PaperBLAST
PaperBLAST Hits for 77 a.a. (ESFLLSKVSF...)
Show query sequence
>77 a.a. (ESFLLSKVSF...)
ESFLLSKVSFVIKKIRLEKGMTQEDLAYKSNLDRTYISGIERNSRNLTIKSLELIMKGLE
VSDVVFFEMLIKEILKH
Running BLASTp...
Found 15 similar proteins in the literature:
3clcB / Q8GGH0 Crystal structure of the restriction-modification controller protein c.Esp1396i tetramer in complex with its natural 35 base-pair operator (see paper)
100% identity, 100% coverage
PluDJC_21265 cell morphology transcriptional regulator XreR1 from Photorhabdus laumondii subsp. laumondii
50% identity, 64% coverage
PDB|2B5A_A restriction-modification system control element Bcll from Bacillus caldolyticus (see paper)
39% identity, 87% coverage
Q81CU4 Transcriptional regulator, MerR family from Bacillus cereus (strain ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NCTC 2599 / NRRL B-3711)
47% identity, 43% coverage
LRHM_1877 helix-turn-helix domain-containing protein from Lacticaseibacillus rhamnosus GG
46% identity, 59% coverage
- Genomic adaptation of the Lactobacillus casei group
Toh, PloS one 2013 - “...protein LBPC_2661 LBPC_2670 8.4 putative cell surface protein, transposase LBCZ_1857 LBCZ_1870 23.6 conserved hypothetical protein LRHM_1877 LRHM_1891 13.2 conserved hypothetical protein, transposase LBCZ_2040 LBCZ_2046 9.2 conserved hypothetical protein LRHM_1959 LRHM_1977 19.3 glycosyltransferase LBCZ_2167 LBCZ_2179 12.2 conserved hypothetical protein, ABC transporter LRHM_2012 LRHM_2019 16.4 conserved hypothetical protein...”
RHE_RS21900 helix-turn-helix domain-containing protein from Rhizobium etli CFN 42
RHE_PA00165 putative transcriptional regulator protein from Rhizobium etli CFN 42
42% identity, 65% coverage
- Rhizobium etli CFN42 and Sinorhizobium meliloti 1021 bioinformatic transcriptional regulatory networks from culture and symbiosis
Taboada-Castro, Frontiers in bioinformatics 2024 - “...RHE_RS27560, RHE_RS28220, RHE_RS00380, RHE_RS27925, and RHE_RS18520; three members of the XRE family: RHE_RS26290, RHE_RS13450, and RHE_RS21900; two AraC family members: RHE_RS07315 and RHE_RS28855; and two ArsR family members: RHE_RS15800 and RHE_RS27600. This highlights the presence of the DNA-directed RNA polymerase sigma-70 factor RHE_RS25560 ( Supplementary Table...”
- Role of plant compounds in the modulation of the conjugative transfer of pRet42a
Bañuelos-Vazquez, PloS one 2020 - “...plant molecules. XRE regulators have been described in pRet42a of R . etli CFN42 as RHE_PA00165 [ 31 ], in pRleVF39b of R . leguminosarum VF39SM as trbR [ 19 ] and in ICE Ml SymR7A of M . loti as qseC [ 62 ]. RHE_PA00165...”
- “...CI proteins) are regulators that have been described in pRet42a of R. etli CFN42 as RHE_PA00165 (Lopez-Fuentes et al., 2015), in pRleVF39b of R. leguminosarum VF39SM as trbR (Ding et al., 2013) and in ICEMlSymR7A of M. loti as qseC (Ramsay et al., 2013). RHE_PA00165 is...”
- Transcriptional Activation of Virulence Genes of Rhizobium etli
Wang, Journal of bacteriology 2017 - “...with a spectinomycin resistance cassette inserted in the RHE_PA00165 locus This study S. B. Gelvin (Purdue University) This study This study R. etli with...”
- “...the spectinomycin resistance gene (35) located in the RHE_PA00165 locus was extracted from an R. etli strain provided by Susana Brom, National Autonomous...”
- Genes encoding conserved hypothetical proteins localized in the conjugative transfer region of plasmid pRet42a from Rhizobium etli CFN42 participate in modulating transfer and affect conjugation from different donors
López-Fuentes, Frontiers in microbiology 2014 - “...formation) and regulation, it has two chp-encoding genes (RHE_PA00163 and RHE_PA00164) and a transcriptional regulator (RHE_PA00165). RHE_PA00163 encodes an uncharacterized protein conserved in bacteria that presents a COG4634 conserved domain, and RHE_PA00164 encodes an uncharacterized conserved protein with a DUF433 domain of unknown function. RHE_PA00165 presents...”
- “...times) but reproducible increase in transfer frequency from Rhizobium donors, while mutants in RHE_PA00164 and RHE_PA00165 lost their ability to transfer the plasmid from some Agrobacterium donors. Our results indicate that the chp-encoding genes located among conjugation genes are indeed related to this function. However, the...”
SeseC_02361 helix-turn-helix domain-containing protein from Streptococcus equi subsp. zooepidemicus ATCC 35246
38% identity, 89% coverage
AZC_3881 putative HTH-type transcriptional regulator from Azorhizobium caulinodans ORS 571
45% identity, 64% coverage
- A Novel Module Promotes Horizontal Gene Transfer in Azorhizobium caulinodans ORS571
Li, Genes 2022 - “...HGT and identified the physiological function of genes designated rihF1a (AZC_3879), rihF1b (AZC_RS26200), and rihR (AZC_3881). In-frame deletion and complementation assays revealed that rihF1a and rihF1b work as a unit ( rihF1 ) that positively affects HGT frequency. The EMSA assay and lacZ -based reporter system...”
- “...rihF1 (AZC_3879 and AZC_RS26200). Interestingly, the homologues of rihF1a , rihF1b , rihF2 , and AZC_3881 are prevalent in different strains ( Figure 2 B,C), implying that these genes may serve as a conserved module in controlling the frequency of HGT. Moreover, XRE family proteins usually...”
NMV_1222 helix-turn-helix domain-containing protein from Neisseria meningitidis 8013
34% identity, 58% coverage
NMB1204 transcriptional regulator from Neisseria meningitidis MC58
34% identity, 58% coverage
NGO0797 putative transcriptional regulator from Neisseria gonorrhoeae FA 1090
34% identity, 59% coverage
- Dual species transcriptomics reveals conserved metabolic and immunologic processes in interactions between human neutrophils and Neisseria gonorrhoeae
Potter, PLoS pathogens 2024 - “..., NGO0509, NGO1002- traA , NGO1090- gp56 , NGO1116- prtR , and NGO1630), transcriptional regulators (NGO0797- xre , NGO1244- marR , and NGO1294- lrp ), respiration and ROS response proteins (NGO1189- hslO , NGO1249- ahpD , NGO1328- cycB , NGO1371- ccoP , and NGO1442- adhA ),...”
- Control of RNA stability by NrrF, an iron-regulated small RNA in Neisseria gonorrhoeae
Jackson, Journal of bacteriology 2013 - “...nrrF mutant FA1090 nrrF mutant NGO0224 NGO0588 NGO0797 NGO0802 NGO1024 NGO1368 NGO1446 NGO1561 NGO1861 NGO2075 ntpA (pyrophosphohydrolase) Hypothetical protein...”
- “...action by NrrF is not clear. Hypothetical proteins. NGO0797 is a member of the helixturn-helix (HTH) xenobiotic response element (XRE) family of transcription...”
- Deep sequencing-based analysis of the anaerobic stimulon in Neisseria gonorrhoeae
Isabella, BMC genomics 2011 - “...family transcriptional regulator Lrp, MtrR nmlR NGO0602 7.2 7.6 Transcriptional regulator nmlR NmlR, FNR xre NGO0797 3.2 3.4 XRE family transcriptional regulator marR NGO1244 5.4 15.2 MarR-family transcriptional regulator RpoH, MtrR nosR a NGO1401/1402 9.4 9.5 Regulator of nitrous oxide reductase pseudogenes FNR lexA NGO1427 4.2...”
- “...bacterioferritin genes, brfA and bfrB , and on the 3' end by an Xre-family repressor (NGO0797) end by an (Figure 5A ). Though not included the FA1090 genome annotation, analysis of the raw RNA-seq data confirms that this transcript is highly induced anaerobically (Table 1 ,...”
AAG42426.1 regulatory protein SptAIC from Salmonella enterica subsp. enterica serovar Paratyphi A (see paper)
40% identity, 73% coverage
pvuIIC / RF|NP_072081.1 transcriptional regulator, PvuIIC from Proteus vulgaris (see 3 papers)
47% identity, 61% coverage
PuuR / VIMSS1544 PuuR regulator of Spermidine biosynthesis, effector Putrescine from Thermotoga maritima MSB8
TM_0656 cupin domain-containing protein from Thermotoga maritima MSB8
TM0656 conserved hypothetical protein from Thermotoga maritima MSB8
38% identity, 32% coverage
SM12261_RS01545 helix-turn-helix domain-containing protein from Streptococcus mitis NCTC 12261
35% identity, 57% coverage
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 798,070 different protein sequences to 1,261,478 scientific articles. Searches against EuropePMC were last performed on May 12 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