PaperBLAST
PaperBLAST Hits for BWI76_RS13245 (80 a.a., MFVELIYDKR...)
Show query sequence
>BWI76_RS13245
MFVELIYDKRNFEGLAGAKEIILTELTKRVHRIFPDADVRVKPMMTLASINTDASKHEKE
QISRAVQEMFEEADMWMQED
Running BLASTp...
Found 12 similar proteins in the literature:
BHE81_21980, VK055_RS06420 DinI family protein from Klebsiella pneumoniae subsp. pneumoniae
80% identity, 100% coverage
- Identifying virulence determinants of multidrug-resistant Klebsiella pneumoniae in Galleria mellonella
Bruchmann, Pathogens and disease 2021 - “...ATCC 43816 that had significantly lower mutant abundance after the Galleria infection and two genes (VK055_RS06420 and VK055_RS19345) that were enriched ( Fig. S4-S6 and Table S6, Supporting Information ). Mutants in 10 genes of the 18-gene K-locus of ATCC 43816 were significantly depleted after G....”
- Transcriptome Analysis Reveals Cr(VI) Adaptation Mechanisms in Klebsiella sp. Strain AqSCr
Lara, Frontiers in microbiology 2021 - “...(BHE81_08655), Nfo (BHE81_10860), Ssb (BHE81_26455), NrdH (BHE81_13045), NrdA (BHE81_13055), NrdB (BHE81_13060), and DinI (BHE81_21170 and BHE81_21980) were upregulated with respect to the controls ( Supplementary Table 5 ). RecA (BHE81_13175) was also upregulated but below the cutoff level, with a log 2 FC = 1.23 (...”
STM2231 Homolog of msgA; ssrB-regulated factor from Salmonella typhimurium LT2
84% identity, 70% coverage
- Application of a High-Throughput Targeted Sequence AmpliSeq Procedure to Assess the Presence and Variants of Virulence Genes in Salmonella
Gao, Microorganisms 2022 - “...( n = 17), rfbJ ( n = 18) rfbX ( n = 18) and STM2231 ( n = 19) were not detected at a high frequency. Phylogenetic analysis of the sequence reads showed that out of 35 strains which consisted of 23 serovars, two S....”
- “...genes playing a role in the attachment ( lpf , stf and sti operons), invasion (STM2231 ), intramacrophage survival ( sse operon) and systemic dissemination ( rfb operon). The use of 80 reference genomes which included the most commonly reported serovars contaminating food, was adequate for...”
- Genomic characterization of Salmonella Cerro ST367, an emerging Salmonella subtype in cattle in the United States
Rodriguez-Rivera, BMC genomics 2014 - “...Typhimurium [ 29 ], and replication in macrophages (SPI-13: [ 30 ]). Furthermore, disruption of STM2231 in SPI-12 and STM3123 in SPI-13 was previously shown to cause significant reduction in fitness in S. Typhimurium SL1344 during intestinal colonization of cattle [ 28 ]. In addition, homologs...”
- Mapping and regulation of genes within Salmonella pathogenicity island 12 that contribute to in vivo fitness of Salmonella enterica Serovar Typhimurium
Tomljenovic-Berube, Infection and immunity 2013 - “...STM3808.S STM2068 STM0586 STM0509 STM0700 STM1424 STM3830 STM2230 STM2231 STM2232 STM2241 ibpB yeeF fes 2.23 2.15 2.12 2.10 2.07 2.04 2.03 0.8144 0.20572...”
- Live attenuated S. Typhimurium vaccine with improved safety in immuno-compromised mice
Periaswamy, PloS one 2012 - “...WITS 17) and; ssaV STM2616 (WITS 1), ssaV STM2998 (WITS 2), ssaV STM2011 (WITS11), ssaV STM2231 (WITS13), ssaV STM2570 (WITS19). Real-time PCR analysis of the sequence tags established the relative abundance of Z234 (black symbols) as compared to the parental strain and the five other double-mutants...”
- Infection of mice by Salmonella enterica serovar Enteritidis involves additional genes that are absent in the genome of serovar Typhimurium
Silva, Infection and immunity 2012 - “...such genes, with possible candidates including STM0274A, STM2599, and STM2231. Thus, not only do these two serovars differ in the details of how they infect...”
- The pKO2 linear plasmid prophage of Klebsiella oxytoca
Casjens, Journal of bacteriology 2004 - “...which is not obviously prophage associated (75), and LT2 gene STM2231, which appears to be part of a badly decayed prophage, Stm6 (Stm6 is our name for a...”
- “...amino acid); (vii) Salmonella defective prophage Stm6 gene STM2231 protein (16 predicted N-terminal amino acids are not shown; its poor Shine-Dalgarno and UUG...”
msgA / AAA82996.1 MsgA from Salmonella enterica subsp. enterica serovar Typhimurium (see paper)
STM14_1492 virulence protein MsgA from Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
NP_460211 macrophage survival gene; reduced mouse virulence from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
STM1241 Macrophage survival gene; reduced mouse virulence from Salmonella typhimurium LT2
STY1883 putative virulence protein from Salmonella enterica subsp. enterica serovar Typhi str. CT18
SC1252 Macrophage survival gene; reduced mouse virulence from Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67
68% identity, 96% coverage
SEEHRA37_09669 virulence protein MsgA from Salmonella enterica subsp. enterica serovar Heidelberg str. SARA37
66% identity, 96% coverage
t1113 putative virulence protein from Salmonella enterica subsp. enterica serovar Typhi Ty2
66% identity, 96% coverage
Ent638_1656 DinI family protein from Enterobacter sp. 638
65% identity, 96% coverage
KFQ06_16010 DinI family protein from Serratia entomophila
60% identity, 100% coverage
NJ56_11895 DinI family protein from Yersinia ruckeri
60% identity, 100% coverage
YPO1232 putative stress response protein from Yersinia pestis CO92
61% identity, 100% coverage
STMMW_10691 DinI-like family protein from Salmonella enterica subsp. enterica serovar Typhimurium str. D23580
STM1056 Gifsy-2 prophage; Homolog of msgA from Salmonella typhimurium LT2
64% identity, 80% coverage
- Characterization of the Prophage Repertoire of African Salmonella Typhimurium ST313 Reveals High Levels of Spontaneous Induction of Novel Phage BTP1
Owen, Frontiers in microbiology 2017 - “...), sodCI ( STMMW_10551 ), sseI ( STMMW_10631- pseudogene), gtgE ( STMMW_10681 ) gtgF ( STMMW_10691 ) Def2 1945242 1951433 6,191 sopE2 ( STMMW_18441 ) ST64B D23580 (BTP3) 2065743 2105830 40,087 sseK3 ( STMMW_19812 ) Def3 (inc. SPI-12) 2354483 2369638 15,155 sspH2 ( STMMW_22721 ) Gifsy-1...”
- Application of a High-Throughput Targeted Sequence AmpliSeq Procedure to Assess the Presence and Variants of Virulence Genes in Salmonella
Gao, Microorganisms 2022 - “..., spaP , spaQ , spaR , spaS , sprB , sptP , sspH2 , STM1056 (msgA) , STM2231 , STM2244 , STM4315 (rtsA) , yejA , yejB , yejE , yejF , ymdA Intramacrophage survival 39 csrA , hfq , mgtA , mgtB , mgtC...”
- “...Where virulence genes are also known by alternate names, these are indicated in parenthesis, namely: STM1056 ( msgA ), STM4315 ( rtsA ), and STM1410 ( ssaX ). microorganisms-10-00369-t005_Table 5 Table 5 Validation of AmpliSeq Salm_227VG based on blind assessment of virulence and serovar designation for...”
- Genome archaeology of two laboratory Salmonella enterica enterica sv Typhimurium
Zaworski, G3 (Bethesda, Md.) 2021 - “...located between 2,728,977 and 2,776,819 (STM2584 to STM2636) and between 1,098,231 and 1,143,702 (STM1005 to STM1056), respectively. These two related prophages are patchily similar to each other; while overall DNA identity is 44.1%, this 42kb region is interspersed with highly divergent segments and unrelated insertions (...”
- Toxicogenomic analysis incorporating operon-transcriptional coupling and toxicant concentration-expression response: analysis of MX-treated Salmonella
Ward, BMC bioinformatics 2007 - “...recN 0.02699 8 11.4 16 yehR 0.05804 1.1 0.8 9.6 ftsK 0.18374 1.3 1.2 1.4 STM1056 0.20943 0.9 1.3 1.5 dinG 0.4182 1 0.7 1.2 uvrB 0.43548 3.7 0.7 1.3 minC 0.46889 1 1 0.9 mfd 0.7057 0.9 1 0.9 ftsY 0.70953 1 1.1 1.1 ybfE...”
- The genome of Salmonella enterica serovar gallinarum: distinct insertions/deletions and rare rearrangements
Wu, Journal of bacteriology 2005 - “...to Gifsy-1 (STM2584 to STM2636), Gifsy-2 (STM1005 to STM1056), Fels-1 (STM893 to STM929), and Fels-2 (STM2694 to STM2772). (The genes of serovar Typhimurium LT2...”
- Genomic comparisons of Salmonella enterica serovar Dublin, Agona, and Typhimurium strains recently isolated from milk filters and bovine samples from Ireland, using a Salmonella microarray
Reen, Applied and environmental microbiology 2005 - “...central regions (STM2702 to STM2730). Gifsy-2 (STM1005 to STM1056) (region X) was present in all serovar Typhimurium strains and all serovar Dublin strains...”
- Identification of novel Salmonella enterica serovar Typhimurium DT104-specific prophage and nonprophage chromosomal sequences among serovar Typhimurium isolates by genomic subtractive hybridization
Hermans, Applied and environmental microbiology 2005 - “...primer set was used to detect a DNA fragment (orf STM1056) in the Gifsy-2 prophage which should be present in all Salmonella strains. An overview of the primers...”
- The pKO2 linear plasmid prophage of Klebsiella oxytoca
Casjens, Journal of bacteriology 2004 - “...(x) Serratia marcescens dinI protein; (xi) Gifsy-2 gene STM1056 protein; and (xi) Stm6 gene STM2244 protein. Downloaded from http://jb.asm.org/ on February 11,...”
- “...that have not conserved this surface (e.g., Gifsy2's STM1056) might either have some other function or be nonfunctional dinI pseudogenes. Interplay between the...”
STY1077 conserved hypothetical protein from Salmonella enterica subsp. enterica serovar Typhi str. CT18
64% identity, 70% coverage
YPO1586 DNA-damage-inducible protein I from Yersinia pestis CO92
YPTB2483 DNA-damage-inducible protein I from Yersinia pseudotuberculosis IP 32953
40% identity, 94% 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