PaperBLAST
PaperBLAST Hits for JDDGAC_01060 (79 a.a., MRFIIRTVML...)
Show query sequence
>JDDGAC_01060
MRFIIRTVMLIALVWIGLLLSGYGVLIGSKENAAELGLQCTYLTARGTSTVQYLHTKSGF
LGITDCPLLRKSNIVVDNG
Running BLASTp...
Found 7 similar proteins in the literature:
YobH / b4536 uncharacterized protein YobH from Escherichia coli K-12 substr. MG1655 (see paper)
99% identity, 100% coverage
AEX15_11230 invasion protein YobH from Salmonella enterica subsp. enterica serovar Kentucky
73% identity, 100% coverage
STM1841 putative outer membrane or exported from Salmonella typhimurium LT2
t1037 putative exported protein from Salmonella enterica subsp. enterica serovar Typhi Ty2
SL1344_1770, STM14_2227 invasion protein YobH from Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344
72% identity, 100% coverage
- Mapping the Regulatory Network for Salmonella enterica Serovar Typhimurium Invasion
Smith, mBio 2016 - “...SprB, all of which are positively regulated. An example of an SprB-regulated gene, STM14_2227 ( STM1841 ), is shown in Fig.S1F . Strikingly, we detected no significant regulation of SPI-4 genes (see TableS1 ), and we detected no binding of SprB within or near SPI-4 (see...”
- “...STM14_0049 nhaR SL0041 STM0040 HilC STM14_1486 SL1177 STM1239 InvF STM14_0398 SL0336 STM0341 SprB STM14_2227 SL1770 STM1841 SprB STM14_3799 SL3112 STM3138 SprB STM14_4215 pckA SL3467 STM3500 SprB STM14_5097 yjbJ SL4176 STM4240 SprB NA STnc520 STnc520 STnc520 SprB STM14_1174 SL0973 STM1034 HilA STM14_1176 SL0975 STM1036 HilA STM14_1177 SL0976...”
- Genome expression analyses revealing the modulation of the Salmonella Rcs regulon by the attenuator IgaA
Mariscotti, Journal of bacteriology 2009 - “...siiE in serovar Ty- phimurium (27). More recently, STM1841, a serovar Typhimurium gene of unknown function, was also shown to have a 30-fold-higher induction...”
- 46(th) Congress of The International Society of Paediatric Oncology (SIOP) 2014 Toronto, Canada, 22(nd) -25(th) October, 2014 SIOP Abstracts
, Pediatric blood & cancer 2014 - HilD induces expression of a novel Salmonella Typhimurium invasion factor, YobH, through a regulatory cascade involving SprB
Banda, Scientific reports 2019 - “...of virulence genes in Salmonella . Results HilD positively controls the expression of yobH ( SL1344_1770 ) Previous RNA-sequencing (RNA-seq) analysis indicates that the HilD transcriptional regulator positively controls the expression of the S . Typhimurium SL1344_1770 gene 28 , which is located outside SPI-1 and...”
- “...Additional RNA-seq and co-expression analyses also support that HilD is involved in the expression of SL1344_1770 39 , 45 . Orthologs of SL1344_1770 , which show high sequence identity and a conserved genomic context, are denominated yobH in Escherichia coli and several other bacteria; thus, we...”
- Mapping the Regulatory Network for Salmonella enterica Serovar Typhimurium Invasion
Smith, mBio 2016 - “...genes for SprB, all of which are positively regulated. An example of an SprB-regulated gene, STM14_2227 ( STM1841 ), is shown in Fig.S1F . Strikingly, we detected no significant regulation of SPI-4 genes (see TableS1 ), and we detected no binding of SprB within or near...”
- “...STM0039 HilC STM14_0049 nhaR SL0041 STM0040 HilC STM14_1486 SL1177 STM1239 InvF STM14_0398 SL0336 STM0341 SprB STM14_2227 SL1770 STM1841 SprB STM14_3799 SL3112 STM3138 SprB STM14_4215 pckA SL3467 STM3500 SprB STM14_5097 yjbJ SL4176 STM4240 SprB NA STnc520 STnc520 STnc520 SprB STM14_1174 SL0973 STM1034 HilA STM14_1176 SL0975 STM1036 HilA...”
SeKA_A1320 invasion protein YobH from Salmonella enterica subsp. enterica serovar Kentucky str. CVM29188
71% identity, 100% coverage
D8682_RS04560 YobH family protein from Buttiauxella sp. 3AFRM03
65% identity, 99% coverage
- Critical Role of Monooxygenase in Biodegradation of 2,4,6-Trinitrotoluene by Buttiauxella sp. S19-1
Xu, Molecules (Basel, Switzerland) 2023 - “...genes up-regulated after TNT exposure included gene D8682_RS01950 (iron (III) transport system permease protein), gene D8682_RS04560 (integral component of membrane), and gene D8682_RS09020 (basic amino acid-specific outer membrane pore). These findings indicate that genes peculiar to membrane transport (belonging to cellular components) may have been mobilized...”
KP1_3469 putative outer membrane or exported from Klebsiella pneumoniae NTUH-K2044
MAKP3_17670 YobH family protein from Klebsiella pneumoniae
65% identity, 100% coverage
- Identification of Genetic Alterations Associated with Acquired Colistin Resistance in Klebsiella pneumoniae Isogenic Strains by Whole-Genome Sequencing
Choi, Antibiotics (Basel, Switzerland) 2020 - “...KPN_02065 and KPN_02066. In B0704-039R1, an IS 5 -like element was inserted between KP1_3468 and KP1_3469. Alterations in KP1_3468 were also seen in B0704-039R2, a colistin-resistant strain derived from the same parent strain as B0704-039R1. However, these changes were in the coding region. Specifically, three nucleotide...”
- “...B0704-039R1, expression of KP1_3468 mRNA was increased 2.51-fold compared with its susceptible parental strain, but KP1_3469 exhibited no significant expression change. Expression of KP1_3468 mRNA was increased by 7.91-fold in B0704-039R2 compared with B0704-039. In B08-063R, increased expression was seen in phoQ (7.49-fold) and the galETK...”
- Stepwise Evolution of a Klebsiella pneumoniae Clone within a Host Leading to Increased Multidrug Resistance
Yoshino, mSphere 2021 - “...) IclR family transcriptional regulator KdgR (MAKP3_17660) Ins (IS Ecp1 ) Del (6,792bp) Hypothetical protein (MAKP3_17670) Del (6,792bp) MgrB (MAKP3_17680) Del (6,792bp) Hypothetical protein (MAKP3_17690) Del (6,792bp) Cold shock-like protein CspC (MAKP3_17700) Del (6,792bp) Cell division protein FtsI (MAKP3_17710) Del (6,792bp) 23S rRNA [guanine(745)-N(1)]-methyltransferase (MAKP3_17720) Del...”
y2568 hypothetical from Yersinia pestis KIM
54% identity, 86% coverage
- Tn5AraOut mutagenesis for the identification of Yersinia pestis genes involved in resistance towards cationic antimicrobial peptides
Guo, Microbial pathogenesis 2011 - “...polymyxin B (PB8-4 and PB8-2) had minitransposon insertions upstream of two single or monocistronic genes, y2568 which encodes a hypothetical protein, and y1522 which encodes an Hcp-like protein that is not linked to any of the five predicted type 6 secretion systems (T6SS) of Y. pestis...”
- “...pbgP operon UDP-4-amino-4-deoxy-L-arabinoseoxoglutarate aminotransferase,etc. + PB8-2 yl522 hcp-\\ke DUF796, T6SS effector hep like + PB8-4 y2568 unknown hypothetical protein + PB8-8 y0634 hflC FtsH protease regulator HflC PM2-3& PM3-2 y3862 pilA phosphate ABC transporter permease PM2-49 y2662 mglB galactose-binding protein PM5-6 y0958 glpQ-Yike glycerophosphoryl diester phosphodiesterase...”
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