PaperBLAST

Full List of Papers Linked to NP_250672.1

exaA / Q9Z4J7 alcohol dehydrogenase (cytochrome c550) monomer (EC 1.1.2.8) from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (see 4 papers)
QEDH_PSEAE / Q9Z4J7 Quinoprotein ethanol dehydrogenase; QEDH; Quinoprotein alcohol dehydrogenase (cytochrome c); Quinoprotein alcohol dehydrogenase (cytochrome c550); EC 1.1.2.8 from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (see 6 papers)
Q9Z4J7 alcohol dehydrogenase (cytochrome c) (EC 1.1.2.8) from Pseudomonas aeruginosa (see paper)
NP_250672 quinoprotein ethanol dehydrogenase from Pseudomonas aeruginosa PAO1
PA1982 quinoprotein alcohol dehydrogenase from Pseudomonas aeruginosa PAO1

• function: Catalyzes the oxidation of ethanol and other primary alcohols to the corresponding aldehydes, except methanol, which is a very poor substrate. Uses a specific inducible cytochrome c550, encoded by the adjacent gene in the locus, as electron acceptor. Is a key enzyme of the carbon and energy metabolism during growth of P.aeruginosa on ethanol as the sole carbon and energy source. Is also able to use secondary alcohols as well as aminoalcohols like ethanolamine and 1- amino-2-propanol, and aldehydes as substrates.
  catalytic activity: a primary alcohol + 2 Fe(III)-[cytochrome c] = an aldehyde + 2 Fe(II)-[cytochrome c] + 2 H(+) (RHEA:51020)
  catalytic activity: ethanol + 2 Fe(III)-[cytochrome c] = acetaldehyde + 2 Fe(II)- [cytochrome c] + 2 H(+) (RHEA:62200)
  catalytic activity: butan-1-ol + 2 Fe(III)-[cytochrome c] = butanal + 2 Fe(II)- [cytochrome c] + 2 H(+) (RHEA:43432)
  catalytic activity: propan-2-ol + 2 Fe(III)-[cytochrome c] = acetone + 2 Fe(II)- [cytochrome c] + 2 H(+) (RHEA:62196)
  catalytic activity: 1-propanol + 2 Fe(III)-[cytochrome c] = propanal + 2 Fe(II)- [cytochrome c] + 2 H(+) (RHEA:62204)
  cofactor: pyrroloquinoline quinone (Binds 1 PQQ group non-covalently per subunit (PubMed:10736230, PubMed:3144289). PQQ is embedded between the ring structure formed from a disulfide bridge between adjacent cysteines Cys-139 and Cys-140 and the indole ring of Trp-282 (PubMed:10736230).)
  cofactor: Ca(2+) (Binds 2 calcium ions per subunit. One is located in the active- site cavity near PQQ and the second calcium binds at the N-terminus and contributes to the stability of the native enzyme.)
  subunit: Homodimer. Interacts with cytochrome c550 (PubMed:19224199).
• PQQ-dependent alcohol dehydrogenase (QEDH) of Pseudomonas aeruginosa is involved in catabolism of acyclic terpenes.
  Chattopadhyay, Journal of basic microbiology 2010 (PubMed)
  • GeneRIF: Inactivation of PA1982 by insertion mutagenesis resulted in inability of the mutant to utilise ethanol and in reduced growth on geraniol.
• Structure of the pyrroloquinoline quinone radical in quinoprotein ethanol dehydrogenase.
  Kay, The Journal of biological chemistry 2006 (PubMed)
  • GeneRIF: Quinoprotein alcohol dehydrogenases use the pyrroloquinoline quinone cofactor to catalyze the oxidation of alcohols.
• Convergent Within-Host Adaptation of Pseudomonas aeruginosa through the Transcriptional Regulatory Network
  Gatt, mSystems 2023
  • “...when growing on ethanol ( 37 ). This PQQ-dependent system comprises a quinoprotein ethanol dehydrogenase (PA1982), cytochrome C550 (PA1983), and an NAD-dependent acetaldehyde dehydrogenase (PA1984). The genes encoding all these components have high HS and low mROS values ( Fig.4A ; TableS2 ) (mROS, 0.2 to...”
• Parallel evolutionary paths to produce more than one Pseudomonas aeruginosa biofilm phenotype
  Thöming, NPJ biofilms and microbiomes 2020
  • “...PA0466 2.9 PA14_38850 PA1983 exaB 6.8 PA14_04650 PA0355 pfpI 3.2 PA14_06180 PA0472 fiuI 2.5 PA14_38860 PA1982 exaA 5.8 PA14_06650 PA0509 nirN 3.0 PA14_07355 PA0565 3.6 PA14_38880 PA1981 5.7 PA14_06660 PA0510 nirE 3.3 PA14_09980 PA4167 dkgB 2.7 PA14_38900 PA1980 exaE 2.9 PA14_06670 PA0511 nirJ 3.5 PA14_10170 PA4159...”
• Engineering thermal stability and solvent tolerance of the soluble quinoprotein PedE from Pseudomonas putida KT2440 with a heterologous whole-cell screening approach
  Wehrmann, Microbial biotechnology 2018
  • “...KT2440 (Takeda etal ., 2013 ; Wehrmann etal ., 2017 ) as well as ExaA (PA1982; Ca 2+ ) of Pseudomonas aeruginosa (Rupp and Grisch, 1988 ; Chattopadhyay etal ., 2010 ), were expressed in E.coli BL21(DE3) cells and activities for all enzymes were determined. With...”
• The Pseudomonas aeruginosa Isohexenyl Glutaconyl Coenzyme A Hydratase (AtuE) Is Upregulated in Citronellate-Grown Cells and Belongs to the Crotonase Family
  Poudel, Applied and environmental microbiology 2015
  • “...dehydrogenase with verified terpene alcohol dehydrogenase activity (PA1982, exaA) were increased in abundance (27). Interestingly, the abundance of a gene...”
  • “...12, 2017 by University of California, Berkeley PA1535 PA1982 PA1984 PA2011 PA2012 PA2013 PA2014 PA2015 PA2886 PA2887 PA2888 PA2889 PA2890 PA2891 PA2892 PA4330...”
• Flexible survival strategies of Pseudomonas aeruginosa in biofilms result in increased fitness compared with Candida albicans
  Purschke, Molecular & cellular proteomics : MCP 2012
  • “...A ToxA (PA1148), quinoprotein ethanol dehydrogenase ExaA (PA1982), heme acquisition protein HasAp (PA3407), and two unknown proteins related to ferric...”
  • “...of the periplasma localized quinoprotein ethanol dehydrogenase ExaA (PA1982) is induced at later time points indicating the appearance of alcohols in the medium...”
• The biofilm-specific antibiotic resistance gene ndvB is important for expression of ethanol oxidation genes in Pseudomonas aeruginosa biofilms
  Beaudoin, Journal of bacteriology 2012
  • “...PA3044 PA2715 PA2700 PA2210 PA1989 PA1987 PA1986 PA1983 PA1982 PA1980 PA1978 PA1976 PA1975 PA1015 PA0931 PA4407 PA4540 PA4857 PA4894 PA5312 PA5397 2.36 2.76...”
• PQQ-dependent alcohol dehydrogenase (QEDH) of Pseudomonas aeruginosa is involved in catabolism of acyclic terpenes
  Chattopadhyay, Journal of basic microbiology 2010 (PubMed)
  • “...isovalerate-grown cells. The spot was identified as PA1982 gene product a pyrroloquinoline quinone (PQQ) dependent ethanol oxidoreductase (QEDH). Inactivation...”
  • “...was restored by transferring an intact copy of the PA1982 gene into the mutant. The PA1982 gene product was purified from recombinant Escherichia coli and...”
• Induction by cationic antimicrobial peptides and involvement in intrinsic polymyxin and antimicrobial peptide resistance, biofilm formation, and swarming motility of PsrA in Pseudomonas aeruginosa
  Gooderham, Journal of bacteriology 2008
  • “...PA1648 PA1649 PA1650 PA1828 PA1881 PA1883 PA1927 PA1976 PA1978 PA1982 PA1983 PA1984 PA1985 PA2124 PA2277 PA2278 PA2339 PA2350 coxA mdcR clpC 3.4 4.8 3.5 3.2 4.8...”
• Transcriptome analysis reveals that multidrug efflux genes are upregulated to protect Pseudomonas aeruginosa from pentachlorophenol stress
  Muller, Applied and environmental microbiology 2007
  • “...PA1281 (cobV) PA1393 (cysC) PA1705 (pcrG) PA1780 (nirD) PA1982 (exaA) PA2166 PA2394 (pvdN) PA2669 PA2906 PA2941 PA3371 PA3547 (algL) PA3954 PA4033 PA4178 PA4217...”
• Cystic fibrosis sputum supports growth and cues key aspects of Pseudomonas aeruginosa physiology
  Palmer, Journal of bacteriology 2005
  • “...PA1894 PA1895 PA1896 PA1897 PA1922 PA1924 PA1925 PA1981 PA1982 PA1983 PA1999 PA2000 PA2006 PA2027 PA2194 PA2384 PA2385 PA2386 PA2392 PA2393 PA2394 PA2395 PA2396...”

New Search

Statistics

How It Works

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

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

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

PaperBLAST also incorporates manually-curated protein functions:

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

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

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

Changes to PaperBLAST since the paper was written:

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

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

Secrets

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

Omissions from the PaperBLAST Database

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

References

PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.

Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.

Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.

UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.

BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.

The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.

The MetaCyc database of metabolic pathways and enzymes.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.

CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.

The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.

The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.

REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
R. J. Roberts et al (2015). Nucleic Acids Research, 10.1093/nar/gku1046.

Deep annotation of protein function across diverse bacteria from mutant phenotypes.
M. N. Price et al (2016). bioRxiv, 10.1101/072470.