PaperBLAST

Full List of Papers Linked to P52873

P52873 Pyruvate carboxylase, mitochondrial from Rattus norvegicus

• Proximity labelling reveals effects of disease-causing mutation on the DNAJC5/cysteine string protein α interactome
  Barker, The Biochemical journal 2024
  • “...(P22734) Hn1(Q6AXU6) Hsph1 (Q66HA8) Map1a (P34926) C2cd2l (Q5U2P5) Hn1* (Q6AXU6) Asap1* (Q1AAU6) Hsp90b1 (Q66HD0) Pc (P52873) Stxbp1* (P61765) Cdv3* (A0A0G2K0B0) Vamp2* (P63045) Stip1 (O35814) Prph (P21807) Pcdh1* (A0A0G2K6T9) Dpysl2* (P47942) Sept11 (A0A0G2JUL7) Pcca (A0A0G2K401) Nudcd2* (Q5M823) Txn1* (P11232) Sept8 (G3V9Z6) Hsp90aa1 (P82995) Myh11 (E9PTU4) Sprr1a* (G3V755)...”
• Proteomics to Metabolomics: A New Insight into the Pathogenesis of Hypertensive Nephropathy
  Eshraghi, Kidney & blood pressure research 2023
  • “...3.476 0.004 G3V734 Decr1 2,4-dienoyl-Coa reductase 1 3.212 0.033 D3Z8F1 Vill Villin like 3.185 0.021 P52873 Pc Pyruvate carboxylase 3.052 0.038 G3V7L4 Cdh16 Cadherin 16 3.049 0.023 F1LQC1 Acox1 Acyl-coenzyme A oxidase 3.041 0.018 P08461 Dlat Dihydrolipoyllysine-residue acetyltransferase 2.998 0.039 PXD012889 (outer cortex) P08932 Kng1 Kininogen...”
  • “...lipoprotein receptor 4.32 0.009 Q68FT3 Pyroxd2 Pyridine nucleotide-disulphide 4.066 0.006 P08461 Dlat Dihydrolipoamide-S-acetyltransferase 4.054 0.016 P52873 Pc Pyruvate carboxylase 3.963 0.047 G3V7L4 Cdh16 Cadherin 16 3.528 0.044 G3V6S5 Mthfd1 Methylenetetrahydrofolate dehydrogenase 3.434 0.007 G3V734 Decr1 2,4-dienoyl-Coa reductase 1 2.972 0.042 P97608 Oplah 5-oxoprolinase, ATP-hydolyzing 2.907 0.042...”
• Diet-Induced Hypercholesterolemia Leads to Cardiac Dysfunction and Alterations in the Myocardial Proteome
  Szabó, International journal of molecular sciences 2022
  • “...Mug1 Murinoglobulin-1 1.96 O35814 Stip1 Stress-induced-phosphoprotein 1 1.91 P09006 Serpina3n Serine protease inhibitor A3N 1.90 P52873 Pc Pyruvate carboxylase 1.54 P02680 Fgg Fibrinogen gamma chain 1.45 P02564 Myh7 Myosin-7 1.42 P06399 Fga Fibrinogen alpha chain 1.42 P01026 C3 Complement C3 1.35 D3ZWC6 Sntb1 Syntrophin, basic 1...”
• Extracellular vesicles released by steatotic hepatocytes alter adipocyte metabolism
  Mleczko, Journal of extracellular biology 2022
  • “...lyase, mitochondrial SDC4_RAT P34901 1.78 1.17E04 Syndecan4 CP2DQ_RAT P10634 1.79 1.03E03 Cytochrome P450 2D26 PYC_RAT P52873 1.82 1.83E03 Pyruvate carboxylase, mitochondrial RS27A_RAT P62982 1.84 8.94E04 Ubiquitin40S ribosomal protein S27a RDH2_RAT P50170 1.86 4.16E04 Retinol dehydrogenase 2 ACOX2_RAT P97562 1.87 3.22E02 Peroxisomal acylcoenzyme A oxidase 2 HYEP_RAT...”
• Brown Adipose Tissue Sheds Extracellular Vesicles That Carry Potential Biomarkers of Metabolic and Thermogenesis Activity Which Are Affected by High Fat Diet Intervention.
  Camino, International journal of molecular sciences 2022
  • “...Medium-chain specific acyl-CoA dehydrogenase, mitochondrial 0.047 2.13 THIL_RAT P17764 Acetyl-CoA acetyltransferase, mitochondrial 0.006 2.12 PYC_RAT P52873 Pyruvate carboxylase, mitochondrial 0.003 2.10 IDH3A_RAT Q99NA5 Isocitrate dehydrogenase [NAD] subunit Alpha, mitochondrial 0.027 2.07 HSP74_RAT O88600 Heat shock 70 kDa protein 4 0.044 2.04 FETA_RAT P02773 Alpha-fetoprotein 0.029 2.01...”
• Red-Fleshed Apples Rich in Anthocyanins and White-Fleshed Apples Modulate the Aorta and Heart Proteome in Hypercholesterolaemic Rats: The AppleCOR Study.
  Catalán, Nutrients 2022
  • “...1.670 0.0022 P43278 H1f0 Histone H1.0 1.259 0.0110 P11980 Pkm Pyruvate kinase PKM 1.268 0.0128 P52873 Pc Pyruvate carboxylase, mitochondrial 1.538 0.0140 Q9EQS0 Taldo1 Transaldolase 1.293 0.0187 M0RBF1 C3 Complement C3 2.158 <0.0001 G3V7K3 Cp Ceruloplasmin 2.244 <0.0001 G3V7N9 C1qb Complement C1q subcomponent subunit B 2.554...”
• Lead-Induced Motor Dysfunction Is Associated with Oxidative Stress, Proteome Modulation, and Neurodegeneration in Motor Cortex of Rats
  Leão, Oxidative medicine and cellular longevity 2021
  • “...and P21571), Citrate Synthase (Q8VHF5), Cytochrome C Oxidase subunits (P00406, P11240, and P10818), Pyruvate carboxylase (P52873), and Pyruvate dehydrogenase (P26284) that are involved in glucose metabolism and affect the cell energy balance, suggesting an impairment on cell energy metabolism. The failure on energy metabolism may impact...”
• Inflammation and apoptosis accelerate progression to irreversible atrophy in denervated intrinsic muscles of the hand compared with biceps: proteomic analysis of a rat model of obstetric brachial plexus palsy.
  Yu, Neural regeneration research 2020
  • “...F1LLZ7, A2RRU1, P97531, G3V8V3, Q4G050, A0A0G2K9C8, Q6P727, Q9Z1N1 0.002 Pyruvate metabolism 17 A0A0G2K5G8 * , P52873 * , Q6P7Q4, P11980, P04636, A0A0G2K4C6, P35745, F7FKI5, P17764, O88989, P42123, P08461, P14408, Q6P6R2, A0A0G2JZH8, P49432, B0BN46 < 0.001 HIF-1 pathway 14 Q3HSE5 * , Q9ET45 * , P15429, M0RD75,...”
• Biological Effects of Korean Red Ginseng Polysaccharides in Aged Rat Using Global Proteomic Approach.
  Lee, Molecules (Basel, Switzerland) 2020
  • “...D4A899 3.2 0.00006 Histone H2A type 2A Hist2h2aa3 P0CC09 5.2 0.00030 Pyruvate carboxylase, mitochondrial Pc P52873 3.2 0.00007 Histone H4 Hist1h4b P62804 5.1 0.00031 Spectrin beta chain Sptbn1 G3V6S0 3.1 0.00007 Pre-mRNA processing factor 40 homolog A (Yeast) (Predicted) Prpf40a D3ZJ92 4.9 0.00037 ATP-binding cassette, subfamily...”
• 2-Methoxyestradiol protects against pressure overload-induced left ventricular hypertrophy
  Maayah, Scientific reports 2018
  • “...carrier protein, mitochondrial 0.67 (0.027) 1.15 (0.41) Q64536 Pyruvate dehydrogenase kinase 0.88 (0.72) 0.46 (0.008) P52873 Pyruvate carboxylase 0.8 (0.382) 0.69 (0.035) P23965 Enoyl-CoA delta isomerase 1 0.48 (0.025) 0.97 (0.921) P45953 Acyl-CoA dehydrogenase 0.59 (0.025) 1.44 (0.15) P14604 Enoyl-CoA hydratase 0.60 (0.039) 1.01 (0.97) Q64591...”
• Palmitate-induced lipotoxicity alters acetylation of multiple proteins in clonal β cells and human pancreatic islets
  Ciregia, Scientific reports 2017
  • “...2 P04785 Protein disulfide-isomerase PDIA1 P4hb 625 61 57 4.6 4.8 2.760.5 6.571.3 0.0098 5 P52873 Pyruvate carboxylase PYC Pc 76 110 130 6.4 6.3 0.700.1 4.360.8 0.002 6 P56720 Sterol regulatory element-binding protein 1 SRBP1 Srebf1 45 100 120 6.2 8.4 1.250.3 2.110.4 0.038 7...”
• Functional proteomic analysis of corticosteroid pharmacodynamics in rat liver: Relationship to hepatic stress, signaling, energy regulation, and drug metabolism.
  Ayyar, Journal of proteomics 2017
  • “...UP P16290 Pgam2 Phosphoglycerate mutase 2 Glycolysis - reversible reaction of 3-phosphoglycerate to 2-phosphoglycerate UP P52873 Pc Pyruvate carboxylase, mitochondrial Gluconeogenesis - irreversible carboxylation of pyruvate to form oxaloacetate UP P12928 Pklr Pyruvate kinase Glycolysis - transfer of phosphate from phosphoenolpyruvate to ADP UP/DOWN P27867 Sord...”
• GSTA3 Attenuates Renal Interstitial Fibrosis by Inhibiting TGF-Beta-Induced Tubular Epithelial-Mesenchymal Transition and Fibronectin Expression.
  Xiao, PloS one 2016
• Role of LRP1 and ERK and cAMP Signaling Pathways in Lactoferrin-Induced Lipolysis in Mature Rat Adipocytes
  Ikoma-Seki, PloS one 2015
  • “...14 678.33 0.17 Citrate synthase, mitochondrial Cs CS 1.01 0.80 1.06 0.13 1.11 0.048 * P52873 45 44 3082.24 0.57 Pyruvate carboxylase Pc PC 1.01 0.87 1.03 0.68 1.05 0.091 Peptide information used for quantitation of these proteins is shown in S1 Table . Details include...”
• Proteomic profiling and pathway analysis of the response of rat renal proximal convoluted tubules to metabolic acidosis
  Schauer, American journal of physiology. Renal physiology 2013
  • “...D3ZNQ6 D3ZNQ6_RAT Ube2m 0.034 2.49 SpC Q920A6 Q9Z2M4 P52873 RISC_RAT DECR2_RAT PYC_RAT Scpep1 Decr2 Pc 0.011/0.049 0.009 0.010 1.88/0.42 0.17 2.56 Both TIC TIC...”
  • “...D3ZPL5 F1LQ78 O88267 P80254 P14173 P83868 Q02974 P52873 PCKGC_RAT TPIS_RAT GSTP1_RAT TAGL2_RAT D3ZPL5_RAT F1LQ78_RAT ACOT1_RAT DOPD_RAT DDC_RAT TEBP_RAT KHK_RAT...”
• Use of biotinylated ubiquitin for analysis of rat brain mitochondrial proteome and interactome.
  Buneeva, International journal of molecular sciences 2012
  • “...in energy generation and carbohydrate metabolism ( n = 13) 1 Pyruvate carboxylase, mitochondrial precursor P52873 25 285.19 M 2 ATP synthase subunit beta, mitochondrial precursor P10719 47 231.07 M 3 ATP synthase subunit alpha, mitochondrial precursor P15999 30 163.32 M 4 Sodium/potassium-transporting ATP-ase subunit alpha-3...”
  • “...Sequence Coverage (%) Search score Sequence/position of a.a. residue/ * 1 Pyruvate carboxylase, mitochondrial precursor P52873 Pc 18 25 285.19 SGEGMGIRLDNASAFQGAVISPHYDSLLVKVIAHG KDHPTAAT K MSR/ K442 /EV K KAYVEANQMLGDLIKVTPSSKIVGDLAQFMV QNGLSR/ K891 /SSTAPVASPNVRRLEY K PIKKVMVANR/ K35 / 2 ATP synthase subunit alpha, mitochondrial precursor P15999 Atp5a1 11 30...”
• Δ9-THC increases endogenous AHA1 expression in rat cerebellum and may modulate CB1 receptor function during chronic use.
  Filipeanu, Journal of neurochemistry 2011
  • “...as a ratio to intact/saline grup) 1-ANOVA Subcellular Localization 1 Intact/9-THC OVX/saline OVX/9-THC pyruvate carboxylase P52873 (PYC_RAT) 254 36 43 0.79 0.60 0.46 0.0075 mitochondria NADH dehydrogenase Q561S0 (NDUAA_RAT) 595 19 47 0.87 0.56 2.51 0.4100 mitochondria, NM23 (NDKB) P19804 (NDKB_RAT) 165 9 57 1.70 2.24...”
• Co-compartmentalization of the astroglial glutamate transporter, GLT-1, with glycolytic enzymes and mitochondria.
  Genda, The Journal of neuroscience : the official journal of the Society for Neuroscience 2011
  • “...11 6 Prohibitin P67778 29,803 4 5 Prohibitin-2 O35129 33,296 9 4 6 Pyruvate carboxylase P52873 129,668 3 3 Pyruvate dehydrogenase E1 component subunit beta P49432 38,964 2 4 7 Sideroflexin-3 Q9JHY2 35,415 3 5 Stomatin-like protein 2 Q4FZT0 38,396 6 3 Trifunctional enzyme subunit alpha...”
• Differential permeabilization effects of Ca2+ and valinomycin on the inner and outer mitochondrial membranes as revealed by proteomics analysis of proteins released from mitochondria
  Yamada, Molecular & cellular proteomics : MCP 2009
  • “...P07756 P00507 P04762 P11884 P22791 P04636 P24329 P07756 P52873 Q63276 P04762 P07756 Q63342 P00507 Q9ER34 Q07116 Q63342 P10860 P07756 P22791 Q02253 P22791 P07756...”
  • “...name 1274 Molecular & Cellular Proteomics 8.6 P07756 P52873 Q5XI78 P84551 Q63342 P97564 Q9ER34 Q64428 Q66HF1 P97852 P18163 P07896 P18886 P48721 Q5BJQ0 Q920L2...”

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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.