PaperBLAST – Find papers about a protein or its homologs

 

PaperBLAST

PaperBLAST Hits for biolip::7cofA Cholesterol esterase from burkholderia stabilis (orthorhombic crystal form) () (320 a.a., ADDYATTRYP...)

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 104 similar proteins in the literature:

7cofA / A0A1Y1BQV9 Cholesterol esterase from burkholderia stabilis (orthorhombic crystal form)
100% identity, 100% coverage

Q75NT4 sterol esterase (EC 3.1.1.13) from Burkholderia cepacia (see paper)
96% identity, 88% coverage

BCAM0949 exported lipase LipA from Burkholderia cenocepacia J2315
I35_RS20825 triacylglycerol lipase from Burkholderia cenocepacia H111
96% identity, 88% coverage

GB|BAA00960.1 triacylglycerol lipase; EC 3.1.1.3 from Pseudomonas sp. KWI-56 (see paper)
94% identity, 88% 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)
96% identity, 86% coverage

A9QXC9 triacylglycerol lipase (EC 3.1.1.3) from Burkholderia cepacia (see paper)
94% identity, 87% coverage

BTH_II0639 lipase from Burkholderia thailandensis E264
89% identity, 88% coverage

BPSS1741 Lipase precursor from Burkholderia pseudomallei K96243
88% identity, 88% coverage

LIP_PSEPS / P0DUB9 Triacylglycerol lipase; Extracellular lipase; Triacylglycerol ester hydrolase; EC 3.1.1.3 from Pseudarthrobacter phenanthrenivorans (Arthrobacter phenanthrenivorans) (see 2 papers)
83% identity, 100% coverage

1tahB / P0DUB8 The crystal structure of triacylglycerol lipase from pseudomonas glumae reveals a partially redundant catalytic aspartate (see paper)
83% identity, 100% 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)
84% identity, 88% coverage

BPSS2319 lipase precursor from Burkholderia pseudomallei K96243
71% identity, 90% coverage

WP_003239806 triacylglycerol lipase from Pseudomonas hydrolytica
45% identity, 99% coverage

FH974_07335 triacylglycerol lipase from Photobacterium ganghwense
45% identity, 99% coverage

H16_A1322 triacylglycerol lipase from Cupriavidus necator H16
H16_A1322 triacylglycerol lipase from Ralstonia eutropha H16
44% identity, 85% coverage

VP1181 lactonizing lipase from Vibrio parahaemolyticus RIMD 2210633
VP_RS05740 triacylglycerol lipase from Vibrio parahaemolyticus RIMD 2210633
44% identity, 99% coverage

VCA0221 lactonizing lipase from Vibrio cholerae O1 biovar eltor str. N16961
46% identity, 94% 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)
46% identity, 99% coverage

MXAN_5522 lactonizing lipase from Myxococcus xanthus DK 1622
45% identity, 98% coverage

PA14_63620 lipase LipC from Pseudomonas aeruginosa UCBPP-PA14
44% identity, 100% coverage

PA4813 lipase LipC from Pseudomonas aeruginosa PAO1
NP_253500 lipase LipC from Pseudomonas aeruginosa PAO1
44% identity, 100% 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
41% identity, 100% coverage

A8QYB2 triacylglycerol lipase (EC 3.1.1.3) from Pseudomonas aeruginosa (see paper)
41% identity, 100% coverage

1ex9A / P26876 Crystal structure of the pseudomonas aeruginosa lipase complexed with rc-(rp,sp)-1,2-dioctylcarbamoyl-glycero-3-o-octylphosphonate (see paper)
41% identity, 99% coverage

Q9L6C7 Triacylglycerol acylhydrolase from Pseudomonas aeruginosa
41% identity, 100% 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)
41% identity, 100% coverage

U876_RS20585 triacylglycerol lipase from Aeromonas hydrophila NJ-35
43% identity, 100% coverage

MUW98_RS20835 triacylglycerol lipase from Aeromonas hydrophila
43% identity, 99% coverage

FUT48_16475 triacylglycerol lipase from Pseudomonas sp. JG-B
40% identity, 99% coverage

ACIAD3309 lipase from Acinetobacter sp. ADP1
40% identity, 98% coverage

A1S_3160 lipase from Acinetobacter baumannii ATCC 17978
40% identity, 94% coverage

YE1842 lipase from Yersinia enterocolitica subsp. enterocolitica 8081
40% identity, 99% coverage

IV454_06595 triacylglycerol lipase from Massilia antarctica
39% identity, 100% coverage

LIP_PSEFR / P08658 Triacylglycerol lipase; Cold-adapted lipase; Extracellular lipase; Triacylglycerol ester hydrolase; EC 3.1.1.3 from Pseudomonas fragi (see 3 papers)
37% identity, 100% coverage

PMI0999 lipase from Proteus mirabilis HI4320
WP_004247922 triacylglycerol lipase from Proteus mirabilis
39% identity, 97% coverage

4hs9A / B4EVM3 Methanol tolerant mutant of the proteus mirabilis lipase (see paper)
38% identity, 97% coverage

PL78_18430 triacylglycerol lipase from Yersinia entomophaga
39% identity, 97% coverage

WP_015093259 triacylglycerol lipase from Pseudomonas sp. UW4
38% identity, 98% coverage

PFLU0569 lipase precursor from Pseudomonas fluorescens SBW25
39% identity, 98% coverage

Pfl01_0571 Alpha/beta hydrolase fold from Pseudomonas fluorescens Pf0-1
39% identity, 99% coverage

EY04_02420 triacylglycerol lipase from Pseudomonas chlororaphis
38% identity, 98% coverage

PSF113_0610 triacylglycerol lipase from Pseudomonas ogarae
39% identity, 99% coverage

WP_011058985 triacylglycerol lipase from Pseudomonas protegens
PFL_0617 lipase from Pseudomonas fluorescens Pf-5
37% identity, 98% coverage

Q88DH1 Lipase from Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)
PP_4854 lipase from Pseudomonas putida KT2440
36% identity, 98% coverage

PSF113_3279 triacylglycerol lipase from Pseudomonas ogarae
36% identity, 99% coverage

LEPBI_I0886 lactonizing lipase (triacylglycerol lipase) from Leptospira biflexa serovar Patoc strain 'Patoc 1 (Paris)'
36% identity, 54% 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
34% identity, 54% 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
32% identity, 37% coverage

ZP_02733109 Esterase/lipase/thioesterase family active site from Gemmata obscuriglobus UQM 2246
26% identity, 98% coverage

XP_504639 YALI0E31515p from Yarrowia lipolytica CLIB122
38% identity, 37% coverage

LEPBI_I0777 putative triglyceride lipase; putative signal peptide from Leptospira biflexa serovar Patoc strain 'Patoc 1 (Paris)'
33% identity, 53% coverage

WP_015677081 lactonizing lipase from Leptospira yanagawae serovar Saopaulo str. Sao Paulo = ATCC 700523
31% identity, 44% coverage

MGL_4063 uncharacterized protein from Malassezia globosa CBS 7966
27% identity, 52% coverage

WP_020775775 triacylglycerol lipase from Leptospira meyeri serovar Semaranga str. Veldrot Semarang 173
33% identity, 44% coverage

MGG_00773 triacylglycerol lipase from Pyricularia oryzae 70-15
37% identity, 34% coverage

PADG_04319 V-type ATPase, G subunit from Paracoccidioides brasiliensis Pb18
35% identity, 24% coverage

MRET_3765 triacylglycerol lipase from Malassezia restricta
35% identity, 22% coverage

C9Z1F6 Putative secreted lipase from Streptomyces scabiei (strain 87.22)
41% identity, 27% coverage

NP_001001804 epoxide hydrolase 4 isoform 1 from Mus musculus
Q6IE26 Epoxide hydrolase 4 from Mus musculus
25% identity, 41% coverage

SCO1735 secreted lipase from Streptomyces coelicolor A3(2)
40% identity, 27% coverage

CH_000489 triacylglycerol lipase; EC 3.1.1.3 from Burkholderia cepacia (see paper)
58% identity, 15% coverage

cg0109 triacylglycerol lipase precursor from Corynebacterium glutamicum ATCC 13032
NCgl0079 triacylglycerol lipase from Corynebacterium glutamicum ATCC 13032
30% identity, 46% coverage

Q8IUS5 Epoxide hydrolase 4 from Homo sapiens
NP_775838 epoxide hydrolase 4 from Homo sapiens
26% identity, 36% coverage

UH47_02215 YSIRK-targeted triacylglycerol lipase from Staphylococcus pseudintermedius
30% identity, 16% coverage

NPW32_RS11105 YSIRK domain-containing triacylglycerol lipase GehC from Staphylococcus epidermidis
28% identity, 18% coverage

SP|Q5HKP6 triacylglycerol lipase; EC 3.1.1.3 from Staphylococcus epidermidis RP62A (see paper)
SERP2297 lipase from Staphylococcus epidermidis RP62A
28% identity, 18% coverage

SE0281 triacylglycerol lipase precursor from Staphylococcus epidermidis ATCC 12228
28% identity, 18% coverage

BJL64_14165, BJL65_15445 YSIRK domain-containing triacylglycerol lipase Lip1 from Staphylococcus aureus
P65289 Lipase 1 from Staphylococcus aureus (strain N315)
28% identity, 17% coverage

SAV2671 triacylglycerol lipase precursor from Staphylococcus aureus subsp. aureus Mu50
SA2463 triacylglycerol lipase precursor from Staphylococcus aureus subsp. aureus N315
28% identity, 17% coverage

LIP1_STAA8 / Q2FUU5 Lipase 1; Glycerol ester hydrolase 1; EC 3.1.1.3 from Staphylococcus aureus (strain NCTC 8325 / PS 47) (see 2 papers)
Q8NUI5 Lipase 1 from Staphylococcus aureus (strain MW2)
SAOUHSC_03006 lipase from Staphylococcus aureus subsp. aureus NCTC 8325
SAUSA300_2603 triacylglycerol lipase precursor from Staphylococcus aureus subsp. aureus USA300_FPR3757
NWMN_2569 lipase precursor from Staphylococcus aureus subsp. aureus str. Newman
SACOL2694 lipase from Staphylococcus aureus subsp. aureus COL
USA300HOU_RS14500 YSIRK domain-containing triacylglycerol lipase Lip1 from Staphylococcus aureus subsp. aureus USA300_TCH1516
28% identity, 17% coverage

MW2590 triacylglycerol lipase precursor from Staphylococcus aureus subsp. aureus MW2
28% identity, 17% coverage

SAR2753 lipase precursor from Staphylococcus aureus subsp. aureus MRSA252
28% identity, 17% coverage

Q6GDD3 Lipase 1 from Staphylococcus aureus (strain MRSA252)
28% identity, 17% coverage

Q6GJZ6 Lipase 2 from Staphylococcus aureus (strain MRSA252)
SAR0317 lipase precursor from Staphylococcus aureus subsp. aureus MRSA252
SAR_RS01585 YSIRK domain-containing triacylglycerol lipase Lip2/Geh from Staphylococcus aureus subsp. aureus MRSA252
29% identity, 16% coverage

CKU_2426 YSIRK domain-containing triacylglycerol lipase Lip1 from Staphylococcus aureus
28% identity, 17% coverage

WP_029418313 triacylglycerol lipase from Bacillus sonorensis
36% identity, 35% coverage

SAU060112_40510 YSIRK domain-containing triacylglycerol lipase Lip1 from Staphylococcus aureus
28% identity, 17% coverage

8k7pA / A0A0U1MWF9 Staphylococcus aureus lipase -psa complex (see paper)
29% identity, 30% coverage

CNAG_07639 triacylglycerol lipase from Cryptococcus neoformans var. grubii H99
33% identity, 19% coverage

LIP2_STAA8 / Q2G155 Lipase 2; Glycerol ester hydrolase 2; EC 3.1.1.3 from Staphylococcus aureus (strain NCTC 8325 / PS 47) (see paper)
SP|Q5HJ48 triacylglycerol lipase; EC 3.1.1.3 from Staphylococcus aureus subsp. aureus COL (see paper)
SAOUHSC_00300 lipase precursor from Staphylococcus aureus subsp. aureus NCTC 8325
28% identity, 17% coverage

SA0309 glycerol ester hydrolase from Staphylococcus aureus subsp. aureus N315
Q7A7P2 Lipase 2 from Staphylococcus aureus (strain N315)
SAV0320 glycerol ester hydrolase from Staphylococcus aureus subsp. aureus Mu50
BJL64_01445, BJL65_01440 YSIRK domain-containing triacylglycerol lipase Lip2/Geh from Staphylococcus aureus
28% identity, 16% coverage

SAUSA300_0320 triacylglycerol lipase precursor from Staphylococcus aureus subsp. aureus USA300_FPR3757
B7H15_01765 YSIRK domain-containing triacylglycerol lipase Lip2/Geh from Staphylococcus aureus
28% identity, 17% coverage

CNE02710 lipase 2 from Cryptococcus neoformans var. neoformans JEC21
33% identity, 20% coverage

Q8NYC2 Lipase 2 from Staphylococcus aureus (strain MW2)
MW0297 glycerol ester hydrolase from Staphylococcus aureus subsp. aureus MW2
28% identity, 17% coverage

CKU_0273 YSIRK domain-containing triacylglycerol lipase Lip2/Geh from Staphylococcus aureus
28% identity, 16% coverage

NWMN_0262 truncated triacylglycerol lipase precursor from Staphylococcus aureus subsp. aureus str. Newman
SACOL0317 lipase precursor, interruption-N from Staphylococcus aureus subsp. aureus COL
28% identity, 18% coverage

CPI83_19975 triacylglycerol lipase from Rhodococcus sp. H-CA8f
29% identity, 34% coverage

WP_020452056 triacylglycerol lipase from Bacillus paralicheniformis
36% identity, 28% coverage

SE0185 glycerol ester hydrolase from Staphylococcus epidermidis ATCC 12228
26% identity, 18% coverage

NPW32_RS02885 YSIRK domain-containing triacylglycerol lipase GehD from Staphylococcus epidermidis
26% identity, 18% coverage

WP_003183220 triacylglycerol lipase from Bacillus licheniformis
35% identity, 35% coverage

SERP2388 lipase from Staphylococcus epidermidis RP62A
SERP_RS11730 YSIRK domain-containing triacylglycerol lipase GehD from Staphylococcus epidermidis RP62A
26% identity, 18% coverage

cg0110 triacylglycerol lipase precursor from Corynebacterium glutamicum ATCC 13032
36% identity, 27% coverage

H0B8D4 Putative secreted lipase from Streptomyces sp. W007
SPW_1544 triacylglycerol lipase from Streptomyces sp. W007
39% identity, 27% coverage

WP_000517067 triacylglycerol lipase from Bacillus cereus B4264
30% identity, 31% coverage

5h6bA / H0B8D4 Crystal structure of a thermostable lipase from marine streptomyces (see paper)
39% identity, 27% coverage

Pden_4983 alpha/beta hydrolase fold from Paracoccus denitrificans PD1222
36% identity, 32% coverage

lip / CAB95850.2 lipase precursor from Bacillus licheniformis (see 2 papers)
35% identity, 28% coverage

TTE0555 predicted acetyltransferases and hydrolases with the alpha/beta hydrolase fold from Thermoanaerobacter tengcongensis MB4
27% identity, 38% coverage

WP_126510627 YSIRK-targeted triacylglycerol lipase from Staphylococcus warneri
26% identity, 18% coverage

WP_043054382 triacylglycerol lipase from Bacillus paralicheniformis
34% identity, 35% coverage

SCO1265 lipase from Streptomyces coelicolor A3(2)
36% identity, 27% coverage

W8FKE7 Lipase from Bacillus pumilus
32% identity, 33% coverage

7r1kA / W8FKE7 Phosphorylated bacillus pumilus lipase a
32% identity, 32% 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