PaperBLAST
PaperBLAST Hits for SMa0833 (46 a.a., MMELHDLAED...)
Show query sequence
>SMa0833
MMELHDLAEDLPSKWTEIMAVAEKAFRAFAELDAVKRELAESENAQ
Running BLASTp...
Found 6 similar proteins in the literature:
SMa0833 conserved hypothetical protein from Sinorhizobium meliloti 1021
100% identity, 100% coverage
- FixJ: a major regulator of the oxygen limitation response and late symbiotic functions of Sinorhizobium meliloti
Bobik, Journal of bacteriology 2006 - “...these 21 genes, located downstream from nifH (nifDKE, nifX, SMa0833, fdxB, orf10.5, and syrA) are affected by the polar effect of nifH mutation itself (4), and...”
- “...itself. The sequence analysis of the upstream regions of SMa0833, fdxB, orf10.5, and syrA did not reveal any consensus NifA box as would be expected if these...”
MAFF_RS24035 CCE_0567 family metalloprotein from Mesorhizobium japonicum MAFF 303099
76% identity, 67% coverage
bsr1749 bsr1749 from Bradyrhizobium japonicum USDA 110
57% identity, 83% coverage
- Identification of the Important Genes of Bradyrhizobium diazoefficiens 113-2 Involved in Soybean Nodule Development and Senescence
Yuan, Frontiers in microbiology 2021 - “...blr1755 MAFF_RS24355 Nitrogen fixation 113-2GL007898 bsr1750 MAFF_RS24040 , Early stages of nodule development MAFF_RS24300 113-2GL007899 bsr1749 MAFF_RS24035 , Early stages of nodule development MAFF_RS24295 113-2GL007902 blr1746 MAFF_RS24215 MCHK_RS32305 SM2011_RS02420 Early stages of nodule development 113-2GL007904 blr1744 MAFF_RS24205 MCHK_RS32315 SM2011_RS02290 Early stages of nodule development 113-2GL007905 blr1743...”
- Metabolomic Profiling of Bradyrhizobium diazoefficiens-Induced Root Nodules Reveals Both Host Plant-Specific and Developmental Signatures
Lardi, International journal of molecular sciences 2016 - “...hypothetical protein 4.3 blr6172 hypothetical protein 4.7 blr7321 hypothetical protein 4.3 blr7327 hypothetical protein 6.0 bsr1749 hypothetical protein 4.4 Intracellular trafficking, secretion, and vesicular transport blr1813 RhcJ protein rhcJ 5.7 blr1819 RhcR protein rhcR 4.5 bsr1820 RhcS protein rhcS 4.9 Other bll1634 unknown protein 4.9 bll1636...”
- Soybean seed extracts preferentially express genomic loci of Bradyrhizobium japonicum in the initial interaction with soybean, Glycine max (L.) Merr
Wei, DNA research : an international journal for rapid publication of reports on genes and genomes 2008 - “...in the presence of either SSE or genistein except for one clone covering genes from bsr1749 to blr1752 (Fig. 2 ). One operon composed of eight ORFs (blr2077bsl2084), which was reported to be likely involved in the biosynthesis of rhizobitoxine-like (RtxA) molecule, 28 as well as...”
WP_010959602 CCE_0567 family metalloprotein from Methylococcus capsulatus
54% identity, 62% coverage
- Hybrid Proteins with Short Conformational Epitopes of the Receptor-Binding Domain of SARS-CoV-2 Spike Protein Promote Production of Virus-Neutralizing Antibodies When Used for Immunization
Karyagina, Biochemistry. Biokhimiia 2022 - “...M. capsulatus (first Rop helix: a.a. 2-34; second Rop helix: a.a. 34-65; PDB: 2JS5_A, RefSeq WP_010959602). Next, sequences coding for either trimerization-mediating -helix of S protein (Tri) (a.a. 958-991, UniProtKB: locus SPIKE_SARS2, accession P0DTC2) or T. maritima ALD (a.a. 2-201, PDB: 1WA3) were introduced. All recombinant...”
- Development of a Platform for Producing Recombinant Protein Components of Epitope Vaccines for the Prevention of COVID-19
Karyagina, Biochemistry. Biokhimiia 2021 - “...the -helix of the Rop-like protein from Methylococcus capsulatus (2-34 aa, PDBcode: 2JS5_A, RefSeq ID: WP_010959602), sequence of the D2 determinant of the receptor-binding motif (RBM) of the Spike protein of the virus SARSCoV2 (470-490 aa, UniProtKB ID: locus SPIKE_SARS2, accession P0DTC2), sequence of the second...”
- “...the Rop-like protein from M. capsulatus (2-34 and 35-66 aa, PDB code: 2JS5_A, RefSeq ID: WP_010959602), a region that includes the RBM protein of the SARS-CoV-2 (433-511 aa, UniProtKB ID: locus SPIKE_SARS2, accession P0DTC2), as well as additional residues representing linker sequences and residues corresponding to...”
asl1434 hypothetical protein from Nostoc sp. PCC 7120
47% identity, 63% coverage
MAFF_RS24295 CCE_0567 family metalloprotein from Mesorhizobium japonicum MAFF 303099
63% 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 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