PaperBLAST
PaperBLAST Hits for ABZR87_RS12965 (67 a.a., MRVRAIQGDT...)
Show query sequence
>ABZR87_RS12965
MRVRAIQGDTVDAICHRVYGRTAGVTEAVLAANPGIADLGPVLPHGTELVMPDISPQPAM
QMVQLWD
Running BLASTp...
Found 14 similar proteins in the literature:
Q8XY29 Probable bacteriophage protein from Ralstonia nicotianae (strain ATCC BAA-1114 / GMI1000)
RSc1934 PROBABLE BACTERIOPHAGE PROTEIN from Ralstonia solanacearum GMI1000
87% identity, 99% coverage
BPX_BPP2 / P51772 Baseplate protein X; Gene X protein; GpX from Escherichia phage P2 (Bacteriophage P2) (see paper)
X / AAD03274.1 gpX from Escherichia virus P2 (see 22 papers)
NP_046763 baseplate hub from Bacteriophage P2
60% identity, 100% coverage
BN49_RS11325 tail protein X from Klebsiella pneumoniae
63% identity, 100% coverage
c0955 Probable phage tail protein from Escherichia coli CFT073
63% identity, 100% coverage
BMULJ_03675 putative bacteriophage tail protein X from Burkholderia multivorans ATCC 17616
53% identity, 96% coverage
- Genomic analysis and relatedness of P2-like phages of the Burkholderia cepacia complex
Lynch, BMC genomics 2010 - “...protein (X) - AGGGAGctgtcctgATG 70 tail X family protein 1-70/70 94 Burkholderia cenocepacia MC0-3 YP_001763504.1 BMULJ_03675 YP_001948083.1 37 28315 28557 unknown - GTGGAGctcatctgATG 80 conserved hypothetical protein 1-80/80 72 Burkholderia multivorans CGD1 ZP_03587617.1 BMULJ_03676 YP_001948084.1 38 28557 29033 capsid completion protein (L) - AACGTGACGAAcccgaccATG 158 head...”
LHK_02587 Fels-2 prophage protein from Laribacter hongkongensis HLHK9
LHK_00414 Fels-2 prophage protein from Laribacter hongkongensis HLHK9
55% identity, 99% coverage
UTI89_C0934 putative phage tail protein from Escherichia coli UTI89
48% identity, 99% coverage
BCAL0107 phage tail protein from Burkholderia cenocepacia J2315
50% identity, 99% coverage
- A Broad-Host-Range Tailocin from Burkholderia cenocepacia
Yao, Applied and environmental microbiology 2017 - “...highly similar to a 24.6-kb region on chromosome 1 of B. cenocepacia J2315 (BCAL0081 to BCAL0107). A close relationship and synteny were observed between BceTMilo and Burkholderia phage KL3 and, by extension, with paradigm temperate myophage P2. Deletion mutants in the gene cluster encoding enzymes for...”
C0J56_06165 tail protein X from Pseudomonas fluorescens
43% identity, 94% coverage
Pchl3084_1211 tail protein X from Pseudomonas chlororaphis subsp. aureofaciens 30-84
43% identity, 94% coverage
PA0627 hypothetical protein from Pseudomonas aeruginosa PAO1
PA14_08140 putative phage protein X from Pseudomonas aeruginosa UCBPP-PA14
40% identity, 96% coverage
- Transcriptional profiling of Pseudomonas aeruginosa mature single- and dual-species biofilms in response to meropenem
Alam, Microbiology (Reading, England) 2023 - “...3.73E-05 0.0007623159776 rplX 1.577791178 0.003955658099 0.03020634629 rpsQ 1.514302023 0.003135531829 0.0252719288 rplN 1.482472974 0.006174262969 0.04190492586 Downregulated PA0627 2.563807744 7.94E-27 6.26E-24 PA0629 2.554150934 7.27E-33 1.34E-29 PA0641 2.55319332 1.46E-27 1.34E-24 PA0628 2.534582315 1.07E-31 1.47E-28 PA0638 2.46361566 3.36E-33 9.27E-30 PA0636 2.444427878 2.44E-22 1.04E-19 PA0635 2.415846681 1.41E-22 6.50E-20 gfnR 2.353411699 6.68E-14...”
- “...3.27E-12 3.37E-10 PA4222 1.708263864 2.26E-12 2.45E-10 PA0563 1.691305244 1.68E-11 1.47E-09 PA0086 1.677560955 4.89E-10 3.46E-08 Downregulated PA0627 2.524464134 1.52E-15 2.79E-13 gfnR 2.418533396 8.72E-23 8.02E-20 PA0641 2.404904976 2.04E-20 7.49E-18 PA0638 2.364308134 4.30E-21 1.98E-18 PA0628 2.298437047 1.97E-20 7.49E-18 PA0635 2.263949045 1.95E-16 3.84E-14 PA0629 2.260720569 5.93E-19 1.92E-16 PA0639 2.220599378 2.18E-21...”
- Quantitative description of a contractile macromolecular machine
Fraser, Science advances 2021 - “...PA0618). PA0616 (the central spike protein, MW = 19.4 kDa, three copies per particle) and PA0627 (MW = 7.5 kDa) are not visible in this SDS-PAGE. ( B ) The killing activity of the WT pyocin and the four mutants with an insertion of one (1aa)...”
- Action of a minimal contractile bactericidal nanomachine
Ge, Nature 2020 - “...and Tri1b ) and one copy of PA0619 ( Tri2 )], sheath initiator (PA0617), glue (PA0627), hub (PA0628) and spike (PA016) ( Fig. 1e , Extended Data Fig. 5 ). PA0626 forms the centerpiece of the baseplate ( Extended Data Fig. 5a ): the central spike...”
- “...at its top the sheath initiator PA0617 protein. A small protein with a LysM fold PA0627 binds to a side of the triplex and glues PA0617, PA0618b and PA0619 together ( Extended Data Fig. 5e ). The (PA0618) 2 -PA0619 triplexes are joined into an iris-like...”
- Fis Contributes to Resistance of Pseudomonas aeruginosa to Ciprofloxacin by Regulating Pyocin Synthesis
Long, Journal of bacteriology 2020 (secret) - Full Transcriptomic Response of Pseudomonas aeruginosa to an Inulin-Derived Fructooligosaccharide
Rubio-Gómez, Frontiers in microbiology 2020 - “...PA0624 Uncharacterized protein 2.3 0.000 PA0625 Uncharacterized protein 2.5 0.000 PA0626 Uncharacterized protein 2.1 0.000 PA0627 Uncharacterized protein 3.7 0.000 PA0628 Uncharacterized protein 2.9 0.000 PA0629 Uncharacterized protein 2.6 0.000 PA0630 Uncharacterized protein 1.8 0.000 PA0631 Uncharacterized protein 2.9 0.000 PA0632 Uncharacterized protein 2.1 0.000 PA0633...”
- Pseudomonas aeruginosa Oligoribonuclease Contributes to Tolerance to Ciprofloxacin by Regulating Pyocin Biosynthesis
Chen, Antimicrobial agents and chemotherapy 2017 - “...PA0620 PA0621 PA0622 PA0623 PA0624 PA0625 PA0626 PA0627 PA0628 PA0629 PA0630 PA0632 PA0633 PA0634 PA0635 PA0636 PA0985 Product Repressor, PtrB Hypothetical...”
- Dissection of the cis-2-decenoic acid signaling network in Pseudomonas aeruginosa using microarray technique
Rahmani-Badi, Frontiers in microbiology 2015 - “...ercS, norD, etfB, hemE, PA0510, PA0516, PA0918, PA1779, PA3025, PA3491, PA4772, PA5491 Bacteriophage production PA0616-PA0623, PA0627, PA063 Tricarboxylic acid (TCA) cycle fumC1, acnA N -AHLs and PQS QS-dependent genes and Virulence lasIR, rhlI, qscR, rsaL, vfr, pqsR (mvfR), pchR, gacA,pqsBCDEH, antAB, rpoS, xcpTVW, secA, pscT, pcrD,...”
- Understanding the antimicrobial mechanism of TiO₂-based nanocomposite films in a pathogenic bacterium
Kubacka, Scientific reports 2014 - “...50 . Finally, a set of three genes ( PA0622 , 5.9-fold; PA0623 , 6.5-fold; PA0627 , 8.8-fold) encoding proteins presumptively involved in genomic prophage-mediated cell death and lysis, as well as a prt N gene (7.8-fold) that encodes a related transcriptional activator 51 , were...”
- More
- F-Type Pyocins Are Diverse Noncontractile Phage Tail-Like Weapons for Killing Pseudomonas aeruginosa
Saha, Journal of bacteriology 2023 (secret) - Pseudomonas aeruginosa Oligoribonuclease Contributes to Tolerance to Ciprofloxacin by Regulating Pyocin Biosynthesis
Chen, Antimicrobial agents and chemotherapy 2017 - “...PA14_08070 PA14_08090 PA14_08100 PA14_08120 PA14_08130 PA14_08140 PA14_08150 PA14_08160 PA14_08180 PA14_08200 PA14_08210 PA14_08220 PA14_08230 PA14_08240...”
DEJ70_05840 tail protein X from Wolbachia pipientis wAlbB
36% identity, 88% coverage
- Genomic and Phenotypic Comparisons Reveal Distinct Variants of Wolbachia Strain wAlbB
Martinez, Applied and environmental microbiology 2022 - “...(DEJ70_05855/unannotated downstream ORF) + + Tape measure (DEJ70_05850) + + gpU (DEJ70_05845) + + gpX (DEJ70_05840) + + Late control D (DEJ70_05835) + + Tail fiber Baseplate wedge 3 tail fiber network Receptor-binding protein (DEJ70_05895DEJ70_05900) + Tail fiber assembly chaperone (DEJ70_05890) + Receptor-binding protein or tail...”
- Complete Genome Sequence of the Wolbachia wAlbB Endosymbiont of Aedes albopictus
Sinha, Genome biology and evolution 2019 - “...protein X, tail tape measure protein, and a major tail tube protein (encoded by DEJ70_05835, DEJ70_05840, DEJ70_05850, and DEJ70_05865, respectively), pseudogenized versions of a tail sheath protein (loci DEJ70_05870 and DEJ70_05880, as well as some of the genes found in Eukaryotic Association Modules of WO phages...”
PP3064 pyocin R2_PP, tail component protein from Pseudomonas putida KT2440
40% identity, 93% coverage
VV1_0086 P2-like prophage tail protein X from Vibrio vulnificus CMCP6
36% identity, 90% 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