PaperBLAST
PaperBLAST Hits for SwissProt::C0ZUQ6 Deoxyribose-phosphate aldolase; DERA; 2-deoxy-D-ribose 5-phosphate aldolase; Phosphodeoxyriboaldolase; Deoxyriboaldolase; EC 4.1.2.4 (Rhodococcus erythropolis (strain PR4 / NBRC 100887)) (221 a.a., MSEAALTRSQ...)
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>SwissProt::C0ZUQ6 Deoxyribose-phosphate aldolase; DERA; 2-deoxy-D-ribose 5-phosphate aldolase; Phosphodeoxyriboaldolase; Deoxyriboaldolase; EC 4.1.2.4 (Rhodococcus erythropolis (strain PR4 / NBRC 100887))
MSEAALTRSQVAAMVDHTLLKPEATAADVTALIDEARSLGVLAVCVSPSMLPIRADGLVT
AAVVGFPSGKHHSLVKGAEARLAVDQGATEIDMVIDVGAAVAGDYSAVLADILTVREAMG
ESAILKVILETAALSDEAIVECCRAAVRAGANFVKTSTGFHPAGGATVEAVELMARTVGP
GVGVKASGGIRTTQAALDMIAAGATRLGLSGTRAVLDGLTD
Running BLASTp...
Found 99 similar proteins in the literature:
DEOC_RHOE4 / C0ZUQ6 Deoxyribose-phosphate aldolase; DERA; 2-deoxy-D-ribose 5-phosphate aldolase; Phosphodeoxyriboaldolase; Deoxyriboaldolase; EC 4.1.2.4 from Rhodococcus erythropolis (strain PR4 / NBRC 100887) (see paper)
C0ZUQ6 deoxyribose-phosphate aldolase (EC 4.1.2.4) from Rhodococcus erythropolis (see paper)
100% identity, 100% coverage
- function: Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5- phosphate.
catalytic activity: 2-deoxy-D-ribose 5-phosphate = D-glyceraldehyde 3-phosphate + acetaldehyde (RHEA:12821)
subunit: Homodimer.
ML2451 deoxyribose-phosphate aldolase from Mycobacterium leprae TN
62% identity, 95% coverage
- Heme and hemoglobin utilization by Mycobacterium tuberculosis
Mitra, Nature communications 2019 - “...designated as ML2436 and ML2437, respectively, and the unmarked avirulent ppe37 mutant was designated as ML2451 (Supplementary Table 2 ). Construction of expression vectors for mycobacteria The dpp ( rv3666c-rv3663c ) and opp ( rv1283c-rv1280c ) operons were amplified using corresponding primers, 016Clone/F and 016Clone/R (Supplementary...”
CpC231_0165 deoxyribose-phosphate aldolase from Corynebacterium pseudotuberculosis C231
D9QDT7 Deoxyribose-phosphate aldolase from Corynebacterium pseudotuberculosis (strain C231)
59% identity, 98% coverage
- Changes in protein abundance are observed in bacterial isolates from a natural host
Rees, Frontiers in cellular and infection microbiology 2015 - “...D9QDT5 deoD CpC231_0163 Purine-nucleoside phosphorylase 1.892 * 0.914 0.979 Nucleotide transport and metabolism D9QDT7 deoC CpC231_0165 Deoxyribose-phosphate aldolase 1.487 * 0.673 2.148 * Nucleotide transport and metabolism D9QDT8 pmmB CpC231_0166 Phosphoglucosamine mutase 1.560 * 0.646 2.103 * Carbohydrate transport and metabolism D9QE16 sdhC CpC231_0245 Succinate dehydrogenase...”
- “...There is also a pair of more abundant proteins that are encoded by adjacent genes CpC231_0165 and CpC231_0166 which have homologs deoC and pmmB in M. tuberculosis . The protein product of pmmB has been suggested as contributing to the production of mannose in the mycobacterial...”
- Changes in protein abundance are observed in bacterial isolates from a natural host
Rees, Frontiers in cellular and infection microbiology 2015 - “...and metabolism D9QDT5 deoD CpC231_0163 Purine-nucleoside phosphorylase 1.892 * 0.914 0.979 Nucleotide transport and metabolism D9QDT7 deoC CpC231_0165 Deoxyribose-phosphate aldolase 1.487 * 0.673 2.148 * Nucleotide transport and metabolism D9QDT8 pmmB CpC231_0166 Phosphoglucosamine mutase 1.560 * 0.646 2.103 * Carbohydrate transport and metabolism D9QE16 sdhC CpC231_0245...”
MSMEG_3089 deoxyribose-phosphate aldolase from Mycobacterium smegmatis str. MC2 155
65% identity, 90% coverage
Rv0478 deoxyribose-phosphate aldolase from Mycobacterium tuberculosis H37Rv
65% identity, 96% coverage
FRAAL1197 2-deoxyribose-5-phosphate aldolase, NAD(P)-linked from Frankia alni ACN14a
52% identity, 94% coverage
- The PEG-responding desiccome of the alder microsymbiont Frankia alni
Ghedira, Scientific reports 2018 - “...TrkA 1.65 Intracellular osmolytes concentration FRAAL0095 Osmotic-stress mechanosensitive channel MscL 4.30 FRAAL1888 Glutamine amidotransferase 2.20 FRAAL1197 2-deoxyribose-5-phosphate aldolase, NAD(P)-linked 2.15 FRAAL5155 Peptidase S51, dipeptidase E 1.91 FRAAL2547 Non-ribosomal peptide synthase 2.20 FRAAL2542 Non-ribosomal peptide synthase 1.80 FRAAL2545 Non-ribosomal peptide synthase 1.60 FRAAL2500 Polyketidecyclase 1.79 Molecular chaperones...”
cg0458 deoxyribose-phosphate aldolase from Corynebacterium glutamicum ATCC 13032
50% identity, 96% coverage
LLKF_1546 deoxyribose-phosphate aldolase from Lactococcus lactis subsp. lactis KF147
44% identity, 95% coverage
- Strain-Dependent Transcriptome Signatures for Robustness in Lactococcus lactis
Dijkstra, PloS one 2016 - “...positive 0.2 LLKF_1805 ccpA catabolite control protein A positive 4.6 LLKF_2245 hypothetical protein negative 2.2 LLKF_1546 deoC deoxyribose-phosphate aldolase positive 3.2 LLKF_1589 putrescine/ornithine aminotransferase negative 0.1 LLKF_0270 nrdD anaerobic ribonucleoside-triphosphate reductase negative 11.7 LLKF_0313 hypothetical protein negative 0.1 LLKF_1486 pp220 phage protein positive 0.5 LLKF_0104 hypothetical...”
RBAM_036480 DeoC from Bacillus amyloliquefaciens FZB42
48% identity, 94% coverage
- Differential proteomics analysis of Bacillus amyloliquefaciens and its genome-shuffled mutant for improving surfactin production
Zhao, International journal of molecular sciences 2014 - “...1062, 1065 Transaldolase gi|154687826 YP_001422987 tal 23,055/5.23 23,336/5.31 86 40 +17.9, +6.5 1067 Hypothetical protein RBAM_036480 gi|154688047 YP_001423208 deoC 23,111/4.90 23,352/5.08 94 40 +24.0 1073 Hypothetical protein KSO_05864 gi|363723690 EHM03828 23,280/4.62 242,110/5.41 112 56 in FMB38 1074 2-AminoethylphosphonatePyruvate transaminase gi|229166259 ZP_04294018 41,797/5.29 27,312/5.61 220 50 in...”
- “...Unknown Nucleotide binding, oxidoreductase activity, zinc ion binding Nucleotide Transport and Metabolism 1067 Hypothetical protein RBAM_036480 F Cytoplasmic Deoxyribonucleotide catabolic process Deoxyribose-phosphate aldolase activity Carbohydrate Transport and Metabolism 1062, 1065 Transaldolase G Cytoplasmic Pentose-phosphate shunt Sedoheptulose-7-phosphate: d -glyceraldehyde-3-phosphate glyceronetransferase activity 1117, 1120 Fructose-bisphosphate aldolase G Cytoplasmic...”
BC_1820 deoxyribose-phosphate aldolase from Bacillus cereus ATCC 14579
46% identity, 93% coverage
DEOC_THEKO / Q877I0 Deoxyribose-phosphate aldolase; DERA; 2-deoxy-D-ribose 5-phosphate aldolase; Phosphodeoxyriboaldolase; Deoxyriboaldolase; EC 4.1.2.4 from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1)) (see paper)
Q877I0 deoxyribose-phosphate aldolase (EC 4.1.2.4) from Thermococcus kodakarensis (see paper)
TK2104 deoxyribose-phosphate aldolase from Thermococcus kodakaraensis KOD1
46% identity, 96% coverage
- function: Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5- phosphate. Could be involved in pentose biosynthesis.
catalytic activity: 2-deoxy-D-ribose 5-phosphate = D-glyceraldehyde 3-phosphate + acetaldehyde (RHEA:12821)
subunit: Homodimer. - Proteome profiling of heat, oxidative, and salt stress responses in Thermococcus kodakarensis KOD1
Jia, Frontiers in microbiology 2015 - “...56.2 26 Methionine synthase II TK1447 12 2.6 5.90 5.9 35.25 35.0 27 Deoxyribose-phosphate aldolase TK2104 27 2.3 5.18 5.2 24.49 26.0 28 Metallophosphoesterase TK0547 19 2.6 5.22 5.3 24.12 23.0 29 Protein disulphide oxidoreductase TK1085 39 3.8 4.72 4.8 25.28 25.6 30 Deblocking aminopeptidase TK0781...”
- “...11 Cell division ATPase TK1421 28 1.8 4.80 5.3 40.03 41.6 12 2-deoxyribose 5-phosphate aldolase TK2104 25 1.9 5.18 5.6 24.49 25.8 13 ATPase TK0701 10 2.0 4.81 4.9 31.93 31.0 14 Transcription regulator TK1962 21 2.4 5.67 5.9 22.02 23.0 15 Hypothetical protein TK0083 41...”
- Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes
Fukui, Genome research 2005 - “...in T. kodakaraensis is deoC for deoxyribose-5-phosphate aldolase (TK2104), deoB for a novel phosphopentomutase (TK1777) (Rashid et al. 2004), and udp for...”
- Presence of a novel phosphopentomutase and a 2-deoxyribose 5-phosphate aldolase reveals a metabolic link between pentoses and central carbon metabolism in the hyperthermophilic archaeon Thermococcus kodakaraensis
Rashid, Journal of bacteriology 2004 - “...revealed the presence of a closely related orthologue (TK2104) of bacterial DERA genes while no orthologue related to previously characterized PPM genes could...”
- “...detected. Expression, purification, and characterization of the TK2104 protein product revealed that this gene actually encoded a DERA, catalyzing the reaction...”
BCE_1975 deoxyribose-phosphate aldolase from Bacillus cereus ATCC 10987
46% identity, 93% coverage
- A transposon mutant library of Bacillus cereus ATCC 10987 reveals novel genes required for biofilm formation and implicates motility as an important factor for pellicle-biofilm formation
Okshevsky, MicrobiologyOpen 2018 - “...inhibitor of FTSZ assembly No BCE_5636 1 5,222,600 jag spoIIIJassociated protein Sporulation No Sugar metabolism BCE_1975 1 1,909,330 deoC / dra Deoxyribose phosphate aldolase Pentose phosphate pathway No BCE_5356 1 4,943,951; 4,943,954 glycosyl transferase domain protein, putative Carbohydrate/sugar metabolism No BCE_5385 1 4,972,962 ugd UDPglucose 6dehydrogenase...”
- “...acid biosynthesis. Possibly involved in transport of dalanine over the membrane 1,476,6831,475,517 1,476,431 Yes No BCE_1975 dra Deoxyribose phosphate aldolase Catalyzes the formation of Dglyceraldehyde 3phosphate and acetaldehyde from 2deoxyDribose 5phosphate in nucleotide catabolism 1,909,2051,909,876 1,909,323 Yes No BCE_5585 Membrane protein, putative Unknown. Pfam notes uncharacterised...”
EF0174 deoxyribose-phosphate aldolase from Enterococcus faecalis V583
47% identity, 94% coverage
- Identification of proteins related to the stress response in Enterococcus faecalis V583 caused by bovine bile
Bøhle, Proteome science 2010 - “...DivIVA EF1002 26.6 4.53 62 16 0.61 1.21 3.5 15 e Energy metabolism Deoxyribose-phosphate aldolase EF0174 23.3 4.65 48 10 1.39 1.28 0.47 16 f Formate acetyltransferase EF1613 84.5 5.31 11 8 1.00 0.95 2.87 17 e Fumarate reductase flavoprotein subunit EF2556 53.8 5.26 10 6...”
- “...proteins are involved in different pathways, including glycolysis (EF 0195, EF1046, EF1961), pentose phosphate pathway (EF0174), pyruvate metabolism (EF1613), oxidative phosphorylation (EF2556, EF1499), and the electron transport chain (EF1405). Proteins identified in the first two pathways are members of the carbohydrate metabolism, and most of these...”
SSA_1036 Deoxyribose-phosphate aldolase, putative from Streptococcus sanguinis SK36
47% identity, 95% coverage
lmo1995 similar to deoxyribose-phosphate aldolase from Listeria monocytogenes EGD-e
46% identity, 93% coverage
SGO_1080 deoxyribose-phosphate aldolase from Streptococcus gordonii str. Challis substr. CH1
A8AX59 Deoxyribose-phosphate aldolase from Streptococcus gordonii (strain Challis / ATCC 35105 / BCRC 15272 / CH1 / DL1 / V288)
46% identity, 95% coverage
- Intracellular Ser/Thr/Tyr phosphoproteome of the oral commensal Streptococcus gordonii DL1
Robertsson, BMC microbiology 2020 - “...aced-3 a) 5.7/5.20 24,000/26547 809 13 62% - Carbohydrate catabolism dera a) Deoxyribose-phosphate aldolase deoC (SGO_1080) A8AX59 4.9/4.84 20,000/23380 691 8 49% Pyruvate conversion ldh-1 a) L-lactatedehydrogenase ldh(SGO_1232) A8AXK9 5.4/5.24 36,000/35267 327 6 28% + ldh-2 5.6/5.24 36,000/35267 436 6 28% + ldh-3 5.8/5.24 36,000/35267 641...”
- Intracellular Ser/Thr/Tyr phosphoproteome of the oral commensal Streptococcus gordonii DL1
Robertsson, BMC microbiology 2020 - “...a) 5.7/5.20 24,000/26547 809 13 62% - Carbohydrate catabolism dera a) Deoxyribose-phosphate aldolase deoC (SGO_1080) A8AX59 4.9/4.84 20,000/23380 691 8 49% Pyruvate conversion ldh-1 a) L-lactatedehydrogenase ldh(SGO_1232) A8AXK9 5.4/5.24 36,000/35267 327 6 28% + ldh-2 5.6/5.24 36,000/35267 436 6 28% + ldh-3 5.8/5.24 36,000/35267 641 8...”
C7E719 deoxyribose-phosphate aldolase (EC 4.1.2.4) from Paenibacillus sp. (see paper)
46% identity, 95% coverage
Cbei_3120 deoxyribose-phosphate aldolase from Clostridium beijerincki NCIMB 8052
46% identity, 94% coverage
- Sigma Factor Regulated Cellular Response in a Non-solvent Producing Clostridium beijerinckii Degenerated Strain: A Comparative Transcriptome Analysis
Zhang, Frontiers in microbiology 2017 - “...number GSE63671). Quantitative Real-Time PCR (qRT-PCR) To validate microarray data, 10 up-regulated (Cbei_4123, Cbei_0411, Cbei_0311, Cbei_3120, Cbei_0441, Cbei_0331, Cbei_4824, Cbei_2740, Cbei_4871, and Cbei_3356) and 10 down-regulated (Cbei_3835, Cbei_1930, Cbei_0677, Cbei_2826, Cbei_2600, Cbei_1583, Cbei_1079, Cbei_0284, Cbei_3832, and Cbei_2261) genes were randomly selected for qRT-PCR. C. beijerinckii (WT-8052...”
DEOC_BACSU / P39121 Deoxyribose-phosphate aldolase; DERA; 2-deoxy-D-ribose 5-phosphate aldolase; Phosphodeoxyriboaldolase; Deoxyriboaldolase; EC 4.1.2.4 from Bacillus subtilis (strain 168) (see paper)
44% identity, 93% coverage
TTE0975 Deoxyribose-phosphate aldolase from Thermoanaerobacter tengcongensis MB4
46% identity, 87% coverage
DR1205, DR_1205 deoxyribose-phosphate aldolase from Deinococcus radiodurans R1
50% identity, 90% coverage
D5AHU8 deoxyribose-phosphate aldolase (EC 4.1.2.4) from Streptococcus suis (see paper)
43% identity, 95% coverage
BH1352 deoxyribose-phosphate aldolase from Bacillus halodurans C-125
45% identity, 95% coverage
- Development of Clostridium saccharoperbutylacetonicum as a Whole Cell Biocatalyst for Production of Chirally Pure (R)-1,3-Butanediol
Grosse-Honebrink, Frontiers in bioengineering and biotechnology 2021 - “...LMSE51C Glucose Aerobic pH controlled fed-batch fermentation of strain from Nemr et al. (2018) with BH1352 harbouring mutations F160Y/M173I Kim et al., 2020 Here, three non-exclusive approaches to increase production of ( R )-1,3-BDO were tested and combined. Firstly, point mutations were applied to increase enzyme...”
- Current state of and need for enzyme engineering of 2-deoxy-D-ribose 5-phosphate aldolases and its impact
Rouvinen, Applied microbiology and biotechnology 2021 - “...DERA aldolases from different organisms were initially screened on the basis of 1,3-BDO production. DERA BH1352 from Bacillus halodurans was chosen for further studies and active site mutations based on the solved crystal structure were created. This was done by targeting hydrophobic residues near the catalytic...”
- Rational engineering of 2-deoxyribose-5-phosphate aldolases for the biosynthesis of (R)-1,3-butanediol
Kim, The Journal of biological chemistry 2020 - “...of the enzymes, with the highest activities in BH1352 from Bacillus halodurans, TM1559 from Thermotoga maritima, and DeoC from Escherichia coli. The crystal...”
- “...the presence of the C-terminal Tyr (Tyr224 in BH1352). The results from structure-based site-directed mutagenesis of BH1352 indicated a key role for the...”
SSU0936 deoxyribose-phosphate aldolase from Streptococcus suis P1/7
43% identity, 95% coverage
- Identification of conditionally essential genes for Streptococcus suis infection in pigs
Arenas, Virulence 2020 - “...SSU1025 zwf Glucose-6-phosphate 1-dehydrogenase 4 2.7 4.3 SSU1839 tkt transketolase 3.3 3.7 SSU1315 Lactonase 9.9 SSU0936 deoC Deoxyribose-phosphate aldolase 7.8 6.9 SSU1269 deoB Phosphopentomutase 7.6 SSU1270 rpiA Ribose-5-phosphate isomerase A 8.7 7.6 4.7 SSU0021 prsA1 Ribose-phosphate pyrophosphokinase 4.3 2.9 4.1 SSU0648 fhs Formate-tetrahydrofolate ligase 5.6 4.4...”
EHI_121800 deoxyribose-phosphate aldolase, putative from Entamoeba histolytica HM-1:IMSS
44% identity, 97% coverage
3ngjD / C4M5C6 Crystal structure of a putative deoxyribose-phosphate aldolase from entamoeba histolytica
44% identity, 97% coverage
DEOC_ACIB4 / B5IEU6 Deoxyribose-phosphate aldolase; DERA; 2-deoxy-D-ribose 5-phosphate aldolase; Phosphodeoxyriboaldolase; Deoxyriboaldolase; EC 4.1.2.4 from Aciduliprofundum boonei (strain DSM 19572 / T469)
46% identity, 95% coverage
- function: Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5- phosphate.
catalytic activity: 2-deoxy-D-ribose 5-phosphate = D-glyceraldehyde 3-phosphate + acetaldehyde (RHEA:12821)
subunit: Homodimer.
HI1116 deoxyribose-phosphate aldolase (deoC) from Haemophilus influenzae Rd KW20
43% identity, 97% coverage
SPD_0737 deoxyribose-phosphate aldolase from Streptococcus pneumoniae D39
45% identity, 95% coverage
- Unraveling the full impact of SPD_0739: a key effector in <i>S. pneumoniae</i> iron homeostasis
Womack, Microbiology spectrum 2024 - “...(spd_0736) , a pyrimidine nucleoside phosphorylase encoded upstream of spd_0739 from a separate operon; deoC (spd_0737) , a deoxyribose-phosphate aldolase; pnrB ( spd_0740) , the permease of the PnrABC transporter (that is likely expressed independently of spd_0739 / pnrA gene) ; and guaA ( spd_1274 ),...”
- “...nucleoside salvaging genes, pyrimidine-nucleoside phosphorylase ( pdp , spd_0736 ), deoxyribose-phosphate aldolase ( deo C, spd_0737 ), and cytidine deaminase ( cdd-1 , spd_0738 ). Pdp catalyzes the phosphorolytic cleavage of pyrimidines into precursors for nucleic acid synthesis ( 53 ); its downregulation in the spd_0739...”
- Conserved surface accessible nucleoside ABC transporter component SP0845 is essential for pneumococcal virulence and confers protection in vivo
Saxena, PloS one 2015 - “...that spd_0739 (the D39 homologue of sp0845 ) is cotranscribed with spd_0735 , spd_0736 , spd_0737 , spd_0738 , spd_0740 , spd_0741 and spd_0742 (data not shown). A comparison with S . mutans UA159 indicated that smu_1124 , smu_1123 and smu_1122 are TIGR4 homologues of sp0842...”
BHWA1_01546 Deoxyribose-phosphate aldolase from Brachyspira hyodysenteriae WA1
43% identity, 94% coverage
CBG46_05965 deoxyribose-phosphate aldolase from Actinobacillus succinogenes
45% identity, 95% coverage
SERP1745 deoxyribose-phosphate aldolase from Staphylococcus epidermidis RP62A
42% identity, 94% coverage
- Role of the SaeRS two-component regulatory system in Staphylococcus epidermidis autolysis and biofilm formation
Lou, BMC microbiology 2011 - “...48 ]. Only Eight genes involved in metabolic process [SERP2414, SERP2360, SERP2192 ( cysH ), SERP1745 ( deoC ), SERP0721 ( pheS ), SERP0371, SERP0365 ( saeR ), and SERP0164] that contained the direct repeat sequence with no more than one mismatch were found (Table 4...”
- “...TTTAA -590 exsD protein SERP0721 pheS -648 GATAA CATGAT GTTAA -663 phenylalanyl-tRNA synthetase, alpha subunit SERP1745 deoC -1091 GTAAA AATAAA GTTAA -1106 deoxyribose-phosphate aldolase SERP2192 cysH -172 GATAA TCAAAA GTTAA -187 phosophoadenylyl-sulfate reductase SERP2360 -114 GTTAA ACCACC GTCAA -129 3-hydroxyacyl-CoA dehydrogenase family protein SERP2414 -270 GTTAA...”
SAUSA300_2090 deoxyribose-phosphate aldolase from Staphylococcus aureus subsp. aureus USA300_FPR3757
43% identity, 94% coverage
SAR0140 deoxyribose-phosphate aldolase from Staphylococcus aureus subsp. aureus MRSA252
43% identity, 95% coverage
- The Staphylococcus aureus response to unsaturated long chain free fatty acids: survival mechanisms and virulence implications
Kenny, PloS one 2009 - “...P-value Virulence Factors and Regulators SAR2745 capA Capsular polysaccharide biosynthesis protein 3.36 2.27E-04 Energy Metabolism SAR0140 deoC1 deoxyribose-phosphate aldolase 4.34 2.49E-03 SAR0217 formate acetyltransferase 2.30 1.50E-03 SAR0394 phosphoglycerate mutase family protein 2.94 1.67E-02 SAR0828 gap1 glyceraldehyde 3-phosphate dehydrogenase 1 2.07 3.53E-03 SAR0924 pgi glucose-6-phosphate isomerase 4.18...”
- “...oxidoreductase family protein 2.00 2.13E-03 SAR2461 pyridine nucleotide-disulphide oxidoreductase family protein 2.59 2.49E-02 Energy Metabolism SAR0140 deoC1 deoxyribose-phosphate aldolase 4.21 4.86E-03 SAR0394 phosphoglycerate mutase family protein 4.79 1.06E-03 SAR0828 gap1 glyceraldehyde 3-phosphate dehydrogenase 1 2.86 2.51E-03 SAR0830 tpiA triosephosphate isomerase 3.40 4.42E-03 SAR0832 eno enolase 3.20...”
Q8NVF5 Deoxyribose-phosphate aldolase 2 from Staphylococcus aureus (strain MW2)
43% identity, 94% coverage
SA1939 deoxyribose-phosphate aldolase from Staphylococcus aureus subsp. aureus N315
P99174 Deoxyribose-phosphate aldolase 2 from Staphylococcus aureus (strain N315)
43% identity, 94% coverage
SA0133 deoxyribose-phosphate aldolase from Staphylococcus aureus subsp. aureus N315
NP_370662 deoxyribose-phosphate aldolase from Staphylococcus aureus subsp. aureus Mu50
KMZ21_00450, NWMN_RS00465 deoxyribose-phosphate aldolase from Staphylococcus aureus subsp. aureus str. Newman
43% identity, 95% coverage
Q9AIP7 deoxyribose-phosphate aldolase (EC 4.1.2.4) from Streptococcus mutans (see paper)
44% identity, 95% coverage
deoC / C0LSK9 deoxyribose-phosphate aldolase (EC 4.1.2.4) from Yersinia sp. EA015 (see paper)
C0LSK9 deoxyribose-phosphate aldolase (EC 4.1.2.4) from Yersinia sp. EA015 (see paper)
45% identity, 94% coverage
Mfl121 deoxyribose-phosphate aldolase from Mesoplasma florum L1
42% identity, 95% coverage
- Genome-scale metabolic modeling reveals key features of a minimal gene set
Lachance, Molecular systems biology 2021 - “...transaldolase (TALA) reaction (pink) was missing in the network. Structural similarity between two 2deoxyribosephosphate aldolases (Mfl121, red in left box; Mfl639, red in right box) to a known transaldolase from the PDB (light blue) served as basis for the addition of this geneassociated reaction in the...”
- “...and the X chain of the phosphomannomutase/phosphoglucomutase of Pseudomonas aeruginosa (1k2yX; PMM/PGM), and (D, E) Mfl121 and Mfl639 proteins and the A chain of the transaldolase of Thermotoga maritima (1vpxA; TM0295), respectively. F FATCAT alignment of the reconstructed structures of both transaldolase Mfl121 (red) and Mfl639...”
Cthe_1943 deoxyribose-phosphate aldolase from Clostridium thermocellum ATCC 27405
42% identity, 94% coverage
LGG_00321 deoxyribose-phosphate aldolase from Lacticaseibacillus rhamnosus GG
LGG_00321 deoxyribose-phosphate aldolase (phosphodeoxyriboaldolase), DERA from Lactobacillus rhamnosus GG
44% identity, 93% coverage
- Growth phase-associated changes in the proteome and transcriptome of Lactobacillus rhamnosus GG in industrial-type whey medium
Laakso, Microbial biotechnology 2011 - “...pyk Pyruvate kinase 3436 4.2 2.004 Others LGG_00052 eda 2Dehydro3deoxyphosphogluconate aldolase/4hydroxy2oxoglutarate aldolase 37 1.7 0.64 LGG_00321 deoC Deoxyribosephosphate aldolase 38 1.9 0.859 LGG_00342 srlD Sorbitol6phosphate 2dehydrogenase 39,40 53.6 7.877 LGG_00757 adhE Aldehydealcohol dehydrogenase 4144 18 5.86 LGG_01322 pdhC Pyruvate dehydrogenase complex E2 component, dihydrolipoyllysineresidue acetyltransferase 45...”
- “...triosephosphate isomerase (TpiA), which catalyses the formation of glyceraldehyde3phosphate from dihydroxyacetone phosphate. Deoxyribosephosphate aldolase (DeoC, LGG_00321), which converts deoxyribose5phosphate to glyceraldehyde3phosphate (a glycolytic intermediate), and its concomitant gene were upregulated upon entry into the stationary phase of growth ( Fig.4A , Table1 ). One of the...”
D1J8C1 Deoxyribose-phosphate aldolase from Metamycoplasma hominis (strain ATCC 23114 / DSM 25592 / NBRC 14850 / NCTC 10111 / PG21)
38% identity, 95% coverage
- Thymidine utilisation pathway is a novel phenotypic switch of Mycoplasma hominis.
Fisunov, Journal of medical microbiology 2022 - “...Liquid culture WT H-34 arginine/ DeoA::TnRM5 thymidine D1J8C2 deoA Thymidine phosphorylase 1.70 1.55 10.55 2.750.30 D1J8C1 deoC Deoxyribose-phosphate aldolase 1 only MCs 0.92 4.090.53 D1J8K5 deoB Phosphopentomutase 0.57 0.28 0.53 0.450.06 D1J8C3 deoD Purine-nucleoside phosphorylase 0.35 1.12 0.70 D1J7L3 MHO_0760 putative glycerol-3-phosphate specific transporter 0.40 only...”
DEOC_THEMA / Q9X1P5 Deoxyribose-phosphate aldolase; DERA; 2-deoxy-D-ribose 5-phosphate aldolase; Phosphodeoxyriboaldolase; Deoxyriboaldolase; EC 4.1.2.4 from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8) (see paper)
TM1559 deoxyribose-phosphate aldolase from Thermotoga maritima MSB8
43% identity, 85% coverage
- function: Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5- phosphate.
catalytic activity: 2-deoxy-D-ribose 5-phosphate = D-glyceraldehyde 3-phosphate + acetaldehyde (RHEA:12821) - Rational engineering of 2-deoxyribose-5-phosphate aldolases for the biosynthesis of (R)-1,3-butanediol
Kim, The Journal of biological chemistry 2020 - “...the highest activities in BH1352 from Bacillus halodurans, TM1559 from Thermotoga maritima, and DeoC from Escherichia coli. The crystal structures of BH1352 and...”
- “...from the alkaliphilic bacterium Bacillus halodurans, as well as TM1559 from Thermotoga maritima and E. coli DeoC as the most active aldolases in the DERA-AKR-...”
- Sequential aldol condensation catalyzed by hyperthermophilic 2-deoxy-d-ribose-5-phosphate aldolase
Sakuraba, Applied and environmental microbiology 2007 - “...purification. The genes encoding DERATma (open reading frame TM1559) and DERAPae (open reading frame PAE1231) were amplified by PCR (the gene information is...”
- A taxonomy of bacterial microcompartment loci constructed by a novel scoring method.
Axen, PLoS computational biology 2014 - “...Dataset S2 ) contains an aldolase 5257% identical to DeoC deoxyribose-phosphate aldolase (EC: 4.1.2.4; UniProtKB: Q9X1P5), a class I aldolase that cleaves 2-deoxyribose 5-phosphate into glyceraldehyde-3-phosphate and acetaldehyde [109] . These loci also contain an AldDH, possibly forming acetyl-CoA from acetaldehyde. Moreover, all but Marinimicrobia contain...”
LSA0795 2 Deoxyribose-5 phosphate aldolase from Lactobacillus sakei subsp. sakei 23K
46% identity, 91% coverage
- Global transcriptome response in Lactobacillus sakei during growth on ribose
McLeod, BMC microbiology 2011 - “...A G TACA -82 loxL1N-loxLI-loxL1C LSA0664-0666 LSA0764 galK TGAAAG CG ATTA AT -30 galK-galE1-galT-galM LSA0764-0767 LSA0795 deoC TGAAAG CG TTAACA -33 deoC-deoB-deoD-lsa0798-lsa0799-deoR-pdp LSA0795-0801 LSA0974 pflB TACGAA CG CTTACA -147 pflB-pflA LSA0974-0973 LSA1048 fruR e TGTAAA CG ATGACA -39 fruR e -fruK e -fruA LSA1048-1050 LSA1141 ppdK...”
DEOC_THET8 / Q5SJ28 Deoxyribose-phosphate aldolase; DERA; 2-deoxy-D-ribose 5-phosphate aldolase; Phosphodeoxyriboaldolase; Deoxyriboaldolase; EC 4.1.2.4 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8) (see paper)
46% identity, 94% coverage
- function: Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5- phosphate.
catalytic activity: 2-deoxy-D-ribose 5-phosphate = D-glyceraldehyde 3-phosphate + acetaldehyde (RHEA:12821)
subunit: Homotetramer, in solution and in the crystal structure.
1ub3A / Q5SJ28 Crystal structure of tetrameric structure of aldolase from thermus thermophilus hb8 (see paper)
47% identity, 90% coverage
- Ligand: 1-hydroxy-pentane-3,4-diol-5-phosphate (1ub3A)
DEOC_PSEU2 / Q4ZMV1 Deoxyribose-phosphate aldolase; DERA; 2-deoxy-D-ribose 5-phosphate aldolase; Phosphodeoxyriboaldolase; Deoxyriboaldolase; EC 4.1.2.4 from Pseudomonas syringae pv. syringae (strain B728a) (see paper)
45% identity, 95% coverage
- function: Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5- phosphate.
function: In vitro, DERA can catalyze the aldol condensation of chloroacetaldehyde (CHAD) and acetaldehyde (ACD), yielding (S)-4- chloro-3-hydroxybutanal ((S)-CHB), which can combine with another aldehyde to form (3R,5S)-6-chloro-2,4,6-trideoxyhexapyranose (CTeHP), a key intermediate for statin drugs.
catalytic activity: 2-deoxy-D-ribose 5-phosphate = D-glyceraldehyde 3-phosphate + acetaldehyde (RHEA:12821)
DEOC_STRP6 / Q5XA31 Deoxyribose-phosphate aldolase; DERA; 2-deoxy-D-ribose 5-phosphate aldolase; Phosphodeoxyriboaldolase; Deoxyriboaldolase; EC 4.1.2.4 from Streptococcus pyogenes serotype M6 (strain ATCC BAA-946 / MGAS10394)
42% identity, 88% coverage
- function: Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5- phosphate.
catalytic activity: 2-deoxy-D-ribose 5-phosphate = D-glyceraldehyde 3-phosphate + acetaldehyde (RHEA:12821)
Mfl639 deoxyribose-phosphate aldolase from Mesoplasma florum L1
36% identity, 94% coverage
- Genome-scale metabolic modeling reveals key features of a minimal gene set
Lachance, Molecular systems biology 2021 - “...missing in the network. Structural similarity between two 2deoxyribosephosphate aldolases (Mfl121, red in left box; Mfl639, red in right box) to a known transaldolase from the PDB (light blue) served as basis for the addition of this geneassociated reaction in the model. The observed essentiality (Ess.)...”
- “...X chain of the phosphomannomutase/phosphoglucomutase of Pseudomonas aeruginosa (1k2yX; PMM/PGM), and (D, E) Mfl121 and Mfl639 proteins and the A chain of the transaldolase of Thermotoga maritima (1vpxA; TM0295), respectively. F FATCAT alignment of the reconstructed structures of both transaldolase Mfl121 (red) and Mfl639 (blue). Source...”
GBSCOH1_RS09680 deoxyribose-phosphate aldolase from Streptococcus agalactiae COH1
41% identity, 88% coverage
- Group B Streptococcus transcriptome when interacting with brain endothelial cells
Vollmuth, Journal of bacteriology 2024 - “...GBS codY (GBSCOH1_RS07970), forward primer 5- CCACCACCATAAATTGGAGCG -3, and reverse primer 5- GGTGGTGGTAACTTACTTGGC -3. deoC (GBSCOH1_RS09680) was used as the housekeeping gene, forward primer 5- CAGCAACATGGCCAGAAATC -3, and reverse primer 5- TTGACGTAAGAGGCTGGAATAC -3. qPCR data were collected on the QuantStudio3 system (Applied Biosystems), and data are...”
TP0264 deoxyribose-phosphate aldolase (deoC) from Treponema pallidum subsp. pallidum str. Nichols
36% identity, 94% coverage
MGA_0363 deoxyribose-phosphate aldolase from Mycoplasma gallisepticum str. R(low)
36% identity, 92% coverage
MPN063 deoxyribose-phosphate aldolase from Mycoplasma pneumoniae M129
35% identity, 92% coverage
sll1776 deoxyribose-phosphate aldolase from Synechocystis sp. PCC 6803
40% identity, 89% coverage
Pcar_2321 deoxyribose-phosphate aldolase from Pelobacter carbinolicus str. DSM 2380
39% identity, 90% coverage
LJ1661 deoxyribose-phosphate aldolase from Lactobacillus johnsonii NCC 533
32% identity, 90% coverage
mru_1685 deoxyribose-phosphate aldolase DeoC from Methanobrevibacter ruminantium M1
34% identity, 90% coverage
Ta0684 deoxyribose-phosphate aldolase related protein from Thermoplasma acidophilum DSM 1728
31% identity, 86% coverage
SCO4914 deoxyribose-phosphate aldolase from Streptomyces coelicolor A3(2)
44% identity, 48% coverage
- The WblC/WhiB7 Transcription Factor Controls Intrinsic Resistance to Translation-Targeting Antibiotics by Altering Ribosome Composition
Lee, mBio 2020 - “...in the WblC-immunoprecipitated DNA samples, not in the HrdB-immunoprecipitated DNAs ( Fig.4E , cvnA1 , SCO4914 , guaB2 , SCO3064 , wblE , and citA promoters). wblC is required to maintain translation and growth rate against subinhibitory concentrations of antibiotics. Given that wblC expression itself is...”
- ArgR of Streptomyces coelicolor is a versatile regulator
Pérez-Redondo, PloS one 2012 - “...a glyceraldehyde-3-phosphate dehydrogenase isoenzyme Gap1 (SCO1947, spot IN 6193). Also, the deoxyribose-phosphate aldolase encoded by SCO4914 (spot IN 6381), the fructose biphosphate aldolase Fba (SCO3649, spot IN 6366), and the second glyceraldehyde-3-phosphate dehydrogenase Gap2 (SCO7511, spot IN 6317), were under-represented in the argR mutant when compared...”
- Quantitative proteomics analysis of Streptomyces coelicolor development demonstrates that onset of secondary metabolism coincides with hypha differentiation
Manteca, Molecular & cellular proteomics : MCP 2010 - “...metabolism Function and KEGG SCO5423 SCO4209 SCO1946 SCO4914 SCO3877 SCO6661 SCO6658 SCO6662 SCO6659 SCO3092 SCO4855 SCO2951 SCO4809 SCO5368 SCO2736 SCO3304...”
- Bioinformatic identification of novel regulatory DNA sequence motifs in Streptomyces coelicolor
Studholme, BMC microbiology 2004 - “...there are matches to the near-palindromic motif CTACgcNCGTAG represented by matrix 1853 (SCO1776, SCO2015, SCO4901, SCO4914 and SCO4917). Furthermore, a match is found upstream of SCO4886. SCO4886 may be the first gene in an operon also containing SCO4889, which encodes a putative cytidine deaminase. A match...”
A0A1Q2T258 deoxyribose-phosphate aldolase (EC 4.1.2.4) from Haloarcula japonica (see paper)
37% identity, 85% coverage
KPN_01702 deoxyribose-phosphate aldolase from Klebsiella pneumoniae subsp. pneumoniae MGH 78578
34% identity, 82% coverage
- Identification of Pathogenicity-Associated Loci in Klebsiella pneumoniae from Hospitalized Patients
Martin, mSystems 2018 - “...KP1_RS09370 PTS fructose transporter subunit IIB 6 (15.8) 32 (42.1) 0.008326 KP1_RS12840 , KPNJ1_RS13410 , KPN_01702 g Deoxyribose-phosphate aldolase 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,...”
- Functional Genomic Screen Identifies Klebsiella pneumoniae Factors Implicated in Blocking Nuclear Factor κB (NF-κB) Signaling
Tomás, The Journal of biological chemistry 2015 - “...function Y/Y P043B5 N -Acetylmuramic acid 6-phosphate etherase KpST66_2662 KPN_01553 Y/Y P037E12 Deoxyribose-phosphate aldolase KpST66_2812 KPN_01702 Y/Y P029H4 Putative Carboxymuconolactone decarboxylase family protein KpST66_1120 KPN_03003 Y/Y P009G9 Propanediol dehydratase medium subunit pduD KpST66_0902 KPN_03206 Y/Y P025D5 Altronate hydrolase KpST66_0586 KPN_03519 Y/Y P006H10 L(+)-tartrate dehydratase subunit (...”
- “...KPN_00870 and KPN_00871 Y/Y P043E6 Between deoR and deoC KpST66_2811 and KpST66_2812 Between KPN_01701 and KPN_01702 Y/Y P038G8 Between aspartate-semialdehyde dehydrogenase and a putative transcriptional regulator KpST66_2862 and KpST66_2863 Between KPN_01773 and KPN_01774 Y/Y P019E6 Between putative transposase IS4 and a putative ARAC-type regulatory protein KpST66_2869...”
KP1_RS12840 deoxyribose-phosphate aldolase from Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044
34% identity, 82% coverage
- Identification of Pathogenicity-Associated Loci in Klebsiella pneumoniae from Hospitalized Patients
Martin, mSystems 2018 - “...157 c 3.347,350 0.01 DeoR family protein/alkaline phosphatase (KP1_RS12850) 10.5 b 1.6267.9 0.014 Deoxyribose-phosphate aldolase (KP1_RS12840) 5.79 b 1.1928.2 0.03 Hypothetical protein (KPNJ1_01715) 5.08 b 1.2720.2 0.021 16.9 c 1.59179 0.019 Putative deoxygluconate dehydrogenase (KPN_01782) 4.5 b 1.3415 0.015 17.8 c 2.2143 0.007 a OR, odds...”
- “...(42.1) 0.008326 KPK_RS16835, VK055_1472, KP1_RS09370 PTS fructose transporter subunit IIB 6 (15.8) 32 (42.1) 0.008326 KP1_RS12840 , KPNJ1_RS13410 , KPN_01702 g Deoxyribose-phosphate aldolase 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...”
DEOC_AERPE / Q9Y948 Deoxyribose-phosphate aldolase; DERA; 2-deoxy-D-ribose 5-phosphate aldolase; Phosphodeoxyriboaldolase; Deoxyriboaldolase; EC 4.1.2.4 from Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1) (see paper)
35% identity, 89% coverage
- function: Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5- phosphate.
catalytic activity: 2-deoxy-D-ribose 5-phosphate = D-glyceraldehyde 3-phosphate + acetaldehyde (RHEA:12821)
subunit: Homotetramer.
SACE_6564 putative deoxyribose-phosphate aldolase from Saccharopolyspora erythraea NRRL 2338
39% identity, 58% coverage
A5F5S6 Deoxyribose-phosphate aldolase from Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)
VC2350 deoxyribose-phosphate aldolase from Vibrio cholerae O1 biovar eltor str. N16961
33% identity, 80% coverage
- Metabolic Reprogramming of Vibrio cholerae Impaired in Respiratory NADH Oxidation Is Accompanied by Increased Copper Sensitivity
Toulouse, Journal of bacteriology 2018 - “...Glyceraldehyde 3-phosphate metabolism A5EZR2 A0A0H3AEL2 A0A0H3AJH0 A5F5U0 A5F5S6 VC no. Gene RF Assigned function VCA0744 VCA0843 VC2349 VC2348 VC2350 glpK...”
- Metabolic Reprogramming of Vibrio cholerae Impaired in Respiratory NADH Oxidation Is Accompanied by Increased Copper Sensitivity
Toulouse, Journal of bacteriology 2018 - “...Gene RF Assigned function VCA0744 VCA0843 VC2349 VC2348 VC2350 glpK gapA-2 deoA deoB deoC 3.4 2.5 2.9 10.6 2 Glycerol kinase Glyceraldehyde 3-phophate...”
- Host-induced epidemic spread of the cholera bacterium
Merrell, Nature 2002 - “...samples are VC0028, VC0941, VC0869, VC0051, VC0647, VC0468, VC2350 and VCA0583, all of which were recently identified in a genetic screen for factors required...”
PMI2416 deoxyribose-phosphate aldolase from Proteus mirabilis HI4320
34% identity, 73% coverage
YPK_3627 deoxyribose-phosphate aldolase from Yersinia pseudotuberculosis YPIII
33% identity, 71% coverage
- Functional versatility of Zur in metal homeostasis, motility, biofilm formation, and stress resistance in Yersinia pseudotuberculosis
Gu, Microbiology spectrum 2024 - “...as peptidoglycan biosynthesis-related D-alanine-D-alanine ligase Ddl (YPK_3516), purine-nucleoside phosphorylase DeoD (YPK_3624), and deoxyribose-phosphate aldolase DeoC (YPK_3627), by directly binding to their promoters. This underscores Zurs regulatory influence on these molecular metabolic pathways. Moreover, Zur negatively regulated the large subunit ribosomal protein bL31-B (YPK_3210) and bL36-B (YPK_3211),...”
- “...bL31-B ( ypk_3210 ), ddl ( ypk_3616 ), deoD ( ypk_3524 ), and deoC ( ypk_3627 ). ( B ) EMSA was performed to analyze the interactions between His6-Zur and various promoters ( ypk_3210 p, ypk_3516 p, and ypk_3627 p). Various amounts of Zur (0, 0.2,...”
PG1996 deoxyribose-phosphate aldolase from Porphyromonas gingivalis W83
39% identity, 58% coverage
- Iron Deficiency Modulates Metabolic Landscape of Bacteroidetes Promoting Its Resilience during Inflammation
Lewis, Microbiology spectrum 2023 - “...PG_RS0823540 PG187879 Cysteine-tRNA ligase, patatin-like phospholipase protein 1.5 0.0340.073 deoC , mnmG , PG_RS08805790 PG199592 PG1996 Nucleotide pyrophosphohydrolase, deoxyribose-phosphate aldolase, d -tyrosyl-tRNA(Tyr)deacylase, MnmG 3.2 2.13807E-05 PG_RS08850 PG2006 Hypothetical protein 2.0 9.4623E-05 PG_RS08855 PG2008 TonB-dependent receptor 1.4 0.089 PG_RS09320 PG2102 T9SS type A sorting domain-containing protein 1.4...”
- Microarray analysis of the transcriptional responses of Porphyromonas gingivalis to polyphosphate
Moon, BMC microbiology 2014 - “...Energy metabolism : Glycolysis/gluconeogenesis PG0130 Phosphoglyceromutase 1.68 Energy metabolism : Purines, pyrimidines, nucleosides, and nucleotides PG1996 Deoxyribose-phosphate aldolase 1.73 Energy 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...”
VP2436 deoxyribose-phosphate aldolase from Vibrio parahaemolyticus RIMD 2210633
34% identity, 76% coverage
VDA_002812 deoxyribose-phosphate aldolase from Photobacterium damselae subsp. damselae CIP 102761
35% identity, 72% coverage
Q91YP3 Deoxyribose-phosphate aldolase from Mus musculus
35% identity, 52% coverage
MHA_0097 deoxyribose-phosphate aldolase from Mannheimia haemolytica PHL213
33% identity, 76% coverage
DEOC_HUMAN / Q9Y315 Deoxyribose-phosphate aldolase; DERA; 2-deoxy-D-ribose 5-phosphate aldolase; Phosphodeoxyriboaldolase; Deoxyriboaldolase; EC 4.1.2.4 from Homo sapiens (Human) (see paper)
Q9Y315 deoxyribose-phosphate aldolase (EC 4.1.2.4) from Homo sapiens (see paper)
NP_057038 deoxyribose-phosphate aldolase isoform 1 from Homo sapiens
34% identity, 52% coverage
- function: Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5- phosphate. Participates in stress granule (SG) assembly. May allow ATP production from extracellular deoxyinosine in conditions of energy deprivation.
catalytic activity: 2-deoxy-D-ribose 5-phosphate = D-glyceraldehyde 3-phosphate + acetaldehyde (RHEA:12821)
subunit: Interacts with YBX1. - A systematic review and meta-analysis of proteomic and metabolomic alterations in anaphylaxis reactions
Gallizzi, Frontiers in immunology 2024 - “...DDB1 DDB1 DNA damage-binding protein 1 NA Q5TDH0 DDI2 DDI2 Protein DDI1 homolog 2 NA Q9Y315 DEOC DERA Deoxyribose-phosphate aldolase NA Q9H3Z4 DNJC5 DNAJC5 DnaJ homolog subfamily C member 5 NA P50570 DYN2 DNM2 Dynamin-2 NA Q14204 DYHC1 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 NA...”
- Longitudinal Assessment of Nasopharyngeal Biomarkers Post-COVID-19: Unveiling Persistent Markers and Severity Correlations.
Redondo-Calvo, Journal of proteome research 2024 - “...ACSA acetyl-coenzyme A synthetase, cytoplasmic 1.98 2.24 ACSS2 Q9NR19 DEOC deoxyribose-phosphate aldolase 2.00 2.24 DERA Q9Y315 RN5A 25A-dependent ribonuclease 2.19 2.26 RNASEL Q05823 GTPB1 GTP-binding protein 1 3.47 2.26 GTPBP1 O00178 AP1B1 AP-1 complex subunit -1 2.72 2.28 AP1B1 Q10567 FCHO2 F-BAR domain only protein 2...”
- Twelfth-Position Deuteration of Nevirapine Reduces 12-Hydroxy-Nevirapine Formation and Nevirapine-Induced Hepatocyte Death
Heck, Journal of medicinal chemistry 2020 - “...FUBP3 1.470.03 0.0198 P00167 cytochrome b5 CYB5A 1.50.11 0.0361 Q13438 protein os-9 OS9 1.530.09 0.0187 Q9Y315 deoxyribose-phosphate aldolase DERA 1.630.06 0.0229 Q4G176 Acyl-CoA synthetase family member3, mitochondrial ACSF3 1.630.09 0.0278 P82979 SAP domain-containing ribonucleoprotein SARNP 1.650.07 0.0043 O75431 metaxin-2 MTX2 1.670.09 0.0465 Q9H6R4 nucleolar protein6 NOL6...”
- Quantitative global proteome and lysine succinylome analyses provide insights into metabolic regulation and lymph node metastasis in gastric cancer.
Song, Scientific reports 2017 - “...1-dehydrogenasepresent (UniProt ID: P11413), 6-phosphofructokinase type C (UniProt ID: Q01813), and deoxyribose-phosphate aldolase (UniProt ID: Q9Y315), are gradually increased in the process of LNM ( Fig. 6b ). Interestingly, we found obvious trends of Ksucc expression levels in these two important pathways. Although most of the...”
- Targeted proteomic approach in prostatic tissue: a panel of potential biomarkers for cancer detection
Aiello, Oncoscience 2016 - “...control the differentiation and maintenance of normal epithelia as well as tumor growth 479 116. Q9Y315 DERA Putative deoxyribose-phosphate aldolase * 908 35231 cytoplasm lyase 189 117. Q15311 RALBP1 RalA-binding protein 1 * 568 76063 membrane signal transduction and ATP catabolic process 213 118. Q08999 RBL2...”
- Hemolysis exacerbates hyperfibrinolysis, whereas platelolysis shuts down fibrinolysis: evolving concepts of the spectrum of fibrinolysis in response to severe injury.
Moore, Shock (Augusta, Ga.) 2015 - “...0 6 Ubiquitin carboxyl-terminal hydrolase 14 P54578 56 kD 10 0 7 Putative deoxyribose-phosphate aldolase Q9Y315 35 kD 10 0 8 Plasminogen * P00747 91 kD 346 13 9 Tropomodulin 1 P28289 41 kD 9 0 10 Histidine triad nucleotide-binding protein 1 P49773 14 kD 7...”
- A case of pericytic neoplasm in the shoulder with a novel DERA-GLI1 gene fusion.
Nitta, Histopathology 2021 (PubMed)- GeneRIF: A case of pericytic neoplasm in the shoulder with a novel DERA-GLI1 gene fusion.
- Genetic variants in TKT and DERA in the nicotinamide adenine dinucleotide phosphate pathway predict melanoma survival.
Gu, European journal of cancer (Oxford, England : 1990) 2020 - GeneRIF: Genetic variants in TKT and DERA in the nicotinamide adenine dinucleotide phosphate pathway predict melanoma survival.
- Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
Rose, Molecular medicine (Cambridge, Mass.) - GeneRIF: Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
STY4918 deoxyribose-phosphate aldolase from Salmonella enterica subsp. enterica serovar Typhi str. CT18
32% identity, 71% coverage
STM4567 2-deoxyribose-5-phosphate aldolase from Salmonella typhimurium LT2
32% identity, 71% coverage
- Mass spectrometry-based quantitative proteomic analysis of Salmonella enterica serovar Enteritidis protein expression upon exposure to hydrogen peroxide
Kim, BMC microbiology 2010 - “...21% STM4414 Inorganic pyrophosphatase ppa 19.68 5.01 43% STM4513 Putative permease yjiG 16.12 7.76 61% STM4567 Deoxyribose-phosphate aldolase deoC 27.68 5.87 47% STM4568 Thymidine phosphorylase deoA 47 4.96 38% STM4569 Phosphopentomutase deoB 44.24 5.15 52% STM4598 Two-component response regulator arcA 45.56 5.47 58% STY2300 CDP-6-deoxy-D-xylo-4-hexulose-3-dehydrase rfbH...”
- “...mutL mutL 41 3% STM4414 Inorganic pyrophosphatase ppa 0% STM4513 Putative permease yjiG -78 15% STM4567 Deoxyribose-phosphate aldolase deoC 0% STM4568 Thymidine phosphorylase deoA -9 2% STM4569 Phosphopentomutase deoB 0% STM4598 Two-component response regulator arcA 10 4% STY2300 CDP-6-deoxy-D-xylo-4-hexulose-3-dehydrase rfbH 0% STY2300 CDP-4-keto-6-deoxy-D-glucose-3-dehydrase ddhC 0% Relative...”
Q8Z0U3 Deoxyribose-phosphate aldolase from Salmonella typhi
32% identity, 73% coverage
DEOC_SALTY / Q8ZJV8 Deoxyribose-phosphate aldolase; DERA; 2-deoxy-D-ribose 5-phosphate aldolase; Phosphodeoxyriboaldolase; Deoxyriboaldolase; EC 4.1.2.4 from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (see paper)
32% identity, 73% coverage
- function: Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5- phosphate.
catalytic activity: 2-deoxy-D-ribose 5-phosphate = D-glyceraldehyde 3-phosphate + acetaldehyde (RHEA:12821)
subunit: Homodimer. - N-dodecanoyl-homoserine lactone influences the levels of thiol and proteins related to oxidation-reduction process in Salmonella
de, PloS one 2018 - “...adk Metabolic process 0.221 0.329 1.820 1.810 0.091 0.215 -0.451 1.037 -1.271 1.260 Deoxyribose-phosphate aldolase Q8ZJV8 deoC Metabolic process -7.031 0.839 ND ND -0.630 0.925 ND ND 7.796 0.767 Pyrimidine/purine nucleoside phosphorylase Q8ZRE7 ppnP Metabolic process ND ND ND ND ND ND 8.356 1.530 ND ND...”
Q7WT44 deoxyribose-phosphate aldolase (EC 4.1.2.4) from Klebsiella pneumoniae (see paper)
31% identity, 78% coverage
F1M1H0 deoxyribose-phosphate aldolase from Rattus norvegicus
35% identity, 53% coverage
BWI76_RS04130 deoxyribose-phosphate aldolase from Klebsiella sp. M5al
32% identity, 73% coverage
- Oxidative Pathways of Deoxyribose and Deoxyribonate Catabolism
Price, mSystems 2019 - “...fitness of 4.0 versus 1.4). Although the genome of K. michiganesis contains a deoxyribose-phosphate aldolase (BWI76_RS04130), it does not seem to encode deoxyribose kinase. This might explain why it did not grow with deoxyribose as the carbon source. We did obtain fitness data with three deoxynucleotides...”
ETEC_4737 deoxyribose-phosphate aldolase from Escherichia coli ETEC H10407
33% identity, 73% coverage
Tlr / b4381 deoxyribose-phosphate aldolase (EC 4.1.2.4) from Escherichia coli K-12 substr. MG1655 (see 16 papers)
deoC / P0A6L0 deoxyribose-phosphate aldolase (EC 4.1.2.4) from Escherichia coli (strain K12) (see 14 papers)
DEOC_ECOLI / P0A6L0 Deoxyribose-phosphate aldolase; DERA; 2-deoxy-D-ribose 5-phosphate aldolase; Phosphodeoxyriboaldolase; Deoxyriboaldolase; EC 4.1.2.4 from Escherichia coli (strain K12) (see 4 papers)
deoC / RF|NP_418798 phosphodeoxyriboaldolase from Escherichia coli K12 (see paper)
b4381 deoxyribose-phosphate aldolase from Escherichia coli str. K-12 substr. MG1655
NP_418798 deoxyribose-phosphate aldolase from Escherichia coli str. K-12 substr. MG1655
33% identity, 73% coverage
- function: Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5- phosphate (PubMed:11598300, PubMed:17905878, PubMed:6749498). Can also catalyze the double aldol condensation of three acetaldehyde molecules, leading to the formation of 2,4,6-trideoxyhexose (Ref.5).
catalytic activity: 2-deoxy-D-ribose 5-phosphate = D-glyceraldehyde 3-phosphate + acetaldehyde (RHEA:12821)
subunit: Monomer and homodimer. - Genome-Scale Mapping of Escherichia coli σ54 Reveals Widespread, Conserved Intragenic Binding
Bonocora, PLoS genetics 2015 - “...20 10.399 IS56 4612117 3 C TGGC ATCGTTA TTGC T 4612106 + b4378 yjjV + b4381 deoC 3229 12.389 IS57 4613489 17 C TGGC TCTGTTT TTGC A 4613489 - b4379 yjjW - b4371 rsmC 7766 11.411 IS58 4627943 2 C TGG AACGCTTCC TGC A 4627937 -...”
- The association of DNA damage response and nucleotide level modulation with the antibacterial mechanism of the anti-folate drug trimethoprim
Sangurdekar, BMC genomics 2011 - “...Site-specific recombinase for fimA promoter segment inversion; bias for ON to OFF phase switching deoC b4381 Deoxyribose-phosphate aldolase; deoxyriboaldolase; binds selenium deoA b4382 Thymidine phosphorylase A total of 18 mutants, based on their relatively high biomass yield in presence of TMP, were identified as sensitive candidates....”
- Protein disorder is positively correlated with gene expression in Escherichia coli
Paliy, Journal of proteome research 2008 - “...degradation), treC (b4239, trehalose degradation), deoC (b4381, deoxyribonucleoside degradation), and fucI (b2802, degradation of sugars). These findings are...”
- YcfR (BhsA) influences Escherichia coli biofilm formation through stress response and surface hydrophobicity
Zhang, Journal of bacteriology 2007 - “...b0331 b0334 b0453 b2392 b1678 b1676 b4234 b4382 b4381 b4384 b2780 b2529 b2530 Predicted GTP-binding transport protein, essential for E. coli growth Putative...”
- Identification of genome-scale metabolic network models using experimentally measured flux profiles
Herrgård, PLoS computational biology 2006 - “...fdoH (b3893), fdoG (b3894), fdhF (b4079), frdD (b4151), frdC (b4152), frdB (b4153), frdA (b4154), deoC (b4381), and deoB (b4383). We thank Trey Ideker, Shankar Subramaniam, Bing Ren, Kenneth Kreutz-Delgado, Costas Maranas, Tony Burgard, and Jennie Reed for valuable discussions. Author contributions. MJH, SSF, and BP conceived...”
- Effect of an artificial RNA marker on gene expression in Escherichia coli
Tucker, Applied and environmental microbiology 2005 - “...gene expression Change in gene expression (fold) Cotranslationb b4381 7.7 106 2.34 deoB b4383 0.000565 1.48 serA b2913 0.007776 1.447 rplL b3986 0.011943 1.387...”
- “...1.358 b4315 b4314 0.003396 0.008934 2.958 2.499 deoC b4381 0.018262 2.025 ykgM tmk b0296 b1098 0.037316 0.049627 1.625 1.625 deoB b4383 0.048425 deoD b4384...”
- Prominent roles of the NorR and Fur regulators in the Escherichia coli transcriptional response to reactive nitrogen species
Mukhopadhyay, Proceedings of the National Academy of Sciences of the United States of America 2004 - “...b3117 b1895 b2717 b0795 b1684 b0127 b4367 b2875 b3106 b4357 b2579 b0484 b3744 b4381 b3774 b0802 b2715 b1200 b1241 b1112 173 338 70 38 2 3 11 2 17 18 1 1 6 5 2 1...”
- Non-natural Aldol Reactions Enable the Design and Construction of Novel One-Carbon Assimilation Pathways in vitro
Mao, Frontiers in microbiology 2021 - “...R , N-terminally His-tagged deoC , inserted between the Nhe I and Xho I sites NP_418798 Yang et al., 2019b pET28a- rpiB Kan R , N-terminally His-tagged rpiB , inserted between the Nhe I and Xho I sites NP_418514 Yang et al., 2019b pET28a- pgi Kan...”
- The primary structure of Escherichia coli K12 2-deoxyribose 5-phosphate aldolase. Nucleotide sequence of the deoC gene and the amino acid sequence of the enzyme.
Valentin-Hansen, European journal of biochemistry 1982 (PubMed)- GeneRIF: N-terminus verified by Edman degradation on mature peptide
- Multi-modal deep learning enables efficient and accurate annotation of enzymatic active sites.
Wang, Nature communications 2024 - “...(UniProt ID: P00655, EC Number M-CSA: 3.1.27.10, EC Number UniProt: 4.6.1.23), deoxyribose-phosphate aldolase (UniProt ID: P0A6L0, EC Number: 4.1.2.4), and galactose mutarotase (UniProt ID: Q96C23, EC Number: 5.1.3.3), along with their corresponding artificially constructed scaffolding enzyme structures designed by Watson et al. 33 using RFdiffusion 35...”
- Protein quaternary structures in solution are a mixture of multiple forms.
Marciano, Chemical science 2022 - “...independently in both dimeric (PDB 1KTN ) and monomeric (PDB 1JCL ) states. In UniProt (P0A6L0) it is ambiguously designated as both a monomer and dimer. 9,47 Using native MS, we observe a concentration dependent monomerdimer equilibrium ( Fig. 2A and B ). Two peaks are...”
- Exposure of E. coli to DNA-Methylating Agents Impairs Biofilm Formation and Invasion of Eukaryotic Cells via Down Regulation of the N-Acetylneuraminate Lyase NanA
Di, Frontiers in microbiology 2016 - “...1.21 2467 0.0089 D-tagatose1,6-bisphosphate aldolase subunit GatZ gatZ P0C8J8 1.20 3721 0.0024 Deoxyribose-phosphate aldolase deoC P0A6L0 1.15 3787 0.0027 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase gpmA P62707 1.12 2062 0.0069 Pyruvate kinase I pykF P0AD61 +1.24 2169 0.0053 Phosphoglucomutase pgm P36938 AMINOACYL-tRNA BIOSYNTHESIS 1.69 3047 0.0044 Phenylalanine tRNA synthetase,...”
- Comprehensively Characterizing the Thioredoxin Interactome In Vivo Highlights the Central Role Played by This Ubiquitous Oxidoreductase in Redox Control
Arts, Molecular & cellular proteomics : MCP 2016 - “...protein MreB 60 kDa chaperonin P0A6A3 P25553 P0A6K6 P0A6L0 P0AAB6 P0ABQ2 B1X7I7 P0C8J8 P0A6F3 P0A6L4 P0A9X4 P0A6F5 dehydratase 1 ATP synthase subunit alpha ATP...”
- The Escherichia coli proteome: past, present, and future prospects
Han, Microbiology and molecular biology reviews : MMBR 2006 - “...DeoB P0A6K6 Phosphopentomutase 5.11/44,369.96 DeoC P0A6L0 Deoxyribose-phosphate aldolase 5.50/27,733.80 5.52/33,657 (5-6) DeoD P0ABP8 Purine nucleoside...”
B5Y277 Deoxyribose-phosphate aldolase from Klebsiella pneumoniae (strain 342)
31% identity, 73% coverage
A0A125YLW2 deoxyribose-phosphate aldolase (EC 4.1.2.4) from Toxoplasma gondii (see paper)
TGME49_270650 deoxyribose-phosphate aldolase from Toxoplasma gondii ME49
36% identity, 70% coverage
- Structural and functional divergence of the aldolase fold in Toxoplasma gondii
Tonkin, Journal of molecular biology 2015 - “...ALDO; PF14_0425), T. gondii DPA ( Tg DPA; TGME49_318750), T. gondii DERA ( Tg DERA; TGME49_270650), N. caninum DPA (NCLIV_010810), N. caninum DERA (NCLIV_036120), P. yoelii DERA ( Py DERA; PY02252), P. berghei DERA (PBANKA_050580), P. chabaudi DERA (PCHAS_050590), P. falciparum DERA (PF10_0210), P. vivax DERA...”
- “...sequences for Ec DERA ( NP_757311.1 ), Py DERA ( PY02252 ), Tg DERA ( TGME49_270650 ), and Tg DPA ( TGME49_318750 ) were aligned and extracted in a similar fashion. Figure 2 Tertiary and quaternary structures of Tg ALD1 and Tg DPA reveal different ancillary...”
1jcjA / P0A6L0 Observation of covalent intermediates in an enzyme mechanism at atomic resolution (see paper)
32% identity, 75% coverage
- Ligand: 1-hydroxy-pentane-3,4-diol-5-phosphate (1jcjA)
DIP0377 Hypothetical protein from Corynebacterium diphtheriae NCTC 13129
40% identity, 56% coverage
DEOC_PYRAE / Q8ZXK7 Deoxyribose-phosphate aldolase; DERA; 2-deoxy-D-ribose 5-phosphate aldolase; Phosphodeoxyriboaldolase; Deoxyriboaldolase; EC 4.1.2.4 from Pyrobaculum aerophilum (strain ATCC 51768 / DSM 7523 / JCM 9630 / CIP 104966 / NBRC 100827 / IM2) (see paper)
PAE1231 deoxyribose-phosphate aldolase from Pyrobaculum aerophilum str. IM2
34% identity, 90% coverage
- function: Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5- phosphate.
catalytic activity: 2-deoxy-D-ribose 5-phosphate = D-glyceraldehyde 3-phosphate + acetaldehyde (RHEA:12821)
subunit: Homodimer. - Sequential aldol condensation catalyzed by hyperthermophilic 2-deoxy-d-ribose-5-phosphate aldolase
Sakuraba, Applied and environmental microbiology 2007 - “...reading frame TM1559) and DERAPae (open reading frame PAE1231) were amplified by PCR (the gene information is available at www.genome.jp /kegg) using the...”
- Presence of a novel phosphopentomutase and a 2-deoxyribose 5-phosphate aldolase reveals a metabolic link between pentoses and central carbon metabolism in the hyperthermophilic archaeon Thermococcus kodakaraensis
Rashid, Journal of bacteriology 2004 - “...phosphorylase PPM Purine nucleoside phosphorylases APE2437 PAE1231 APE0993, APE2105 PAE1476, PAE3111 SSO1519, SSO2706 ST0975, ST2449 Euryarchaeota Archaeoglobus...”
- Distribution and phylogenies of enzymes of the Embden-Meyerhof-Parnas pathway from archaea and hyperthermophilic bacteria support a gluconeogenic origin of metabolism
Ronimus, Archaea (Vancouver, B.C.) 2003 - “...aerophilum does, however, contain a putative deoxyribose aldolase (PAE1231) that has been shown to possess sequence similarity to DhnAlike aldolases and which...”
KVC_2446 deoxyribose-phosphate aldolase from Ketogulonicigenium vulgare
33% identity, 62% coverage
Igni_1079 deoxyribose-phosphate aldolase from Ignicoccus hospitalis KIN4/I
39% identity, 62% coverage
- Multi-omics analysis provides insight to the Ignicoccus hospitalis-Nanoarchaeum equitans association
Rawle, Biochimica et biophysica acta. General subjects 2017 - “...Igni_0363 Hypothetical protein t Igni_1361 Glucokinase p Igni_0415 Glucose-6-phosphate isomerase t Igni_0678 Fumarase Fumarate m Igni_1079 Deoxyribose-phosphate aldolase t,p Igni_0257 Acyl-coenzyme A synthetase/AMP-(fatty) acid ligase-like protein t Igni_0256 AMP-dependent synthetase and ligase t,p Igni_0983 Isopropylmalate/citramalate/homocitrate synthase p Igni_1256 Pyruvate/ketoisovalerate oxidoreductase, gamma subunit t Igni_0728 N-acetyl-gamma-glutamyl-phosphate reductase...”
NCLIV_036120 putative deoxyribose-phosphate aldolase from Neospora caninum Liverpool
33% identity, 76% coverage
- Structural and functional divergence of the aldolase fold in Toxoplasma gondii
Tonkin, Journal of molecular biology 2015 - “...TGME49_318750), T. gondii DERA ( Tg DERA; TGME49_270650), N. caninum DPA (NCLIV_010810), N. caninum DERA (NCLIV_036120), P. yoelii DERA ( Py DERA; PY02252), P. berghei DERA (PBANKA_050580), P. chabaudi DERA (PCHAS_050590), P. falciparum DERA (PF10_0210), P. vivax DERA (PVX_001945), P. knowlesi DERA (PKH_060570)]. Sequences for Oryctolagus...”
PVX_001945 deoxyribose-phosphate aldolase, putative from Plasmodium vivax
32% identity, 68% coverage
- Structural and functional divergence of the aldolase fold in Toxoplasma gondii
Tonkin, Journal of molecular biology 2015 - “...P. berghei DERA (PBANKA_050580), P. chabaudi DERA (PCHAS_050590), P. falciparum DERA (PF10_0210), P. vivax DERA (PVX_001945), P. knowlesi DERA (PKH_060570)]. Sequences for Oryctolagus cuniculus aldolase A (Rabbit muscle aldolase, Oc ALDOA; NP_001075707.1), Pf Aldolase ( Pf ALDO) and Tg ALD1, and for Escherichia coli DERA (...”
- Revealing natural antisense transcripts from Plasmodium vivax isolates: evidence of genome regulation in complicated malaria
Boopathi, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2013 (PubMed)- “...PVX_080515 ribose 5-phosphate epimerase PVX_001945 deoxyribose-phosphate aldolase PVX_094915 GDP-L-fucose synthetase PVX_111455 glucosamine-fructose-6-phosphate...”
PF3D7_1021600 deoxyribose-phosphate aldolase, putative from Plasmodium falciparum 3D7
30% identity, 68% coverage
PBANKA_050580 deoxyribose-phosphate aldolase, putative from Plasmodium berghei ANKA
28% identity, 71% coverage
- An Integrated Approach to Explore Composition and Dynamics of Cholesterol-rich Membrane Microdomains in Sexual Stages of Malaria Parasite
Fratini, Molecular & cellular proteomics : MCP 2017 - “...UAP56 (PBANKA_030680) and the putative deoxyribose-phosphate aldolase (PBANKA_050580, from now on named PbDPA), detected only in gametocyte DRMs. To further...”
- Structural and functional divergence of the aldolase fold in Toxoplasma gondii
Tonkin, Journal of molecular biology 2015 - “...(NCLIV_010810), N. caninum DERA (NCLIV_036120), P. yoelii DERA ( Py DERA; PY02252), P. berghei DERA (PBANKA_050580), P. chabaudi DERA (PCHAS_050590), P. falciparum DERA (PF10_0210), P. vivax DERA (PVX_001945), P. knowlesi DERA (PKH_060570)]. Sequences for Oryctolagus cuniculus aldolase A (Rabbit muscle aldolase, Oc ALDOA; NP_001075707.1), Pf Aldolase...”
SPO3367, YP_168563 deoxyribose-phosphate aldolase from Silicibacter pomeroyi DSS-3
32% identity, 60% coverage
- An Updated genome annotation for the model marine bacterium Ruegeria pomeroyi DSS-3
Rivers, Standards in genomic sciences 2014 - “...decarboxylase pyrF ORF position YP_168540 SPO3344 Cys/Met metabolism PLP-dependent enzyme family protein ORF position YP_168563 SPO3367 Deoxyribose-phosphate aldolase deoC ORF position YP_168618 SPO3422 ATP-dependent protease La domain protein ORF position YP_168712 SPO3517 Preprotein translocase, SecE subunit secE ORF position YP_168722 SPO3527 Universal stress protein family protein...”
- “...5'-phosphate decarboxylase pyrF ORF position YP_168540 SPO3344 Cys/Met metabolism PLP-dependent enzyme family protein ORF position YP_168563 SPO3367 Deoxyribose-phosphate aldolase deoC ORF position YP_168618 SPO3422 ATP-dependent protease La domain protein ORF position YP_168712 SPO3517 Preprotein translocase, SecE subunit secE ORF position YP_168722 SPO3527 Universal stress protein family...”
SPO3367 deoxyribose-phosphate aldolase from Ruegeria pomeroyi DSS-3
32% identity, 50% coverage
- An Updated genome annotation for the model marine bacterium Ruegeria pomeroyi DSS-3
Rivers, Standards in genomic sciences 2014 - “...decarboxylase pyrF ORF position YP_168540 SPO3344 Cys/Met metabolism PLP-dependent enzyme family protein ORF position YP_168563 SPO3367 Deoxyribose-phosphate aldolase deoC ORF position YP_168618 SPO3422 ATP-dependent protease La domain protein ORF position YP_168712 SPO3517 Preprotein translocase, SecE subunit secE ORF position YP_168722 SPO3527 Universal stress protein family protein...”
PCHAS_050590 deoxyribose-phosphate aldolase, putative from Plasmodium chabaudi chabaudi
29% identity, 73% coverage
- Structural and functional divergence of the aldolase fold in Toxoplasma gondii
Tonkin, Journal of molecular biology 2015 - “...(NCLIV_036120), P. yoelii DERA ( Py DERA; PY02252), P. berghei DERA (PBANKA_050580), P. chabaudi DERA (PCHAS_050590), P. falciparum DERA (PF10_0210), P. vivax DERA (PVX_001945), P. knowlesi DERA (PKH_060570)]. Sequences for Oryctolagus cuniculus aldolase A (Rabbit muscle aldolase, Oc ALDOA; NP_001075707.1), Pf Aldolase ( Pf ALDO) and...”
PKH_060570 deoxyribose-phosphate aldolase, putative from Plasmodium knowlesi strain H
32% identity, 56% coverage
MGA_1328 deoxyribose-phosphate aldolase domain-containing protein from Mycoplasma gallisepticum str. R(low)
38% identity, 34% coverage
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 789,361 different protein sequences to 1,256,019 scientific articles. Searches against EuropePMC were last performed on January 10 2025.
PaperBLAST builds a database of protein sequences that are linked
to scientific articles. These links come from automated text searches
against the articles in EuropePMC
and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot,
BRENDA,
CAZy (as made available by dbCAN),
BioLiP,
CharProtDB,
MetaCyc,
EcoCyc,
TCDB,
REBASE,
the Fitness Browser,
and a subset of the European Nucleotide Archive with the /experiment tag.
Given this database and a protein sequence query,
PaperBLAST uses protein-protein BLAST
to find similar sequences with E < 0.001.
To build the database, we query EuropePMC with locus tags, with RefSeq protein
identifiers, and with UniProt
accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use
queries of the form "locus_tag AND genus_name" to try to ensure that
the paper is actually discussing that gene. Because EuropePMC indexes
most recent biomedical papers, even if they are not open access, some
of the links may be to papers that you cannot read or that our
computers cannot read. We query each of these identifiers that
appears in the open access part of EuropePMC, as well as every locus
tag that appears in the 500 most-referenced genomes, so that a gene
may appear in the PaperBLAST results even though none of the papers
that mention it are open access. We also incorporate text-mined links
from EuropePMC that link open access articles to UniProt or RefSeq
identifiers. (This yields some additional links because EuropePMC
uses different heuristics for their text mining than we do.)
For every article that mentions a locus tag, a RefSeq protein
identifier, or a UniProt accession, we try to select one or two
snippets of text that refer to the protein. If we cannot get access to
the full text, we try to select a snippet from the abstract, but
unfortunately, unique identifiers such as locus tags are rarely
provided in abstracts.
PaperBLAST also incorporates manually-curated protein functions:
- Proteins from NCBI's RefSeq are included if a
GeneRIF
entry links the gene to an article in
PubMed®.
GeneRIF also provides a short summary of the article's claim about the
protein, which is shown instead of a snippet.
- Proteins from Swiss-Prot (the curated part of UniProt)
are included if the curators
identified experimental evidence for the protein's function (evidence
code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that
describe the protein's function are shown (with bold headings).
- Proteins from BRENDA,
a curated database of enzymes, are included if they are linked to a paper in PubMed
and their full sequence is known.
- Every protein from the non-redundant subset of
BioLiP,
a database
of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself
does not include descriptions of the proteins, those are taken from the
Protein Data Bank.
Descriptions from PDB rely on the original submitter of the
structure and cannot be updated by others, so they may be less reliable.
(For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every
ligand is represented among a group of structures with similar sequences, but for
PaperBLAST, we use the non-redundant set provided by BioLiP.)
- Every protein from EcoCyc, a curated
database of the proteins in Escherichia coli K-12, is included, regardless
of whether they are characterized or not.
- Proteins from the MetaCyc metabolic pathway database
are included if they are linked to a paper in PubMed and their full sequence is known.
- Proteins from the Transport Classification Database (TCDB)
are included if they have known substrate(s), have reference(s),
and are not described as uncharacterized or putative.
(Some of the references are not visible on the PaperBLAST web site.)
- Every protein from CharProtDB,
a database of experimentally characterized protein annotations, is included.
- Proteins from the CAZy database of carbohydrate-active enzymes
are included if they are associated with an Enzyme Classification number.
Even though CAZy does not provide links from individual protein sequences to papers,
these should all be experimentally-characterized proteins.
- Proteins from the REBASE database
of restriction enzymes are included if they have known specificity.
- Every protein with an evidence-based reannotation (based on mutant phenotypes)
in the Fitness Browser is included.
- Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators)
with experimentally-determined DNA binding sites from the
PRODORIC database of gene regulation in prokaryotes.
- Putative transcription factors from RegPrecise
that have manually-curated predictions for their binding sites. These predictions are based on
conserved putative regulatory sites across genomes that contain similar transcription factors,
so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
- Coding sequence (CDS) features from the
European Nucleotide Archive (ENA)
are included if the /experiment tag is set (implying that there is experimental evidence for the annotation),
the nucleotide entry links to paper(s) in PubMed,
and the nucleotide entry is from the STD data class
(implying that these are targeted annotated sequences, not from shotgun sequencing).
Also, to filter out genes whose transcription or translation was detected, but whose function
was not studied, nucleotide entries or papers with more than 25 such proteins are excluded.
Descriptions from ENA rely on the original submitter of the
sequence and cannot be updated by others, so they may be less reliable.
Except for GeneRIF and ENA,
the curated entries include a short curated
description of the protein's function.
For entries from BioLiP, the protein's function may not be known beyond binding to the ligand.
Many of these entries also link to articles in PubMed.
For more information see the
PaperBLAST paper (mSystems 2017)
or the code.
You can download PaperBLAST's database here.
Changes to PaperBLAST since the paper was written:
- November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
- February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
- June 2022: incorporated some coding sequences from ENA with the /experiment tag.
- March 2022: incorporated BioLiP.
- April 2020: incorporated TCDB.
- April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
- February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
- January 2018: incorporated BRENDA.
- December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
- September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.
Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.
PaperBLAST cannot provide snippets for many of the papers that are
published in non-open-access journals. This limitation applies even if
the paper is marked as "free" on the publisher's web site and is
available in PubmedCentral or EuropePMC. If a journal that you publish
in is marked as "secret," please consider publishing elsewhere.
Many important articles are missing from PaperBLAST, either because
the article's full text is not in EuropePMC (as for many older
articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an
article that characterizes a protein's function but is missing from
PaperBLAST, please notify the curators at UniProt
or add an entry to GeneRIF.
Entries in either of these databases will eventually be incorporated
into PaperBLAST. Note that to add an entry to UniProt, you will need
to find the UniProt identifier for the protein. If the protein is not
already in UniProt, you can ask them to create an entry. To add an
entry to GeneRIF, you will need an NCBI Gene identifier, but
unfortunately many prokaryotic proteins in RefSeq do not have
corresponding Gene identifers.
References
PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.
Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.
Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.
UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.
BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.
The MetaCyc database of metabolic pathways and enzymes.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.
CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.
The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.
The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.
REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
R. J. Roberts et al (2015). Nucleic Acids Research, 10.1093/nar/gku1046.
Deep annotation of protein function across diverse bacteria from mutant phenotypes.
M. N. Price et al (2016). bioRxiv, 10.1101/072470.
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory