PaperBLAST
PaperBLAST Hits for 71 a.a. (MSSPNTETLT...)
Show query sequence
>71 a.a. (MSSPNTETLT...)
MSSPNTETLTQMIEEISQKLNMLNVGVIKAEDFSDEKIEDLTYLHRMVMKKESFSPSEMQ
AIAQELASLRK
Running BLASTp...
Found 8 similar proteins in the literature:
GK0418 hypothetical protein from Geobacillus kaustophilus HTA426
51% identity, 96% coverage
BC0449 hypothetical protein from Bacillus cereus ATCC 14579
W8Y592 UPF0435 protein BTDB27_000199 from Bacillus thuringiensis DB27
45% identity, 96% coverage
lmo1707 lmo1707 from Listeria monocytogenes EGD-e
37% identity, 97% coverage
Q71YW0 UPF0435 protein LMOf2365_1731 from Listeria monocytogenes serotype 4b (strain F2365)
37% identity, 97% coverage
BH2488 hypothetical protein from Bacillus halodurans C-125
45% identity, 89% coverage
- Similarity-based gene detection: using COGs to find evolutionarily-conserved ORFs
Powell, BMC bioinformatics 2006 - “...COG id Organism b Genomic coordinates Annotated locus tag Explanation for similarity 458 Bhal 2607307-2607975 BH2488 ambiguous-- smc may be annotated as too long 2939 Lmon 2784312-2784674 MYPU_4520 opposite strand dnaG 3041 Mgen 400107-399841 MG320.1 opposite strand tRNA cluster 715 Mmob 474080-474634 MMOB3820 opposite strand tRNA...”
SAUSA300_1861 hypothetical protein from Staphylococcus aureus subsp. aureus USA300_FPR3757
SAOUHSC_02093 hypothetical protein from Staphylococcus aureus subsp. aureus NCTC 8325
40% identity, 77% coverage
- Identification of novel genetic factors that regulate c-di-AMP production in <i>Staphylococcus aureus</i> using a riboswitch-based biosensor
Kviatkovski, mSphere 2024 - “...55962 1S1F10 SAUSA300_2273 Na + /H + antiporter family 2443962 1S1G10 SAUSA300_1859 Acyl-CoA hydrolase 2021204 SAUSA300_1861, SAUSA300_1860 ( pepS ), SAUSA300_1859 1S1E11 SAUSA300_0945 menD (menaquinone synthase) 1034224 SAUSA300_0945, SAUSA300_0946 ( mend ), SAUSA300_0947, SAUSA300_0947 ( menB ) 1S2D4 SAUSA300_0014 gdpP (phosphodiesterase) 18539 1S2E4 SAUSA300_1662 Aminotransferase/cysteine desulfurase...”
- Novel Regulation of Alpha-Toxin and the Phenol-Soluble Modulins by Peptidyl-Prolyl cis/trans Isomerase Enzymes in Staphylococcus aureus
Keogh, Toxins 2019 - “...Purines, pyrimidines, nucleosides, and nucleotides SAUSA300_0364 YchF 0.26 Unknown function SAUSA300_1144 TrmFO 0.24 Unknown function SAUSA300_1861 0.24 Conserved hypothetical protein SAUSA300_1007 0.24 Unknown function SAUSA300_0329 0.24 Unknown function SAUSA300_0732 0.23 Conserved hypothetical protein SAUSA300_0538 0.23 Energy metabolism SAUSA300_2251 0.22 Energy metabolism SAUSA300_2025 RsbU 0.22 Cellular processes...”
- Antimicrobial Peptide Induced-Stress Renders Staphylococcus aureus Susceptible to Toxic Nucleoside Analogs
Rodríguez-Rojas, Frontiers in immunology 2020 - “...57 ). Other genes showing a differentially low level of expression are SAOUHSC_01986, SAOUHSC_01986, SAOUHSC_008020, SAOUHSC_02093, SAOUHSC_02535, and SAOUHSC_01414 which code for uncharacterized proteins ( 51 ). SAOUHSC_01030 is a putative glutaredoxin domain-containing protein but it is not characterized either. The gene SAOUHSC_02576 codes for a...”
SAR1970 conserved hypothetical protein from Staphylococcus aureus subsp. aureus MRSA252
40% identity, 77% coverage
SA1696 hypothetical protein from Staphylococcus aureus subsp. aureus N315
40% identity, 77% coverage
- S-Nitrosoglutathione Reduces the Density of Staphylococcus aureus Biofilms Established on Human Airway Epithelial Cells
Wolf, ACS omega 2023 - “...to promote differentiation into a mucociliary phenotype. Bacteria S. aureus isolated from human sinonasal samples (SA1696 and SA1692) was purchased from ATCC (Manassas, MD) and stored as glycerol stocks at 80 C. We also isolated an S. aureus strain from excised polyp tissue (SANP), and the...”
- “...bronchial epithelial cells. Mucociliary-differentiated CF bronchial epithelial cells were infected apically with S. aureus isolates SA1696, SA1692, SANP, or a mixture of all three isolates and incubated for 24 h. The cells were then treated apically with GSNO (50, 100, or 250 M) or appropriate placebo...”
- Characterizing the effects of inorganic acid and alkaline shock on the Staphylococcus aureus transcriptome and messenger RNA turnover
Anderson, FEMS immunology and medical microbiology 2010 - “...2.5 2.5 ruvA SA1697 Holliday junction DNA helicase RuvA sa_c9430s8244_a_at * 2.9 2.5 30 ruvB SA1696 Holliday junction DNA helicase RuvB sa_c7140s6251_at * 2.5 15 stable ssb SA0438 single-stranded DNA-binding protein sa_c9288s8130_a_at 7.7 2.5 2.5 topA SA1267 DNA topoisomerase I sa_c2521s2102_a_at * 2.8 2.5 30 xseB...”
- “...5.0 2.5 2.5 ruvA SA1697 Holliday junction DNA helicase sa_c9430s8244_a_at * 4.1 2.5 2.5 ruvB SA1696 Holliday junction DNA helicase sa_c2429s2013_at 2.4 2.5 2.5 scpA SA1538 segregation and condensation protein A sa_c2426s2008_a_at 2.5 2.5 2.5 scpB SA1537 segregation and condensation protein B sa_c7140s6251_at * 4.5 15...”
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 793,807 different protein sequences to 1,259,118 scientific articles. Searches against EuropePMC were last performed on March 13 2025.
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.
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.
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