PaperBLAST – Find papers about a protein or its homologs

 

PaperBLAST

PaperBLAST Hits for WP_016936851.1 triacylglycerol lipase (Bacillus siamensis) (214 a.a., MKQIKSKILA...)

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 31 similar proteins in the literature:

JD965_RS01465 triacylglycerol lipase from Bacillus siamensis
100% identity, 100% coverage

ESTA_BACSU / P37957 Lipase EstA; Lipase A; Triacylglycerol lipase; EC 3.1.1.3 from Bacillus subtilis (strain 168) (see 5 papers)
NP_388152 secreted alkaliphilic lipase from Bacillus subtilis subsp. subtilis str. 168
BSU02700 secreted alkaliphilic lipase from Bacillus subtilis subsp. subtilis str. 168
78% identity, 100% coverage

W8FKE7 Lipase from Bacillus pumilus
75% identity, 98% coverage

lip / CAB95850.2 lipase precursor from Bacillus licheniformis (see 2 papers)
73% identity, 100% coverage

5ct4A / P37957 Wild-type bacillus subtilis lipase a with 5% [bmim][cl] (see paper)
83% identity, 84% coverage

7r1kA / W8FKE7 Phosphorylated bacillus pumilus lipase a
82% identity, 84% coverage

ESTB_BACSU / Q79F14 Extracellular esterase EstB; Extracellular esterase LipB; Lipase B; Triacylglycerol lipase; EC 3.1.1.3 from Bacillus subtilis (strain 168) (see 2 papers)
Q79F14 acylglycerol lipase (EC 3.1.1.23) from Bacillus subtilis (see paper)
BSU08350 secreted esterase / lipase from Bacillus subtilis subsp. subtilis str. 168
70% identity, 97% coverage

WP_029418313 triacylglycerol lipase from Bacillus sonorensis
69% identity, 96% coverage

Q8RJP5 triacylglycerol lipase (EC 3.1.1.3) from Priestia megaterium (see paper)
69% identity, 97% coverage

WP_043054382 triacylglycerol lipase from Bacillus paralicheniformis
66% identity, 97% coverage

WP_003183220 triacylglycerol lipase from Bacillus licheniformis
66% identity, 97% coverage

WP_020452056 triacylglycerol lipase from Bacillus paralicheniformis
65% identity, 97% coverage

OOZ19_29350 triacylglycerol lipase from Saccharopolyspora sp. NFXS83
29% identity, 87% coverage

DR2078 lipase, putative from Deinococcus radiodurans R1
27% identity, 73% coverage

IV454_31865 triacylglycerol lipase from Massilia antarctica
25% identity, 87% coverage

5h6bA / H0B8D4 Crystal structure of a thermostable lipase from marine streptomyces (see paper)
36% identity, 44% coverage

H0B8D4 Putative secreted lipase from Streptomyces sp. W007
SPW_1544 triacylglycerol lipase from Streptomyces sp. W007
36% identity, 37% coverage

C9Z1F6 Putative secreted lipase from Streptomyces scabiei (strain 87.22)
32% identity, 53% coverage

SCO1735 secreted lipase from Streptomyces coelicolor A3(2)
31% identity, 53% coverage

sll1969 unknown protein from Synechocystis sp. PCC 6803
31% identity, 53% coverage

SCO1265 lipase from Streptomyces coelicolor A3(2)
32% identity, 41% coverage

TTE0555 predicted acetyltransferases and hydrolases with the alpha/beta hydrolase fold from Thermoanaerobacter tengcongensis MB4
33% identity, 26% coverage

cg0109 triacylglycerol lipase precursor from Corynebacterium glutamicum ATCC 13032
NCgl0079 triacylglycerol lipase from Corynebacterium glutamicum ATCC 13032
33% identity, 31% coverage

O16380 Lipase from Caenorhabditis elegans
30% identity, 27% coverage

cg0110 triacylglycerol lipase precursor from Corynebacterium glutamicum ATCC 13032
28% identity, 34% coverage

WP_015793408 triacylglycerol lipase from Catenulispora acidiphila DSM 44928
27% identity, 52% coverage

7v3kC / A3TMR7 Crystal structure of maj1
25% identity, 46% coverage

A3TMR7 Putative lipase from Janibacter sp. HTCC2649
25% identity, 41% coverage

HMPREF0675_4855 triacylglycerol lipase from Cutibacterium acnes SK137
39% identity, 21% coverage

CAA67627.1 triacylglycerol lipase from Cutibacterium acnes (see paper)
PPA2105 triacylglycerol lipase from Cutibacterium acnes KPA171202
PPA2105 triacylglycerol lipase precursor from Propionibacterium acnes KPA171202
32% identity, 32% coverage

A9QXC9 triacylglycerol lipase (EC 3.1.1.3) from Burkholderia cepacia (see paper)
27% 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