PaperBLAST

Full List of Papers Linked to VIMSS58699

PA2249 branched-chain alpha-keto acid dehydrogenase (lipoamide component) from Pseudomonas aeruginosa PAO1
Q9I1M0 Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)

• Catabolite repression control protein antagonist, a novel player in Pseudomonas aeruginosa carbon catabolite repression control
  Sonnleitner, Frontiers in microbiology 2023
  • “...2.66 3.14E-08 bkdA1 2-oxoisovalerate dehydrogenase (alpha subunit) PA2248 2.64 3.32E-07 bkdA2 2-oxoisovalerate dehydrogenase (beta subunit) PA2249 2.51 9.12E-07 bkdB Branched-chain alpha-keto acid dehydrogenase (lipoamide component) PA2250 2.78 4.13E-06 lpdV Lipoamide dehydrogenase-Val PA2338 4.24 9.03E-16 PA 2338 Probable binding protein component of ABC maltose/mannitol transporter PA2339 4.97...”
• ECF Sigma Factor HxuI Is Critical for In Vivo Fitness of Pseudomonas aeruginosa during Infection
  Cai, Microbiology spectrum 2022
  • “...8E-24 PA1522 xdhC Xanthine dehydrogenase accessory protein 2.07 3.09E-15 PA2003 bdhA 3-Hydroxybutyrate dehydrogenase 2.07 7.56E-15 PA2249 bkdB Branched-chain alpha-keto acid dehydrogenase complex component 2.17 4.46E-14 PA2250 lpdV Branched-chain alpha-keto acid dehydrogenase complex component 2.31 8.19E-16 PA2446 gcvH2 Glycine cleavage system protein H 2.14 3.3E-10 PA3415 Probable...”
• The development of a new parameter for tracking post-transcriptional regulation allows the detailed map of the Pseudomonas aeruginosa Crc regulon
  Corona, Scientific reports 2018
  • “...3,61 1,96 5,58 Catabolism bkdA2 PA2248 2-oxoisovalerate dehydrogenase (beta subunit) 3,98 2,79 7,95 Catabolism bkdB PA2249 Branched-chain alpha-keto acid dehydrogenase (lipoamide component) 3,99 2,17 6,18 Catabolism lpdV PA2250 Lipoamide dehydrogenase-Val 4,12 2,35 6,69 Transport PA2252 Probable AGCS sodium/alanine/glycine symporter 3,32 0,89 5,85 Catabolism ansA PA2253 L-asparaginase...”
• Mitochondrial targeting increases specific activity of a heterologous valine assimilation pathway in Saccharomyces cerevisiae
  Solomon, Metabolic engineering communications 2016
  • “...and plasmids were maintained in E. coli XL1B. acd1 (PA0746), bkdA1 (PA2247), bkdA2 (PA2248), bkdB (PA2249), and lpdV (PA2250), encoding the acyl-CoA dehydrogenase and branched chain keto acid dehydrogenase complex, respectively, from Pseudomonas aeruginosa PA01, were PCR amplified from plasmid template (pMMA202) provided by Mitsubishi Rayon....”
• Small Colony Variants and Single Nucleotide Variations in Pf1 Region of PB1 Phage-Resistant Pseudomonas aeruginosa
  Lim, Frontiers in microbiology 2016
  • “...bkdA1 2-oxoisovalerate dehydrogenase (alpha subunit) -2.7 1.E-02 PA2248 bkdA2 2-oxoisovalerate dehydrogenase (beta subunit) -3.4 4.E-03 PA2249 bkdB Branched-chain alpha-keto acid dehydrogenase (lipoamide component) -3.4 1.E-03 PA2250 lpdV Lipoamide dehydrogenase-Val -3.0 4.E-03 PA2553 Probable acyl-CoA thiolase -5.6 3.E-03 PA2554 Probable short-chain dehydrogenase -2.2 1.E-02 PA3569 mmsB 3-hydroxyisobutyrate...”
• Inhibition of Pseudomonas aeruginosa swarming motility by 1-naphthol and other bicyclic compounds bearing hydroxyl groups
  Oura, Applied and environmental microbiology 2015
  • “...PA2007 PA2008 PA2009 PA2014 PA2015 PA2016 PA2247 PA2248 PA2249 PA2250 PA2321 PA2554 PA2555 PA3183 PA3194 PA3195 PA3559 PA3584 PA3723 PA3924 PA4022 PA5056 PA5435...”
• Comparative systems biology analysis to study the mode of action of the isothiocyanate compound Iberin on Pseudomonas aeruginosa
  Tan, Antimicrobial agents and chemotherapy 2014
  • “...PA1493 PA1999 PA2000 PA2008 PA2009 PA2197 PA2247 PA2248 PA2249 ahpF PA2277 PA2278 PA2310 PA2311 PA2312 PA2327 PA2359 PA2444 PA2445 PA2483 PA2490 PA2491 PA2493...”
• Novel targets of the CbrAB/Crc carbon catabolite control system revealed by transcript abundance in Pseudomonas aeruginosa
  Sonnleitner, PloS one 2012
  • “...2,36 3,81 3,23 2-oxoisovalerate dehydrogenase (alpha subunit) PA2248 bkdA2 2,6 3,51 2-oxoisovalerate dehydrogenase (beta subunit) PA2249 bkdB 2,48 3,22 branched-chain alpha-keto acid dehydrogenase PA2250 lpdV 2,62 3,07 lipoamide dehydrogenase-Val PA2533 2,13 probable sodium:alanine symporter AACAAGAAUAA (20 to 10) PA3038 4,13 16,75 2,11 probable porin AAUAACAA (7...”
• Nutritional cues control Pseudomonas aeruginosa multicellular behavior in cystic fibrosis sputum
  Palmer, Journal of bacteriology 2007
  • “...aruD 2.7 3.4 PA2001 PA2007 PA2008 PA2009 PA2247 PA2248 PA2249 PA2250 PA3766 PA4470 PA5302 PA5304 atoB maiA fahA hmgA bkdA1 bkdA2 bkdB lpdV fumC1 dadX dadA...”
• Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits
  Dessimoz, Nucleic acids research 2006
  • “...(1: NMB1342, 3: NMB0956), Pasteurella multocida (1: PM0894, 3: PM0278), Pseudomonas aeruginosa (1: PA5016, 2: PA2249, 3: PA1586), Rhizobium loti (2: mll4471, 3: mll4300, 4a: mlr0385, 4b: mll3627), Rhizobium meliloti (2: SMc03203, 3a: SMc02483, 3b: SMb20019, 4: SMc01032), Rickettsia conorii (3: RC0226, 4: RC0764), Rickettsia prowazekii...”
• Cystic fibrosis sputum supports growth and cues key aspects of Pseudomonas aeruginosa physiology
  Palmer, Journal of bacteriology 2005
  • “...PA0897 PA0898 PA2001 PA2007 PA2008 PA2009 PA2247 PA2248 PA2249 PA2250 PA3766 PA4470 PA5302 PA5304 Glucose transport and metabolism PA2322 PA2323 PA3181 PA3186...”
• Microarray analysis of global gene expression in mucoid Pseudomonas aeruginosa
  Firoved, Journal of bacteriology 2003
  • “...(pyrB) Phosphoribosylamine-glycine ligase (purD) PA1384 PA0509 PA3459 PA2007 PA0511 PA2249 PA5025 PA0402 PA4855 7 6 5 5 5 5 4 5 4 2E-04 2E-05 2E-04 5E-05 1E-03...”
• Proteomic profiling spotlights the molecular targets and the impact of the natural antivirulent umbelliferone on stress response, virulence factors, and the quorum sensing network of Pseudomonas aeruginosa
  Kasthuri, Frontiers in cellular and infection microbiology 2022
  • “...ANOVA ( p ) Max fold change Q9I0A2 50S ribosomal protein L20 RplT 0.046 1.757 Q9I1M0 Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex BkdB 0.040 1.820 Q9I502 ProlinetRNA ligase ProS 0.047 1.125 Q9I2U1 ATP-dependent Clp protease proteolytic subunit 1 clpP1 0.004 3.201 P40947 Single-stranded...”

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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.