PaperBLAST
PaperBLAST Hits for VIMSS319109 blr3898 (121 a.a., MMPYVDGFVL...)
Show query sequence
>VIMSS319109 blr3898
MMPYVDGFVLAVPKDKIEAYKALAKTACAVWMEHGALDYVECIGDDVPYGELTSFPRAVM
AKEDELVVFSWIVYRDRKTRDAVNKKVMADPRLKLDGMPFDGKRMIYGGFTTLLRASDVI
S
Running BLASTp...
Found 3 similar proteins in the literature:
blr3898 blr3898 from Bradyrhizobium japonicum USDA 110
100% identity, 100% coverage
- Transcriptomic Characterization of Bradyrhizobium diazoefficiens Bacteroids Reveals a Post-Symbiotic, Hemibiotrophic-Like Lifestyle of the Bacteria within Senescing Soybean Nodules
Franck, International journal of molecular sciences 2018 - “...bll3172, bll4771, bll6387, bll6597, bll8078, blr0490, blr0998, blr2666, blr2834, blr2882, blr2923, blr3110, blr3499, blr3603, blr3634, blr3898, blr4361, blr5112, blr7482, blr7579, bsr1885, bll0052, bll0242, bll0244, bll0493, bll1533, bll2075, bll2188, bll4292, bll6051, blr4337, blr7208, and blr7482. ijms-19-03918-t001_Table 1 Table 1 Categories of Expressed and Constitutive Genes. Each identified...”
NGR_c22640 RNA signal recognition particle 4.5S RNA from Rhizobium sp. NGR234
71% identity, 93% coverage
YbaA / b0456 DUF1428 domain-containing protein YbaA from Escherichia coli K-12 substr. MG1655
TC 3.A.5.1.1 / P0AAQ6 Uncharacterized protein ybaA, component of General secretory pathway (Sec-SRP) complex from Escherichia coli (strain K12) (see 3 papers)
SF5M90T_427 DUF1428 domain-containing protein from Shigella flexneri 5a str. M90T
b0456 hypothetical protein from Escherichia coli str. K-12 substr. MG1655
S0408 hypothetical protein from Shigella flexneri 2a str. 2457T
ECs0509 hypothetical protein from Escherichia coli O157:H7 str. Sakai
57% identity, 93% coverage
- substrates: proteins
tcdb comment: A biphasic pulling force may act on TMSs during translocon-mediated membrane integration (Ismail et al. 2012). Intermediate structures for the insertion of integral membrane proteins have been visualized (Bischoff et al. 2014). Insertion of the Type II single span (N-terminus, in, C-terminus, out) protein, RodZ, requires only SecYEG, SecA and the pmf, but not SecB, SecDF, YidC or FtsY (Rawat et al. 2015). The combined effects of ribosome and peptide binding to SecYEG may allow for co-translational membrane insertion of successive transmembrane segments (Ge et al. 2014). SecA penetrates deeply into the SecYEG channel during insertion, contacting transmembrane helices and periplasmic loops (Banerjee et al. 2017) - RNA-seq analysis of the influence of anaerobiosis and FNR on Shigella flexneri
Vergara-Irigaray, BMC genomics 2014 - “...pore protein -2.98 SF5M90T_4307 putative inner membrane protein -3.40 SF1231 conserved hypothetical protein -3.71 -1.60 SF5M90T_427 ybaA conserved hypothetical protein -3.88 Phage related S1668 relF prophage maintenance protein 1.75 SF5M90T_1793 putative phage integrase protein 1.45 -1.60 SF5M90T_1056 hypothetical bacteriophage protein 1.14 SF5M90T_740 putative bacteriophage protein -1.93...”
- 5-azacytidine induces transcriptome changes in Escherichia coli via DNA methylation-dependent and DNA methylation-independent mechanisms
Militello, BMC microbiology 2016 - “...1.84 1.90E-04 b0506 allR Repressor for all (allantoin) and gcl (glyoxylate) operons; glyoxylate-inducible 1.93 1.10E-03 b0456 ybaA DUF1428 family protein 1.98 2.30E-03 Table 3 RT-qPCR analysis of gene expression changes in 5-azacytidine treated and dcm knockout Escherichia coli Gene Phase fc (log 2 )+aza/-aza (array) fc...”
- YcfR (BhsA) influences Escherichia coli biofilm formation through stress response and surface hydrophobicity
Zhang, Journal of bacteriology 2007 - “...ybiM ybaA yceK yjbJ yjdN ygaM ymgE b0806 b0456 b1050 b4045 b4107 b2672 b1195 Hypothetical protein Hypothetical protein Hypothetical protein Highly abundant...”
- Genetic analysis of the 5-azacytidine sensitivity of Escherichia coli K-12
Bhagwat, Journal of bacteriology 1987 - “...recA56 srlC relAl spoTI metBI W6 upp-11 rpsL254 S0408 srlC::TnlO recA56 S0408 udk-2 S0415 srlC::TnlO recA56 S0408 cdd-5 S0441 srlC::TnlO recA56 A(lac-cod-pro)...”
- “...F- uvrA ArecA galK rpsL BH127 GM31 BH128 RP4182 BH112 W6 S0408 BH117 S0415 BH121 S0441 BH118 JM108 a Source F. Daldal F. Daldal CGSCa CGSC CGSC CGSC M. G....”
- Global transcriptional response of Escherichia coli O157:H7 to growth transitions in glucose minimal medium
Bergholz, BMC microbiology 2007 - “...glnK -3.73 1 ECs1356 terE -2.90 1 ECs0507 ybaY 3.19 2 ECs1423 - 2.34 2 ECs0509 ybaA 2.56 2 ECs1438 yceP 4.78 2 ECs0518 aefA 2.12 2 ECs1466 yceD -2.86 1 ECs1467 rpmF -2.36 1 ECs2307 ydgG -2.69 1 ECs1500 potC -2.14 1 ECs2308 pntB -2.80...”
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
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.
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