PaperBLAST
PaperBLAST Hits for ABZR87_RS04155 (71 a.a., MNPEDLQRLV...)
Show query sequence
>ABZR87_RS04155
MNPEDLQRLVTTQMPFGKYKGRLIADLPGHYLNWFAREGFPPGQIGRLLALMQELDHNGL
KGLLDPLRQGR
Running BLASTp...
Found 8 similar proteins in the literature:
BP1193 conserved hypothetical protein from Bordetella pertussis Tohama I
75% identity, 99% coverage
- Genomic epidemiology of Iranian Bordetella pertussis: 50 years after the implementation of whole cell vaccine
Safarchi, Emerging microbes & infections 2019 - “...BP2233, BP2428, BP2539, BP3329 6 P1 (3), P4 (1), P27 (1) Genic (8) 7 nsSNPs: BP1193, BP1362, BP1374( fla FIII ), BP1924, BP2162, BP3843, BP3856 Deletion: BP0041p (1) 1 sSNPs: BP0425 5 P1 (4), P4 (1), P8 (1), P27 (2) Genic (6) 6 sSNPs: BP0170, BP1322,...”
RMET_RS20695 DUF3820 family protein from Cupriavidus metallidurans CH34
78% identity, 88% coverage
PP0796 conserved hypothetical protein from Pseudomonas putida KT2440
71% identity, 73% coverage
PA3612 hypothetical protein from Pseudomonas aeruginosa PAO1
53% identity, 93% coverage
- Crystal structure of a putative quorum sensing-regulated protein (PA3611) from the Pseudomonas-specific DUF4146 family
Das, Proteins 2014 - “...based on genomic context using STRING 47 ( http://string.embl.de ) indicates that PA3611 interacts with PA3612 (score ~0.8, a 73-residue protein of unknown function classified in PF12843, DUF3820). Also, PA3611 and PA3612 may form a single transcriptional unit based on the prediction that they form an...”
- “...quorum sensing and PA3611 was found to be up regulated in quorum sensing, PA3611 (and PA3612) may be involved in quorum sensing via modulation of PotDs function, with implications specific to biofilm formation in Pseudomonas. A computational assessment of PA3611 using a Support Vector Machine method...”
YP2613 conserved hypothetical protein from Yersinia pestis biovar Medievalis str. 91001
48% identity, 88% coverage
- Evidence for two evolutionary lineages of highly pathogenic Yersinia species
Rakin, Journal of bacteriology 1995 - “...Germany; Y. pseudotuberculosis YP252 (serotype O1A) and YP2613 (serotype O1B) were obtained from S. Korovkin, Saratov, Russia; Y. pseudotuberculosis YP68...”
- “...O1 Y. pseudotuberculosis YP252, O1A Y. pseudotuberculosis YP2613, O1B Y. pseudotuberculosis Erlangen, O2 Y. pseudotuberculosis YP146, O3 Y. pseudotuberculosis...”
VCA0163 conserved hypothetical protein from Vibrio cholerae O1 biovar eltor str. N16961
48% identity, 90% coverage
- Impact of Gene Repression on Biofilm Formation of Vibrio cholerae
Pombo, Frontiers in microbiology 2022 - “...Hypothetical protein 1 VCA0127-132 VCA0128 D-Ribose transporter ATP-binding protein, ribose transport system ATP-binding protein 1 VCA0163 Hypothetical protein 2 VCA0168 Pseudogene 2 VCA0186 Hypothetical protein 1 VCA0281-282 VCA0281 Integrase 2 VCA0308 dGTPase-like protein 1 VCA0331 Hypothetical protein 1 VCA0334 Hypothetical protein 1 VCA0341 Biphenyl-2,3-diol 1,2-dioxygenase 1...”
- The quorum sensing transcription factor AphA directly regulates natural competence in Vibrio cholerae
Haycocks, PLoS genetics 2019 - “...(VCA0064) r 83056 83013 gtaggaatttcatttcatac (VCA0074) r 105925 105897 gtatgaaaccttagtcatgg (VCA0098) 180601 180618 ctctgcatccagatgcagga (VCA0162) VCA0163 215501 215472 tcattcaagcgtttgcatag (VCA0198) r VCA0199 220027 219980 tgtggaaacttgttgaatag (VCA0202) 270051 270033 catttccacaggtttcataa VCA0249 a VCA0249 a 292440 292420 tgtggaaacttgttgaatag (VCA0275) 310741 310644 ctatggttttttttgcatag VCA0291 VCA0291 354757 354789 ctatgcgcttttttgcttag VCA0367...”
FE46_RS04325 DUF3820 family protein from Flavobacterium psychrophilum
41% identity, 89% coverage
YpeB / b4546 PF12843 family protein YpeB from Escherichia coli K-12 substr. MG1655 (see paper)
b4546 hypothetical protein from Escherichia coli str. K-12 substr. MG1655
46% identity, 96% coverage
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