PaperBLAST
PaperBLAST Hits for PFLU_RS30645 (61 a.a., MRSRELIDLL...)
Show query sequence
>PFLU_RS30645
MRSRELIDLLVAEGWFEVAVTGSHHQFKHPVKRGRITVPHPKSEIAKGTLHSIFKSAGLN
Y
Running BLASTp...
Found 13 similar proteins in the literature:
KZA74_07675 type II toxin-antitoxin system HicA family toxin from Acinetobacter baumannii
57% identity, 98% coverage
NGO1628 hypothetical protein, putative phage associated protein from Neisseria gonorrhoeae FA 1090
54% identity, 97% coverage
- Quantitative Proteomics of the 2016 WHO Neisseria gonorrhoeae Reference Strains Surveys Vaccine Candidates and Antimicrobial Resistance Determinants
El-Rami, Molecular & cellular proteomics : MCP 2019 - “...NGO1239 WHO_F_ 02198c MdaB NGO1966 NGO7315 NGO0143 NGO1628 NGO0059 Downregulated Cluster V Upregulated Downloaded from https://www.mcponline.org at UNIV OF...”
- Computational analysis of bacterial RNA-Seq data
McClure, Nucleic acids research 2013 - “...results and as identified from the RNA-seq data. For 5 of the 10 genes (NGO1577, NGO1628, NGO1762, NGO1812 and NGO1858), the length of the 5 UTR identified by our approach is within 7 nt of the length of the 5 UTR as estimated from the primer...”
- Deep sequencing-based analysis of the anaerobic stimulon in Neisseria gonorrhoeae
Isabella, BMC genomics 2011 - “...34.0 16.0 Putative phage associated protein NGO1627 6.6 4.4 Conserved hypothetical protein (probable phage origin) NGO1628 7.6 4.9 Putative phage associated protein NGO1633 26.9 137.3 Putative phage associated protein NGO1634 27.4 18.8 Putative phage associated protein NGO1635 58.1 5.4 Putative phage associated protein NGO1636 26.4 10.0...”
- “...NGO1559 3.6 2.5 Probable outer membrane protein arsR NGO1562 4.2 -2.3 ArsR family transcriptional regulator NGO1628 6.3 2.1 Conserved hypothetical protein NGO1633 82.1 2.1 Putative phage associated protein NGO1688 -3.1 3.7 Conserved hypothetical protein folA NGO1694 3.3 -2.0 Dihydrofolate reductase (FolA) NGO1807 -3.3 -3.0 Amino-acid transporter...”
- Characterization of the dsDNA prophage sequences in the genome of Neisseria gonorrhoeae and visualization of productive bacteriophage
Piekarowicz, BMC microbiology 2007 - “...133 hypothetical protein HP2p14 protein [ Haemophilus phage (pfam UPFO150 family) HP2] 34,54% on 129 NGO1628 15901771590593 60 conserved hypothetical protein [HP1p18] protein [ Haemophilus (COG1724) phage HP1] 60,74% on 51 NGO1629 15906021591249 272 NS NGO1634 15913691591770 183 hypothetical protein hypothetical protein [P27p17] [Bacteriophage P27] 30,51%...”
A1S_2020 hypothetical protein from Acinetobacter baumannii ATCC 17978
58% identity, 85% coverage
- The HicAB System: Characteristics and Biological Roles of an Underappreciated Toxin-Antitoxin System
Encina-Robles, International journal of molecular sciences 2024 - “...aeruginosa PA1 NC_022808 PA1S_RS06915 (hicA)/PA1S_RS31585 (hicB) Prophage [ 27 ] Acinetobacter baumannii ATCC 17978 NC_009085 A1S_2020 (hicA)/A1S_2019 (hicB) Prophage [ 77 ] Burkholderia pseudomallei K96243 NC_006351 BPS_RS20815 (hicA)/BPS_RS20820 (hicB) Prophage-IS/Tn [ 24 , 25 , 41 ] Streptococcus pneumoniae TIGR4 NC_003028 SP_RS08870 (hicA)/SP_RS08865 (hicB) IS/Tn [...”
- A corepressor participates in LexA-independent regulation of error-prone polymerases in Acinetobacter
Peterson, Microbiology (Reading, England) 2020 - “...RecA for their regulation (the notable exceptions being recA itself, and the hypothetical phage gene A1S_2020). Finally, one-third ( n =20) of the 57 genes whose expression was differentially induced in JH1700 cells but not in WT cells were located in seven potential operons or gene...”
- Prophage induction and differential RecA and UmuDAb transcriptome regulation in the DNA damage responses of Acinetobacter baumannii and Acinetobacter baylyi
Hare, PloS one 2014 - “...recA and umuDAb 2.1 A1S_0421 Protein chain initiation factor IF-1 * recA and umuDAb 2.1 A1S_2020 Hypothetical protein umuDAb 7.0 *Indicates that the induced gene is not part of a prophage region. ** See reference [27] . In contrast to the dispersal of induced genes throughout...”
- “...exhibited only a recA -dependent path of inducing geneswith the exception of recA itself and A1S_2020, which were induced 2.0 to 2.2 fold, respectively, in the recA mutant. However, the 17978 induced transcriptome contained two DNA-damage induced regulons: i) 123 genes regulated by recA (i.e. umuDAb...”
- Molecular mechanisms of ethanol-induced pathogenesis revealed by RNA-sequencing
Camarena, PLoS pathogens 2010 - “...COG3958 A1S_1291 2.3 Hypothetical protein, pfam03781:DUF323 A1S_0043 2.5 Phospholipase C A1S_0997 2.4 Predicted esterase, COG3150 A1S_2020 2.2 RNA binding protein, HicA family A1S_3543 2.2 Hypothetical protein 1 A1S_2195 2.6 Hypothetical protein 6 A1S_3024 2.4 Hypothetical protein A1S_3231 4.3 Acetyl-CoA hydrolase/transferase domain COG0427 A1S_1641 2.2 Fatty acid...”
SMc04441 HYPOTHETICAL PROTEIN from Sinorhizobium meliloti 1021
57% identity, 97% coverage
- Characterization of HicAB toxin-antitoxin module of Sinorhizobium meliloti
Thomet, BMC microbiology 2019 - “...In this study, we focused on the TA module HicAB of S. meliloti corresponding to SMc04441 and SMc04269 hypothetical proteins as defined by Capela et al., [ 32 ]. The HicAB modules are highly subjected to horizontal gene transfer and are widely distributed in free-living Bacteria-...”
- “...[ 21 ]. In this study, we show that the operon consisting of the ORFs SMc04441 and SMc04269 in S. meliloti encodes a TA module composed of the functional toxin HicA and antitoxin HicB. Results hicAB of S. meliloti encodes a functional TA system In order...”
BPS_RS20815 type II toxin-antitoxin system HicA family toxin from Burkholderia pseudomallei K96243
BPSS0390 conserved hypothetical protein from Burkholderia pseudomallei K96243
59% identity, 97% coverage
- The HicAB System: Characteristics and Biological Roles of an Underappreciated Toxin-Antitoxin System
Encina-Robles, International journal of molecular sciences 2024 - “...baumannii ATCC 17978 NC_009085 A1S_2020 (hicA)/A1S_2019 (hicB) Prophage [ 77 ] Burkholderia pseudomallei K96243 NC_006351 BPS_RS20815 (hicA)/BPS_RS20820 (hicB) Prophage-IS/Tn [ 24 , 25 , 41 ] Streptococcus pneumoniae TIGR4 NC_003028 SP_RS08870 (hicA)/SP_RS08865 (hicB) IS/Tn [ 28 ] Escherichia coli plasmid pJIE143 JN194214 hicA/hicB Plasmid [ 78...”
- Unraveling the role of toxin-antitoxin systems in <i>Burkholderia pseudomallei</i>: exploring bacterial pathogenesis and interactions within the HigBA families
Chapartegui-González, Microbiology spectrum 2024 - “...for a ribosomal protein ( rplC ); BPSL3426, two-component regulator; and the type II toxins BPSS0390 ( hicA ), BPSS1060 ( higB ), and BPSL0175 ( higB ). Only a few genes are repressed in BPSL3261 compared with BPSL3343, and all of them are identified as...”
- “...BPS_RS18025), among the genes significantly repressed in BPSL3260 BPSL3261, we found BPSS0394 (antitoxin BrnA) and BPSS0390 (toxin HicA), and different genes that encodes for ribosomal-related proteins (BPSL0915, BPSL1461, BPSL1942, BPSL1943, BPSL2444, BPSL3194, BPSL3196, BPSL3197, BPSL3209, and BPSL3217). It is important to highlight a putative new TA...”
- Evaluating the Contribution of the Predicted Toxin-Antitoxin System HigBA to Persistence, Biofilm Formation, and Virulence in Burkholderia pseudomallei
Chapartegui-González, Infection and immunity 2022 (secret) - Predicting toxins found in toxin-antitoxin systems with a role in host-induced Burkholderia pseudomallei persistence
Ross, Scientific reports 2020 - “...the published results, we only had an overlap of 8 toxins (BPSL0549A, BPSL0562, BPSL1564, BPSL2333, BPSS0390, BPSS0845a, BPSS2142, and BPSS1226), which may be due to the stringent size and gene structure filters used by the RASTA analysis (Supplemental Figure S3 A and B) 28 . Further,...”
- “...BPSS2196. Seven of the genes in clusters 2 and 3 (BPS1584, BPSS0395, BPSL0559, BPSL2333, BPSS1060, BPSS0390, and BPSL0175) have been previously tested by either our lab or in the study by Butt et al . and some were shown to induce antibiotic-mediated persistence and influence persistence...”
- Mutagenesis and functional characterisation of toxin HicA from the HicBA TA system in Burkholderia pseudomallei
Bare, 2016 - Toxin-Antitoxin Systems in Clinical Pathogens
Fernández-García, Toxins 2016 - “...BPSS1060 (RelE2 Bp ) halted growth when expressed in E. coli , whereas expression of BPSS0390 (HicA Bp ) or BPSS1584 (HipA Bp ) (in an E. coli DhipBA background) caused a reduction in the number of culturable bacteria [ 63 ]. The HicAB Bp system...”
- Identification of type II toxin-antitoxin modules in Burkholderia pseudomallei
Butt, FEMS microbiology letters 2013 (PubMed)- “...cease when expressed in Escherichia coli, whereas expression of BPSS0390 (HicA) or BPSS1584 (HipA) (in an E. coli DhipBA background) caused a reduction in the...”
- “...Fw BPSL0559 Rv BPSL2333 Fw BPSL2333 Rv BPSS0395 Fw BPSS0395 Rv BPSS0390 Fw BPSS0390 Rv HipBA R HipBA F FEMS Microbiol Lett 338 (2013) 86-94 of of of of of...”
EAMY_1828 hypothetical protein from Erwinia amylovora CFBP1430
ROD_25752 hypothetical protein from Citrobacter rodentium ICC168
56% identity, 97% coverage
SAJRA307_03820 type II toxin-antitoxin system HicA family toxin from Staphylococcus aureus
53% identity, 93% coverage
YPO1818 conserved hypothetical protein from Yersinia pestis CO92
53% identity, 49% coverage
PMI0818 hypothetical protein from Proteus mirabilis HI4320
53% identity, 97% coverage
TDE1838 conserved hypothetical protein from Treponema denticola ATCC 35405
47% identity, 91% coverage
BP0939 conserved hypothetical protein from Bordetella pertussis Tohama I
53% identity, 97% coverage
ZMOB_RS10035 type II toxin-antitoxin system HicA family toxin from Zymomonas mobilis subsp. mobilis ATCC 10988
46% identity, 97% coverage
slr1999 hypothetical protein from Synechocystis sp. PCC 6803
41% identity, 42% 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