonase (APA386B_2110); (16) gluconate kinase (APA386B_1158); (17) phosphogluconate dehydrogenase (APA386B_1154); (18) ribulose-phosphate 3-epimerase (APA386B_2378); (19) ribose-5-phosphate isomerase A (APA386B_1157); (20) transketolase (APA386B_1152 and APA386B_1521); (21) transaldolase (APA386B_1153) (22) glucose-6-phosphate dehydrogenase (APA386B_729); (23) 6-phosphogluconolactonase (APA386B_1156); (24) glycerol kinase (Apa396B_92); (25) glycerol-3-phosphate dehydrogenase (APA386B_1931 and APA386B_94);...”

lmo1818 similar to ribulose-5-phosphate 3-epimerase from Listeria monocytogenes EGD-e
51% identity, 95% coverage

• Listeria monocytogenes genes supporting growth under standard laboratory cultivation conditions and during macrophage infection
  Fischer, Genome research 2022
  • “...only enzyme in this lower part of the pathway that is required for growth is lmo1818 , which encodes one out of six paralogous ribulose-phosphate 3-epimerase genes and was the only paralog expressed under standard growth conditions in a previous transcriptome analysis ( Hauf et al....”

RPE_SYNY3 / P74061 Ribulose-phosphate 3-epimerase; EC 5.1.3.1 from Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa) (see paper)
P74061 ribulose-phosphate 3-epimerase (EC 5.1.3.1) from Synechocystis sp. PCC 6803 (see paper)
rpe / PDB|1TQJ_A ribulose-phosphate 3-epimerase from Synechocystis sp. (see paper)
sll0807 pentose-5-phosphate-3-epimerase from Synechocystis sp. PCC 6803
51% identity, 90% coverage

• function: Catalyzes the reversible epimerization of D-ribulose 5- phosphate to D-xylulose 5-phosphate.
  catalytic activity: D-ribulose 5-phosphate = D-xylulose 5-phosphate (RHEA:13677)
  cofactor: a divalent metal cation (Binds 1 divalent metal cation per subunit.)
  subunit: Homohexamer.
• Ribulose-1,5-bisphosphate regeneration in the Calvin-Benson-Bassham cycle: Focus on the last three enzymatic steps that allow the formation of Rubisco substrate
  Meloni, Frontiers in plant science 2023
  • “...Chlamydomonas reinhardtii (Cr) RPE (PDB ID: 7B1W; UNIPROT: A8IKW6), Synechocystis PCC 6803 (Syn) RPE (UNIPROT: P74061), Physcomitrium patens (Pp) RPE (UNIPROT: A9RCK8), Arabidopsis thaliana (At) RPE (UNIPROT: Q9SAU2), and Spinacia oleracea (So) RPE (UNIPROT: Q43157). For the sake of clarity, the alignment was initiated by variably...”
• Site-2 Protease Slr1821 Regulates Carbon/Nitrogen Homeostasis during Ammonium Stress Acclimation in Cyanobacterium Synechocystis sp. PCC 6803
  Lin, International journal of molecular sciences 2023
  • “...( slr0783 ), sedoheptulose bisphosphatase ( slr2094 ), transketolase ( sll1070 ), phosphopentose epimerase ( sll0807 ) and phosphoribulose kinase ( sll1525 ). While WT only notably repressed 11% of photosynthesis genes, it had no significant regulation on genes related with antenna proteins, porphyrin and chlorophyll...”
• Towards the rate limit of heterologous biotechnological reactions in recombinant cyanobacteria
  Barone, Biotechnology for biofuels and bioproducts 2023
  • “...been observed as upregulated: tktA ( sll1070 ), devB ( sll1479 ), and cfxE ( sll0807 ). In the later light period, the upregulation of rpiA was noted [ slr0194 , encoding the ribose 5-phosphate isomerase (RPI)] [ 34 ]. Nevertheless, the stimulating effect of D-Glu...”
• Diurnal Regulation of Cellular Processes in the Cyanobacterium Synechocystis sp. Strain PCC 6803: Insights from Transcriptomic, Fluxomic, and Physiological Analyses
  Saha, mBio 2016
  • “...tktA ( sll1070 ), encoding transketolase, devB ( sll1479 ), encoding 6-phosphogluconolactonase, and cfxE ( sll0807 ), encoding pentose-5-phosphate-3-epimerase, were upregulated in the earlier light period (with peaks at L1), while rpiA ( slr0194 ), encoding ribose 5-phosphate isomerase, was upregulated in the later light period...”
• Expression profiling of the bloom-forming cyanobacterium Nodularia CCY9414 under light and oxidative stress conditions
  Kopf, The ISME journal 2015
  • “...(0.0) Slr0606 (e 101) None Slr1329HL (0.0) Slr0008 (e 171) Sll0807 (e 144) Sll1381 (3e 53) Slr0193 (e 48) Sll0765 (e 110) None None Sll1380 (e 23) Sll1142 (e...”
• Gene expression patterns of sulfur starvation in Synechocystis sp. PCC 6803
  Zhang, BMC genomics 2008
  • “...protein ssr2799 ( rpl27 )) 15 sll1184( ho1 ), slr0444( aroA ), slr1176( agp ), sll0807( cfxE ), slr1545( rpoE ), Cytochrome b 6/f complex subunit smr0003( petM ), Photosystem I (smr0005( psaM ), ssl0563( psaC )), Photosystem II (sll1867( psbA3 ), sml0001( psbI ), sml0002(...”
• Role of sigma factors in controlling global gene expression in light/dark transitions in the cyanobacterium Synechocystis sp. strain PCC 6803
  Summerfield, Journal of bacteriology 2007
  • “...1.9 3.2 1.9 4.1 5.0 1.7 OPP pathway sll0329 slr1843 slr1734 sll0807 slr1793 sll1070 gnd zwf opcA rpe tal tktA 3.7 2.9 2.9 2.2 1.9 1.7 3.4 3.1 2.6 1.9 2.6 2.0...”
• Highly expressed and alien genes of the Synechocystis genome
  Mrázek, Nucleic acids research 2001
  • “...[0.92] 686 CO2 concentrating mechanism protein (ccmM) sll0807 1.10 229 Pentose 5-phosphate 3-epimerase (cfxE) sll0018 1.27 358 Fructose 1,6-bisphosphate...”

CPE1736 ribulose-phosphate 3-epimerase from Clostridium perfringens str. 13
49% identity, 96% coverage

• Use of an EZ-Tn5-based random mutagenesis system to identify a novel toxin regulatory locus in Clostridium perfringens strain 13
  Vidal, PloS one 2009
  • “...Tu S13Tn5-05 CPE1142, hypothetical protein S13Tn5-06 16S RNAr S13Tn5-07 CPE1892, 50S ribosomal protein L20 S13Tn5-09 CPE1736, ribulose phosphate 3-epimerase S13Tn5-10 CPE0027, hypothetical protein S13Tn5-11 CPE2524, methionyl-tRNA synthetase S13Tn5-12 CPE0643, hypothetical protein S13Tn5-13 CPE2348, phosphate butyryltransferase Disruption of the C. perfringens agr B gene using EZ-Tn 5...”

Q9ZTP5 Ribulose-phosphate 3-epimerase, chloroplastic from Oryza sativa subsp. japonica
LOC4331761 ribulose-phosphate 3-epimerase, chloroplastic from Oryza sativa Japonica Group
50% identity, 78% coverage

• SWATH-MS-based quantitative proteomics reveals a uniquely intricate defense response in Cnaphalocrocis medinalis-resistant rice
  Cheah, Scientific reports 2020
  • “...Qingliu compared with TN1 (Supplementary Table S4a ). Notably, the two dark reaction-affiliated proteins (O64422, Q9ZTP5) were differentially expressed only at this time point (Supplementary Table S4a ). Fructose-1,6-bisphosphatase (O64422) was upregulated in Qingliu compared with TN1, whereas ribulose-phosphate 3-epimerase (Q9ZTP5) was downregulated in Qingliu compared...”
• iTRAQ-Based Quantitative Proteome Revealed Metabolic Changes in Winter Turnip Rape (Brassica rapa L.) under Cold Stress.
  Xu, International journal of molecular sciences 2018
  • “...protein 3 - - 0.388785817 Carbon fixation in photosynthetic organisms Q8RWV0 Transketolase-1 - 1.696959938 0.611169392 Q9ZTP5 Ribulose-phosphate 3-epimerase - - 0.597820343 Photosynthesis Q96334 Oxygen-evolving enhancer protein 2 - - 0.449814881 P83504 Oxygen-evolving enhancer protein 1 - - 0.375329761 Q8W0Y8 Photosystem II reaction center PSB28 - -...”
• Selection of an Appropriate Protein Extraction Method to Study the Phosphoproteome of Maize Photosynthetic Tissue.
  Luís, PloS one 2016
  • “...protein M9, chloroplastic 4.98 24 822 104 P43188 Adenylate kinase, chloroplastic 4.95 24 851 106 Q9ZTP5 Ribulose-phosphate 3-epimerase, chloroplastic 5.73 24 934 107 P12302 Oxygen-evolving enhancer protein 2, chloroplastic 5.94 20 197 108 Q32904 Chlorophyll a-b binding protein 3, chloroplastic 8.84 29 588 109 Q6ER94 2-Cys...”
• cDNA-AFLP analysis of plant and pathogen genes expressed in grapevine infected with Plasmopara viticola
  Polesani, BMC genomics 2008
  • “...4.78E-34 232 TA AT TC57434 161 - Nucleotide sugar epimerase-like protein 8.83E-12 1630 TT CT Q9ZTP5 105 - Pentose-5-phosphate 3-epimerase 5.85E-10 * 1610 TT CA TC54570 167 - Sedoheptulose-bisphosphatase (Q940F8) 1.37E-27 1668 TT GT TC54602 412 - Fructose-bisphosphate aldolase (Q6RUF6) 1.47E-50 100 TC AG TC54851 224...”
• Transcriptomics and physiology reveal the mechanism of potassium indole-3-butyrate (IBAK) mediating rice resistance to salt stress
  Zhou, BMC plant biology 2023
  • “...phosphate pathwayin CKY and IBAKY, of which 10 were upregulated, and 4 were downregulated. Both LOC4331761 (ribulose-phosphate 3-epimerase, chloroplastic-like) and LOC4332364 (fructose-1,6-bisphosphatase, chloroplastic-like) were upregulated after using IBAK under salt stress (Fig. 7 b). Fig. 7 Heat map of gene expression in different pathways. a starch...”
  • “...and other biomolecules to maintain the normal function and growth of cells. In this study, LOC4331761 and LOC4332364 had higher expression levels in CKY and IBAKY. Upregulated LOC4331761 is ribulose-phosphate 3-epimerase, chloroplastic-like. Ribulose-phosphate 3-epimerase is responsible for catalyzing the reversible epimerization of D-ribulose 5-phosphate to D-xylulose...”

RPE_SOLTU / Q43843 Ribulose-phosphate 3-epimerase, chloroplastic; Pentose-5-phosphate 3-epimerase; PPE; R5P3E; RPE; EC 5.1.3.1 from Solanum tuberosum (Potato) (see 2 papers)
48% identity, 76% coverage

• function: Catalyzes the reversible epimerization of D-ribulose 5- phosphate to D-xylulose 5-phosphate.
  catalytic activity: D-ribulose 5-phosphate = D-xylulose 5-phosphate (RHEA:13677)
  cofactor: Co(2+) Fe(2+) Mn(2+) Zn(2+) (Binds 1 divalent metal cation per subunit. Active with Co(2+), Fe(2+), Mn(2+) and Zn(2+).)
  subunit: Homohexamer.

SYNW1115 ribulose-5-phosphate 3-epimerase from Synechococcus sp. WH 8102
47% identity, 83% coverage

• Genetic identification of a high-affinity Ni transporter and the transcriptional response to Ni deprivation in Synechococcus sp. strain WH8102
  Dupont, Applied and environmental microbiology 2012
  • “...fabF (synw0142), phosphoribulose kinase (prk, synw0785), cbbE (synw1115), hemA (synw1117), and glyC (synw1118). In contrast, only fabF and hemA were...”

1rpxA / Q43843 D-ribulose-5-phosphate 3-epimerase from solanum tuberosum chloroplasts (see paper)
48% identity, 92% coverage

• Ligand: sulfate ion (1rpxA)

SMb20195 putative pentose-5-phosphate-3-epimerase protein from Sinorhizobium meliloti 1021
57% identity, 87% coverage

• Transcriptome analysis of the role of GlnD/GlnBK in nitrogen stress adaptation by Sinorhizobium meliloti Rm1021
  Yurgel, PloS one 2013
  • “...of the reductive pentose phosphate pathway or Calvin Benson Bassham cycle (CBB cycle): ribulose-phosphate 3-epimerase SMb20195, ppe ATPase, cbbSL small and large subunits of the RuBisCO complex, cbbA fructose-1,6-bisphosphate aldolase, cbbT transketolase, and cbbP phosphoribulokinase. This pathway is the most important mode of autotrophic CO 2...”
• Identification of Sinorhizobium meliloti early symbiotic genes by use of a positive functional screen
  Zhang, Applied and environmental microbiology 2006
  • “...synthesis SMb20195 (ppe)...................................................................................................................Pentose phosphate...”

BSU15790 ribulose-phosphate 3-epimerase from Bacillus subtilis subsp. subtilis str. 168
49% identity, 92% coverage

• Microbes vary strategically in their metalation of mononuclear enzymes
  Rohaun, Proceedings of the National Academy of Sciences of the United States of America 2024
  • “...SI Appendix , Tables S1 and S2 , respectively. The rpe genes from B. subtilis (BSU15790), L. lactis (L_RS10085), and S. cerevisiae (YJL121C) were identified by BLAST analysis using E. coli rpe sequence as query. The mutant E. coli rpe gene deletion (JW3349-2) was obtained from...”
• The Blueprint of a Minimal Cell: MiniBacillus
  Reuß, Microbiology and molecular biology reviews : MMBR 2016
  • “...suum Malic enzyme Malate dehydrogenase (decarboxylating) BSU13010 BSU15790 BSU17890 BSU23850 BSU23860 No No No No No 3.1.1.31 5.1.3.1 2.2.1.1 1.1.1.49 1.1.1.44...”

I1H9A1 ribulose-phosphate 3-epimerase from Brachypodium distachyon
49% identity, 77% coverage

• Identifying Endogenous Proteins of Perennial Ryegrass (Lolium perenne) with Ex Vivo Antioxidant Activity
  Pedersen, Proteomes 2025
  • “...Q-like (ycf33) 1 A0A0Q3H912 A Reduction of alkyl hydroperoxides [ 66 ] Ribulose-phosphate 3-epimerase (RPE) I1H9A1 N Calvin cycle enzyme [ 67 ] Sedoheptulose-1,7-biphosphatase (SBP) I1HTG2 N Calvin cycle enzyme [ 68 ] 1 Uncharacterized protein ycf33 shows high similarity to peroxiredoxin Q by BLAST analysis....”

RPE_SPIOL / Q43157 Ribulose-phosphate 3-epimerase, chloroplastic; Pentose-5-phosphate 3-epimerase; PPE; R5P3E; RPE; EC 5.1.3.1 from Spinacia oleracea (Spinach) (see 4 papers)
Q43157 ribulose-phosphate 3-epimerase (EC 5.1.3.1) from Spinacia oleracea (see 2 papers)
48% identity, 75% coverage

• function: Catalyzes the reversible epimerization of D-ribulose 5- phosphate to D-xylulose 5-phosphate.
  catalytic activity: D-ribulose 5-phosphate = D-xylulose 5-phosphate (RHEA:13677)
  cofactor: Co(2+) Fe(2+) Mn(2+) Zn(2+) (Binds 1 divalent metal cation per subunit. Active with Co(2+), Fe(2+), Mn(2+) and Zn(2+).)
  subunit: Homooctamer.
• Ribulose-1,5-bisphosphate regeneration in the Calvin-Benson-Bassham cycle: Focus on the last three enzymatic steps that allow the formation of Rubisco substrate
  Meloni, Frontiers in plant science 2023
  • “...RPE (UNIPROT: A9RCK8), Arabidopsis thaliana (At) RPE (UNIPROT: Q9SAU2), and Spinacia oleracea (So) RPE (UNIPROT: Q43157). For the sake of clarity, the alignment was initiated by variably omitting the N-terminal residues and residue numbering is based on the sequence of CrRPE. Conserved residues are highlighted in...”
• Redox Conformation-Specific Protein-Protein Interactions of the 2-Cysteine Peroxiredoxin in Arabidopsis.
  Liebthal, Antioxidants (Basel, Switzerland) 2020
  • “...helicase homolog RECG Q9ZVG0 LlFtsZ protein Q9LRC5 Transketolase O20250 Triosephosphate isomerase P48496 * Ribulose-phosphate 3-epimerase Q43157 D-3-phosphoglycerate dehydrogenase Q9FSS6 O-acetylserine (thiol)-lyase B P32260 28 kDa ribonucleoprotein P28644 * Elongation factor Tu Q43467 Elongation factor G-1 P34811 * 30S ribosomal protein S1 P29344 * 30S ribosomal protein...”
• iTRAQ-Based Quantitative Proteome Revealed Metabolic Changes in Winter Turnip Rape (Brassica rapa L.) under Cold Stress.
  Xu, International journal of molecular sciences 2018
  • “...metabolism Q00326 Myrosinase 0.518096445 - 0.495250588 Pentose phosphate pathway Q8RWV0 Transketolase-1, chloroplastic - - 0.611169392 Q43157 Ribulose-phosphate 3-epimerase - - 0.553787078 Photosynthesisantenna proteins P27525 Chlorophyll a-b binding protein CP24 - 0.574349177 1.601593552 P04778 Chlorophyll a-b binding protein 1 - - 1.818756629 Isoflavonoid biosynthesis Q940Z5 Phenolic glucosidemalonyl...”
• Protein profile of Beta vulgaris leaf apoplastic fluid and changes induced by Fe deficiency and Fe resupply
  Ceballos-Laita, Frontiers in plant science 2015
  • “...Glucose metabolic process 2 Ribose-5-phosphate isomerase Q8RU73 C nCS PPS, non-oxidative branch 1 Ribulose-phosphate 3-epimerase Q43157 C nCS Calvin cycle; PPS, oxidative branch 3 Transketolase O20250, Q14K68 C, nCS, nCS Calvin cycle; PPS, oxidative branch 1 Phosphoglycerate kinase P29409 C Calvin cycle, glycolytic process 1 Sedoheptulose-1,7-bisphosphatase...”
• Comparative proteomics analysis of proteins expressed in the I-1 and I-2 internodes of strawberry stolons
  Fang, Proteome science 2011
  • “...P28391 magnesium ion binding Ceratopetalum gummiferum 51.3/6.2 24.0/6.9 104 22 11/63 64 Ribulose-phosphate 3-epimerase, chloroplastic Q43157 ribulose-phosphate 3-epimerase activity Spinacia oleracea 30.6/8.2 27.2/7.9 58 31 6/51 82 Triosephosphate isomerase, chloroplastic Q9M4S8 triose-phosphate isomerase activity Fragaria ananassa 33.7/7.6 31.5/5.2 154 51 16/71 90 Oxygen-evolving enhancer protein 1,...”
• Proteomics gives insight into the regulatory function of chloroplast thioredoxins
  Balmer, Proceedings of the National Academy of Sciences of the United States of America 2003
  • “...column, starting with transketolase, are O20250, P48496, Q43157, Q9FSS6, P32260, P28644, Q43467, P34811, P29344, P82403, Q94KU2. *The first number represents...”

RPE_ARATH / Q9SAU2 Ribulose-5-phosphate-3-epimerase, chloroplastic; R5P3E; Pentose-5-phosphate 3-epimerase; Protein EMBRYO DEFECTIVE 2728; EC 5.1.3.1 from Arabidopsis thaliana (Mouse-ear cress) (see 2 papers)
NP_200949 D-ribulose-5-phosphate-3-epimerase from Arabidopsis thaliana
AT5G61410 RPE; catalytic/ ribulose-phosphate 3-epimerase from Arabidopsis thaliana
48% identity, 76% coverage

• function: Essential protein required during embryogenesis (PubMed:15266054). Catalyzes the reversible epimerization of D-ribulose 5-phosphate to D-xylulose 5-phosphate (By similarity). Essential for the early steps of nematode feeding sites (NFS, multinucleated root cells) formation induced by the root-knot nematodes Heterodera schachtii, Meloidogyne incognita, M.javanica and M.hapla (PubMed:9843485).
  catalytic activity: D-ribulose 5-phosphate = D-xylulose 5-phosphate (RHEA:13677)
  cofactor: Co(2+) Fe(2+) Mn(2+) Zn(2+) (Binds 1 divalent metal cation per subunit. Active with Co(2+), Fe(2+), Mn(2+) and Zn(2+).)
  subunit: Homooctamer.
  disruption phenotype: Defective embryo arrested at cotyledon stage (PubMed:15266054). Reduced germination capacity, leading to the development of some dwarf seedlings unable to grow on soil (PubMed:9843485). Reduced sensitivity to nematodes associated with reduced number of cysts and limited number of galls upon infection with Meloidogyne incognita and Heterodera schachtii (PubMed:9843485).
• Ribulose-1,5-bisphosphate regeneration in the Calvin-Benson-Bassham cycle: Focus on the last three enzymatic steps that allow the formation of Rubisco substrate
  Meloni, Frontiers in plant science 2023
  • “...(Syn) RPE (UNIPROT: P74061), Physcomitrium patens (Pp) RPE (UNIPROT: A9RCK8), Arabidopsis thaliana (At) RPE (UNIPROT: Q9SAU2), and Spinacia oleracea (So) RPE (UNIPROT: Q43157). For the sake of clarity, the alignment was initiated by variably omitting the N-terminal residues and residue numbering is based on the sequence...”
• The Influence of Symbiosis on the Proteome of the Exaiptasia Endosymbiont Breviolum minutum.
  Mashini, Microorganisms 2023
  • “...Q06135 1,3-beta-glucanosyltransferase (GAS2) 3.44 B0Y8K2 1,4-beta-D-glucan cellobiohydrolase B (CBHB) 1.78 A0A1Q9CUD0 Putative glucose-6-phosphate 1-epimerase 1.76 Q9SAU2 Ribulose-5-phosphate-3-epimerase (R5P3E) 1.16 B4R9R7 Guanosine monophosphate synthetase (GMP) 0.92 P11029 Acetyl-CoA carboxylase (ACC) 1.03 Q9Y7Y7 1,3-beta-glucanosyltransferase (GAS4) 1.10 Q54WR9 Type-3 glutamine synthetase 1.49 Q12613 Glutamine synthetase (GS) 1.50 Q00955 Acetyl-CoA...”
• Disclosing proteins in the leaves of cork oak plants associated with the immune response to Phytophthora cinnamomi inoculation in the roots: A long-term proteomics approach
  Coelho, PloS one 2021
  • “...anhydrase 1, chloroplastic BCA1 A0A1P8BG37 3.388 2.750 0.041 -0.2 Photosystem II stability/assembly factor, chloroplast A0A1P8BG37 Q9SAU2 1.863 1.309 0.026 -0.2 D-ribulose-5-phosphate-3-epimerase Q9SAU2/RPE a UniProt accession, protein name and protein initials arise from the annotation using the Arabidopsis proteome database as a reference. For more details on...”
  • “...Cytoplasm Carbohydrate metabolism 0.2 4.6 Q42525 Hexokinase-1 (HXK1) Cytoplasm Nucleous Glycolysis; Stress signalling -0.3 4.6 Q9SAU2 D-ribulose-5-phosphate-3-epimerase (Q9SAU2/RPE) Chloroplast Photosynthesis -0.2 Cellular metabolic compound salvage (3) 3 P10795 Ribulose bisphosphate carboxylase small chain 1A (RBS1A/RBCS1A) Chloroplast Photorespiration; Photosynthesis -3.1 3 P25697 Phosphoribulokinase (KPPR/PRK) Chloroplast Photosynthesis; Plant...”
• Iron-dependent modifications of the flower transcriptome, proteome, metabolome, and hormonal content in an Arabidopsis ferritin mutant
  Sudre, Journal of experimental botany 2013
  • “...290/5/5 18 36.0/5.1 35.8/5.1 21 Q9SAJ4 At1g79550 3.8 Phosphoglycerate kinase 908/43/17 54 42.2/5.5 39.2/5.8 22 Q9SAU2 At5g61410 4.7 d -Ribulose-5-P-3-epimerase 377/16/8 29 30.1/8.2 22.1/6.9 23 Q9M9K1 At3g08590 3.9 Phosphoglyceromutase 2 734/16/15 41 60.9/5.5 67.2/6.1 Mn 24 Q7DLW9 3.1 -Fructosidase 669/14/12 18 73.8/5.4 51.7/5.3 25 Q1WIQ6 At2g24270...”
• A genome-wide expression profile of salt-responsive genes in the apple rootstock Malus zumi
  Li, International journal of molecular sciences 2013
  • “...5 1 I glucose-1-phosphate adenylyltransferase NP_197423 81% 2.34 10 7 1 I ribulose-phosphate 3-epimerase, RPE NP_200949. 83% 5.20 10 4 a S means suppression, I means induction; b p -value indicates probability of a gene showing significantly differentially expression between salt-treated samples and untreated samples at...”
• Homoeolog expression divergence contributes to time of day changes in transcriptomic and glucosinolate responses to prolonged water limitation in Brassica napus
  Ricono, The Plant journal : for cell and molecular biology 2025
  • “...altered expression within a single accession (St), where a BnC copy of the ortholog DRIBULOSE5PHOSPHATE3EPIMERASE (At5g61410), was enriched in M3 while the BnA copy was enriched in M1. This was not the case for other overlapping orthologs such as TRANSKETOLASE1 (At3g60750) that have the same responsive...”
• Dynamics of mRNA fate during light stress and recovery: from transcription to stability and translation
  Smith, The Plant journal : for cell and molecular biology 2024
  • “..., AT5G42270 , AT3G63140 , AT3G11630 , AT4G24770 , AT1G65960 , AT3G54050 , AT4G01150 , AT5G61410 , AT1G11860 , AT4G32260 , AT5G60600 , AT5G42980 , AT3G55800 , AT3G46780 , AT3G16140 , AT4G20360 , AT3G14420 , AT1G56070 , AT5G66190 , AT3G02470 , AT1G30380 , AT4G03280 , AT2G30950...”
• Engineering plant immune circuit: walking to the bright future with a novel toolbox
  Vuong, Plant biotechnology journal 2023
  • “...2009 ) 74 PME3 AT3G14310 TDNA insertion H.schachtii Hewezi etal .( 2008 ) 75 RPE AT5G61410 TDNA insertion M.incognita Favery etal .( 1998 ) Pests: Arthropods 76 AtWSCP AT1G72290 TDNA insertion Porcellio scaber , Armadillidium vulgare BoexFontvieille etal .( 2015 ) 77 AGO1 AT1G48410 EMS M.persicae...”
• Reduction in chloroplastic ribulose-5-phosphate-3-epimerase decreases photosynthetic capacity in Arabidopsis
  Li, Frontiers in plant science 2022
  • “...in the CBC and OPPP ( Favery etal., 1998 ). In the Arabidopsis genome, only At5g61410 was designated as RPE and located in plastids. The Arabidopsis chloroplast RPE deletion mutant rpe can be germinated only when exogenous carbohydrates are added and are dwarf-like with light-green leaves...”
  • “...(ATCG00480, PHY0312), PetC (AT4G03280, PHY2293S), NDHH (ATCG01110, PHY2018A), PGRL1 (AT4G22890, PHY0234A), RbcL (ATCG00490, PHY0346), RPE (AT5G61410, PHY0616), FBA2 (AT4G38970, PHY0406S), PGK1 (AT3G12780, PHY0405S), PRK (AT1G32060, PHY0100A), RCA (AT2G39730, PHY0400S), RPI (AT3G04790, PHY0402S), TPI (AT2G21170, PHY0409S), TKL1 (AT3G60750, PHY0407S), GAPA1 (AT3G26650, PHY0408S), SBPase (AT3G55800, PHY0410S) were obtained...”
• Integrative Modeling of Gene Expression and Metabolic Networks of Arabidopsis Embryos for Identification of Seed Oil Causal Genes
  Cloutier, Frontiers in plant science 2021
  • “...(ACC, AT1G36160) ( Baud et al., 2003 ) and the other for ribulose-5-phosphate epimerase (EPI, AT5G61410) ( Favery et al., 1998 ). Cytosolic ACCase is responsible for the malonyl-CoA pool necessary for the production of very long chain fatty acids found in TAG and in cuticular...”
• Genome-Wide Association Mapping Unravels the Genetic Control of Seed Vigor under Low-Temperature Conditions in Rapeseed (Brassica napus L.)
  Luo, Plants (Basel, Switzerland) 2021
  • “...carboxyl-terminal hydrolase protein gene, and protease gene were detected in our study. The D-ribulose-5-phosphate-3-epimerase gene AT5G61410 and 3-phosphoglycerate kinase gene AT5G61450 , both located on the flanking region of the lead SNP BnvaA0320140457 associated with PC3 traits, are well known to regulate the energy supply involved...”
  • “...AT5G58330 Malate dehydrogenese PC2 28.27 BnaC02g10830D AT5G58290 26S protease regulatory subunit PC3 BnvaA0320140457 81.91 BnaA03g40170D AT5G61410 D-ribulose-5-phosphate-3-epimerase PC3 42.95 BnaA03g40210D AT5G61450 3-Phosphoglycerate kinase PC3 4.76 BnaA03g40290D AT5G61520 Sugar transporter PC3 45.08 BnaA03g40380D AT5G61600 Ethylene-responsive transcription factor ERF104 PC3 136.63 BnaA03g40560D AT3G49700 1-aminocyclopropane-1-carboxylate synthase PC3 BnvaA0903085508 4.61...”
• Integration of QTL Mapping and Gene Fishing Techniques to Dissect the Multi-Main Stem Trait in Rapeseed (Brassica napus L.)
  Zhao, Frontiers in plant science 2019
  • “...GGT2 BnaA08g16660D AT5G10720 HK5 BnaA08g14480D AT5G48820 ICK6 cqMMS.A10-1 BnaA10g02750D AT1G04610 YUC3 BnaA10g12480D AT5G59480 HAD BnaA10g23990D AT5G61410 RPE BnaA10g29350D AT5G57950 HLR cqMMS.C1 BnaC01g21630D AT3G51030 TRX1 BnaC01g21860D AT4G16280 FCA BnaC01g22100D AT4G16110 RR2 BnaC01g22110D AT1G27320 HK3 BnaC01g24570D AT3G46510 PUB13 BnaC01g26510D AT3G50070 CYCD3.3 BnaC01g26840D AT1G54990 AXR4 BnaC01g27460D AT5G13010 EMB3011 BnaC01g32740D...”
• The plastidial pentose phosphate pathway is essential for postglobular embryo development in Arabidopsis
  Andriotis, Proceedings of the National Academy of Sciences of the United States of America 2019
  • “...+334 At3g04790 RPI3 d -Ribose-5-phosphate isomerase 8 rpi3-1 emb3119-1 Nssen +631 rpi3-2 emb3119-2 Col +4 At5g61410 RPE3 d -Ribose-5-phosphate epimerase 9 rpe3-2 emb2728-2 Col +146 rpe3-3 SAIL_240_G08 Col +147 # At3g60750 TKL1 Transketolase 10 tkl1-1 WiscDsLox453_456I14 Col +2750 tkl1-2 SAIL_58_D02 Col +509 At3g55010 PUR5 AIR synthase...”
• More

I3DTP3 ribulose-phosphate 3-epimerase (EC 5.1.3.1); L-ribulose-5-phosphate 3-epimerase (EC 5.1.3.22) from Bacillus methanolicus (see paper)
47% identity, 92% coverage

Cj0451 ribulose-phosphate 3-epimerase from Campylobacter jejuni subsp. jejuni NCTC 11168
46% identity, 96% coverage

• In vivo and in silico determination of essential genes of Campylobacter jejuni
  Metris, BMC genomics 2011
  • “...cj1607, cj1610, cj1652c FBA & transposon mutagenesis of Stahl and Stintzi cj0132, cj0147c, cj0308c, cj0356c, cj0451, cj0503c, cj0722c, cj0845c, cj0861c, cj0925, cj1201, cj1239, cj1290c, cj1291c, cj1531, cj1535c FBA & the 2 transposon mutagenesis methods cj0231c, cj0545, cj0707, cj0810, cj0855, cj0895c, cj1644, cj1676 The "metabolic genes" refer...”

A8IKW6 Ribulose-phosphate 3-epimerase from Chlamydomonas reinhardtii
46% identity, 82% coverage

• Ribulose-1,5-bisphosphate regeneration in the Calvin-Benson-Bassham cycle: Focus on the last three enzymatic steps that allow the formation of Rubisco substrate
  Meloni, Frontiers in plant science 2023
  • “...performed with ESPript ( http://espript.ibcp.fr ) using Chlamydomonas reinhardtii (Cr) RPE (PDB ID: 7B1W; UNIPROT: A8IKW6), Synechocystis PCC 6803 (Syn) RPE (UNIPROT: P74061), Physcomitrium patens (Pp) RPE (UNIPROT: A9RCK8), Arabidopsis thaliana (At) RPE (UNIPROT: Q9SAU2), and Spinacia oleracea (So) RPE (UNIPROT: Q43157). For the sake of...”
• Quantitative proteomics of a B₁₂ -dependent alga grown in coculture with bacteria reveals metabolic tradeoffs required for mutualism
  Helliwell, The New phytologist 2018
  • “...1.2.1.12) (EC 4.3.2.1) 1.47 A8IPI7 HPR1 Hydroxypyruvate reductase 1.51 A8IRK4 SEBP1 Sedoheptulose1,7bisphosphatase (EC 3.1.3.37) 1.53 A8IKW6 RPE1 Ribulosephosphate 3epimerase (EC 5.1.3.1) 1.57 A8I5A0 CPLD45 Predicted protein 1.58 A8IKQ0 FBP1 Fructose1,6bisphosphatase (EC 3.1.3.11) 1.65 Q42690 FBA1 Fructosebisphosphate aldolase 1, chloroplastic (EC 4.1.2.13) 1.71 A8IRQ1 RPI1 Ribose5phosphate isomerase...”

A9RCK8 Ribulose-phosphate 3-epimerase from Physcomitrium patens
47% identity, 87% coverage

• Ribulose-1,5-bisphosphate regeneration in the Calvin-Benson-Bassham cycle: Focus on the last three enzymatic steps that allow the formation of Rubisco substrate
  Meloni, Frontiers in plant science 2023
  • “...7B1W; UNIPROT: A8IKW6), Synechocystis PCC 6803 (Syn) RPE (UNIPROT: P74061), Physcomitrium patens (Pp) RPE (UNIPROT: A9RCK8), Arabidopsis thaliana (At) RPE (UNIPROT: Q9SAU2), and Spinacia oleracea (So) RPE (UNIPROT: Q43157). For the sake of clarity, the alignment was initiated by variably omitting the N-terminal residues and residue...”

DR1401 ribulose-phosphate 3-epimerase from Deinococcus radiodurans R1
47% identity, 72% coverage

• Oxidative stress resistance in Deinococcus radiodurans
  Slade, Microbiology and molecular biology reviews : MMBR 2011
  • “...acid dehydratase (Edd) DR1596 DR1595 DR2256 DR1337 DR1401 DR0845 DR1205 DR1132 TCA cycle Citrate synthase (GltA) Aconitase (AcnA) Isocitrate dehydrogenase (Icd)...”

7b1wF / A8IKW6 Crystal structure of plastidial ribulose epimerase rpe1 from the model alga chlamydomonas reinhardtii (see paper)
47% identity, 92% coverage

• Ligand: zinc ion (7b1wF)

Dde_2632 Ribulose-phosphate 3-epimerase from Desulfovibrio desulfuricans G20
46% identity, 96% coverage

• Integration of text mining and biological network analysis: Identification of essential genes in sulfate-reducing bacteria
  Saxena, Frontiers in microbiology 2023
  • “..., glyA , hisC , ispH , dde_0789, dde_0140, dde_1449, dde_1537, dde_1569, dde_2112, dde_2120, dde_2453, dde_2632, dde_2631 (shown in Figure 4C ). In this metabolism, most of the genes were observed in the purine and pyrimidine metabolism, biosynthesis of amino acid, biosynthesis of secondary metabolites, and...”

Q97IC0 Ribulose-phosphate 3-epimerase from Clostridium acetobutylicum (strain ATCC 824 / DSM 792 / JCM 1419 / IAM 19013 / LMG 5710 / NBRC 13948 / NRRL B-527 / VKM B-1787 / 2291 / W)
CAC1730 Pentose-5-phosphate-3-epimerase, YLOR B.subtilis ortholog from Clostridium acetobutylicum ATCC 824
44% identity, 96% coverage

• Reassessment of the role of CaCO₃ in n-butanol production from pretreated lignocellulosic biomass by Clostridium acetobutylicum
  Su, Scientific reports 2020
  • “...Hypothetical protein Q97MY3 4.67 50.00 Protein containing cell adhesion domain Q97EM4 4.77 84.89 Ribulose-phosphate 3-epimerase Q97IC0 5.76 a a Not detected after CaCO 3 addition. Based on proteomics analysis results, Fig. 4 summarized the effect of CaCO 3 addition on the metabolic pathway of C. acetobutylicum...”
• Transcriptional analysis of micronutrient zinc-associated response for enhanced carbohydrate utilization and earlier solventogenesis in Clostridium acetobutylicum
  Wu, Scientific reports 2015
  • “...( galM ), respectively, were elevated by 3.19-, 2.44- and 2.77-fold. Additionally, three other genes CAC1730, CAC2610 and CAC2612 encoding a ribulose-phosphate 3-epimerase ( rpe ), a xylose isomerase ( xylA ) and a xylulose kinase ( xylB ), were 1.52-, 2.29- and 2.31-fold upregulated. Despite...”
• Combined overexpression of genes involved in pentose phosphate pathway enables enhanced D-xylose utilization by Clostridium acetobutylicum
  Jin, Journal of biotechnology 2014 (PubMed)
  • “...utilization. Among all the candidate genes, the CAC1347, CAC1348, CAC1730 and CAC2880 were validated to encode genes tal, tkl, rpe and rpi, four key genes...”
  • “...genes in C . acetobutylicum . The CAC1347 and CAC1730 genes were experimentally confirmed to encode TAL and RPE enzymes. Combined overexpression of these four...”
• Genome-scale model for Clostridium acetobutylicum: Part I. Metabolic network resolution and analysis
  Senger, Biotechnology and bioengineering 2008
  • “...List 7: (from DAHP) CAC0894, CAC0713/CAC0899, CAC0897, CAC0898, CAC0895, CAC0896. List 8: CAC2680, CAC0944, CAC1348, CAC1730, CAC0726, CAC0819/CAC3221. List 9: CAC0936, CAC0943, CAC0942, CAC0940, CAC0939, CAC0938, CAC1369, CAC2727, CAC0937. List 10: CAC3162/CAC3163, CAC3161, CAC3159, CAC3160, CAC3157/CAC3158. List 11: CAC1234, CAC0893, CAC1369/CAC3031/CAC1001/CAC1819/CAC2832. List 12: CAC1234, CAC0217, CAC1369/CAC3031/CAC1001/CAC1819/CAC2832....”

L_RS10085 ribulose-phosphate 3-epimerase from Lactococcus lactis subsp. lactis Il1403
51% identity, 89% coverage

• Microbes vary strategically in their metalation of mononuclear enzymes
  Rohaun, Proceedings of the National Academy of Sciences of the United States of America 2024
  • “...Tables S1 and S2 , respectively. The rpe genes from B. subtilis (BSU15790), L. lactis (L_RS10085), and S. cerevisiae (YJL121C) were identified by BLAST analysis using E. coli rpe sequence as query. The mutant E. coli rpe gene deletion (JW3349-2) was obtained from the Keio collection...”

gll3548 ribulose-phosphate 3-epimerase from Gloeobacter violaceus PCC 7421
45% identity, 93% coverage

• Computational prediction of Pho regulons in cyanobacteria
  Su, BMC genomics 2007
  • “...Slr1181 sll1555 PCC7120 alr0528-0537 glr3061 all3132 all0542 alr1171 alr5272 alr1170 alr5224 all0638 all0637 PCC7421 gvip499 gll3548 gll0367 PCC7942 Synpcc7942_0424 Synpcc7942_2048 Synpcc7942_0169 Synpcc7942_1356-1357 Synpcc7942_2356 Synpcc7942_1355 -2049 CC9605 Syncc9605_1756 Syncc9605_1831 Syncc9605_0307 Syncc9605_0442-0444 Syncc9605_2579 MED4 PMM1438-1439 PMM0709 PMM0572 MIT9312 PMT9312_1542-1550 PMT9312_0721 PMT9312_0577 MIT9313 PMT1046 NATL2A PMN2A_0435 WH8102 SYNW0817 SYNW1999-22001...”

E1Z7S4 Ribulose-phosphate 3-epimerase from Chlorella variabilis
CHLNCDRAFT_56033 ribulose-phosphate 3-epimerase mature form from Chlorella variabilis
47% identity, 91% coverage

• Real-time iTRAQ-based proteome profiling revealed the central metabolism involved in nitrogen starvation induced lipid accumulation in microalgae
  Rai, Scientific reports 2017
  • “...0.7230.09 32 E1Z7C4 Putative uncharacterized protein (Ribose-5-phosphate isomerase) (b),(d) CHLNCDRAFT_34303 1 1.1640.11 2.1640.77 2.5840.15 33 E1Z7S4 Ribulose-phosphate 3-epimerase CHLNCDRAFT_56033 1 0.8000.02 1.0150.16 1.6420.33 34 E1ZKS0 Enolase CHLNCDRAFT_136652 2 1.6880.12 2.2440.81 1.7231.50 35 E1Z1Z7 Putative uncharacterized protein CHLNCDRAFT_29144 1.0220.44 1.4330.03 3.0320.67 36 E1ZKB3 Triosephosphate isomerase (b),(c),(d) CHLNCDRAFT_36334...”
  • “...101 4 Carbohydrate metabolism 20 E1Z5R5, E1ZCC9, E1ZT20, A0A087SEW0, A0A087SHU5, A0A087SU66, E1Z2U6, E1Z5A0, E1Z6L2, E1Z7C4, E1Z7S4, E1ZF27, E1ZKS0, E1ZN90, E1ZQQ5, E1ZRS4, F2YGL1, E1Z1Z7, E1ZKB3, E1ZRS1 Several of the enzymes associated with glycolysis, reductive PPP and TCA cycle are up-regulated to fulfil the energy needs of the...”
• Real-time iTRAQ-based proteome profiling revealed the central metabolism involved in nitrogen starvation induced lipid accumulation in microalgae
  Rai, Scientific reports 2017
  • “...Putative uncharacterized protein (Ribose-5-phosphate isomerase) (b),(d) CHLNCDRAFT_34303 1 1.1640.11 2.1640.77 2.5840.15 33 E1Z7S4 Ribulose-phosphate 3-epimerase CHLNCDRAFT_56033 1 0.8000.02 1.0150.16 1.6420.33 34 E1ZKS0 Enolase CHLNCDRAFT_136652 2 1.6880.12 2.2440.81 1.7231.50 35 E1Z1Z7 Putative uncharacterized protein CHLNCDRAFT_29144 1.0220.44 1.4330.03 3.0320.67 36 E1ZKB3 Triosephosphate isomerase (b),(c),(d) CHLNCDRAFT_36334 2 1.2230.69 2.1841.52...”

A5VKQ0 Ribulose-phosphate 3-epimerase from Limosilactobacillus reuteri (strain DSM 20016)
47% identity, 94% coverage

• Redox Balance in Lactobacillus reuteri DSM20016: Roles of Iron-Dependent Alcohol Dehydrogenases in Glucose/ Glycerol Metabolism
  Chen, PloS one 2016
  • “...56374 - - - 3 A5VMD1 6-Phosphogluconate dehydrogenase lreu_1766 478 53399 - - - 4 A5VKQ0 Ribulose-5-phosphate-3-epimerase lreu_1167 217 23422 - - - 5 A5VM51 Phosphoketolase lreu_1686 803 91404 - - - 6 A5VIJ3 Phosphate acetyltransferase lreu_0398 324 34700 -1.22 -0.99 -1.18 7 A5VIB7 Aldehyde dehydrogenase...”

Csac_2074 Ribulose-phosphate 3-epimerase from Caldicellulosiruptor saccharolyticus DSM 8903
47% identity, 94% coverage

• Hydrogenomics of the extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus
  van, Applied and environmental microbiology 2008
  • “...of the PPP uses ribulose phosphate 3-epimerase (Csac_2074), ribose-5-phosphate isomerase (Csac_ 1200), the N-terminal (Csac_1351) and C-terminal (Csac_ 1352)...”

GOX1352 Ribulose-phosphate 3-epimerase from Gluconobacter oxydans 621H
46% identity, 96% coverage

• Global mRNA decay and 23S rRNA fragmentation in Gluconobacter oxydans 621H
  Kranz, BMC genomics 2018
  • “...(GOX1707); ppc , phosphoenolpyruvate carboxylase (GOX0102); pyk , pyruvate kinase (GOX2250); rpe , ribulosephosphate 3-epimerase (GOX1352); rpi , ribose 5-phosphate isomerase (GOX1708); sldA , polyol dehydrogenase subunit SldA (GOX0854); sldB , polyol dehydrogenase subunit SldB (GOX0855); tal / pgi , bifunctional transaldolase (GOX1704); tkt , transketolase...”

TTHA0106 ribulose-phosphate 3-epimerase from Thermus thermophilus HB8
Q5SM37 Ribulose-phosphate 3-epimerase from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
47% identity, 98% coverage

• A Transfer Learning-Based Approach for Lysine Propionylation Prediction
  Li, Frontiers in physiology 2021
  • “...Q5SIC8 Fructose 1,6-bisphosphatase II (glpX) Q5SM35 Transketolase (TTHA0108) Q5SHF7 Fructose-1,6-bisphosphate aldolase (TTHA1773) Q5SM37 Ribulose-phosphate 3-epimerase (TTHA0106) Q5SLJ4 Glucokinase (TTHA0299) Q5SJM8 Hypothetical protein (TTHA0980) P56194 Histidyl-tRNA synthetase (hisS) 3.2378 Q5SLY2 Leucyl-tRNA synthetase (leuS) Q5SJX7 Seryl-tRNA synthetase (TTHA0875) P56881 Threonyl-tRNA synthetase (thrS) P56206 Glycyl-tRNA synthetase (TTHA0543) P56690 Isoleucyl-tRNA...”
• Lysine propionylation is a prevalent post-translational modification in Thermus thermophilus
  Okanishi, Molecular & cellular proteomics : MCP 2014
  • “...TTHA1928 Carbohydrate transport and metabolism TTHA0002 TTHA0003 TTHA0106 TTHA0108 TTHA0116 TTHA0299 TTHA0481 TTHA0650 TTHA0905 ORF K67 K31 K148, K240, K241,...”
• A Transfer Learning-Based Approach for Lysine Propionylation Prediction
  Li, Frontiers in physiology 2021
  • “...A (TTHA1299) 3.8325 Q5SIC8 Fructose 1,6-bisphosphatase II (glpX) Q5SM35 Transketolase (TTHA0108) Q5SHF7 Fructose-1,6-bisphosphate aldolase (TTHA1773) Q5SM37 Ribulose-phosphate 3-epimerase (TTHA0106) Q5SLJ4 Glucokinase (TTHA0299) Q5SJM8 Hypothetical protein (TTHA0980) P56194 Histidyl-tRNA synthetase (hisS) 3.2378 Q5SLY2 Leucyl-tRNA synthetase (leuS) Q5SJX7 Seryl-tRNA synthetase (TTHA0875) P56881 Threonyl-tRNA synthetase (thrS) P56206 Glycyl-tRNA synthetase...”

LGG_01665 ribulose-phosphate 3-epimerase from Lactobacillus rhamnosus GG
50% identity, 94% coverage

• Proteomics and transcriptomics characterization of bile stress response in probiotic Lactobacillus rhamnosus GG
  Koskenniemi, Molecular & cellular proteomics : MCP 2011
  • “...LGG_01323 LGG_01367 LGG_01421 LGG_01433 LGG_01604 LGG_01665 LGG_01786 LGG_01823 LGG_01823 LGG_01823 LGG_01864 LGG_01864 LGG_02234 LGG_02045 LGG_02296 LGG_02296...”
  • “...(Pgk, LGG_00934), and ribulose-phosphate 3-epimerase (Rpe, LGG_01665) were increased, and L-lactate dehydrogenase (Ldh, LGG_02523), enolase (Eno, LGG_00936),...”

EIO_2692, KVC_2798, KVH_13715, KVU_2194 ribulose-phosphate 3-epimerase from Ketogulonicigenium vulgare
50% identity, 93% coverage

• Reconstruction and analysis of carbon metabolic pathway of Ketogulonicigenium vulgare SPU B805 by genome and transcriptome
  Wang, Scientific reports 2018
  • “...RpiA PPP 5.3.1.6 KVC_0880 KvSKV_03890 KVH_03920 KVU_0356 EIO_0823 Rpe PPP 5.1.3.1 KVC_2798 KvSKV_03940 KVH_13715 KVU_2194 EIO_2692 TktA PPP 2.2.1.1 KVC_2247 KvSKV_10835 KVH_10920 KVU_1671 EIO_2112 Tal PPP 2.2.1.2 KVC_1789 KvSKV_RS08555 KVH_08530 KVU_1236 EIO_1771 AceE TCA 1.2.4.1 KVC_1207, 1208 KvSKV_05525 KVH_05560 KVU_0668, 0669 EIO_1168, 1169 GltA TCA 2.3.3.1...”
  • “...KvSKV_03940 KVH_03970 KVU_0365 EIO_0834 RpiA PPP 5.3.1.6 KVC_0880 KvSKV_03890 KVH_03920 KVU_0356 EIO_0823 Rpe PPP 5.1.3.1 KVC_2798 KvSKV_03940 KVH_13715 KVU_2194 EIO_2692 TktA PPP 2.2.1.1 KVC_2247 KvSKV_10835 KVH_10920 KVU_1671 EIO_2112 Tal PPP 2.2.1.2 KVC_1789 KvSKV_RS08555 KVH_08530 KVU_1236 EIO_1771 AceE TCA 1.2.4.1 KVC_1207, 1208 KvSKV_05525 KVH_05560 KVU_0668, 0669 EIO_1168,...”
  • “...KVU_0365 EIO_0834 RpiA PPP 5.3.1.6 KVC_0880 KvSKV_03890 KVH_03920 KVU_0356 EIO_0823 Rpe PPP 5.1.3.1 KVC_2798 KvSKV_03940 KVH_13715 KVU_2194 EIO_2692 TktA PPP 2.2.1.1 KVC_2247 KvSKV_10835 KVH_10920 KVU_1671 EIO_2112 Tal PPP 2.2.1.2 KVC_1789 KvSKV_RS08555 KVH_08530 KVU_1236 EIO_1771 AceE TCA 1.2.4.1 KVC_1207, 1208 KvSKV_05525 KVH_05560 KVU_0668, 0669 EIO_1168, 1169 GltA...”
  • “...EIO_0834 RpiA PPP 5.3.1.6 KVC_0880 KvSKV_03890 KVH_03920 KVU_0356 EIO_0823 Rpe PPP 5.1.3.1 KVC_2798 KvSKV_03940 KVH_13715 KVU_2194 EIO_2692 TktA PPP 2.2.1.1 KVC_2247 KvSKV_10835 KVH_10920 KVU_1671 EIO_2112 Tal PPP 2.2.1.2 KVC_1789 KvSKV_RS08555 KVH_08530 KVU_1236 EIO_1771 AceE TCA 1.2.4.1 KVC_1207, 1208 KvSKV_05525 KVH_05560 KVU_0668, 0669 EIO_1168, 1169 GltA TCA...”

PG1595 ribulose-phosphate 3-epimerase from Porphyromonas gingivalis W83
46% identity, 97% coverage

• Microarray analysis of the transcriptional responses of Porphyromonas gingivalis to polyphosphate
  Moon, BMC microbiology 2014
  • “...metabolism : Pentose phosphate pathway PG1747 Ribose 5-phosphate isomerase B, putative 2.45 PG0230 Transaldolase 2.05 PG1595 Ribulose-phosphate 3-epimerase 2.22 Energy metabolism: Sugars PG1633 Galactokinase 1.89 Energy metabolism : TCA cycle PG1614 Succinate dehydrogenase 2.25 PG1615 Succinate dehydrogenase 1.60 Energy metabolism : Other PG1522 Mandelate racemase/muconate lactonizing...”
• Role of the Porphyromonas gingivalis extracytoplasmic function sigma factor, SigH
  Yanamandra, Molecular oral microbiology 2012
  • “...Results Bioinformatic characterization of P. gingivalis SigH The sigH gene of P. gingivalis (designated as PG1595 on the Oralgen database [ oralgen.lanl.gov ] and PG1827 on the JCVI database [ jcvi.org ] codes for a 213 aa protein. Based on sequence similarity determined using the BLAST...”
• Metal uptake in host-pathogen interactions: role of iron in Porphyromonas gingivalis interactions with host organisms
  Lewis, Periodontology 2000 2010
  • “...PG0879.1 (sigma 24 factor), PG0984 (RpoN, sigma 54 factor), PG1158, PG1449 (SigG, ECF subfamily), and PG1595 (SigH, ECF subfamily) (results from the Oralgen website, www.oralgen.lanl.gov ). While RpoD (sigma 70), known as the primary sigma factor, and RpoN (sigma 54) are required for transcription of a...”

AMETH_4130 ribulose-phosphate 3-epimerase from Amycolatopsis methanolica 239
50% identity, 88% coverage

• A systematic study of the whole genome sequence of Amycolatopsis methanolica strain 239^T provides an insight into its physiological and taxonomic properties which correlate with its position in the genus
  Tang, Synthetic and systems biotechnology 2016
  • “..., AMED_2263 AORI_5659 , AORI_5660 AJAP_11180 , AJAP_11185 AMETH_4518 AMETH_4092 AMED_2809 AORI_2796 AJAP_24810 rpe AMETH_4520 AMETH_4130 AMED_2771 AORI_2761 AJAP_25030 rpi AMETH_4529 AMETH_1699 AMED_6811 AORI_1928 AJAP_29895 AORI_6417 AJAP_06835 AMETH_2243 , AMETH_6524 AORI_7455 AJAP_38990 gnd AMETH_0006 AMED_0003 AORI_0003 AJAP_00020 talA AMETH_4093 AMED_2808 AORI_2795 AJAP_24815 pgi AMETH_4094 AMED_2807 AORI_2794...”

RiCNE_00410 ribulose-phosphate 3-epimerase from Rickettsia endosymbiont of Culicoides newsteadi
43% identity, 95% coverage

• Torix group Rickettsia are widespread in Culicoides biting midges (Diptera: Ceratopogonidae), reach high frequency and carry unique genomic features
  Pilgrim, Environmental microbiology 2017
  • “...pathway (PPP), including transketolase, transaldolase, ribulosephosphate 3epimerase and a ribose 5phosphate isomerase B (RiCNE_05410, RiCNE_04320, RiCNE_00410 and RiCNE_09330, respectively) (Fig. 3 ). The oxidative phase is completely absent, as for other Rickettsia . Only one gene of the PPP (coding for the ribose 5phosphate isomerase B)...”
  • “...amino acid identity with Ehrlichia homologs, RiCNE_04320 shared 59% identity with Sulfitobacter sp. EhC04 and RiCNE_00410 shared 58% identity with an uncultured proteobacterium). Additional phylogenetic analyses of the individual PPP protein sequences clearly cluster the RiCNE sequences within the alphaproteobacteria and the Rickettsiales, and partial PPPs...”

TNMX_12225 ribulose-phosphate 3-epimerase from Thermus sp. NMX2.A1
46% identity, 95% coverage

• Whole Genome Comparison of Thermus sp. NMX2.A1 Reveals Principle Carbon Metabolism Differences with Closest Relation Thermus scotoductus SA-01
  Müller, G3 (Bethesda, Md.) 2016
  • “...Figure S1 ). DELTA-BLAST using the smaller of the two epimerases from Thermus sp. NMX2.A1 (TNMX_12225) produced at least 500 positive results for ribulose-phosphate 3-epimerase from a wide variety of bacteria. When the larger epimerase (TNMX_12230) was subjected to the same DELTA BLAST, it showed that...”

BT_3946 ribulose-phosphate 3-epimerase from Bacteroides thetaiotaomicron VPI-5482
44% identity, 96% coverage

• Endogenous superoxide is a key effector of the oxygen sensitivity of a model obligate anaerobe
  Lu, Proceedings of the National Academy of Sciences of the United States of America 2018
  • “...the conditions of these experiments.) The B. thetaiotaomicron rpe (BT_3946) and sod (BT_0655) genes were identified by BLAST analysis using E. coli rpe and sodB...”

GJQ69_09515 ribulose-phosphate 3-epimerase from Caproicibacterium lactatifermentans
47% identity, 94% coverage

• Revealing the Characteristics of Glucose- and Lactate-Based Chain Elongation for Caproate Production by Caproicibacterium lactatifermentans through Transcriptomic, Bioenergetic, and Regulatory Analyses
  Wang, mSystems 2022
  • “...81 TTTTTTAAGAATTAACAC 9.07 rnfCDGEAB GJQ69_04335 1,032 367 1.04 Electron transport complex 101 TTATTCAATCTTTAACAA 14.29 rpe GJQ69_09515 118 624 3.05 Ribulose-phosphate 3-epimerase 123 TTTTTAACCGCTTAATCA 9.55 hydA GJQ69_02965 1,136 1,893 1.55 [FeFe]-hydrogenase 117 TTGTTATAATAAAAACAA 9.09 GJQ69_09080 122 81 0.07 SDR family NAD(P)-dependent oxidoreductase 148 TTGTAAAACAAAAAACAA 9.35 10.1128/msystems.00534-22.7 FIGS4...”

spr1797 Pentose-5-phosphate-3-epimerase from Streptococcus pneumoniae R6
43% identity, 98% coverage

• Predicted functions and linkage specificities of the products of the Streptococcus pneumoniae capsular biosynthetic loci
  Aanensen, Journal of bacteriology 2007
  • “...phosphate 3-epimerase (Rpe) (2), and the rpe gene (spr1797) is present in the S. pneumoniae R6 genome (GenBank accession number AE007317). NDP-Ara-ol-1P is...”

AL01_09060 ribulose-phosphate 3-epimerase from Bombella intestini
47% identity, 94% coverage

• Whole-Genome Sequence Analysis of Bombella intestini LMG 28161T, a Novel Acetic Acid Bacterium Isolated from the Crop of a Red-Tailed Bumble Bee, Bombus lapidarius
  Li, PloS one 2016
  • “...(AL01_06120); 35, ribose-5-phosphate isomerase (AL01_06135); 36, glucose-6-phosphate dehydrogenase (AL01_02790); 37, 6-phosphogluconolactonase (AL01_06130); 38, ribulose-phosphate 3-epimerase (AL01_09060); 39, polyol:NADP oxidoreductase (AL01_07080); 40, phosphomannomutase (AL_0102400); 41, mannose-1-phosphate guanyltransferase (AL01_07360); 42, carbohydrate kinase (AL01_03675); 43, mannose06-phosphate isomerase (AL01_00140); 44, 2-dehydro-3-deoxyphosphogluconate aldolase (AL01_04330). All genes encoding the enzymes of the...”

Q89S24 Ribulose-phosphate 3-epimerase from Bradyrhizobium diazoefficiens (strain JCM 10833 / BCRC 13528 / IAM 13628 / NBRC 14792 / USDA 110)
blr2588 ribulose-phosphate 3-epimerase from Bradyrhizobium japonicum USDA 110
51% identity, 86% coverage

• Induction by Bradyrhizobium diazoefficiens of Different Pathways for Growth in D-mannitol or L-arabinose Leading to Pronounced Differences in CO₂ Fixation, O₂ Consumption, and Lateral-Flagellum Production
  Cogo, Frontiers in microbiology 2018
  • “...blr2586 Q9ZI33 cbbS Ribulose bisphosphate carboxylase small chain. In only Mtl In only Mtl blr2588 Q89S24 cbbE Ribulose-phosphate 3-epimerase. In only Mtl - blr2815 Q89RF7 Putative transketolase family protein. Pyruvate dehydrogenase E1 component. In only Mtl In only Mtl blr3224 Q89QA6 ABC transporter ATP-binding protein. Putative...”
• Pleiotropic Effects of PhaR Regulator in Bradyrhizobium diazoefficiens Microaerobic Metabolism
  Quelas, International journal of molecular sciences 2024
  • “...(EMP) pathway. Regarding the CBB cycle, we found that the entire cbb operon (blr2581 to blr2588) was expressed under the growth conditions of our assays (microoxia in the presence of mannitol), but was downregulated in the phaR mutant ( Table S3 ). In this line, the...”
• Induction by Bradyrhizobium diazoefficiens of Different Pathways for Growth in D-mannitol or L-arabinose Leading to Pronounced Differences in CO₂ Fixation, O₂ Consumption, and Lateral-Flagellum Production
  Cogo, Frontiers in microbiology 2018
  • “...Mtl blr2586 Q9ZI33 cbbS Ribulose bisphosphate carboxylase small chain. In only Mtl In only Mtl blr2588 Q89S24 cbbE Ribulose-phosphate 3-epimerase. In only Mtl - blr2815 Q89RF7 Putative transketolase family protein. Pyruvate dehydrogenase E1 component. In only Mtl In only Mtl blr3224 Q89QA6 ABC transporter ATP-binding protein....”
• Whole-genome transcriptional profiling of Bradyrhizobium japonicum during chemoautotrophic growth
  Franck, Journal of bacteriology 2008
  • “...blr2455 (aceA) blr2585 (cbbL) blr2588 bll6941 (hupL) bll7911 ACAAGTACAAGGTTCCGCGCAT CGACGAGCGCGCCATTCTAT ACCAACAGCGTCGCAGAAATCA TATTCTGCACGCCAAGGCTCAA...”
  • “...(blr2585) cbbS (blr2586) cbbX (blr2587) cbbE (blr2588) bll1137 bll4865 aceA (blr2455) ppc (blr2955) Putative D-fructose-1,6-bisphosphatase protein Putative...”

AORI_2761 ribulose-phosphate 3-epimerase from Amycolatopsis keratiniphila
47% identity, 96% coverage

• A systematic study of the whole genome sequence of Amycolatopsis methanolica strain 239^T provides an insight into its physiological and taxonomic properties which correlate with its position in the genus
  Tang, Synthetic and systems biotechnology 2016
  • “...AORI_5659 , AORI_5660 AJAP_11180 , AJAP_11185 AMETH_4518 AMETH_4092 AMED_2809 AORI_2796 AJAP_24810 rpe AMETH_4520 AMETH_4130 AMED_2771 AORI_2761 AJAP_25030 rpi AMETH_4529 AMETH_1699 AMED_6811 AORI_1928 AJAP_29895 AORI_6417 AJAP_06835 AMETH_2243 , AMETH_6524 AORI_7455 AJAP_38990 gnd AMETH_0006 AMED_0003 AORI_0003 AJAP_00020 talA AMETH_4093 AMED_2808 AORI_2795 AJAP_24815 pgi AMETH_4094 AMED_2807 AORI_2794 AJAP_24820 zwf...”

AJAP_25030 ribulose-phosphate 3-epimerase from Amycolatopsis japonica
47% identity, 96% coverage

• A systematic study of the whole genome sequence of Amycolatopsis methanolica strain 239^T provides an insight into its physiological and taxonomic properties which correlate with its position in the genus
  Tang, Synthetic and systems biotechnology 2016
  • “..., AORI_5660 AJAP_11180 , AJAP_11185 AMETH_4518 AMETH_4092 AMED_2809 AORI_2796 AJAP_24810 rpe AMETH_4520 AMETH_4130 AMED_2771 AORI_2761 AJAP_25030 rpi AMETH_4529 AMETH_1699 AMED_6811 AORI_1928 AJAP_29895 AORI_6417 AJAP_06835 AMETH_2243 , AMETH_6524 AORI_7455 AJAP_38990 gnd AMETH_0006 AMED_0003 AORI_0003 AJAP_00020 talA AMETH_4093 AMED_2808 AORI_2795 AJAP_24815 pgi AMETH_4094 AMED_2807 AORI_2794 AJAP_24820 zwf AMETH_4095...”

HPG27_RS07685 ribulose-phosphate 3-epimerase from Helicobacter pylori G27
45% identity, 94% coverage

• Acid-regulated gene expression of Helicobacter pylori: Insight into acid protection and gastric colonization
  Marcus, Helicobacter 2018
  • “...HP1102 0.95 0.07 0.38 0.77 0.06 0.07 0.81 0.03 0.02 6-phosphogluconolactonase ( pgl, devB ) HPG27_RS07685 HP1386 1.50 0.07 0.04 1.92 0.05 0.01 2.21 0.07 0.01 ribulose-phosphate 3-epimerase ( rpe ) HPG27_RS07415 HP1495 1.89 0.16 0.03 1.75 0.22 0.08 2.44 0.48 0.11 transaldolase ( tal )...”

SP_1983 ribulose-phosphate 3-epimerase from Streptococcus pneumoniae TIGR4
42% identity, 98% coverage

• An in vivo atlas of host-pathogen transcriptomes during Streptococcus pneumoniae colonization and disease
  D'Mello, Proceedings of the National Academy of Sciences of the United States of America 2020
  • “...is ultimately converted into cytidine diphosphate-ribitol by other genes within the operon together with genes SP_1983, SP_1270, and SP_1271. Of all of the genes within this pathway, only SP_1983 was not DE above cutoff. Cytidine diphosphate-ribitol is essential for bacteria wall synthesis ( 21 ) and,...”

XP_004368096 ribulosephosphate 3-epimerase from Acanthamoeba castellanii str. Neff
46% identity, 93% coverage

• A practical implementation of large transcriptomic data analysis to resolve cryptic species diversity problems in microbial eukaryotes
  Tekle, BMC evolutionary biology 2018
  • “...14.7 0.1 2840 XP_004344004 XP_637130 Phosphoglycerate kinase 0 0 0 13.0 0.4 15.0 0 3192 XP_004368096 XP_642255 Ribulosephosphate 3-epimerase 0.3 0 0.1 12.0 0.4 13.0 0.2 3202 XP_004368095 XP_646606 Proteasome 26S subunit 0 0 0 9.4 0 12.5 0.1 3401 XP_004341728 XP_628938 COP9 signalosome complex 0...”

Ssal_00221 ribulose-phosphate 3-epimerase from Streptococcus salivarius 57.I
43% identity, 95% coverage

• Impact of growth pH and glucose concentrations on the CodY regulatory network in Streptococcus salivarius
  Geng, BMC genomics 2018
  • “...7.3 2.6 1.6 Ssal_02096 3.7 2.8 6.0 3.1 Others Ssal_00088 rpsS 0.04 0.48 0.16 0.22 Ssal_00221 rpe 0.28 0.44 0.17 0.27 Ssal_00318 0.13 0.24 0.36 0.18 Ssal_00689 0.11 0.48 0.32 0.23 Ssal_00700 0.06 0.35 0.14 0.10 Ssal_00703 0.06 0.34 0.24 0.19 Ssal_00750 ece1 0.34 0.47 0.21...”

AMED_2771 ribulose-phosphate 3-epimerase from Amycolatopsis mediterranei U32
47% identity, 96% coverage

• A systematic study of the whole genome sequence of Amycolatopsis methanolica strain 239^T provides an insight into its physiological and taxonomic properties which correlate with its position in the genus
  Tang, Synthetic and systems biotechnology 2016
  • “...AMED_2263 AORI_5659 , AORI_5660 AJAP_11180 , AJAP_11185 AMETH_4518 AMETH_4092 AMED_2809 AORI_2796 AJAP_24810 rpe AMETH_4520 AMETH_4130 AMED_2771 AORI_2761 AJAP_25030 rpi AMETH_4529 AMETH_1699 AMED_6811 AORI_1928 AJAP_29895 AORI_6417 AJAP_06835 AMETH_2243 , AMETH_6524 AORI_7455 AJAP_38990 gnd AMETH_0006 AMED_0003 AORI_0003 AJAP_00020 talA AMETH_4093 AMED_2808 AORI_2795 AJAP_24815 pgi AMETH_4094 AMED_2807 AORI_2794 AJAP_24820...”

SAK_RS09050 ribulose-phosphate 3-epimerase from Streptococcus agalactiae A909
SAK_1798 ribulose-phosphate 3-epimerase from Streptococcus agalactiae A909
42% identity, 98% coverage

• CsbD, a Novel Group B Streptococcal Stress Response Factor That Contributes to Bacterial Resistance against Environmental Bile Salts
  Jia, Journal of bacteriology 2023
  • “...12.12 11.91 11.63 11.87 11.67 Glycolipid metabolism SAK_RS07690 DGK 12.06 10.76 3.66 13.62 3.66 13.64 SAK_RS09050 Ribulose-phosphate 3-epimerase 11.20 11.48 17.24 16.50 17.24 16.31 SAK_RS07290 Glycosyltransferase family 2 protein 10.74 11.03 22.40 20.52 22.40 20.71 SAK_RS04180 Glycosyltransferase 10.21 10.77 26.98 27.28 26.98 27.61 SAK_RS04445 Phosphoglycerate mutase...”
• The Role of Regulator Catabolite Control Protein A (CcpA) in Streptococcus agalactiae Physiology and Stress Response
  Roux, Microbiology spectrum 2022
  • “...rbsK ( SAK_0170 ), ribokinase; rpiA ( SAK_1270 ), ribose 5-phosphate isomerase A; rpe ( SAK_1798 ), ribulose-phosphate 3-epimerase; tkt ( SAK_0350 ), transketolase; SAK_0262 , 0263 , putative transketolase, N- and C-terminal subunits; SAK_1756 , transketolase; pgi ( SAK_0475 ), glucose-6-phosphate isomerase; fbp ( SAK_0666...”

2fliC / Q9A1H8 The crystal structure of d-ribulose 5-phosphate 3-epimerase from streptococus pyogenes complexed with d-xylitol 5-phosphate (see paper)
43% identity, 96% coverage

• Ligands: zinc ion; d-xylitol-5-phosphate (2fliC)

OJAG_00210 ribulose-phosphate 3-epimerase from Oerskovia enterophila
46% identity, 97% coverage

• Genome sequencing and description of Oerskovia enterophila VJag, an agar- and cellulose-degrading bacterium
  Jag, Standards in genomic sciences 2017
  • “...D-xylulose-5-phosphate via a xylulokinase (OJAG_26780). D-xylulose-5-phosphate would be converted to D-ribulose-5-phosphate by a ribulose-5-phosphate 3-epimerase (OJAG_00210), and then metabolized via the pentose phosphate pathway, or D-xylulose-5-phosphate would be converted to L-ribulose -5-posphate via a L-ribulose-5-phosphate 4-epimerase (OJAG_27380). This also fits into the overall picture since xylose...”

lmo0505 similar to ribulose-5-phosphate 3-epimerase from Listeria monocytogenes EGD-e
44% identity, 89% coverage

• 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...”

SSU1785 ribulose-phosphate 3-epimerase from Streptococcus suis P1/7
45% identity, 91% coverage

• Transcriptomic Analysis Reveals Selective Metabolic Adaptation of Streptococcus suis to Porcine Blood and Cerebrospinal Fluid
  Koczula, Pathogens (Basel, Switzerland) 2017
  • “...of the PPP, such as SSU0181 , SSU0182 , zwf ( SSU1025 ), rpe ( SSU1785 ), and deoB ( SSU1269 ), showed increased expression ( Figure 1 A, Table S2 ). This observation suggests an increasing PPP activity. The higher activity might result from the...”

HP1386 D-ribulose-5-phosphate 3 epimerase (rpe) from Helicobacter pylori 26695
45% identity, 94% coverage

• Acid-regulated gene expression of Helicobacter pylori: Insight into acid protection and gastric colonization
  Marcus, Helicobacter 2018
  • “...0.95 0.07 0.38 0.77 0.06 0.07 0.81 0.03 0.02 6-phosphogluconolactonase ( pgl, devB ) HPG27_RS07685 HP1386 1.50 0.07 0.04 1.92 0.05 0.01 2.21 0.07 0.01 ribulose-phosphate 3-epimerase ( rpe ) HPG27_RS07415 HP1495 1.89 0.16 0.03 1.75 0.22 0.08 2.44 0.48 0.11 transaldolase ( tal ) HPG27_RS01820...”
• Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single- and double-deletion mutants
  Thiele, Journal of bacteriology 2005
  • “...(RPI), HP1386 (RPE) ADD...”
• Acid-adaptive genes of Helicobacter pylori
  Wen, Infection and immunity 2003
  • “...2.23 3.11 9.17 3.60 2.38 3.34 HP1100 HP1166 HP1222 HP1345 HP1386 0.99 0.99 1.01 0.87 1.39 0.95 1.07 1.51 1.28 1.34 2.87 1.52 3.07 2.56 HP1461 HP1508 1.03 1.02...”
• Metabolism and genetics of Helicobacter pylori: the genome era
  Marais, Microbiology and molecular biology reviews : MMBR 1999
  • “...essential for nucleotide synthesis (Fig. 1). The genes HP1386, HP1102, HP1101, HP1495, HP1088, and HP0354, orthologous to rpe, devB, g6pD, tal, tktA, and tktB,...”
  • “...the inner core; HP0003 (kdsA), HP0230 (kdsB), and HP1386 (rpe) for the 3-deoxy-D-mannooctulosonic acid (KDO) residue region of the inner core; and HP0159,...”

ACPL_6461 ribulose-phosphate 3-epimerase from Actinoplanes sp. SE50/110
46% identity, 94% coverage

• Reconstruction and in silico analysis of an Actinoplanes sp. SE50/110 genome-scale metabolic model for acarbose production
  Wang, Frontiers in microbiology 2015
  • “...and the inhibition of glycolysis. Thus, genes in the pentose phosphate pathway, such as ACPL_1861, ACPL_6461, ACPL_1328, were candidates for overexpression to improve acarbose production. In addition, the flux of the reaction catalyzed by alanine aminotransferase (EC: 2.6.1.2), which forms glutamate, increased with increasing acarbose production....”
  • “...engineering to improve acarbose production. It was shown that the overexpression of genes ACPL_1861 (6-phosphoglucanolactonase), ACPL_6461 (ribulose phosphate 3-epimerase), ACPL_1328 (ribose 5-phosphate isomerase) and ACPL_6750 (aminotransferase) promoted acarbose producing. However, no candidate genes to be knockout were found through single and double gene deletions. The overexpression...”

cg1801 ribulose-phosphate 3-epimerase from Corynebacterium glutamicum ATCC 13032
NCgl1536 ribulose-phosphate 3-epimerase from Corynebacterium glutamicum ATCC 13032
44% identity, 96% coverage

• CRISPRi-Library-Guided Target Identification for Engineering Carotenoid Production by Corynebacterium glutamicum
  Göttl, Microorganisms 2021
  • “...plasmid carrying the ramB (cg0444) sgRNA This work pS_dCas9_ rpe pS_dCas9 plasmid carrying the rpe (cg1801) sgRNA This work pS_dCas9_ rpi pS_dCas9 plasmid carrying the rpi (cg2658) sgRNA This work pS_dCas9_ rsdA pS_dCas9 plasmid carrying the rsdA (cg0697) sgRNA This work pS_dCas9_ rshA pS_dCas9 plasmid carrying...”
• Methanol-Essential Growth of Corynebacterium glutamicum: Adaptive Laboratory Evolution Overcomes Limitation due to Methanethiol Assimilation Pathway
  Hennig, International journal of molecular sciences 2020
  • “...coding sequence (CDS) cg1806 metK MDS2T8 S-adenosylmethionine synthetase S288N cg1929 res MDS2T8 Site-specific recombinase R91H cg1801 rpe MDS2T14 Ribulose-5-phosphate epimerase Insertion of a 1.4 kb transposon ijms-21-03617-t002_Table 2 Table 2 Bacterial strains used in this study. Strain Relevant Characteristics Reference E. coli DH5 lac U169 (80...”
• High-throughput screening of a Corynebacterium glutamicum mutant library on genomic and metabolic level
  Reimer, PloS one 2014
  • “...in glycolysis ( NCgl1526 encoding the glyceraldehyde-3-phosphate dehydrogenase, EC 1.2.1.12), the pentose phosphate pathway ( NCgl1536 encoding the ribulose-phosphate 3-epimerase, EC 5.1.3.1) or the valine, leucine and isoleucine pathway ( NCgl1219 encoding the dihydroxy-acid dehydratase, EC 4.2.1.9 and NCgl0245 encoding the 2-isopropylmalate synthase, EC 2.3.3.13). Also...”

Blon_1368 Ribulose-phosphate 3-epimerase from Bifidobacterium longum subsp. infantis ATCC 15697
42% identity, 100% coverage

• Inefficient Metabolism of the Human Milk Oligosaccharides Lacto-N-tetraose and Lacto-N-neotetraose Shifts Bifidobacterium longum subsp. infantis Physiology
  Özcan, Frontiers in nutrition 2018
  • “...of those genes compared to lactose ( p < 0.05), except for Blon_1722, Blon_1096, and Blon_1368 that did not significantly differ ( p > 0.05). This is interesting as the biomass and growth rate achieved with LNT or lactose did not significantly differ ( p >...”

Rv1408 ribulose-phosphate 3-epimerase from Mycobacterium tuberculosis H37Rv
49% identity, 85% coverage

• From immunology to artificial intelligence: revolutionizing latent tuberculosis infection diagnosis with machine learning
  Li, Military Medical Research 2023
  • “...validation cohort, ATB ( n =92), LTBI ( n =93), HCs ( n =94) China Rv1408, R0248, Rv2026c, Rv2716, Rv2031c, Rv2928, and Rv2121c Logistic regression and hierarchical clustering 96.77% in training cohort and 93.33% in validation cohort 93.75% in training cohort and 93.1% in validation cohort...”
  • “...algorithm, Cao et al. [ 265 ] expanded the number of MTB antigens to 7 (Rv1408, R0248, Rv2026c, Rv2716, Rv2031c, Rv2928, Rv2121c) when constructing their discriminative LTBI diagnostic model. Additionally, they used both logistic regression and hierarchical clustering as ML algorithms. The combination of these 7...”
• Using Omics to Study Leprosy, Tuberculosis, and Other Mycobacterial Diseases
  Ahamad, Frontiers in cellular and infection microbiology 2022
  • “...serum from individuals with active TB and latent TB infection and found that RV2031c, RV2421c,and RV1408 were possible serum biomarkers for distinguishing active TB from latent TB infection ( Cao etal., 2018 ). Another serum biomarkers study found that proteins including S100 calcium-binding protein (S100-A9), superoxide...”
• Host and Bacterial Iron Homeostasis, an Underexplored Area in Tuberculosis Biomarker Research
  Baatjies, Frontiers in immunology 2021
  • “...TB disease Luminex assay on saliva supernatants Cao etal. ( 39 ) No stimulation Rv2002, Rv1408, Rv0389, Rv2421c, Rv0248c, Rv2026c, Rv2716, Rv2097c, Rv2031c, Rv2906c, Rv2928 LTBI vs active TB Serum profiling on Mtb proteome microarray and ELISA Day etal. ( 55 ) Unstimulated ESAT-6, CFP-10, TB10.4,...”
  • “...analysis of 11 candidate antigens were consistent with the microarray analysis. Antibodies specific for Rv2031c, Rv1408, and Rv2421c had highest areas under the curve (AUCs) of 0.8520, 0.8152, and 0.7970, respectively. The authors identified several antigens with potential as serum biomarkers for discriminating between active TB...”
• Differential Diagnosis of Latent Tuberculosis Infection and Active Tuberculosis: A Key to a Successful Tuberculosis Control Strategy
  Gong, Frontiers in microbiology 2021
  • “...serum biomarkers for distinguishing between LTBI and aTB, and their results indicated that antigens Rv2031c, Rv1408, and Rv2421c had higher AUCs of 0.8520, 0.8152, and 0.7970, respectively. With the development of high-resolution quantitative proteomics and label-free quantitative proteomics, a growing number of protein signatures that can...”
• Immune Biomarkers for Diagnosis and Treatment Monitoring of Tuberculosis: Current Developments and Future Prospects
  Yong, Frontiers in microbiology 2019
  • “...patients with active TB when compared to patients with LTBI. Further analysis showed that RV2031c, RV1408 and RV2421c were able to discriminate between active TB and LTBI ( Cao et al., 2018 ). By studying 1011 host serum biomarkers, Liu et al. found that 153 protein...”
  • “...= 92%, specificity = 91% PPE17 More antigenic antigen than ESAt-6 and CFP-10 MDP-1 RV2031c, RV1408, RV2421c IgG against these three Ags were initial identified by screening done by proteomics Host cytokines responses against ex-vivo stimulation of MTB Ags Tuberculin skin test (TST) Poor sensitivity among...”
• Screening of Serum Biomarkers for Distinguishing between Latent and Active Tuberculosis Using Proteome Microarray
  Cao, Biomedical and environmental sciences : BES 2018 (PubMed)
  • “...using ELISA and showed consistent results in microarray analysis. ROC analysis showed that antigens Rv2031c, Rv1408, and Rv2421c had higher areas under the curve (AUCs) of 0.8520, 0.8152, and 0.7970, respectively. In addition, both antigen combination and logistic regression analysis improved the diagnostic ability. Several antigens...”
• Deciphering the metabolic response of Mycobacterium tuberculosis to nitrogen stress
  Williams, Molecular microbiology 2015
  • “...Rv1915, Rv3565 u3 0.01 1 1 Phthiocerol precursor ligase Rv2930 Down d1 <0.001 9 5 Rv1408, Rv1436, Rv1437, Rv1438, Rv1449, Rv1611, Rv1612, Rv1613 d2 0.037 2 1 Phosphatidylglycerol synthase Rv1822, Rv2289, Rv2746 d3 0.037 2 1 Pyridoxine 5 phosphate oxidase Rv2607 d4 0.037 2 1 Pyridoxal...”

lmo2659 similar to ribulose-phosphate 3-epimerase from Listeria monocytogenes EGD-e
44% identity, 94% coverage

• Identification of a peptide-pheromone that enhances Listeria monocytogenes escape from host cell vacuoles
  Xayarath, PLoS pathogens 2015
  • “...9 Lmo2459 Glyceraldehyde-3-phosphate dehydrogenase SecA2 16 74.40 36 Lmo0539 Tagatose 1,6-diphosphate aldolase 12 52.70 38 Lmo2659 Dihydroacetone kinase 8 52.30 35 Lmo0554 Oxidoreductase 11 45.00 43 Lmo2416 Lipoprotein SecA 4 21.20 40 Group 11 Lmo2415 FeS Assembly ATPase SufC 12 55.20 29 Lmo9211 Ctcgeneral stress protein...”
• Identification of new noncoding RNAs in Listeria monocytogenes and prediction of mRNA targets
  Mandin, Nucleic acids research 2007
  • “...that pairs with the mRNA (black). On the nucleotidic sequence, the translation start codon of lmo2659 is indicated by a grey box, the translation stop codon of lmo2660 by an open box. Data are otherwise presented as in Figure 5 A. ( B ) Duplex formation...”
• Microarray-based characterization of the Listeria monocytogenes cold regulon in log- and stationary-phase cells
  Chan, Applied and environmental microbiology 2007
  • “...those consisting of lmo2664 and lmo2663 and lmo2661 to lmo2659; see above) also showed higher transcript levels in stationary-phase cells at 4C than in cells at...”
  • “...of lmo2661, lmo2660, and lmo2659 (encoding ribulose-5-phosphate-3-epimerase, transketolase, and ribulose-phosphate-3-epimerase, respectively), also showed...”

BL0753 ribulose-phosphate 3-epimerase from Bifidobacterium longum NCC2705
43% identity, 95% coverage

• Low-pH adaptation and the acid tolerance response of Bifidobacterium longum biotype longum
  Sánchez, Applied and environmental microbiology 2007
  • “...WT ratiog rpe BL0529 BL1630 BL0988 BL0716 BL1644 BL0715 BL0978 BL1341 BL0753 50 60 55 25 34 65 39 30 36 3.49E 13 8.17E 12 2.64E 10 1.08E 10 1.02E 05 1.00E...”

Q9X243 Ribulose-phosphate 3-epimerase from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)
42% identity, 95% coverage

• Stoichiometric Conversion of Maltose for Biomanufacturing by In Vitro Synthetic Enzymatic Biosystems
  Li, Biodesign research 2022
  • “...for the expression of ribulose 5-phosphate 3-epimerase (RPE) from Thermotoga maritima MSB8 (UniProt entry number: Q9X243) were constructed by simple cloning [ 28 ]. Primers for PCR were synthesized by Azenta Life Sciences (Suzhou, China), and their sequences were listed in Table S1 . Plasmids for...”

CTN_RS04470 ribulose-phosphate 3-epimerase from Thermotoga neapolitana DSM 4359
42% identity, 97% coverage

• CO₂-Induced Transcriptional Reorganization: Molecular Basis of Capnophillic Lactic Fermentation in Thermotoga neapolitana
  d'Ippolito, Frontiers in microbiology 2020
  • “...CTN_RS00550 5.83 6-Phosphogluconate dehydratase a CTN_RS03140 1.26 2-Dehydro-3-deoxyphosphogluconate aldolase OPP CTN_RS01150 1.40 6-Phosphogluconate dehydrogenase. Decarboxylating CTN_RS04470 1.64 Ribulose-phosphate-epimerase CTN_RS07445 NDE Ribose-5-phosphate isomerase CTN_RS04700 1.81 Transketolase CTN_RS08090 1.60 Transketolase. C-terminal subunit CTN_RS08085 2.66 Transketolase. N-terminal subunit CTN_RS07710 5.74 Fructose-6-phosphate aldolase CTN_RS01915 NDE Fructose-6-phosphate aldolase Other genes CTN_RS01940...”

SA1065 hypothetical protein from Staphylococcus aureus subsp. aureus N315
Q2FZ62 Ribulose-phosphate 3-epimerase from Staphylococcus aureus (strain NCTC 8325 / PS 47)
SAV1222 ribulose-5-phosphate 3-epimerase homolog from Staphylococcus aureus subsp. aureus Mu50
SAOUHSC_01189 ribulose-phosphate 3-epimerase from Staphylococcus aureus subsp. aureus NCTC 8325
SACOL1235 ribulose-phosphate 3-epimerase from Staphylococcus aureus subsp. aureus COL
CH51_RS06555 ribulose-phosphate 3-epimerase from Staphylococcus aureus
42% identity, 94% coverage

• Studies of the in vitro antibacterial activities of several polyphenols against clinical isolates of methicillin-resistant Staphylococcus aureus
  Su, Molecules (Basel, Switzerland) 2014
  • “...125 125 1000 >2000 >4000 >4000 9 SA1061 125 125 1000 >2000 >4000 >4000 20 SA1065 31.2 62.5 500 >2000 >4000 >4000 21 SA1131 125 125 1000 >2000 >4000 >4000 22 SA1133 125 125 500 >2000 >4000 >4000 23 SA1134 62.5 125 500 >2000 >4000 >4000...”
  • “...SA1057 62.5/62.5 1 ad 18 SA1060 62.5/62.5 1 ad 19 SA1061 62.5/31.2 0.75 ad 20 SA1065 15.6/31.2 1 ad 21 SA1131 62.5/62.5 1 ad 22 SA1133 62.5/62.5 1 ad 23 SA1134 31.2/62.5 1 ad 24 SA1140 31.2/62.5 1 ad 25 SA1143 62.5/62.5 1 ad 26 SA1147...”
• Global transcriptome analysis of Staphylococcus aureus biofilms in response to innate immune cells
  Scherr, Infection and immunity 2013
  • “...SA1839 SA1523 SA0513 SA1752 SA2131 SA0314 SA1323 SA1832 SA1065 SA1954 SA2634 SA1637 SA1966 SA0024 SA1241 SA0551 SA1494 SA0002 SA1771 SA1028 SA1316 SA1150 SA2735...”
• Exposure of clinical MRSA heterogeneous strains to β-lactams redirects metabolism to optimize energy production through the TCA cycle
  Keaton, PloS one 2013
  • “...into glucose-6-P. SAR2247 mtlD 5.2 mannitol-1-phosphate 5-dehydrogenase Catalyzes: D-mannitol-1-P+NAD+=D-fructose-6-P+NADH SA1336 2 glucose-6-phosphate 1-dehydrogenase Catalyzes: D-glucose-6-P+NADP+=D-glucono-1,5-lactone-6-P+NADPH SA1065 cfxE 2.3 hypothetical protein pentose phosphate pathway SACOL1124 lctP 2.4 hypothetical protein Transports L-lactate across the membrane. SA0106 20.3 hypothetical protein homolog of L-lactate permease lctP SA2156 4.6 hypothetical protein...”
• Transcriptome and functional analysis of the eukaryotic-type serine/threonine kinase PknB in Staphylococcus aureus
  Donat, Journal of bacteriology 2009
  • “...genes, we tested expression of downstream genes (SA1064, SA1065, and SA1066) by performing a reverse transcription (RT)-PCR analysis. We did not observe any...”
• Antibacterial Activity of Juglone against Staphylococcus aureus: From Apparent to Proteomic
  Wang, International journal of molecular sciences 2016
  • “...thioredoxin SAOUHSC_00834 6 6 12.10 0.758 0.046 Q2FXI6 thioredoxin SAOUHSC_01860 8 8 11.80 0.781 0.003 Q2FZ62 ribulose-phosphate 3-epimerase SAOUHSC_01189 2 2 23.60 0.750 0.038 Q2FWJ9 threonine dehydratase biosynthetic ilvA 3 3 46.90 0.751 0.016 Q2FV58 4,4-diaponeurosporenoate glycosyltransferase crtQ 2 2 42.50 0.782 0.016 DNA replication and...”
• Inhibition of Staphylococcus aureus biofilm formation by gurmarin, a plant-derived cyclic peptide
  Chang, Frontiers in cellular and infection microbiology 2022
  • “...SACOL0454 2.34 Sodium dicarboxylate symporter family protein 0.03 SAV2129 2.26 Similar to spermine/spermidine acetyltransferase 0.04 SAV1222 2.23 ribuloase-5-phosphate 3-epimerase homolog cfxE 0.02 MW0477 2.23 Hypothetical protein ctsR 0.02 SAV1480 2.21 Thioredoxin reductase-like protein trxB 0.02 SAV2317 2.17 Hypothetical protein 0.02 SAV2351 2.1 Hypothetical protein 0.01 SAV1747...”
• Antibacterial Activity of Juglone against Staphylococcus aureus: From Apparent to Proteomic
  Wang, International journal of molecular sciences 2016
  • “...6 12.10 0.758 0.046 Q2FXI6 thioredoxin SAOUHSC_01860 8 8 11.80 0.781 0.003 Q2FZ62 ribulose-phosphate 3-epimerase SAOUHSC_01189 2 2 23.60 0.750 0.038 Q2FWJ9 threonine dehydratase biosynthetic ilvA 3 3 46.90 0.751 0.016 Q2FV58 4,4-diaponeurosporenoate glycosyltransferase crtQ 2 2 42.50 0.782 0.016 DNA replication and transcription Q2FWH6 DNA-binding...”
• The yjeQ gene is required for virulence of Staphylococcus aureus
  Campbell, Infection and immunity 2006
  • “...elements for the ribulose phosphate 3-epimerase gene (SAcol1235). Primers SA1234-B and SA1234-C contained regions that were complementary to an erythromycin...”
• Staphylococcus aureus PhoU Homologs Regulate Persister Formation and Virulence
  Shang, Frontiers in microbiology 2020
  • “...CH51_RS14700 2-Dehydropantoate 2-reductase 2.63 ND CH51_RS11580 Carbohydrate kinase 2.33 ND CH51_RS11585 Sucrose-6-phosphate hydrolase 2.17 ND CH51_RS06555 Ribulose-phosphate 3-epimerase 2.16 ND CH51_RS08720 Glycine dehydrogenase 2.94 ND CH51_RS02915 Serine acetyltransferase 2.52 ND CH51_RS00820 Formate dehydrogenase 2.06 ND CH51_RS09725 Formate-tetrahydrofolate ligase 2.07 ND CH51_RS05415 Bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase 2.04...”

BHWA1_00002 ribulose-phosphate 3-epimerase from Brachyspira hyodysenteriae WA1
41% identity, 92% coverage

• Genome sequence of the pathogenic intestinal spirochete brachyspira hyodysenteriae reveals adaptations to its lifestyle in the porcine large intestine
  Bellgard, PloS one 2009
  • “...following putative CDS were identified in B. hyodysenteriae : i) ribulose-5-phosphate epimerase ( rep : BHWA1_00002); ii) ribose-5-phosphate isomerase ( rpiB: BHWA1_01037); iii) transketolase ( tkt: BHWA1_00091 and BHWA1_00092); and iv) transaldolase (BHWA1_01968); these enzymes combine to convert glucose-6-phosphate to ribulose-5-phosphate. The orthologs for transketolase and...”
  • “...and rfaD (BHWA1_00678) for synthesis of the inner core; kdsA (BHWA1_00088), kdsB (BHWA1_01886) and rpe (BHWA1_00002) for the 3-deoxy-D-mann-2-octulsonic acid (Kdo) region of the inner core; and a putative rfaJ (BHWA1_02200), pgi (BHWA1_01137) and galE (BHWA1_01537) for outer core synthesis. The genes rfbA , rfbB ,...”

AMETH_4520 ribulose-phosphate 3-epimerase from Amycolatopsis methanolica 239
44% identity, 96% coverage

• A systematic study of the whole genome sequence of Amycolatopsis methanolica strain 239^T provides an insight into its physiological and taxonomic properties which correlate with its position in the genus
  Tang, Synthetic and systems biotechnology 2016
  • “...AMED_2262 , AMED_2263 AORI_5659 , AORI_5660 AJAP_11180 , AJAP_11185 AMETH_4518 AMETH_4092 AMED_2809 AORI_2796 AJAP_24810 rpe AMETH_4520 AMETH_4130 AMED_2771 AORI_2761 AJAP_25030 rpi AMETH_4529 AMETH_1699 AMED_6811 AORI_1928 AJAP_29895 AORI_6417 AJAP_06835 AMETH_2243 , AMETH_6524 AORI_7455 AJAP_38990 gnd AMETH_0006 AMED_0003 AORI_0003 AJAP_00020 talA AMETH_4093 AMED_2808 AORI_2795 AJAP_24815 pgi AMETH_4094 AMED_2807...”
  • “...certain genes, such as those encoding transketolase ( tkt AMETH_4518 ), ribulose-phosphate 3-epimerase ( rpe AMETH_4520 ) and ribose 5-phosphate isomerase ( rpi AMETH_4529 ), have corresponding isoenzymes with similar functions in other parts of the genomes of both A.methanolica strain 239 T and the three...”

Pro0839 Pentose-5-phosphate-3-epimerase from Prochlorococcus marinus str. SS120
40% identity, 87% coverage

• Glucose uptake and its effect on gene expression in prochlorococcus
  Gómez-Baena, PloS one 2008
  • “...nagB 3.1.1.31 Pro0844 6-phosphogluconate dehydrogenase gnd 1.1.1.44 Pro0843 Phosphoribulokinase prk 2.7.1.19 Pro0861 Pentose-5-phosphate-3-epimerase rpe 5.1.3.1 Pro0839 Ribose-5-phosphate isomerase rpi 5.3.1.6 Pro1644 Transketolase tktA 2.2.1.1 Pro1770 Transaldolase tal 2.2.1.2 Pro0519 Triosephosphate isomerase tpi 5.3.1.1 Pro0901 Glyceraldehyde-3-phosphate dehydrogenase gap3 1.2.1.12 Pro1577 3-phosphoglycerate kinase pgk 2.7.2.3 Pro0221 Phosphoglycerate mutase...”

A9PIC8 Ribulose-phosphate 3-epimerase from Populus trichocarpa
42% identity, 97% coverage

• The proteome of Populus nigra woody root: response to bending
  Trupiano, Annals of botany 2012
  • “...138* Ribulose-5-phosphate-3-epimerase,putative Phi class glutathione transferase GSTF5 A9PIC8 B9IBH2 Populus trichocarpa Populus trichocarpa TMS TMS 2 3 17 17...”

4nu7C 2.05 angstrom crystal structure of ribulose-phosphate 3-epimerase from toxoplasma gondii. (see paper)
41% identity, 93% coverage

• Ligand: zinc ion (4nu7C)

YjcU / b4085 D-allulose-6-phosphate 3-epimerase from Escherichia coli K-12 substr. MG1655 (see 4 papers)
alsE / P32719 D-allulose-6-phosphate 3-epimerase from Escherichia coli (strain K12) (see 3 papers)
ALSE_ECOLI / P32719 D-allulose-6-phosphate 3-epimerase; EC 5.1.3.- from Escherichia coli (strain K12) (see 2 papers)
alsE / RF|NP_418509 D-allulose-6-phosphate 3-epimerase from Escherichia coli K12 (see 3 papers)
NP_418509 allulose-6-phosphate 3-epimerase from Escherichia coli str. K-12 substr. MG1655
40% identity, 94% coverage

• function: Catalyzes the reversible epimerization of D-allulose 6- phosphate to D-fructose 6-phosphate. Can also catalyze with lower efficiency the reversible epimerization of D-ribulose 5-phosphate to D- xylulose 5-phosphate.
  catalytic activity: D-allulose 6-phosphate = keto-D-fructose 6-phosphate (RHEA:28426)
  cofactor: Co(2+) Mn(2+) Zn(2+) (Binds 1 divalent metal cation per subunit. Activity is highest with Co(2+) > Mn(2+) > Zn(2+).)
  subunit: Homohexamer. Trimer of dimers.
• Non-natural Aldol Reactions Enable the Design and Construction of Novel One-Carbon Assimilation Pathways in vitro
  Mao, Frontiers in microbiology 2021
  • “...Kan R , N-terminally His-tagged alsE , inserted between Nhe I and Xho I sites NP_418509 This study pET28a- fpk Kan R , N-terminally His-tagged fpk , inserted between the Nhe I and Hind III sites BAF39468 Yang et al., 2019b Table 2 Primers used in...”

3ct7A / P32719 Crystal structure of d-allulose 6-phosphate 3-epimerase from escherichia coli k-12 (see paper)
40% identity, 96% coverage

• Ligand: magnesium ion (3ct7A)

TP0945 ribulose-phosphate 3-epimerase (cfxE) from Treponema pallidum subsp. pallidum str. Nichols
43% identity, 91% coverage

• The binary protein interactome of Treponema pallidum--the syphilis spirochete
  Titz, PloS one 2008
  • “...TP0046 and TP0048 have also been functionally implicated in bacterial motility and the ortholog of TP0945 shows a motility phenotype in E. coli [14] . This suggests that the locus around TP0048 has a functional involvement in bacterial motility, and demonstrates that genomic loci links can...”
• The protein network of bacterial motility
  Rajagopala, Molecular systems biology 2007
  • “...possible that RpmJ links protein synthesis to the flagellar protein export machinery. Another one, Rpe (TP0945) is a ribulose-phosphate 3-epimerase. Surprisingly, this protein also showed a strong reduction in motility when deleted. Rpe could have a role in providing energy for the flagellar motor. Novel interactions...”

MJ0680 pentose-5-phosphate-3-epimerase from Methanocaldococcus jannaschii DSM 2661
40% identity, 93% coverage

• Ribose-5-phosphate biosynthesis in Methanocaldococcus jannaschii occurs in the absence of a pentose-phosphate pathway
  Grochowski, Journal of bacteriology 2005
  • “...ribose-5-phosphate epimerase MJ1603, and ribulose-5-phosphate 3-epimerase MJ0680 or (ii) a second pathway involving carboxylation of erythrose-4-phosphate (4,...”
• Transaldolase of Methanocaldococcus jannaschii
  Soderberg, Archaea (Vancouver, B.C.) 2004
  • “...X MJ0679 X X X AF0943 NT01HS1713 NT02MA2464 MJ1603 NT01MK1964 NT01MM0099 NT01MT0629 X X X MJ0680 X X X X X X X X X X X NT01HS1935 X X X X X E E E E E C C C C X...”

M5WTG1 Ribulose-phosphate 3-epimerase from Prunus persica
41% identity, 97% coverage

• Proteomic analysis reveals a role of melatonin in promoting cucumber seed germination under high salinity by regulating energy production.
  Zhang, Scientific reports 2017
  • “...2.19 0.01513 0.30 0.02392 Alpha-xylosidase 1-like W9SB70 6.36 0.00003 7.26 0.00008 Ribulose-phosphate 3- cytoplasmic isoform M5WTG1 5.86 0.07207 1.89 0.34807 UTPglucose-1-phosphate uridylyltransferase Q19TV8 0.29 0.00084 2.90 0.07416 Isocitrate dehydrogenase B9GHS2 2.03 0.01631 5-methyltetrahydropteroyltriglutamatehomocysteine methyltransferase M5WFB9 12.42 0.00693 Lipid metabolic process Aspartic proteinase O04057 4.09 0.00003 15.40...”

SE0897 ribulose-phosphate 3-epimerase from Staphylococcus epidermidis ATCC 12228
41% identity, 92% coverage

• Factors characterizing Staphylococcus epidermidis invasiveness determined by comparative genomics
  Yao, Infection and immunity 2005
  • “...0.0185603 0.0220505 0.02653 0.02653 0.0286499 0.0289139 SE0135 SE1065 SE0897 SE0079 5 2 6 6 13 9 14 14 0.0334195 0.0353177 0.0365301 0.0365301 SE2232 SE0142...”

AT3G01850 ribulose-phosphate 3-epimerase, cytosolic, putative / pentose-5-phosphate 3-epimerase, putative from Arabidopsis thaliana
39% identity, 97% coverage

• Changes in annual transcriptome dynamics of a clone of Japanese cedar (Cryptomeria japonica D. Don) planted under different climate conditions
  Nose, PloS one 2023
  • “...CUST_7163_PI429951308 reCj21779:MSWR:isotig21631 AT4G13430 0.0 IIL1 isopropyl malate isomerase large subunit 1 temp-7d -0.86 CUST_11543_PI429951308 reCj26221:MSW-:isotig26073 AT3G01850 6.6E-131 - Aldolase-type TIM barrel family protein temp-max -0.84 CUST_9836_PI429951308 reCj24485:--W-:isotig24337 AT5G38530 0.0 TSBtype2 tryptophan synthase beta type 2 temp-0h -0.82 CUST_1398_PI429951308 reCj12804:M---:isotig12659 AT5G19550 0.0 ASP2 aspartate aminotransferase 2 temp-30d...”
• Reduction in chloroplastic ribulose-5-phosphate-3-epimerase decreases photosynthetic capacity in Arabidopsis
  Li, Frontiers in plant science 2022
  • “...and Smith, 2019 ). In addition to RPE, two other proteins encoded by At1g63290 and At3g01850 were proposed to be cytosolic RPE (cyRPE) ( Kruger and von Schaewen, 2003 ; Baune etal., 2020 ). Cytosolic RPEs have also been shown to be involved in the OPPP...”
• The isothiocyanate sulforaphane induces respiratory burst oxidase homologue D-dependent reactive oxygen species production and regulates expression of stress response genes
  Arruebarrena, Plant direct 2022
  • “...hydrolase homologue 22 AT1G18075 MIR159B 3.22 Encodes a microRNA that targets several MYB family members. AT3G01850 2.86 Aldolasetype TIM barrel family protein AT1G28710 2.80 Nucleotidediphosphosugar transferase family protein AT4G13720 2.75 Inosine triphosphate pyrophosphatase family protein Note : Ten days old Arabidosis seedlings sprayed with 400 or...”
• Transcriptome Analysis of Air Space-Type Variegation Formation in Trifolium pratense
  Zhang, International journal of molecular sciences 2022
  • “...composed of the LHCB subfamily proteins. The Calvin cycle part was composed of CP12-1, AT1G73110, AT3G01850, UKL5, RBCS1B, GAPA, FBP, FBA7, and AT3G60750 ( Figure 5 a). The LHCB subfamily proteins and the proteins translated from the genes related to the Calvin cycle were associated with...”
• Network mapping of root-microbe interactions in Arabidopsis thaliana
  He, NPJ biofilms and microbiomes 2021
  • “...0 25 1 9 1 6 Hrd1A AT1G05380 SS5 AT5G11430 AT5G35555 AT1G72230 UBP22 JAZ6 CSTF77 AT3G01850 AT3G12350 IGPD DELTA-VPE AT4G15640 DEL2 AT4G16050 MAIN AT5G19930 CAP1 SBT5.4 DEL2 Gene AT4G31360 AT4G25610 NAC058 AT5G20660 AT2G34185 AT5G19480 AT4G00320 UPL4 AT3G13662 PEPR2 AT5G11750 Aggression QTLs 1 2 0 1 7...”
• Proteomic and metabolomic analyses provide insight into the off-flavour of fruits from citrus trees infected with 'Candidatus Liberibacter asiaticus'
  Yao, Horticulture research 2019
  • “...EC 4.1.2.13 0.57 1.16E04 gi|568831440 AT5G40760 G6PD6 Glucose-6-phosphate dehydrogenase 6 EC 1.1.1.49 0.52 1.55E02 gi|568831566 AT3G01850 F28J7.18 Ribulose-phosphate 3-epimerase EC 5.1.3.1 0.65 1.13E02 gi|568833896 AT1G71170 F23N20.16 6-Phosphogluconate dehydrogenase-like protein EC 1.1.1.44 0.56 1.83E04 gi|568836722 AT4G37870 PCK1 Phosphoenolpyruvate carboxykinase 1 EC 4.1.1.49 0.58 2.19E02 gi|568837718 AT5G52560 USP...”
• A "footprint" of plant carbon fixation cycle functions during the development of a heterotrophic fungus
  Lyu, Scientific reports 2015
  • “...EC: 2.7.2.3 phosphoglycerate kinase SS1G_02281 AT4G37870 (0), AT5G65690 (4E-180) EC: 4.1.1.49 phosphoenolpyruvate carboxykinase (ATP) SS1G_01844 AT3G01850 (6E-60), AT1G63290 (2E-56), AT5G61410 (5E-42) EC: 5.1.3.1 ribulose-phosphate 3-epimerase SS1G_11433 AT3G55440 (1E-78), AT2G21170 (6E-71) EC: 5.3.1.1 triose-phosphate isomerase SS1G_08408 AT1G71100 (1E-19), AT2G01290 (4E-19) AT3G04790 (3E-15) EC: 5.3.1.6 ribose-5-phosphate isomerase SS1G_08975...”
• Divergent evolutionary fates of major photosynthetic gene networks following gene and whole genome duplications
  Coate, Plant signaling & behavior 2011
  • “...-0.11 0.24 AT5G61410 0.68 -0.76 AT1G63290 -0.42 0.58 AT3G01850 -0.27 0.11 AT1G12230 0.45 -0.44 AT5G13420 -0.46 0.79 Pearson correlation coefficients (r) for...”
• More

O14105 Ribulose-phosphate 3-epimerase from Schizosaccharomyces pombe (strain 972 / ATCC 24843)
39% identity, 96% coverage

• Proteasome regulation of petite-negativity in fission yeast.
  Amberg, bioRxiv : the preprint server for biology 2024
  • “...arg4 0.26 0.033 arginine specific carbamoyl-phosphate synthase Arg4 O74413 SPCC1223.14 0.26 0.028 chorismate synthase Aro2 O14105 SPAC31G5.05c 0.26 0.019 ribulose phosphate 3-epimerase Rpe1 P78780 SPCC1827.06c 0.26 0.029 aspartate semialdehyde dehydrogenase Hom2 O60155 prs1 0.24 0.036 cytoplasmic proline-tRNA ligase Prs1 P87228 SPCC364.07 0.24 0.030 D-3 phosphoglycerate dehydrogenase...”

RPE_YEAST / P46969 Ribulose-phosphate 3-epimerase; Pentose-5-phosphate 3-epimerase; PPE; RPE; EC 5.1.3.1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 2 papers)
P46969 ribulose-phosphate 3-epimerase (EC 5.1.3.1) from Saccharomyces cerevisiae (see paper)
YJL121C D-ribulose-5-phosphate 3-epimerase, catalyzes a reaction in the non-oxidative part of the pentose-phosphate pathway; mutants are sensitive to oxidative stress from Saccharomyces cerevisiae
39% identity, 91% coverage

• function: Catalyzes the reversible epimerization of D-ribulose 5- phosphate to D-xylulose 5-phosphate (By similarity). Involved in the protective response to oxidative stress.
  catalytic activity: D-ribulose 5-phosphate = D-xylulose 5-phosphate (RHEA:13677)
  cofactor: Co(2+) Fe(2+) Mn(2+) Zn(2+) (Binds 1 divalent metal cation per subunit. Active with Co(2+), Fe(2+), Mn(2+) and Zn(2+).)
• Identification of Genetic Modifiers of TDP-43: Inflammatory Activation of Astrocytes for Neuroinflammation
  Kim, Cells 2021
  • “...DNA repair protein RAD51 RAD51 26 YJL065C DLS1 P40366 Protein DLS1 CHRAC1 27 YJL121C RPE1 P46969 Ribulose-phosphate 3-epimerase RPE 28 YJR035W RAD26 P40352 DNA repair and recombination protein RAD26 ERCC6 29 YIL007C NAS2 P40555 Probable 26S proteasome regulatory subunit p27 PSMD9 30 YNL130C CPT1 P17898 Cholinephosphotransferase...”
• Microbes vary strategically in their metalation of mononuclear enzymes
  Rohaun, Proceedings of the National Academy of Sciences of the United States of America 2024
  • “..., respectively. The rpe genes from B. subtilis (BSU15790), L. lactis (L_RS10085), and S. cerevisiae (YJL121C) were identified by BLAST analysis using E. coli rpe sequence as query. The mutant E. coli rpe gene deletion (JW3349-2) was obtained from the Keio collection ( 57 ) at...”
• Identification of Genetic Modifiers of TDP-43: Inflammatory Activation of Astrocytes for Neuroinflammation
  Kim, Cells 2021
  • “...RAD51 P25454 DNA repair protein RAD51 RAD51 26 YJL065C DLS1 P40366 Protein DLS1 CHRAC1 27 YJL121C RPE1 P46969 Ribulose-phosphate 3-epimerase RPE 28 YJR035W RAD26 P40352 DNA repair and recombination protein RAD26 ERCC6 29 YIL007C NAS2 P40555 Probable 26S proteasome regulatory subunit p27 PSMD9 30 YNL130C CPT1...”
• The Pentose Phosphate Pathway in Yeasts-More Than a Poor Cousin of Glycolysis
  Bertels, Biomolecules 2021
  • “...(?) 54 kDa 85%/81% NADP + n.d. Ribulosephosphate epimerase (RPE) EC 5.1.3.1 S. cerevisiae RPE1 (YJL121C) NC_001142.9 (?) 26 kDa - 19002200 [ 28 , 37 ] K. lactis KlRPE1 (KLLA0E15071g) (?) 26 kDa 69% Ribosephosphate ketol isomerase (RKI) EC 5.3.1.6 S. cerevisiae RKI1 (YOR095C) NC_001147.6...”
• Systematic analysis of nuclear gene function in respiratory growth and expression of the mitochondrial genome in S. cerevisiae
  Stenger, Microbial cell (Graz, Austria) 2020
  • “...VMA9 YCL005W-A Other function BIT2 YBR270C KCS1 YDR017C RHO4 YKR055W COY1 YKL179C KEX1 YGL203C RPE1 YJL121C CTL1 YMR180C LCB4 YOR171C RTS1 YOR014W CTR9 YOL145C LEM3 YNL323W RTT103 YDR289C CUS2 YNL286W MAF1 YDR005C SFM1 YOR021C DAK2 YFL053W NGL2 YMR285C SFP1 YLR403W EGT2 YNL327W NPR2 YEL062W SLY41 YOR307C...”
• Laboratory Evolution of a Biotin-Requiring Saccharomyces cerevisiae Strain for Full Biotin Prototrophy and Identification of Causal Mutations
  Bracher, Applied and environmental microbiology 2017
  • “...YBR196C (PGI1), YER178W (PDA1), YFL039C (ACT1), and YJL121C (RPE1)], processed with Pilon (66). Accession number(s). The sequencing data are available under...”
• A Genome-Wide Screen with Nicotinamide to Identify Sirtuin-Dependent Pathways in Saccharomyces cerevisiae
  Choy, G3 (Bethesda, Md.) 2015
  • “...YNL041C 0.20 0.30 0.25 SAC1 YKL212W 0.00 0.05 0.02 CPS1 YJL172W 0.33 0.50 0.41 RPE1 YJL121C 0.07 0.27 0.17 HTZ1 YOL012C 0.41 0.48 0.44 JHD2 YJR119C 0.31 0.32 0.32 + DPB3 YBR278W 0.41 0.42 0.41 EAF1 YDR359C 0.29 0.13 0.21 + MNN10 YDR245W 0.12 0.13 0.13...”
• The protein transportation pathway from Golgi to vacuoles via endosomes plays a role in enhancement of methylmercury toxicity
  Hwang, Scientific reports 2014
  • “...IC50 of deletion cells/IC50 of control cells Metabolic pathway PSD2 YGR170W Phosphatidylserine decarboxylase 0.78 RPE1 YJL121C D-ribulose-5-phosphate 3-epimerase 0.67 ETR1 YBR026C 2-enoyl thioester reductase 0.68 Protein CKB2 YOR039W Subunit of the casein kinase 2 0.65 phosphorylation PFK1 YGR240C Subunit of the phosphofructokinase 0.74 Transporter BAP2 YBR068C...”
• Inaccurately assembled cytochrome c oxidase can lead to oxidative stress-induced growth arrest
  Bode, Antioxidants & redox signaling 2013
  • “...Reduced Strong Minor None None Other metabolic enzymes YJL121C RPE1 Reduced Reduced Strong Minor Strong Minor YIL155C GUT2 Reduced Reduced Strong Minor Strong...”
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NCU00519 ribulose-phosphate 3-epimerase from Neurospora crassa OR74A
40% identity, 84% coverage

• Glucose Starvation Alters Heat Shock Response, Leading to Death of Wild Type Cells and Survival of MAP Kinase Signaling Mutant
  Plesofsky, PloS one 2016
  • “...Transketol 0.85 4.91E-06 NCU06712 Pre5 1.17 0.181 NCU03100 6PGluconDH 0.82 7.08E-06 NCU03028 Dph1 1.29 0.030 NCU00519 RibulP3Epi 0.77 0.045 NCU01919 Ubiq C-Hydro 1.12 0.036 NCU03651 NADPMalicE 0.65 0.091 CELL DEATH TCA CYCLE NCU01419 QuinOxiR Pig3 0.77 0.049 NCU08471 SuccCoAlig 1.09 0.006 NCU05850 AIF 0.59 1.16E-09 NCU03004...”

RPE1_ORYSJ / Q9SE42 Ribulose-phosphate 3-epimerase, cytoplasmic isoform; Cyt-RPEase; Pentose-5-phosphate 3-epimerase; PPE; RPEcyt; Ribulose-5-phosphate-epimerase; EC 5.1.3.1 from Oryza sativa subsp. japonica (Rice) (see 2 papers)
Q9SE42 ribulose-phosphate 3-epimerase (EC 5.1.3.1) from Oryza sativa (see 2 papers)
42% identity, 93% coverage

• function: Catalyzes the reversible epimerization of D-ribulose 5- phosphate to D-xylulose 5-phosphate.
  catalytic activity: D-ribulose 5-phosphate = D-xylulose 5-phosphate (RHEA:13677)
  cofactor: Co(2+) Fe(2+) Mn(2+) Zn(2+) (Binds 1 divalent metal cation per subunit. Active with Co(2+), Fe(2+), Mn(2+) and Zn(2+).)
  subunit: Homodimer.
• Proteomic Analysis of a Rice Mutant sd58 Possessing a Novel d1 Allele of Heterotrimeric G Protein Alpha Subunit (RGA1) in Salt Stress with a Focus on ROS Scavenging
  Peng, International journal of molecular sciences 2019
  • “...1.070666181 1.389299887 Carbon metabolism Q7X8A1 Glyceraldehyde-3-phosphate dehydrogenase 19 15 53.23 269 1.185175004 0.893344399 1.068761987 1.417896607 Q9SE42 Ribulose-phosphate 3-epimerase 4 4 25.88 12 1.125852891 0.92458396 1.103994095 1.344318091 Q7XZW5 Malate dehydrogenase 15 13 52.26 77 1.236084716 0.958486603 1.042411695 1.344316299 Q40677 Fructose-bisphosphate aldolase 19 18 53.35 220 1.164792195 0.983320615...”

1h1yB / Q9SE42 The structure of the cytosolic d-ribulose-5-phosphate 3-epimerase from rice complexed with sulfate (see paper)
42% identity, 94% coverage

• Ligand: sulfate ion (1h1yB)

DDB_G0278275, XP_642255 ribulose phosphate 3-epimerase from Dictyostelium discoideum AX4
41% identity, 92% coverage

• A practical implementation of large transcriptomic data analysis to resolve cryptic species diversity problems in microbial eukaryotes
  Tekle, BMC evolutionary biology 2018
  • “...0.1 2840 XP_004344004 XP_637130 Phosphoglycerate kinase 0 0 0 13.0 0.4 15.0 0 3192 XP_004368096 XP_642255 Ribulosephosphate 3-epimerase 0.3 0 0.1 12.0 0.4 13.0 0.2 3202 XP_004368095 XP_646606 Proteasome 26S subunit 0 0 0 9.4 0 12.5 0.1 3401 XP_004341728 XP_628938 COP9 signalosome complex 0 0...”
• The amoebal MAP kinase response to Legionella pneumophila is regulated by DupA
  Li, Cell host & microbe 2009
  • “...E2-4 enzyme 2.01 5.50 1.82 Carbon metabolism Reduced Expression DDB_G0288289 RliF; Beta-xylosidase 0.49 0.18 0.26 DDB_G0278275 Ribulose phosphate-3-epimerase 0.36 0.26 0.62 DDB_G0272781 Phosphomannomutase 0.46 0.32 0.74 DDB_G0270018 Dehydrogenase signature 0.41 0.49 0.76 DDB_G0278341 Citrate lyase b-subunit 0.19 0.47 3.07 Enhanced Expression DDB_G0284277 Dehydrogenase signature (2 genes)...”

XP_002907019 ribulose-phosphate 3-epimerase from Phytophthora infestans T30-4
43% identity, 91% coverage

• Still acting green: continued expression of photosynthetic genes in the heterotrophic Dinoflagellate Pfiesteria piscicida (Peridiniales, Alveolata)
  Kim, PloS one 2013
  • “...triquetra Dinophyta 320C018635 7 712 AAW79354 5.95E-108 Heterocapsa triquetra Dinophyta Ribulose-phosphate 3-epimerase 320C010448 10 829 XP_002907019 1.05E-91 Phytophthora infestans Oomycota Phosphoglycerate kinase 320C003700 12 719 AAW79324 1.88E-76 Heterocapsa triquetra Dinophyta 320C003327 11 897 BAE07167 1.55E-157 Karenia brevis Dinophyta 320C004509 9 301 AAW79324 1.56E-45 Heterocapsa triquetra Dinophyta...”

RPE_HUMAN / Q96AT9 Ribulose-phosphate 3-epimerase; Ribulose-5-phosphate-3-epimerase; EC 5.1.3.1 from Homo sapiens (Human) (see paper)
Q96AT9 ribulose-phosphate 3-epimerase (EC 5.1.3.1) from Homo sapiens (see paper)
NP_954699 ribulose-phosphate 3-epimerase isoform 1 from Homo sapiens
39% identity, 96% coverage

• function: Catalyzes the reversible epimerization of D-ribulose 5- phosphate to D-xylulose 5-phosphate.
  catalytic activity: D-ribulose 5-phosphate = D-xylulose 5-phosphate (RHEA:13677)
  cofactor: Fe(2+) Mn(2+) Zn(2+) Co(2+) (Binds 1 divalent metal cation per subunit. Active with Fe(2+), and probably also with Mn(2+), Zn(2+) and Co(2+).)
  subunit: Homodimer.
• Liver Graft Proteomics Reveals Potential Incipient Mechanisms behind Early Renal Dysfunction after Liver Transplantation
  Norén, International journal of molecular sciences 2022
  • “...nuclear phosphoprotein 32 family member B 0.78 0.01 Cell differentiation Cell proliferation, apoptosis, cell cycle Q96AT9 RPE Ribulose-phosphate 3-epimerase 0.78 0.03 Metabolic process Biosynthesis of amino acids Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 0.78 0.02 Cell communication Rho gap activity Q9Y608 LRRFIP2 Leucine-rich repeat flightless-interacting protein...”
• The benefit of combining curcumin, bromelain and harpagophytum to reduce inflammation in osteoarthritic synovial cells
  Brochard, BMC complementary medicine and therapies 2021
  • “...0.66 GMFB Glia maturation factor beta false 1 2 1 false Protein up-regulated by LPS Q96AT9 51.49 RPE Ribulose-phosphate 3-epimerase false 0 0 3 false O14684 4.09 PTGES Prostaglandin E synthase false 8 4 0 false P43490 3.35 NAMPT Nicotinamide phphoribyltransferase true 8 0 4 false...”
• Proteomic Analysis in Morquio A Cells Treated with Immobilized Enzymatic Replacement Therapy on Nanostructured Lipid Systems
  Álvarez, International journal of molecular sciences 2019
  • “...proteasome non-ATPase regulatory subunit 7 0.0118 2,1633 O75368 SH3 domain-binding glutamic acid-rich-like protein 0.0004 2.0888 Q96AT9 Ribulose-phosphate 3-epimerase 0.0115 2.0690 P48147 Prolyl endopeptidase 0.0276 2.0209 P30498 HLA class I histocompatibility antigen, B-78 alpha chain 0.0315 1.8355 P04179 Superoxide dismutase [Mn], mitochondrial 0.0153 1.8015 Q7Z4H8 KDEL motif-containing...”
• Global Characterization of Protein Secretion from Human Macrophages Following Non-canonical Caspase-4/5 Inflammasome Activation.
  Lorey, Molecular & cellular proteomics : MCP 2017
• Novel Biomarker Proteins in Chronic Lymphocytic Leukemia: Impact on Diagnosis, Prognosis and Treatment.
  Admoni-Elisha, PloS one 2016
• Biophysical and Structural Characterization of Ribulose-5-phosphate Epimerase from Leishmania donovani
  Narsimulu, ACS omega 2022
  • “...out for the different organisms such as T. cruzi (XP_804346), P. falciparum (XP_001350598), H. sapiens (NP_954699), and L. donovani ( XP_003863992 ) by the Clustal Omega alignment tool ( https://www.ebi.ac.uk/Tools/msa/clustalo/ ) to understand the sequence homology and residues involved in binding with the substrate and product....”

3qc3A / Q96AT9 Crystal structure of a d-ribulose-5-phosphate-3-epimerase (np_954699) from homo sapiens at 2.20 a resolution
39% identity, 97% coverage

• Ligands: zinc ion; fe (iii) ion (3qc3A)

HTIA_0711 ribulose-phosphate 3-epimerase from Halorhabdus tiamatea SARL4B
43% identity, 92% coverage

• Pentose degradation in archaea: Halorhabdus species degrade D-xylose, L-arabinose and D-ribose via bacterial-type pathways
  Sutter, Extremophiles : life under extreme conditions 2020
  • “...HTIA_1041 HTIA_p2891 WP_136689521 Ribokinase HTIA_0439 WP_135662271 WP_136687548 Ribose-5-phosphate isomerase Huta_0832 HTIA_0710 WP_135665987 WP_136689787 D-Ribulose-5-phosphate-3-epimerase Huta_0833 HTIA_0711 WP_135665983 WP_136689785 Transaldolase Huta_0859 HTIA_0717 WP_135665975 WP_136687890 Transketolase Huta_0861 Huta_0860 HTIA_0719 HTIA_0718 WP_135665971 WP_167880040 WP_135665973 WP_169051793 WP_136687892 WP_136687891 Sequence comparison and phylogenetic affiliation of xylose isomerase from H. utahensis Xylose...”
  • “...H. tiamatea is absent in H. utahensis . HTIA_0710 and Huta_0832 encode ribose-5-phosphate isomerase and HTIA_0711 and Huta_0833 encode D-ribulose-5-phosphate-3-epimerase (grey arrows) HTIA_0439 encoding putative ribokinase in H. tiamatea was overexpressed and the recombinant protein was purified. Ribokinase was characterized as dimeric protein of 70kDa composed...”

Q8VEE0 Ribulose-phosphate 3-epimerase from Mus musculus
39% identity, 96% coverage

• Analysis of the Effect of Intestinal Ischemia and Reperfusion on the Rat Neutrophils Proteome.
  Tahir, Frontiers in molecular biosciences 2018
  • “...migration inhibitory factor EC 5.3.2.1 P30904 Mif 2 0.461822345 0.148221794 0.610044139 Ribulose-phosphate 3-epimerase EC 5.1.3.1 Q8VEE0 Rpe 4 0.174094827 0.354098654 0.180003827 NAD(P)H-hydrate epimerase EC 5.1.99.6 B0BNM1 Apoa1bp 4 0.03634563 0.110532371 0.074186741 LIGASES AspartatetRNA ligase, cytoplasmic EC 6.1.1.12 P15178 Dars 1 0.047262581 0.090565223 0.043302641 LeucinetRNA ligase, cytoplasmic...”

CT121 Ribulose-P Epimerase from Chlamydia trachomatis D/UW-3/CX
39% identity, 87% coverage

• Comprehensive Flux Modeling of Chlamydia trachomatis Proteome and qRT-PCR Data Indicate Biphasic Metabolic Differences Between Elementary Bodies and Reticulate Bodies During Infection
  Yang, Frontiers in microbiology 2019
  • “...1 . TABLE 1 Primers used for the PCR analysis. Oligo Gene Order Sequence 53 CT121 araD fwd GTCCGGAGCAGATCTTATTCAT rev TCAAAATGCACAATGATACGATCC CT750 tktB fwd CTAAAGATTCTCGATGGGTGAATA rev TGTAGTGGCTTCTACACCATCA CT313 tal fwd CTCTGACTTTTGTTTTAGATAAGATC rev TTTTAACTAATAAACGTTTCTTATCTCCT CT505 gapA fwd GGAGAAAGAAAGATCCGTTTCTTA rev TCCCATAACAAACGTAGGGACA CT714 gpdA fwd AGAATCTTTCTTTCACATACCACAT rev CGATTTCGCTTAGGAGTAAGC CT807...”
  • “...TABLE 6 Candidate genes for RT-qPCR validation. CT no. Gene Reaction EC no. Annotation Pathway CT121 araD R01529 5.1.3.1 Ribulose-phosphate 3-epimerase PPP CT750 tktB R01830 2.2.1.1 Transketolase CT313 tal R01827 2.2.1.2 Transaldolase CT378 pgi R02740 5.3.1.9 glucose-6-phosphate isomerase EMP CT205 pfkA_1 R04779 2.7.1.11 6-phosphofructokinase CT505 gapA...”
• The ompA gene in Chlamydia trachomatis differs in phylogeny and rate of evolution from other regions of the genome
  Brunelle, Infection and immunity 2006
  • “...adk hemZ gap thdF uvrC mrsA CT044 CT045 CT121 CT128 CT485 CT505 CT698 CT791 CT815 Noncoding regions ssb-pepA rpoB-r17 rs4-yceA thdF-psdD glyQ-pgsA porB ompA...”
• Chlamydia trachomatis lacks an adaptive response to changes in carbon source availability
  Nicholson, Infection and immunity 2004
  • “...1.37 0.01 1.33 0.01 Pentose-phosphate pathway CT063 gnd CT121 araA CT185 zwf CT186 devB CT213 rpiA CT313 tal CT331 dxs CT750 tktB 6-Phosphogluconate...”

CTL0376 ribulose-phosphate 3-epimerase from Chlamydia trachomatis 434/Bu
39% identity, 89% coverage

• Robust Heat Shock Response in Chlamydia Lacking a Typical Heat Shock Sigma Factor
  Huang, Frontiers in microbiology 2021
  • “...232 1.54 2.460.39 5.82E-03 trxB * CTL0354 Thioredoxin reductase TttAGTTT-N12-GTCGAAAC 76 1.66 nd na araD CTL0376 Ribulose-phosphate 3-epimerase TAAAaTTT-N11-ATtGAAGT 42 1.61 nd na ctl0399 CTL0399 T3SS exported membrane protein TcAAtATT-N12-ATCGATAA 393 2.18 3.040.75 1.92E-02 ctl0417a CTL0417a Hypothetical protein cAAAGAAC-N11-GCaGATGC 472 1.75 nd na ihfA CTL0519 DNA-binding...”

KP1_2791 D-allulose-6-phosphate 3-epimerase from Klebsiella pneumoniae NTUH-K2044
39% identity, 96% coverage

• YjcC, a c-di-GMP phosphodiesterase protein, regulates the oxidative stress response and virulence of Klebsiella pneumoniae CG43
  Huang, PloS one 2013
  • “...KP1_0853 Ascorbate specific PTS family enzyme 3.1 KP1_2793 D-arabinitol dehydrogenase 2.9 KP1_3760 Allulose-6-phosphate 3-epimerase 2.3 KP1_2791 Xylulokinase 2 KP1_3759 Transporter ABC transporter ATP-binding protein 2.5 KP1_5267 Putative transport protein/kinase ydjN 2 KP1_2272 Amino acid biosynthesis Sulfate adenylate transferase subunit 2 cysD 2.4 KP1_4384 Nucleotide biosynthesis and...”

AT1G63290 ribulose-phosphate 3-epimerase, cytosolic, putative / pentose-5-phosphate 3-epimerase, putative from Arabidopsis thaliana
40% identity, 96% coverage

• Reduction in chloroplastic ribulose-5-phosphate-3-epimerase decreases photosynthetic capacity in Arabidopsis
  Li, Frontiers in plant science 2022
  • “...( Andriotis and Smith, 2019 ). In addition to RPE, two other proteins encoded by At1g63290 and At3g01850 were proposed to be cytosolic RPE (cyRPE) ( Kruger and von Schaewen, 2003 ; Baune etal., 2020 ). Cytosolic RPEs have also been shown to be involved in...”
• A "footprint" of plant carbon fixation cycle functions during the development of a heterotrophic fungus
  Lyu, Scientific reports 2015
  • “...phosphoglycerate kinase SS1G_02281 AT4G37870 (0), AT5G65690 (4E-180) EC: 4.1.1.49 phosphoenolpyruvate carboxykinase (ATP) SS1G_01844 AT3G01850 (6E-60), AT1G63290 (2E-56), AT5G61410 (5E-42) EC: 5.1.3.1 ribulose-phosphate 3-epimerase SS1G_11433 AT3G55440 (1E-78), AT2G21170 (6E-71) EC: 5.3.1.1 triose-phosphate isomerase SS1G_08408 AT1G71100 (1E-19), AT2G01290 (4E-19) AT3G04790 (3E-15) EC: 5.3.1.6 ribose-5-phosphate isomerase SS1G_08975 AT1G53240 (4E-88),...”
• The membrane-tethered transcription factor ANAC089 serves as redox-dependent suppressor of stromal ascorbate peroxidase gene expression
  Klein, Frontiers in plant science 2012
  • “...AT3G24170 0.592559 6.6e 32 Glutathione reductase, putative AT2G45440 0.585632 4.9e 31 Dihydrodipicolinate synthase 2 (DHDPS2) AT1G63290 0.569233 4.8e 29 Ribulose-phosphate 3-epimerase, cytosolic, putative AT4G16265 0.560068 5.5e 28 DNA-directed RNA polymerase II, putative AT1G18320 0.559598 6.3e 28 Mitochondrial import inner membrane translocase subunit Tim17 AT3G17609 0.551960 4.5e...”
• Divergent evolutionary fates of major photosynthetic gene networks following gene and whole genome duplications
  Coate, Plant signaling & behavior 2011
  • “...0.68 -0.65 AT1G71100 -0.11 0.24 AT5G61410 0.68 -0.76 AT1G63290 -0.42 0.58 AT3G01850 -0.27 0.11 AT1G12230 0.45 -0.44 AT5G13420 -0.46 0.79 Pearson correlation...”
• Coronatine-insensitive 1 (COI1) mediates transcriptional responses of Arabidopsis thaliana to external potassium supply
  Armengaud, Molecular plant 2010
  • “...p450, putative 11.6 0.7 0.6 1.9 1.5 At5g23970 Acyltransferase family 12.8 0.7 0.8 1.8 1.5 At1g63290 D-ribulose-5-phosphate-3-epimerase 0.3 0.8 0.3 1.7 1.7 At4g25050 ACP4 Acyl carrier-like protein 6.2 0.8 0.9 1.6 1.8 At1g72610 GLP1 Germin-like protein 8.5 0.8 0.5 1.6 1.9 At5g65730 Xyloglucan endo-transglycosylase 13.3 0.6...”
• Comprehensive transcriptional profiling of NaCl-stressed Arabidopsis roots reveals novel classes of responsive genes
  Jiang, BMC plant biology 2006
  • “...all components of the PPP was also decreased (Table 3 ), including D-ribulose-5-phosphate 3-epimerase (At3g01850, At1g63290), ribose 5-phosphate isomerase (At2g01290, At3g04790), 6-phosphogluconolactonase (At5g24410, At3g02360), and glucose-6-phosphate-1-dehydrogenase (G6PDH) ( Additional File 1 ). The PPP is an important source of NADPH, especially in non-photosynthetic tissues, and therefore...”
• Full-length messenger RNA sequences greatly improve genome annotation
  Haas, Genome biology 2002
  • “...Exon number Exon length (nucleotides) Micro-exon sequence At5g51700 RAR1 Ceres:99615 2 of 6 3 AG<GGA>GT At1g63290 D-ribulose-5-phosphate-3-epimerase Ceres:37843 2 of 8 5 AG<GACGG>GT At3g01850 D-ribulose-5-phosphate-3-epimerase Ceres:2398 2 of 9 5 AG<GACGG>GT At4g01610 Cysteine protease Ceres:20761 5 of 11 5 AG<ATCAG>GT At5g14030 Expressed protein Ceres:16313. 5 of...”

A0A1D6I841 Ribulose-phosphate 3-epimerase from Zea mays
38% identity, 85% coverage

• 2-DE-based proteomic analysis of protein changes associated with etiolated mesocotyl growth in Zea mays
  Niu, BMC genomics 2019
  • “...APx1-cytosolic ascorbate peroxidase 13,47 B4FQX1 -1,4-glucan-protein synthase UDP-L-arabinose metabolic process, plant-type cell wall biogenesis 16 A0A1D6I841 Ribulose-phosphate 3-epimerase Carbohydrate metabolic process 49 A0A1R3MB28 Malate dehydrogenase 46 P49235 -D-glucoside glucohydrolase 29,30 Q9FR39 Profilin-5 17 B4FRS8 Germin-like protein subfamily T member 1 Manganese ion binding, nutrient reservoir activity...”

WP_136689785 ribulose-phosphate 3-epimerase from Halorhabdus amylolytica
41% identity, 90% coverage

• Pentose degradation in archaea: Halorhabdus species degrade D-xylose, L-arabinose and D-ribose via bacterial-type pathways
  Sutter, Extremophiles : life under extreme conditions 2020
  • “...WP_136689521 Ribokinase HTIA_0439 WP_135662271 WP_136687548 Ribose-5-phosphate isomerase Huta_0832 HTIA_0710 WP_135665987 WP_136689787 D-Ribulose-5-phosphate-3-epimerase Huta_0833 HTIA_0711 WP_135665983 WP_136689785 Transaldolase Huta_0859 HTIA_0717 WP_135665975 WP_136687890 Transketolase Huta_0861 Huta_0860 HTIA_0719 HTIA_0718 WP_135665971 WP_167880040 WP_135665973 WP_169051793 WP_136687892 WP_136687891 Sequence comparison and phylogenetic affiliation of xylose isomerase from H. utahensis Xylose isomerase of...”

Huta_0833 ribulose-phosphate 3-epimerase from Halorhabdus utahensis DSM 12940
42% identity, 92% coverage

• Pentose degradation in archaea: Halorhabdus species degrade D-xylose, L-arabinose and D-ribose via bacterial-type pathways
  Sutter, Extremophiles : life under extreme conditions 2020
  • “...Huta_1149 HTIA_1041 HTIA_p2891 WP_136689521 Ribokinase HTIA_0439 WP_135662271 WP_136687548 Ribose-5-phosphate isomerase Huta_0832 HTIA_0710 WP_135665987 WP_136689787 D-Ribulose-5-phosphate-3-epimerase Huta_0833 HTIA_0711 WP_135665983 WP_136689785 Transaldolase Huta_0859 HTIA_0717 WP_135665975 WP_136687890 Transketolase Huta_0861 Huta_0860 HTIA_0719 HTIA_0718 WP_135665971 WP_167880040 WP_135665973 WP_169051793 WP_136687892 WP_136687891 Sequence comparison and phylogenetic affiliation of xylose isomerase from H. utahensis...”
  • “...operative in most bacteria. In the genome of H. utahensis two clustered genes, Huta_0832 and Huta_0833, encoding putative ribose-5-phosphate isomerase and d -ribulose-5-phosphate-3-epimerase are annotated; a gene homologous to ribokinase from E. coli could not be identified. In contrast to H. utahensis , we found that...”

WP_135665983 ribulose-phosphate 3-epimerase from Halorhabdus rudnickae
42% identity, 88% coverage

• Pentose degradation in archaea: Halorhabdus species degrade D-xylose, L-arabinose and D-ribose via bacterial-type pathways
  Sutter, Extremophiles : life under extreme conditions 2020
  • “...HTIA_p2891 WP_136689521 Ribokinase HTIA_0439 WP_135662271 WP_136687548 Ribose-5-phosphate isomerase Huta_0832 HTIA_0710 WP_135665987 WP_136689787 D-Ribulose-5-phosphate-3-epimerase Huta_0833 HTIA_0711 WP_135665983 WP_136689785 Transaldolase Huta_0859 HTIA_0717 WP_135665975 WP_136687890 Transketolase Huta_0861 Huta_0860 HTIA_0719 HTIA_0718 WP_135665971 WP_167880040 WP_135665973 WP_169051793 WP_136687892 WP_136687891 Sequence comparison and phylogenetic affiliation of xylose isomerase from H. utahensis Xylose isomerase...”

SS1G_01844 hypothetical protein from Sclerotinia sclerotiorum 1980 UF-70
38% identity, 83% coverage

• A "footprint" of plant carbon fixation cycle functions during the development of a heterotrophic fungus
  Lyu, Scientific reports 2015
  • “...are ribose-5-phosphate isomerase (EC: 5.3.1.6, SS1G_08408), triose-phosphate isomerase (EC: 5.3.1.1, SS1G_11433), ribulose-phosphate 3-epimerase (EC: 5.1.3.1, SS1G_01844), transketolase (EC: 2.2.1.1, SS1G_10246), phosphoglycerate kinase (EC: 2.7.2.3, SS1G_01105), fructose-bisphosphate aldolase (EC: 4.1.2.13, SS1G_06561 and SS1G_06400), fructose-bisphosphatase or sedoheptulose-bisphosphatase (EC: 3.1.3.11 or EC: 3.1.3.37, SS1G_11369) and glyceraldehyde-3-phosphate dehydrogenase (phosphorylating or...”
  • “...(1E-106), EC: 2.7.2.3 phosphoglycerate kinase SS1G_02281 AT4G37870 (0), AT5G65690 (4E-180) EC: 4.1.1.49 phosphoenolpyruvate carboxykinase (ATP) SS1G_01844 AT3G01850 (6E-60), AT1G63290 (2E-56), AT5G61410 (5E-42) EC: 5.1.3.1 ribulose-phosphate 3-epimerase SS1G_11433 AT3G55440 (1E-78), AT2G21170 (6E-71) EC: 5.3.1.1 triose-phosphate isomerase SS1G_08408 AT1G71100 (1E-19), AT2G01290 (4E-19) AT3G04790 (3E-15) EC: 5.3.1.6 ribose-5-phosphate isomerase...”

FAD_0295 ribulose-phosphate 3-epimerase from Ferroplasma acidiphilum
38% identity, 88% coverage

• Metabolic and evolutionary patterns in the extremely acidophilic archaeon Ferroplasma acidiphilum Y^T
  Golyshina, Scientific reports 2017
  • “...isomerase (FAD_0562); 24, phosphoglucomutase/phosphomannomutase (FAD_0602); 25, transketolase (FAD_14771476); 26, transaldolase (FAD_1201; FAD_1475); 27, ribulose-phosphate 3-epimerase (FAD_0295). Abbreviations used: Fd, electron carrier ferredoxin; NAD, nicotinamide adenine dinucleotide; CoA, Coenzyme-A; PEP, phosphoenolpyruvate; UQ, ubiquinone. Enzymes labeled in blue are potentially involved in anaplerotic assimilation of CO 2 ....”

NP_001137381 ribulose-phosphate 3-epimerase-like protein 1 from Homo sapiens
38% identity, 96% coverage

• Associations of RPEL1 and miR-1307 gene polymorphisms with disease susceptibility, glucocorticoid efficacy, anxiety, depression, and health-related quality of life in Chinese systemic lupus erythematosus patients.
  Yan, Lupus 2022 (PubMed)
  • GeneRIF: Associations of RPEL1 and miR-1307 gene polymorphisms with disease susceptibility, glucocorticoid efficacy, anxiety, depression, and health-related quality of life in Chinese systemic lupus erythematosus patients.

CPn0185 Ribulose-P Epimerase from Chlamydophila pneumoniae CWL029
39% identity, 89% coverage

• Growth of Chlamydia pneumoniae Is Enhanced in Cells with Impaired Mitochondrial Function
  Käding, Frontiers in cellular and infection microbiology 2017
  • “...Cpn0102 cydA cytochrome D ubiquinol oxidase subunit I 1,178 2,530 Cpn0106 phoH ATPase 1,056 1,515 Cpn0185 rpe ribulose-phosphate 3-epimerase 134 283 Cpn0238 zwf glucose-6-phosphate 1-dehydrogenase 1,134 1,977 Cpn0624 gapA glyceraldehyde-3-phosphate dehydrogenase 2,291 3,241 TRANSPORTER Cpn0023 yjjK ABC transporter ATPase 872 1,532 Cpn0061 ptsN_2 PTS IIA protein...”
• Gene expression profiles of Chlamydophila pneumoniae during the developmental cycle and iron depletion-mediated persistence
  Mäurer, PLoS pathogens 2007
  • “...Genes involved with the pentose phosphate pathway, including zwf ( Cpn0238 [cluster 5]), rpe ( Cpn0185 [cluster 7]), and tal ( Cpn0083 [cluster 8]), were expressed in both mid and late classes. The gene for glucose-6-phosphate isomerase, pgi (Cpn1025), a dimeric enzyme catalyzing the reversible isomerization...”

XP_001350598 ribulose-phosphate 3-epimerase, putative from Plasmodium falciparum 3D7
35% identity, 95% coverage

• Biophysical and Structural Characterization of Ribulose-5-phosphate Epimerase from Leishmania donovani
  Narsimulu, ACS omega 2022
  • “...alignment was carried out for the different organisms such as T. cruzi (XP_804346), P. falciparum (XP_001350598), H. sapiens (NP_954699), and L. donovani ( XP_003863992 ) by the Clustal Omega alignment tool ( https://www.ebi.ac.uk/Tools/msa/clustalo/ ) to understand the sequence homology and residues involved in binding with the...”
• Structure of a ribulose 5-phosphate 3-epimerase from Plasmodium falciparum.
  Caruthers, Proteins 2006 (PubMed)
  • GeneRIF: The structure is a classicbarrel fold. A coordinated Zn ion and a bound sulfate ion in the active site of the enzyme allow for a greater understanding of the mechanism of action.

1tqxA / Q8I5L3 Crystal structure of pfal009167 a putative d-ribulose 5-phosphate 3- epimerase from p.Falciparum (see paper)
35% identity, 96% coverage

• Ligands: sulfate ion; zinc ion (1tqxA)

D8PP98 Ribulose-phosphate 3-epimerase from Schizophyllum commune (strain H4-8 / FGSC 9210)
37% identity, 95% coverage

• Improving the Proteome-Mining of Schizophyllum commune to Enhance Medicinal Mushroom Applications
  Desiderio, Journal of fungi (Basel, Switzerland) 2025
  • “...A2 PSMs Sample B D8PMS0 6-phosphogluconate dehydrogenase, decarboxylating (EC 1.1.1.44) 15.7 * 35.7 14.3 * D8PP98 Ribulose-phosphate 3-epimerase (EC 5.1.3.1) 1.7 2.0 2.7 D8PNV4 Glucose-6-phosphate 1-dehydrogenase (EC 1.1.1.49) 0.7 * 15.7 1.7 * D8PNV6 Glucose-6-phosphate 1-dehydrogenase (EC 1.1.1.49) 1.0 3.7 0.0 * D8PN33 6-phosphogluconolactonase (6PGL) (EC...”

MMP1114 Pentose-5-phosphate 3-epimerase from Methanococcus maripaludis S2
37% identity, 93% coverage

• Metabolic processes of Methanococcus maripaludis and potential applications
  Goyal, Microbial cell factories 2016
  • “...6-phosphogluconate dehydrogenase] and high activities of non-oxidative enzymes [transketolase (MMP1113, MMP1115), transaldolase (MMP1308), ribose-5-phosphate 3-epimerase (MMP1114), and ribulose-5-phosphate isomerase (MMP1189)] [ 41 , 50 ] . Tumbula et al. [ 67 ] supported this observation by ruling out oxidative PPP based on the labelling patterns of...”

PY17X_1437500 ribulose-phosphate 3-epimerase, putative from Plasmodium yoelii
34% identity, 96% coverage

• Why is Babesia not killed by artemisinin like Plasmodium?
  Si, Parasites & vectors 2023
  • “...clear that more malaria parasites expressing glucose-6-phosphate dehydrogenase-6-phosphogluconolactonase (PY17X_1321300), 6-phosphogluconate dehydrogenase, decarboxylating (PY17X_1322200), ribulose-phosphate 3-epimerase (PY17X_1437500), ribose-5-phosphate isomerase (PY17X_1115400), and transketolase (PY17X_0110700) were eliminated 24h post-artemether treatment than B. microti (Fig. 2 e). Babesia microti that express DNA synthesis-, antioxidation-, and glycolysis-related genes are not susceptible...”

KP1_RS12830 D-allulose 6-phosphate 3-epimerase from Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044
36% identity, 88% coverage

• Identification of Pathogenicity-Associated Loci in Klebsiella pneumoniae from Hospitalized Patients
  Martin, mSystems 2018
  • “...31 (81.5) 43 (56.6) 0.009493 KP1_RS12835, KPNJ1_RS13415, KPN_01701 Alkaline phosphatase/deoR 31 (81.5) 43 (56.6) 0.009493 KP1_RS12830 KPNJ1_RS13420, KPN_01700 Allulose-6-phosphate 3-epimerase 31 (81.5) 43 (56.6) 0.009493 KP1_RS12825, KPNJ1_RS13425, KPN_01699 Carbohydrate kinase (ribokinase) 31 (81.5) 43 (56.6) 0.009493 KP1_RS12820, KPNJ1_RS13430, KPN_01698 Permease 31 (81.5) 43 (56.6) 0.009493 KP1_RS26720...”

SUB0285 ribulose-phosphate 3-epimerase from Streptococcus uberis 0140J
34% identity, 88% coverage

• Evidence for niche adaptation in the genome of the bovine pathogen Streptococcus uberis
  Ward, BMC genomics 2009
  • “...a mannitol-specific PTS (SUB0288 and SUB0289) as part of an operon with a ribulose-phosphate 3-epimerase (SUB0285), 6-phospho-3-hexuloisomerase (SUB0286) and a mannitol-1-phosphate 5-dehydrogenase (SUB0287). These five CDSs do not have orthologous matches in the other streptococci. The metabolic genes in this cluster encode functions for conversion of...”

PAAG_01632 ribulose-phosphate 3-epimerase from Paracoccidioides lutzii Pb01
37% identity, 84% coverage

• Transcriptional profile of Paracoccidioides spp. in response to itraconazole
  da, BMC genomics 2014
  • “...Succinyl 3-ketoacid-coenzime A transferase ( SCOT ) PAAG_05093 2.6e-17 +1 Ribulose-phosphate 3-epimerase ( RP3E ) PAAG_01632 6.5e-42 -17 Aconitase ( ACO ) PAAG_05328 5.8e-18 -2 D-amino-acid oxidase ( DAAO ) PAAG_02361 2.4e-38 -3 Er-associated proteolytic system protein ( ERAD ) PAAG_04633 8.6e-40 -4 Isovaleryl-CoA dehydrogenase (...”

EMQU_2813 D-allulose 6-phosphate 3-epimerase from Enterococcus mundtii QU 25
35% identity, 88% coverage

• Complete genome sequence of Enterococcus mundtii QU 25, an efficient L-(+)-lactic acid-producing bacterium
  Shiwa, DNA research : an international journal for rapid publication of reports on genes and genomes 2014
  • “...a transketolase (EMQU_2812) and a transaldolase (EMQU_2814). Furthermore, this cluster contains an allulose-6-phosphate 3-epimerase gene (EMQU_2813), genes for a fructose-like phosphotransferase system (EMQU_2815-2819), and a putative transcriptional regulator (EMQU_2820). Transketolase is a key enzyme in the PP/glycolytic pathway, and the QU 25 chromosome additionally harbours one...”

C9J9T0 ribulose-phosphate 3-epimerase from Homo sapiens
39% identity, 82% coverage

• LC‑MS/MS proteomic analysis revealed novel associations of 37 proteins with T2DM and notable upregulation of immunoglobulins.
  Abdulwahab, International journal of molecular medicine 2019
  • “...P-value (ANOVA) MFC 30 P01861 Ig -4 chain C region 8 3 0.0002 2.360 31 C9J9T0 Ribulose-5-phosphate-3-epimerase, isoform CRA_a 1 1 0.0007 2.914 32 Q96LX7-3 Isoform 4 of Coiled-coil domain-containing protein 17 2 1 0.0013 2.842 33 Q9HAS0 Protein Njmu-R1 2 2 0.0053 1.615 34 P19827...”

B1745_06310 ribulose-phosphate 3-epimerase from Lactobacillus amylolyticus
36% identity, 95% coverage

• Adaptive mechanism of Lactobacillus amylolyticus L6 in soymilk environment based on metabolism of nutrients and related gene-expression profiles
  Fei, Food science & nutrition 2022
  • “...1.32 B1745_02465 galE UDPglucose4epimerase 1.30 B1745_07245 poxL pyruvate oxidase 1.29 B1745_04860 pgl 3carboxymuconate cyclase 1.29 B1745_06310 rpe ribulose phosphate epimerase 1.22 B1745_00870 aldose 1epimerase 1.19 B1745_07130 bdhAB aldo/keto reductase 1.19 B1745_03235 lysozyme lysin 1.12 B1745_01565 gntK, idnK gluconate kinase 1.09 B1745_04605 pta phosphate acetyltransferase 1.09 B1745_05160...”

E9B3Z3 Ribulose-phosphate 3-epimerase from Leishmania mexicana (strain MHOM/GT/2001/U1103)
39% identity, 83% coverage

• Quantitative proteomic analysis of amastigotes from Leishmania (L.) amazonensis LV79 and PH8 strains reveals molecular traits associated with the virulence phenotype
  de, PLoS neglected tropical diseases 2017
  • “...subunit A4H800 2,00 Up LV79 ATP synthase subunit alpha Q4QJF1 1,99 Up LV79 Ribulose-phosphate 3-epimerase E9B3Z3 1,95 Up LV79 Putative thimet oligopeptidase A4HF12 1,88 Up LV79 Putative RNA helicase A4HC04 1,88 Up LV79 Putative uncharacterized protein E9AY45 1,87 Up LV79 Conserved TPR domain protein E9B146 1,72...”

llmg_0957 ribulose-phosphate 3-epimerase from Lactococcus lactis subsp. cremoris MG1363
35% identity, 97% coverage

• Transcriptome landscape of Lactococcus lactis reveals many novel RNAs including a small regulatory RNA involved in carbon uptake and metabolism
  van, RNA biology 2016
  • “...a PTS transporter ( llmg_0963 ), 2 -glucosidases ( llmg_0959/0960 ), a ribulose-phosphate 3-epimerase ( llmg_0957 ), a ribose-5-phosphate isomerase B ( llmg_0962 ) and an AraC transcriptional regulator ( llmg_0962 ). Table1 provides a complete list of differentially expressed genes upon pulse-expression of LLMGnc_147. Since...”
  • “...6.07 3.66 151 9.10E-35 8.60E-32 67.1 103.2 llmg_0959 5.87 3.56 111 7.20E-26 4.10E-23 58.5 74.38 llmg_0957 5.8 3.61 193 7.20E-44 1.00E-40 55.6 132.84 llmg_0958 5.42 3.97 123 1.40E-28 9.80E-26 42.8 83.07 llmg_0962 4.69 0.89 30.3 3.70E-08 1.30E-05 25.9 16.21 llmg_0963 4.54 0.26 17.5 2.90E-05 4.30E-03 23.3...”
• Complete genome sequence of the prototype lactic acid bacterium Lactococcus lactis subsp. cremoris MG1363
  Wegmann, Journal of bacteriology 2007
  • “...llmg_0489 llmg_0490 llmg_0666 llmg_0737 llmg_0738 llmg_0957 llmg_0958 llmg_0959 llmg_0960 llmg_0961 llmg_0963 llmg_1009 llmg_1010 llmg_1011 llmg_1162 llmg_1163...”

XP_003863992 ribulose-5-phosphate 3-epimerase, putative from Leishmania donovani
38% identity, 81% coverage

• Biophysical and Structural Characterization of Ribulose-5-phosphate Epimerase from Leishmania donovani
  Narsimulu, ACS omega 2022
  • “...leishmaniasis. 5 Methods 5.1 Sequence and Phylogenetic Analysis The protein sequence of Ld RPE ( XP_003863992 ) was retrieved from the NCBI database ( https://www.ncbi.nlm.nih.gov/protein ) and submitted to ProtParam ( https://web.expasy.org/protparam/ ) and TOPCONS ( http://topcons.cbr.su.se/ ) tools for sequence analysis. Simultaneously, the multiple sequence...”
  • “...such as T. cruzi (XP_804346), P. falciparum (XP_001350598), H. sapiens (NP_954699), and L. donovani ( XP_003863992 ) by the Clustal Omega alignment tool ( https://www.ebi.ac.uk/Tools/msa/clustalo/ ) to understand the sequence homology and residues involved in binding with the substrate and product. Further, a phylogenetic study of...”

KPN_01700 putative ribulose-phosphate 3-epimerase from Klebsiella pneumoniae subsp. pneumoniae MGH 78578
37% identity, 86% coverage

• Identification of Pathogenicity-Associated Loci in Klebsiella pneumoniae from Hospitalized Patients
  Martin, mSystems 2018
  • “...43 (56.6) 0.009493 KP1_RS12835, KPNJ1_RS13415, KPN_01701 Alkaline phosphatase/deoR 31 (81.5) 43 (56.6) 0.009493 KP1_RS12830 KPNJ1_RS13420, KPN_01700 Allulose-6-phosphate 3-epimerase 31 (81.5) 43 (56.6) 0.009493 KP1_RS12825, KPNJ1_RS13425, KPN_01699 Carbohydrate kinase (ribokinase) 31 (81.5) 43 (56.6) 0.009493 KP1_RS12820, KPNJ1_RS13430, KPN_01698 Permease 31 (81.5) 43 (56.6) 0.009493 KP1_RS26720 , KPK_RS27195...”

TGME49_247670 ribulose-phosphate 3 epimerase family protein from Toxoplasma gondii ME49
42% identity, 43% coverage

• CSGID Solves Structures and Identifies Phenotypes for Five Enzymes in Toxoplasma gondii
  Lykins, Frontiers in cellular and infection microbiology 2018
  • “...( http://toxodb.org/toxo/ ), including these gene IDs: Tg PGM: TGME49_297060, Tg NDK: TGME49_295350, Tg RPE: TGME49_247670, Tg RPI: TGME49_239310, Tg OAT: TGME49_269110. Results Structural genomic pipeline for Toxoplasma The NIAID Structural Genomics Centers selected 265 proteins for the Toxoplasma Structural Genomic Pipeline in three phases (Figure...”

SCLAV_p0975 ribulose-phosphate 3-epimerase from Streptomyces clavuligerus
38% identity, 89% coverage

• Transcriptomic analysis of Streptomyces clavuligerus ΔccaR::tsr: effects of the cephamycin C-clavulanic acid cluster regulator CcaR on global regulation
  Alvarez-Álvarez, Microbial biotechnology 2014
  • “...<1E 06 1.75 <1E 06 SCLAV_4529 glcP Glucose permease 1.79 <1E 06 0.60 7.97E 02 SCLAV_p0975 Ribulose-phosphate 3-epimerase 1.25 <1E 06 1.36 <1E 06 Nitrogen metabolism SCLAV_4534 amtB Ammonium transporter 4.10 <1E 06 5.04 <1E 06 SCLAV_4535 glnB Putative nitrogen regulatory protein P-II 4.39 <1E 06...”

LMOf2365_2641 ribulose-phosphate 3-epimerase family protein from Listeria monocytogenes str. 4b F2365
36% identity, 94% coverage

• Catabolite control protein C contributes to virulence and hydrogen peroxide-induced oxidative stress responses in Listeria monocytogenes
  Ogunleye, Frontiers in microbiology 2024
  • “...subunit: Fructose-bisphosphate aldolase class-II 1.6 4.0E-02 LMOf2365_2168 D-tagatose-1,6-bisphosphate aldolase subunit: Fructose-bisphosphate aldolase class-II 2.0 8.0E-03 LMOf2365_2641 Ribulose-phosphate 3 epimerase family 1.8 1.9E-02 LMOf2365_0365 ( rpiB 1) Ribose-5-P isomerase B 1.9 1.4E-02 Amino acids biosynthesis, 2-oxocarboxylic acid metabolism LMOf2365_0363 Probable transaldolase 2: Transaldolase 2.1 8.2E-03 LMOf2365_0395 Probable...”
• Identification of genetic elements required for Listeria monocytogenes growth under limited nutrient conditions and virulence by a screening of transposon insertion library
  Narayanan, Frontiers in microbiology 2022
  • “...73.39 proA ::Tn LMOf2365_1276 Glutamate-5-semialdehyde dehydrogenase 67.2 72.85 100 53.2 74.7 49.71 94.56 2641 ::Tn LMOf2365_2641 Ribulose-phosphate 3-epimerase family protein 82.2 74.43 104 90.89 56.90 53.61 74.40 gcvT ::Tn LMOf2365_1365 Glycine cleavage system T protein 117 102 121 115.5 20.81 51.07 84.68 LP2387 ::Tn LMOf2365_2387 Putative...”

lmo0735 similar to Ribulose-5-Phosphate 3-Epimerase from Listeria monocytogenes EGD-e
LMON_0740 ribulose-phosphate 3-epimerase from Listeria monocytogenes EGD
35% identity, 97% coverage

• RECON gene disruption enhances host resistance to enable genome-wide evaluation of intracellular pathogen fitness during infection
  Stamm, mBio 2024
  • “...in Lm and expected expression under indicated conditions. ( B ) Relative gene expression of lmo0735 and lmo0737 in Lm grown to mid-log phase in BHI or BHI supplemented with 1% D-allose. Data are normalized to BHI for each gene. * P < 0.05 by Mann-Whitney...”
  • “...CFU at 72 hpi. Fewer CFU were recovered from livers of mice infected with alsR lmo0735 compared to alsR alone ( Fig. 4G ; Fig. S4J). In contrast, alsR lmo0736 , alsR lmo0737 , alsR lmo0738, and alsR lmo0739 CFU were similar to alsR CFU (...”
• Horizontal Gene Transfer and Loss of Serotype-Specific Genes in Listeria monocytogenes Can Lead to Incorrect Serotype Designations with a Commonly-Employed Molecular Serotyping Scheme
  Brown, Microbiology spectrum 2023
  • “...of approximately 38% ( 33 ), while the GC content of others (e.g., lmo0734 , lmo0735 ) was much lower ( Fig.3 ). Genes downstream of lmo0739 continued to have abnormally low GC content ( Fig.3 ), suggesting that this entire chromosomal region may have been...”
• Identification and Characterization of als Genes Involved in D-Allose Metabolism in Lineage II Strain of Listeria monocytogenes
  Zhang, Frontiers in microbiology 2018
  • “...pIMK2 lmo0734 0735 0737 0738 0739 pAL6 pIMK2 lmo0734 0736 0737 0738 0739 pAL7 pIMK2 lmo0735 0736 0737 0738 0739 STRAINS (SEROTYPE) EGD-e (1/2a) lmo0734, 0735, 0736, 0737, 0738, 0739 ICDC-LM188 (1/2b) None RS801 (1/2b) ICDC-LM188::pAL1 RS802 (1/2b) ICDC-LM188::pAL2 RS803 (1/2b) ICDC-LM188::pAL3 RS804 (1/2b) ICDC-LM188::pAL4 RS805...”
  • “...RS805, RS806, and RS807 did not (Supplementary Figure 1B ). This revealed that genes lmo0734, lmo0735 , and lmo0736 were essential for D-allose metabolism of L. monocytogenes . The recombinant strains RS801, RS802, RS803, and RS804 showed different growth rates in MWB medium with 0.2% D-allose...”
• A Comprehensive Evaluation of the Genetic Relatedness of Listeria monocytogenes Serotype 4b Variant Strains
  Burall, Frontiers in public health 2017
  • “...Based on motif analyses, these genes encode a transcriptional regulator (lmo0734), a putative ribulose-5-phosphate 3-epimerase (lmo0735), a putative ribose-5-phosphate isomerase (lmo0736), phosphotransferase system IIABC (lmo0738), and a glucosidase (lmo0739). The protein encoded by lmo0737 has no annotated function. Prior work generating a deletion of this region...”
  • “...a shift from 100% threonine to approximately half possessing a serine residue at position 240. Lmo0735 had a near complete (99%) transition from lysine to arginine at position 215. Lmo0737 in 4bV had serine in all but one strain, instead of a proline, at site 237....”
• Strand specific RNA-sequencing and membrane lipid profiling reveals growth phase-dependent cold stress response mechanisms in Listeria monocytogenes
  Hingston, PloS one 2017
  • “...protein lmo2522 4 -1.33 2.20 0.95 4.50 1.70 G5 late-stationary phase LMON_0740 D-allulose-6-phosphate 3-epimerase + lmo0735 2 -0.81 -1.52 -2.11 -1.19 10.05 LMON_0741 D-allose-6-phosphate isomerase + lmo0736 2 -0.52 -1.36 -1.52 -0.35 10.41 LMON_0742 Hypothetical protein + lmo0737 2 0.04 -0.98 -1.86 1.08 10.49 LMON_0743 PTS...”
• Listeria monocytogenes differential transcriptome analysis reveals temperature-dependent Agr regulation and suggests overlaps with other regulons
  Garmyn, PloS one 2012
  • “...genes with higher transcript levels. These genes are under the negative control of B except lmo0735, lmo0736, lmo0737 and lmo0738 . Seventeen genes under the positive control of B were included in the set of genes with lower transcript level. Finally, 11 genes positively regulated by...”
• Atypical Listeria monocytogenes serotype 4b strains harboring a lineage II-specific gene cassette
  Lee, Applied and environmental microbiology 2012
  • “...upregulated in the stationary phase at 37C. Furthermore, lmo0735, -0736, -0738, and -0739 were upregulated in the intestines of infected mice while lmo0739 was...”
• Listeria monocytogenes grown at 7° C shows reduced acid survival and an altered transcriptional response to acid shock compared to L. monocytogenes grown at 37° C
  Ivy, Applied and environmental microbiology 2012
  • “...38 1 5 7 2 0 1 1 lmo0299, lmo0735, lmo1114 lmo0049, lmo0728, lmo2445 lmo0680, lmo1406, minD lmo0770, murC, ndk lmo2210 lmo0998, lmo1597, lmmo1965 lmo952,...”
• More
• Strand specific RNA-sequencing and membrane lipid profiling reveals growth phase-dependent cold stress response mechanisms in Listeria monocytogenes
  Hingston, PloS one 2017
  • “...2.33 LMON_2534 Cell wall-binding protein lmo2522 4 -1.33 2.20 0.95 4.50 1.70 G5 late-stationary phase LMON_0740 D-allulose-6-phosphate 3-epimerase + lmo0735 2 -0.81 -1.52 -2.11 -1.19 10.05 LMON_0741 D-allose-6-phosphate isomerase + lmo0736 2 -0.52 -1.36 -1.52 -0.35 10.41 LMON_0742 Hypothetical protein + lmo0737 2 0.04 -0.98 -1.86...”

lmo2661 similar to ribulose-5-phosphate 3-epimerase from Listeria monocytogenes EGD-e
36% identity, 94% coverage

• In vivo transcriptional profiling of Listeria monocytogenes and mutagenesis identify new virulence factors involved in infection
  Camejo, PLoS pathogens 2009
  • “...four genes involved in the non-oxidative phase of the pentose phosphate pathway ( lmo2660 , lmo2661 , lmo2662 and lmo2674 ). The final step of glycolysis leads to pyruvate, which is then converted to acetyl-CoA by the pyruvate dehydrogenase complex. We found this complex partly up...”
• Microarray-based characterization of the Listeria monocytogenes cold regulon in log- and stationary-phase cells
  Chan, Applied and environmental microbiology 2007
  • “...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 4C than...”
  • “...and that consisting of lmo2661, lmo2660, and lmo2659 (encoding ribulose-5-phosphate-3-epimerase, transketolase, and ribulose-phosphate-3-epimerase,...”

LACR_1639 Pentose-5-phosphate-3-epimerase from Lactococcus lactis subsp. cremoris SK11
34% identity, 97% coverage

• Genome-scale diversity and niche adaptation analysis of Lactococcus lactis by comparative genome hybridization using multi-strain arrays
  Siezen, Microbial biotechnology 2011
  • “...in FG2, HP, LMG6897T LACR_1637 6Phosphobetaglucosidase (EC 3.2.1.86) LACR_1638 rpiB Ribose5phosphate isomerase B (EC 5.3.1.6) LACR_1639 rpe Ribulose5phosphate 3epimerase (EC 5.1.3.1) LACR_1640 Transcription regulator, LacI family LACR_2591 Hypothetical protein LACR_2592 Hypothetical protein LACR_2593 Hypothetical protein LACR_2594 Hypothetical protein a. For the conserved OGs, members from a...”

LOC101490106 ribulose-phosphate 3-epimerase, cytoplasmic isoform-like from Cicer arietinum
44% identity, 70% coverage

• Overexpression of Chickpea Defensin Gene Confers Tolerance to Water-Deficit Stress in Arabidopsis thaliana
  Kumar, Frontiers in plant science 2019
  • “...protein kinase HERK 1-like protein-coding 80 LOC101508898 3.48617 101508898 Ca1 reticuline oxidase-like protein-like protein-coding 81 LOC101490106 4.69002 101490106 Ca1 ribulose-phosphate 3-epimerase, cytoplasmic isoform-like protein-coding 82 LOC101488811 2.10436 101488811 Ca1 serine carboxypeptidase-like 45-like protein-coding 83 LOC101493761 2.52261 101493761 Ca6 serine hydroxymethyltransferase 1-like protein-coding 84 LOC101513097 3.47589 101513097...”

LMOf2365_0528 ribulose-phosphate 3-epimerase family protein from Listeria monocytogenes str. 4b F2365
34% identity, 92% coverage

• Catabolite control protein C contributes to virulence and hydrogen peroxide-induced oxidative stress responses in Listeria monocytogenes
  Ogunleye, Frontiers in microbiology 2024
  • “...Pentose phosphate pathway (PPP) LMOf2365_0363 Fructose-6-phosphate aldolase 2.1 8.2E-03 LMOf2365_0379 D-tagatose-1,6-bisphosphate aldolase class-II 1.5 6.2E-03 LMOf2365_0528 Ribulose-phosphate 3 epimerase family 2.1 9.3E-03 LMOf2365_1054 Putative transketolase C-terminal section 1.7 1.0E-02 LMOf2365_2167 D-tagatose-1,6-bisphosphate aldolase subunit: Fructose-bisphosphate aldolase class-II 1.6 4.0E-02 LMOf2365_2168 D-tagatose-1,6-bisphosphate aldolase subunit: Fructose-bisphosphate aldolase class-II 2.0...”
  • “...transaldolase 2: Transaldolase 2.1 8.2E-03 LMOf2365_0395 Probable triosephosphate isomerase 2 ( tpiA -1) 2.0 1.3E-02 LMOf2365_0528 Ribulose-phosphate 3 epimerase family 2.1 9.3E-03 LMOf2365_1654 Anthranilate synthase component 2: Glutamine amidotransferase class-I ( trpG ) 1.5 4.9E-02 LMOf2365_1655 Anthranilate synthase component 1, N terminal region ( trpE )...”

lmo0499 similar to ribulose-5-phosphate 3 epimerase from Listeria monocytogenes EGD-e
32% identity, 92% coverage

• The transcriptional response of Listeria monocytogenes during adaptation to growth on lactate and diacetate includes synergistic changes that increase fermentative acetoin production
  Stasiewicz, Applied and environmental microbiology 2011
  • “...protein gene lmo0742 Pentose phosphate epimerase gene (lmo0499 rpe), cytochrome d oxidase subunit gene (lmo2718 cydA) lmo0433 (inlA), two-component system genes...”
• Glycerol metabolism and PrfA activity in Listeria monocytogenes
  Joseph, Journal of bacteriology 2008
  • “...lmo0429a,b lmo0431 inlAb,d inlBb,d lmo0456 lmo0458 lmo0498 lmo0498 lmo0499 YG-B 5416 JOSEPH ET AL. J. BACTERIOL. TABLE 2--Continued Fold induction Gene Function...”

DEALK_13610 ribulose-phosphate 3-epimerase from Dehalogenimonas alkenigignens
37% identity, 91% coverage

• Genome sequence of the organohalide-respiring Dehalogenimonas alkenigignens type strain (IP3-3(T))
  Key, Standards in genomic sciences 2016
  • “...HypD (DEALK_04300), DNA gyrase subunit A (DEALK_05640), excinuclease ABC subunit A (DEALK_13870), and ribulose-phosphate 3-epimerase (DEALK_13610). Of the conserved signature proteins (CSPs) that were reported previously to be specific for the class Dehalococcoidia [ 25 ], however, several did not have homologs in D. alkenigignens IP3-3...”

CD2319 putative ribulose-phosphate 3-epimerase from Clostridium difficile 630
CD630_23190, CDIF630erm_02557 ribulose-phosphate 3-epimerase from Clostridioides difficile
32% identity, 89% coverage

• Global transcriptional control by glucose and carbon regulator CcpA in Clostridium difficile
  Antunes, Nucleic acids research 2012
  • “...kinase; fumB (CD1004), fumarate hydratase subunit B; CD1005, putative nicotinamide adenine dinucleotide-dependent malic enzyme; rpe (CD2319), putative ribulose-phosphate 3-epimerase; rpiB1 (CD2320), ribose-5-phosphate isomerase B1; rpiB2 (CD3480), ribose-5-phosphate isomerase B2; rbsK (CD0299), ribokinase; tkt (CD2321), transketolase, central and C-terminal; tkt (CD2322), transketolase, N-terminal; CD0764CD0768, PTS sorbitol IIC,...”
• Iron Regulation in Clostridioides difficile
  Berges, Frontiers in microbiology 2018
  • “...CD630_08860 CDIF630erm_01006 amyB Amylopullulanase -0.12 -0.29 -2.68 0.05 CD630_23180 CDIF630erm_02556 Phosphohexomutase 2.01 0.58 1.56 0.21 CD630_23190 CDIF630erm_02557 rpe Ribulose-phosphate 3-epimerase 1.24 ON 1.19 ON CD630_23200 CDIF630erm_02558 rpiB1 Ribose-5-phosphate isomerase B 3.19 0.00 2.23 -0.02 CD630_23210 CDIF630erm_02559 Transketolase 1.75 0.44 2.01 0.22 CD630_23220 CDIF630erm_02560 tkt Transketolase 1.48...”
  • “...CDIF630erm_01006 amyB Amylopullulanase -0.12 -0.29 -2.68 0.05 CD630_23180 CDIF630erm_02556 Phosphohexomutase 2.01 0.58 1.56 0.21 CD630_23190 CDIF630erm_02557 rpe Ribulose-phosphate 3-epimerase 1.24 ON 1.19 ON CD630_23200 CDIF630erm_02558 rpiB1 Ribose-5-phosphate isomerase B 3.19 0.00 2.23 -0.02 CD630_23210 CDIF630erm_02559 Transketolase 1.75 0.44 2.01 0.22 CD630_23220 CDIF630erm_02560 tkt Transketolase 1.48 0.23...”

C9J6A7 Ribulose-5-phosphate-3-epimerase (Fragment) from Homo sapiens
35% identity, 71% coverage

• Downregulation of lncRNA APCDD1L-AS1 due to DNA hypermethylation and loss of VHL protein expression promotes the progression of clear cell renal cell carcinoma.
  Yang, International journal of biological sciences 2022
  • “...P16401, P10412, P16403 GO:0032554 purine deoxyribonucleotide binding 0.03277154 P10412 GO:0016854 racemase and epimerase activity 0.03277154 C9J6A7 GO:0032564 dATP binding 0.03277154 P10412 GO:0004133 glycogen debranching enzyme activity 0.03277154 A0A0M4G3H8 GO:0016862 intramolecular oxidoreductase activity interconverting keto- and enol-groups 0.03277154 P14174 GO:0004135 amylo-alpha-1,6-glucosidase activity 0.03277154 A0A0M4G3H8 GO:0004516 nicotinate phosphoribosyltransferase...”

YjhK / b4301 KpLE2 phage-like element; putative epimerase SgcE from Escherichia coli K-12 substr. MG1655 (see paper)
b4301 ribulose-phosphate 3-epimerase from Escherichia coli str. K-12 substr. MG1655
30% identity, 96% coverage

• The genome sequence of E. coli W (ATCC 9637): comparative genome analysis and an improved genome-scale reconstruction of E. coli
  Archer, BMC genomics 2011
  • “...e.g. reaction "RPE" from iAF1260 can be catalyzed by the enzyme encoded by b3386 or b4301. However, in W, an ortholog for b4301 is not present while an ortholog for b3386 is present so the reaction still occurs within the cell. Click here for file Additional...”

pRL120033 putative D-allulose-6-phosphate 3-epimerase from Rhizobium leguminosarum bv. viciae 3841
33% identity, 87% coverage

• The Use of Transposon Insertion Sequencing to Interrogate the Core Functional Genome of the Legume Symbiont Rhizobium leguminosarum
  Perry, Frontiers in microbiology 2016
  • “...Ribulose-phosphate 3-epimerase VGI 0.38 2.33 GD 0.63 9.2 NE 3.3.9 Putative ribulose phosphate 3-epimerase 4.3 pRL120033 D-allulose-6-phosphate 3-epimerase PGN 1 20.6 NE 1 21 NE 3.3.9 Putative D-allulose-6-phosphate 3-epimerase 4.4, 4.6 RL2718 Transketolase GN 1 16.23 NE 0.92 14.83 NE 3.3.15 Putative transketolase, alpha subunit, terpenoid...”

STY1447 putative ribulose-5-phosphate 3-epimerase from Salmonella enterica subsp. enterica serovar Typhi str. CT18
33% identity, 90% coverage

• Gallbladder carriage generates genetic variation and genome degradation in Salmonella Typhi
  Thanh, PLoS pathogens 2020
  • “...isolates, including STY0429 ( SbcC exonuclease), STY0661 ( dmsC molybdopterin containing oxidoreductase membrane anchor subunit), STY1447 (putative ribulose-5-phosphate 3-epimerase) and STY2760 ( ratA putative exported protein) ( Table 2 ). 10.1371/journal.ppat.1008998.t002 Table 2 Nonsynonymous mutations associated with positive selection in gallbladder isolates. Position in CT18 S/NS...”
  • “...NS STY1242 PTS, glucose specific IIBC component transport carbohydrate A112T H136R G316S complement (13991421399774) NS STY1447 ribulose-5-phosphate 3 epimerase unknown E164K I101V complement (22200422221727) NS STY2389 two-component system sensor kinase broad regulatory function P11L V49A complement (23313732334009) NS STY2499 DNA gyrase submit A DNA replication and...”
• Analysis of the hypervariable region of the Salmonella enterica genome associated with tRNA(leuX)
  Bishop, Journal of bacteriology 2005
  • “...sgc system at a different position in the genome (STY1447 to STY1450 and STY1452). Delineation of the borders of the tRNAleuX islands was supported for a number...”

NP_001265212 ribulose-phosphate 3-epimerase isoform 2 from Homo sapiens
32% identity, 71% coverage

• Conversion of D-ribulose 5-phosphate to D-xylulose 5-phosphate: new insights from structural and biochemical studies on human RPE.
  Liang, FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2011
  • GeneRIF: The binary complexes of RPE reported here will aid in the design of small molecules for modulating the activity of the enzyme and altering flux through the pentose phosphate pathway.

t3538 putative ribulose-phosphate 3-epimerase from Salmonella enterica subsp. enterica serovar Typhi Ty2
26% identity, 84% coverage

• A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi
  Perkins, PLoS genetics 2009
  • “...crucial for macrophage persistence in Mycobacterium tuberculosis [47] . Three genes t3544 , t3543 and t3538 that are predicted components of a ribose/arabinose transport operon were also increased in expression. Furthermore, predicted genes t1788 - 90 were greatly increased in expression in the ompR mutant. These...”

LSRE_SALTY / Q8ZKP8 Putative epimerase LsrE; EC 5.1.3.- from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (see 2 papers)
STM4080 putative ribulose-5-phosphate 3-epimerase from Salmonella typhimurium LT2
26% identity, 84% coverage

• cofactor: a divalent metal cation (Binds 1 divalent metal cation per subunit.)
• FabR regulates Salmonella biofilm formation via its direct target FabB
  Hermans, BMC genomics 2016
  • “...1-6-phosphate aldolase 2.60 AI-2 metabolism 5 STM4079 yneC/lsrG Isomerase for processing of phospho-AI-2 2.49 7 STM4080 lsrE Putative ribulose-5-phosphate 3-epimerase 2.24 10 STM4077 yneA/lsrB ABC transport protein, solute-binding component 2.13 12 STM4071 Hypothetical protein 2.02 13 STM4072 ydeV/lsrK Sugar kinase 1.87 17 STM4076 ydeZ/lsrD ABC transporter,...”
• Transcriptome analysis of genes controlled by luxS/autoinducer-2 in Salmonella enterica serovar Typhimurium
  Jesudhasan, Foodborne pathogens and disease 2010
  • “...(ego) lsrB (yneA) lsrC (ydeY) lsrD (ydeZ) lsrE (STM4080) lsrF (yneB) lsrG (yneZ) lsrK (ydeV) lsrR (ydeW) Putative identification of JCVI database Mid-log Early...”
• Rcs signalling-activated transcription of rcsA induces strong anti-sense transcription of upstream fliPQR flagellar genes from a weak intergenic promoter: regulatory roles for the anti-sense transcript in virulence and motility
  Wang, Molecular microbiology 2009
  • “...dniR 3.6 2.2 ydeW 7.0 2.0 ecnB 2.5 0.6 yeaG 2.6 0.9 ego, ydeY,Z, yneA~C, STM4080 ( ego ) 2.520 0.14.6 yebF 2.2 0.5 fbaB 4.1 1.4 yehZ ( yehZ ) 2.1 0.7 galP 2.2 0.6 ygiM 2.3 0.8 ggt 5.6 5.0 yhbO 2.0 0.9 katE...”
• Identification of new flagellar genes of Salmonella enterica serovar Typhimurium
  Frye, Journal of bacteriology 2006
  • “...0.46 86. STM4080 .................................................................................... 0.55 87. yjcH...”

MG_112 ribulose-phosphate 3-epimerase from Mycoplasma genitalium G37
31% identity, 80% coverage

• Transcriptional response to metal starvation in the emerging pathogen Mycoplasma genitalium is mediated by Fur-dependent and -independent regulatory pathways
  Martínez-Torró, Emerging microbes & infections 2020
  • “..., MG_023). Similarly, we detected decreased transcript levels of the ribulose-phosphate 3-epimerase ( rpe , MG_112) and the UTP-glucose-1-phosphate uridylyltransferase ( galU , MG_453) genes. Therefore, metal depletion prompts an important remodelling of the metabolic flux in M. genitalium . Furthermore, we found that transcription of...”
• Transcriptional response of Mycoplasma genitalium to osmotic stress
  Zhang, Microbiology (Reading, England) 2011
  • “...MG_082 rplA Ribosomal protein L1 2.60 0.00002 0.00136 MG_111 pgi Glucose-6-phosphate isomerase 4.16 0.00002 0.00136 MG_112 rpe Ribulose-phosphate 3-epimerase 3.55 0.00002 0.00136 MG_124 trx Thioredoxin 3.23 0.00359 0.00136 MG_125 Cof-like hydrolase, putative 2.80 0.00004 0.00136 MG_139 Metallo-beta-lactamase superfamily protein 2.04 0.00475 0.00136 MG_187 ABC transporter, ATP-binding...”

HSM_1950 ribulose-phosphate 3-epimerase from Haemophilus somnus 2336
HSM_1950 ribulose-phosphate 3-epimerase from Histophilus somni 2336
24% identity, 84% coverage

• Identification and initial characterization of Hfq-associated sRNAs in Histophilus somni strain 2336
  Subhadra, PloS one 2023
  • “...102 Y Y HSM_1868 HSM_1869 A [ 8 ] HS179 2210181 2210317 137 Y Y HSM_1950 HSM_1951 B [ 8 ] a The start# and end# represent the boundaries of an identified transcriptionally active region (TAR), which is a potential sRNA region. b sRNA sequences conserved:...”

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How It Works

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

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

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

PaperBLAST also incorporates manually-curated protein functions:

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

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

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

Changes to PaperBLAST since the paper was written:

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

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

Secrets

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

Omissions from the PaperBLAST Database

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

References

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.