PaperBLAST
PaperBLAST Hits for Pf6N2E2_4080 (81 a.a., MGIIGTIFIG...)
Show query sequence
>Pf6N2E2_4080
MGIIGTIFIGLIVGLLARFLKPGDDSMGWIMTILLGIGGSLAATYGGQALGIYQAGQGAG
FIGALVGAVVLLVIYGLIKRN
Running BLASTp...
Found 9 similar proteins in the literature:
HZ99_RS16790 GlsB/YeaQ/YmgE family stress response membrane protein from Pseudomonas canadensis
93% identity, 100% coverage
PA5424 hypothetical protein from Pseudomonas aeruginosa PAO1
88% identity, 100% coverage
- Transcriptional Responses of Pseudomonas aeruginosa to Inhibition of Lipoprotein Transport by a Small Molecule Inhibitor
Lorenz, Journal of bacteriology 2020 - “...PA4877 8.3 10.5 Hypothetical protein PA2180 8.3 14.0 Hypothetical protein PA2134 8.3 13.5 Hypothetical protein PA5424 8.2 12.1 Conserved hypothetical protein PA3231 8.2 12.8 Hypothetical protein PA3040 8.1 11.3 Conserved hypothetical protein PA2149 8.0 11.5 Hypothetical protein PA4880 7.5 14.2 Probable bacterioferritin PA2148 7.5 10.4 Conserved...”
- Transcriptomic Analyses Elucidate Adaptive Differences of Closely Related Strains of Pseudomonas aeruginosa in Fuel
Gunasekera, Applied and environmental microbiology 2017 - “...pvdE, PA3235, PA2779, PA3819, PA3451, PA0038, PA0276, PA3986, PA5424, PA0109, and PA2024). DNA sequence analyses of P. aeruginosa ATCC 33988 alkB1 and alkB2...”
- Identification of genes in the σ²² regulon of Pseudomonas aeruginosa required for cell envelope homeostasis in either the planktonic or the sessile mode of growth
Wood, mBio 2012 - “...predicted lipoprotein 7.5/3.0 714:387:3,732 PA5178 Hypothetical, LysM domain 9.6/7.1 452:284:2,532 PA5212 Hypothetical, unclassified 15.9/7.8 1,555:44:5,758 PA5424 d Hypothetical, predicted inner membrane protein 8.3/7.4 807:660:3,904 a PAO1 gene names and descriptions were obtained from the Pseudomonas Genome Database ( 33 ) and are listed numerically. Sequence-defined transposon...”
- “...or none in the algT mutant (i.e., PA0567, PA0920, PA2177, PA3040, PA3459, PA3795, PA4717, and PA5424) ( Table 1 ). Thus, their P- lacZ reporters were examined under conditions of cell wall stress in wild-type PAO1 and in an algT (PDO-LS586) mutant ( Table 2 )....”
BCAM1775 putative transglycosylase associated protein from Burkholderia cenocepacia J2315
59% identity, 93% coverage
G8E09_19180 GlsB/YeaQ/YmgE family stress response membrane protein from Acinetobacter pittii
53% identity, 95% coverage
- Phenotypic Variation and Carbapenem Resistance Potential in OXA-499-Producing Acinetobacter pittii
Zhang, Frontiers in microbiology 2020 - “...0.0012 0.0318 G8E09_12925 OprD family porin 1.73 0.0001 0.0064 G8E09_10340 Hypothetical protein 1.72 0.0001 0.0067 G8E09_19180 GlsB/YeaQ/YmgE family stress response membrane protein 1.71 0.0020 0.0463 G8E09_01795 Hemerythrin domain-containing protein 1.71 0.0008 0.0244 G8E09_12835 Heavy-metal-associated domain-containing protein -1.70 0.0002 0.0091 G8E09_07185 Hypothetical protein 1.67 0.0008 0.0229 G8E09_18175...”
BP0987 putative membrane protein from Bordetella pertussis Tohama I
48% identity, 98% coverage
- The multifaceted RisA regulon of Bordetella pertussis
Coutte, Scientific reports 2016 - “..., while the remaining genes were not identified as BvgA/S-regulated genes. With the exception of bp0987 , the gene with the strongest decrease in transcript abundance in BPSMRisA (42 fold), all the other genes showed only a 5-fold decrease in transcript abundance ( Fig. 1B )....”
STM14_2173 GlsB/YeaQ/YmgE family stress response membrane protein from Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
42% identity, 95% coverage
- Proteome remodelling by the stress sigma factor RpoS/σS in Salmonella: identification of small proteins and evidence for post-transcriptional regulation
Lago, Scientific reports 2017 - “...63 Yes yaiA 12 -Proteobacteria STM14_1271 YccJ-like protein IPR025600 75 Yes yccJ 1114 - Proteobacteria STM14_2173 Transglycosylase motif IPR007341, 3TM fragments 84 ymgE 1114 Bacteria and Archaea STM14_2188 45 Yes Enterobacteriaceae STM14_2189 32 Salmonella STM14_2239 Start codon re-annotated, 88% identity with E . coli YebV, DUF1480...”
- “...coding capacity of the uncharacterized small ORFs, for which no protein was identified by LC-MS (STM14_2173, STM14_2189, STM14_5292, STM14_5469, STM14_5479, STM14_5481), was assessed by immunodetection of the corresponding 3xFlag-tagged proteins. Proteins were detected for all of them, except STM14_5469 and STM14_5479 (Fig. 1b ). In the...”
YPO1181 putative membrane protein from Yersinia pestis CO92
42% identity, 70% coverage
YPTB1222 putative membrane protein from Yersinia pseudotuberculosis IP 32953
42% identity, 91% coverage
MSMEG_3022 transglycosylase associated protein from Mycobacterium smegmatis str. MC2 155
39% identity, 68% coverage
- Expression of a unique M. tuberculosis DNA MTase Rv1509 in M. smegmatis alters the gene expression pattern and enhances virulence
Manjunath, Frontiers in microbiology 2024 - “...whose functions have been predicted based on in-silico data ( Table 4 ). The gene MSMEG_3022 (a transglycosylase-associated protein) was significantly downregulated (nearly 6-fold) in Ms_Rv1509 compared to the vector control. Such proteins are known to play a role in septa formation during bacterial cell division...”
- “...DNA binding MSMEG_3141 28,966.79 7,583.247 656.1065 210.2984 36.1 5.16565 Conserved domain protein Rv1473A Transcriptional mechanism MSMEG_3022 27,341.28 7,054.566 328.9183 104.5347 67.89 6.06297 Transglycosylase associated protein Absent in Mtb Septa formation Rv1509 enhances the survival of M. smegmatis inside RAW264.7 macrophages To study the role of Rv1509...”
- Gene Expression, Bacteria Viability and Survivability Following Spray Drying of Mycobacterium smegmatis
Lauten, Materials (Basel, Switzerland) 2010 - “...ATP-binding protein opuCA 1.0 10.1 0.006 98% MSMEG_2958 conserved hypothetical protein 1.0 10.3 0.003 98% MSMEG_3022 transglycosylase associated protein 1.6 10.5 0.008 94% MSMEG_3184 malto-oligosyltrehalose trehalohydrolase treZ 0.8 9.4 0.012 90% MSMEG_3185 putative maltooligosyl trehalose synthase 0.8 10.2 0.006 95% MSMEG_3186 glycogen debranching enzyme GlgX glgX...”
- “...protein CACGACGGTTCGCCAGGTCGCCGCGCGGGTAT 31 1.4 1.3 96% 1.0 1.1 98% 1.2 3.1 28% 0.1 5.1 0% MSMEG_3022 transglycosylase associated protein GCCGCCGTTTACGCCGCCGACAGCCGGGGTAT 37 1.7 2.8 34% 1.6 1.4 94% 2.4 3.3 7% -0.4 4.5 2% MSMEG_3289 gp61 protein CCTTGACGTTTGAACGTGCAGCGGGAGGGTAC 36 1.1 1.7 96% 0.5 0.7 8% 0.4 1.1...”
- The SigF regulon in Mycobacterium smegmatis reveals roles in adaptation to stationary phase, heat, and oxidative stress
Hümpel, Journal of bacteriology 2010 - “...MSMEG_2415 MSMEG_2830 MSMEG_2924 MSMEG_2927 MSMEG_2958 MSMEG_3022 MSMEG_3185 MSMEG_3255 MSMEG_3419 MSMEG_3439 MSMEG_4618 MSMEG_5402 MSMEG_5543 MSMEG_5550...”
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