PaperBLAST – Find papers about a protein or its homologs

 

PaperBLAST

PaperBLAST Hits for VIMSS329899 carboxylesterase (249 a.a., MMLKQPEPFF...)

Other sequence analysis tools:

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

Fitness BLAST: loading...

Found 30 similar proteins in the literature:

F9UM18 feruloyl esterase (EC 3.1.1.73) from Lactiplantibacillus plantarum (see paper)
lp_0796 carboxylesterase from Lactobacillus plantarum WCFS1
lp_0796 carboxylesterase from Lactiplantibacillus plantarum WCFS1
100% identity, 100% coverage

3dltA / B2CZF3 Snapshots of esterase d from lactobacillus rhamnosus: insights into a rotation driven catalytic mechanism
48% identity, 98% coverage

WP_011232515 carboxylesterase from Geobacillus kaustophilus HTA426
GK3045 carboxylesterase from Geobacillus kaustophilus HTA426
32% identity, 99% coverage

EST_GEOSE / Q06174 Carboxylesterase; EC 3.1.1.1 from Geobacillus stearothermophilus (Bacillus stearothermophilus) (see 2 papers)
Q06174 carboxylesterase (EC 3.1.1.1) from Geobacillus stearothermophilus (see paper)
31% identity, 99% coverage

1tqhA / Q06174 Covalent reaction intermediate revealed in crystal structure of the geobacillus stearothermophilus carboxylesterase est30 (see paper)
31% identity, 97% coverage

lmo2450 similar to carboxylesterase from Listeria monocytogenes EGD-e
31% identity, 99% coverage

SAOUHSC_00802 carboxylesterase precursor, putative from Staphylococcus aureus subsp. aureus NCTC 8325
Q2G025 Carboxylesterase, putative from Staphylococcus aureus (strain NCTC 8325 / PS 47)
NWMN_0748 hypothetical protein from Staphylococcus aureus subsp. aureus str. Newman
SACOL0845 carboxylesterase from Staphylococcus aureus subsp. aureus COL
30% identity, 99% coverage

SE0564 carboxyesterase precursor-like protein from Staphylococcus epidermidis ATCC 12228
31% identity, 99% coverage

SA0734 hypothetical protein from Staphylococcus aureus subsp. aureus N315
31% identity, 99% coverage

SAR0835 putative carboxylesterase from Staphylococcus aureus subsp. aureus MRSA252
30% identity, 99% coverage

SAB0735 probable carboxylesterase precursor from Staphylococcus aureus RF122
30% identity, 99% coverage

8ftpA / A0A0H2XJL0 Fphh, staphylococcus aureus fluorophosphonate-binding serine hydrolases h, apo form (see paper)
30% identity, 98% coverage

Q65EQ1 Esterase/lipase/thioesterase from Bacillus licheniformis (strain ATCC 14580 / DSM 13 / JCM 2505 / CCUG 7422 / NBRC 12200 / NCIMB 9375 / NCTC 10341 / NRRL NRS-1264 / Gibson 46)
28% identity, 99% coverage

Aflv_2499 Esterase/lipase from Anoxybacillus flavithermus WK1
28% identity, 99% coverage

EST_BACSU / O32232 Carboxylesterase; EC 3.1.1.1 from Bacillus subtilis (strain 168) (see paper)
26% identity, 99% coverage

lmo2452 similar to carboxylesterase from Listeria monocytogenes EGD-e
32% identity, 96% coverage

SA0416 hypothetical protein from Staphylococcus aureus subsp. aureus N315
25% identity, 99% coverage

SAUSA300_0430 hypothetical protein from Staphylococcus aureus subsp. aureus USA300_FPR3757
SAOUHSC_00417 hypothetical protein from Staphylococcus aureus subsp. aureus NCTC 8325
25% identity, 99% coverage

SAR0457 conserved hypothetical protein from Staphylococcus aureus subsp. aureus MRSA252
25% identity, 99% coverage

4ke8C / P82597 Crystal structure of monoglyceride lipase from bacillus sp. H257 in complex with monopalmitoyl glycerol analogue (see paper)
32% identity, 45% coverage

MGLP_BAC25 / P82597 Thermostable monoacylglycerol lipase; MGLP; bMGL; EC 3.1.1.23 from Bacillus sp. (strain H-257) (see 3 papers)
P82597 acylglycerol lipase (EC 3.1.1.23) from Bacillus sp. (in: Bacteria) (see 4 papers)
T260_16665 carboxylesterase from Geobacillus thermopakistaniensis
32% identity, 44% coverage

YP_003253705 BAAT/Acyl-CoA thioester hydrolase from Geobacillus sp. Y412MC61
32% identity, 44% coverage

G3JWZ2 carboxylesterase (EC 3.1.1.1) from Geobacillus thermodenitrificans (see paper)
32% identity, 45% coverage

TPANIC_0902 carboxylesterase from Treponema pallidum subsp. pallidum str. Nichols
TP0902 carboxylesterase (est) from Treponema pallidum subsp. pallidum str. Nichols
33% identity, 39% coverage

TM_1022 carboxylesterase from Thermotoga maritima MSB8
TM1022 esterase from Thermotoga maritima MSB8
31% identity, 39% coverage

YP_075874 esterase from Symbiobacterium thermophilum IAM 14863
29% identity, 40% coverage

Q6N0W4 Alpha/beta fold hydrolase from Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)
RPA4646 putative carboxylesterase from Rhodopseudomonas palustris CGA009
28% identity, 40% coverage

Rv3177 POSSIBLE PEROXIDASE (NON-HAEM PEROXIDASE) from Mycobacterium tuberculosis H37Rv
24% identity, 64% coverage

MT3266 hydrolase, alpha/beta hydrolase fold family from Mycobacterium tuberculosis CDC1551
24% identity, 61% coverage

SCO2123 esterase/lipase from Streptomyces coelicolor A3(2)
30% identity, 37% coverage

New Search

For advice on how to use these tools together, see Interactive tools for functional annotation of bacterial genomes.

Statistics

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.

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:

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:

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.

by Morgan Price, Arkin group
Lawrence Berkeley National Laboratory