PaperBLAST – Find papers about a protein or its homologs

 

PaperBLAST

PaperBLAST Hits for VIMSS6630293 lipase 2 (587 a.a., MGTTLSPFRY...)

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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 43 similar proteins in the literature:

CNE02710 lipase 2 from Cryptococcus neoformans var. neoformans JEC21
100% identity, 100% coverage

CNAG_07639 triacylglycerol lipase from Cryptococcus neoformans var. grubii H99
93% identity, 100% coverage

MGL_4063 uncharacterized protein from Malassezia globosa CBS 7966
39% identity, 70% coverage

MRET_3765 triacylglycerol lipase from Malassezia restricta
45% identity, 57% coverage

TGL2_YEAST / P54857 Triacylglycerol lipase 2; Lipase 2; Neutral lipid hydrolase; EC 3.1.1.3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 4 papers)
NP_010343, YDR058C Protein with lipolytic activity towards triacylglycerols and diacylglycerols when expressed in E. coli; role in yeast lipid degradation is unclear from Saccharomyces cerevisiae
NP_010343 triglyceride lipase from Saccharomyces cerevisiae S288C
31% identity, 51% coverage

XP_504639 YALI0E31515p from Yarrowia lipolytica CLIB122
31% identity, 49% coverage

PADG_04319 V-type ATPase, G subunit from Paracoccidioides brasiliensis Pb18
28% identity, 71% coverage

MGG_00773 triacylglycerol lipase from Pyricularia oryzae 70-15
30% identity, 49% coverage

ZP_02733109 Esterase/lipase/thioesterase family active site from Gemmata obscuriglobus UQM 2246
29% identity, 48% coverage

LIC_12988 alpha/beta fold hydrolase from Leptospira interrogans serovar Copenhageni str. Fiocruz LV130
LIC12988 lipase from Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130
28% identity, 47% coverage

7cofA / A0A1Y1BQV9 Cholesterol esterase from burkholderia stabilis (orthorhombic crystal form)
36% identity, 21% coverage

PA14_63620 lipase LipC from Pseudomonas aeruginosa UCBPP-PA14
33% identity, 20% coverage

PA4813 lipase LipC from Pseudomonas aeruginosa PAO1
NP_253500 lipase LipC from Pseudomonas aeruginosa PAO1
33% identity, 20% coverage

LIP_BURCE / P22088 Triacylglycerol lipase; Extracellular lipase; Triacylglycerol ester hydrolase; EC 3.1.1.3 from Burkholderia cepacia (Pseudomonas cepacia) (see 8 papers)
lipA / GI|557867 triacylglycerol lipase; EC 3.1.1.3 from Burkholderia cepacia (see 5 papers)
35% identity, 20% coverage

GB|BAA00960.1 triacylglycerol lipase; EC 3.1.1.3 from Pseudomonas sp. KWI-56 (see paper)
35% identity, 20% coverage

BCAM0949 exported lipase LipA from Burkholderia cenocepacia J2315
I35_RS20825 triacylglycerol lipase from Burkholderia cenocepacia H111
35% identity, 21% coverage

LIP_PSEPS / P0DUB9 Triacylglycerol lipase; Extracellular lipase; Triacylglycerol ester hydrolase; EC 3.1.1.3 from Pseudarthrobacter phenanthrenivorans (Arthrobacter phenanthrenivorans) (see 2 papers)
35% identity, 20% coverage

MXAN_5522 lactonizing lipase from Myxococcus xanthus DK 1622
32% identity, 22% coverage

1tahB / P0DUB8 The crystal structure of triacylglycerol lipase from pseudomonas glumae reveals a partially redundant catalytic aspartate (see paper)
35% identity, 20% coverage

LIP_BURPL / P0DUB8 Triacylglycerol lipase; Extracellular lipase; Triacylglycerol ester hydrolase; EC 3.1.1.3 from Burkholderia plantarii (see 6 papers)
lipA / GB|CAA49812.1 Triacylglycerol lipase; EC 3.1.1.3 from Burkholderia glumae (see 4 papers)
35% identity, 20% coverage

Q75NT4 sterol esterase (EC 3.1.1.13) from Burkholderia cepacia (see paper)
36% identity, 21% coverage

BPSS1741 Lipase precursor from Burkholderia pseudomallei K96243
34% identity, 20% coverage

A9QXC9 triacylglycerol lipase (EC 3.1.1.3) from Burkholderia cepacia (see paper)
35% identity, 20% coverage

H16_A1322 triacylglycerol lipase from Cupriavidus necator H16
H16_A1322 triacylglycerol lipase from Ralstonia eutropha H16
34% identity, 21% coverage

BTH_II0639 lipase from Burkholderia thailandensis E264
32% identity, 20% coverage

LEPBI_I0886 lactonizing lipase (triacylglycerol lipase) from Leptospira biflexa serovar Patoc strain 'Patoc 1 (Paris)'
26% identity, 47% coverage

LEPBI_I0777 putative triglyceride lipase; putative signal peptide from Leptospira biflexa serovar Patoc strain 'Patoc 1 (Paris)'
23% identity, 47% coverage

PL78_18430 triacylglycerol lipase from Yersinia entomophaga
32% identity, 20% coverage

BPSS2319 lipase precursor from Burkholderia pseudomallei K96243
34% identity, 21% coverage

U876_RS20585 triacylglycerol lipase from Aeromonas hydrophila NJ-35
28% identity, 49% coverage

MUW98_RS20835 triacylglycerol lipase from Aeromonas hydrophila
28% identity, 49% coverage

VCA0221 lactonizing lipase from Vibrio cholerae O1 biovar eltor str. N16961
32% identity, 24% coverage

YE1842 lipase from Yersinia enterocolitica subsp. enterocolitica 8081
34% identity, 20% coverage

LIP_VIBCH / P15493 Triacylglycerol lipase; Extracellular lipase; Triacylglycerol ester hydrolase; EC 3.1.1.3 from Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) (see 2 papers)
32% identity, 24% coverage

FUT48_16475 triacylglycerol lipase from Pseudomonas sp. JG-B
28% identity, 20% coverage

IV454_06595 triacylglycerol lipase from Massilia antarctica
30% identity, 21% coverage

1ex9A / P26876 Crystal structure of the pseudomonas aeruginosa lipase complexed with rc-(rp,sp)-1,2-dioctylcarbamoyl-glycero-3-o-octylphosphonate (see paper)
30% identity, 25% coverage

FH974_07335 triacylglycerol lipase from Photobacterium ganghwense
30% identity, 24% coverage

WP_003239806 triacylglycerol lipase from Pseudomonas hydrolytica
30% identity, 20% coverage

LIP_PSEAE / P26876 Triacylglycerol lipase; Extracellular lipase; Triacylglycerol ester hydrolase; EC 3.1.1.3 from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (see 3 papers)
P26876 triacylglycerol lipase (EC 3.1.1.3) from Pseudomonas aeruginosa (see 2 papers)
NP_251552 lactonizing lipase from Pseudomonas aeruginosa PAO1
PA14_27100 lactonizing lipase precursor from Pseudomonas aeruginosa UCBPP-PA14
PA2862 lactonizing lipase precursor from Pseudomonas aeruginosa PAO1
30% identity, 25% coverage

LIP_PSEU0 / P26877 Triacylglycerol lipase; Extracellular lipase; Lactonizing lipase; Lipase P; Triacylglycerol ester hydrolase; EC 3.1.1.3 from Pseudomonas sp. (strain 109) (see paper)
30% identity, 25% coverage

A8QYB2 triacylglycerol lipase (EC 3.1.1.3) from Pseudomonas aeruginosa (see paper)
30% identity, 25% coverage

Q9L6C7 Triacylglycerol acylhydrolase from Pseudomonas aeruginosa
30% identity, 25% 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