PaperBLAST
PaperBLAST Hits for MPMX20_02134 (63 a.a., MKKMAGVLTV...)
Show query sequence
>MPMX20_02134
MKKMAGVLTVAVAALLTGCTPRIEVAAPKEPITINMNVKIEHEIHIKVDKDVETLLKSRS
DLF
Running BLASTp...
Found 6 similar proteins in the literature:
SG1474 putative lipoprotein from Salmonella enterica subsp. enterica serovar Gallinarum str. 287/91
73% identity, 100% coverage
Z2327 orf, hypothetical protein from Escherichia coli O157:H7 EDL933
BHW77_14595 YnbE family lipoprotein from Escherichia coli
77% identity, 90% coverage
- Characterizing the Escherichia coli O157:H7 proteome including protein associations with higher order assemblies
Pieper, PloS one 2011 - “...23478 L (IM or OM) PP 110 46 LAGC 37 E 2 putative lipoprotein YnbE Z2327 ynbE 6815 L (IM or OM) unkn 109 0 LVGC 17 T 2 conserved lipoprotein YmbA Z1302 ymbA 19949 L (IM or OM) unkn 107 0 LAGC 11 S 2...”
- Comparative genomics reveals structural and functional features specific to the genome of a foodborne Escherichia coli O157:H7
Sharma, BMC genomics 2019 - “...YYZ-2008 113.4 31 2,514,1932,627,682 BHW77_13055 and BHW77_13845 51.50 NC_011356 12/Enterobacteria phage BP-4795 60 29 2,800,1432,860,221 BHW77_14595 and BHW77_14980 50.25 NC_004813 13/Enterobacteria phage BP-4795 57.4 32 2,967,2683,024,670 BHW77_15525 and BHW77_15920 50.94 NC_004813 14/Enterobacteria phage P88 24.8 18 3,361,8913,386,762 BHW77_17640 and BHW77_17830 50.31 NC_026014 15/ Escherichia virus Lambda...”
YnbE / b1382 lipoprotein YnbE from Escherichia coli K-12 substr. MG1655 (see 3 papers)
b1382 predicted lipoprotein from Escherichia coli str. K-12 substr. MG1655
NP_415900 lipoprotein YnbE from Escherichia coli str. K-12 substr. MG1655
P64448 Uncharacterized protein YnbE from Escherichia coli (strain K12)
73% identity, 100% coverage
- Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coli K12 through accurate full-length transcripts assembling
Li, BMC genomics 2013 - “...one of our seven samples (Additional file 14 ), and 21 ( b0050, b0137, b1356, b1382, b1419, b1446, b1457, b1607, b1952, b1998, b3471, b3638, b3937, b4325, b4335, b4336, b4593, b4596, b4610, b4615 and b4620 ) of them were expressed in all the seven samples, suggesting that...”
- 18th Congress of the European Hematology Association, Stockholm, Sweden, June 13–16, 2013
, Haematologica 2013 - Genome-wide analysis of lipoprotein expression in Escherichia coli MG1655
Brokx, Journal of bacteriology 2004 - “...b0735 b0741 b0772 b0830 b1050 b1063 b1079 b1104 b1105 b1209 b1283 b1382 b1431 b1491 b1510 49.65 P 569.75 P 211 P 1,508.05 P 467.95 P 43.3 P 266 P 12.75 P 68.8...”
- YdbH and YnbE form an intermembrane bridge to maintain lipid homeostasis in the outer membrane of Escherichia coli.
Kumar, Proceedings of the National Academy of Sciences of the United States of America 2024 - GeneRIF: YdbH and YnbE form an intermembrane bridge to maintain lipid homeostasis in the outer membrane of Escherichia coli.
- YdbH and YnbE form an intermembrane bridge to maintain lipid homeostasis in the outer membrane of <i>Escherichia coli</i>
Kumar, Proceedings of the National Academy of Sciences of the United States of America 2024 - “...25 ) was leveraged to acquire the model structures for YdbH (UniProt P52645), YnbE (UniProt P64448), and YdbL (UniProt P76076) using the https://alphafold.ebi.ac.uk website. With the support of the Unity server at the Ohio State University, AlphaFold-Multimer (5) was used employing the full-length protein sequence of...”
- Functional Prediction of Biological Profile During Eutrophication in Marine Environment
Sbaoui, Bioinformatics and biology insights 2022 - “...protein YkfF P75677 CP4-6 prophage; protein YmdC P75919 Putative synthase with phospholipase D/nuclease domain YnbE P64448 Lipoprotein YnfD P76172 DUF1161 domain-containing protein YtfJ P39187 Conserved hypothetical protein The predictive analysis has been performed using the bacterium strain E coli K12 as model organism for the aquatic...”
YPK_1920 putative lipoprotein from Yersinia pseudotuberculosis YPIII
73% identity, 77% coverage
- Fis Is Essential for Yersinia pseudotuberculosis Virulence and Protects against Reactive Oxygen Species Produced by Phagocytic Cells during Infection
Green, PLoS pathogens 2016 - “...**** ns ** **** arnDT *** ns **** ns Other dusB-fis **** *** ** **** YPK_1920 **** ns **** ns YPK_2066 * ns ns ns flgD ns ns ns ns YPK_2594 ** ns **** ns psaEFABC **** **** * ns YPK_3600 ns ns ns ns YPK_3656...”
- “...been previously characterized in Yersinia infection models, including YPK_2594 , which has no predicted function, YPK_1920 , which is predicted to encode a lipoprotein, YPK_3765 , which is predicted to encode a murein peptide ligase, and the dusB-fis operon, which encodes the nucleoid associated protein Fis,...”
YPO2327 putative lipoprotein from Yersinia pestis CO92
73% identity, 78% coverage
- An integrated computational-experimental approach reveals Yersinia pestis genes essential across a narrow or a broad range of environmental conditions
Senior, BMC microbiology 2017 - “...protein YPO1213 nrdB ribonucleotide-diphosphate reductase subunit beta YPO1391 cmk cytidylate kinase YPO2159 ypo2159 hypothetical protein YPO2327 ypo2327 lipoprotein YPO2350 pspB phage shock protein B YPO2883 ndk nucleoside diphosphate kinase YPO2894 iscA iron-sulfur cluster assembly protein YPO2907 glyA serine hydroxymethyltransferase YPO3173 thii thiamine biosynthesis protein ThiI YPO3696...”
- “...these genes identified as essential at 37C but not at 28C (YPO0331, YPO1102, YPO2159 and YPO2327) could not be predicted on the basis of motif or homology matches, although YPO2327 is predicted to be a lipoprotein and is therefore likely to be surface located. These proteins...”
SO2063 hypothetical protein from Shewanella oneidensis MR-1
56% identity, 68% coverage
- Validation of Shewanella oneidensis MR-1 small proteins by AMT tag-based proteome analysis
Romine, Omics : a journal of integrative biology 2004 (PubMed)- “...while those that map to hypotheticals SO2669 and SO2063, conserved hypotheticals SO0335 and SO2176, and the SlyX protein (SO1063) were observed at frequencies...”
- “...are annotated as hypothetical (SO0315, SO0515, SO0755, SO1479, SO2063, SO2669, SO2974.1, SO3777, SO4490, and SO4494.1), and eight are annotated TABLE 3. ORF...”
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