PaperBLAST
PaperBLAST Hits for VIMSS201566 conserved hypothetical protein (93 a.a., MTDINQVIDQ...)
Show query sequence
>VIMSS201566 conserved hypothetical protein
MTDINQVIDQMPVEVYDRLRSAAELGKWEDGTVLTEAQRESTLQVVMLYQARRLEQTDHF
TIGAGGKLNELSKAELKKQFRGESIAEFKADDL
Running BLASTp...
Found 9 similar proteins in the literature:
SO2422 conserved hypothetical protein from Shewanella oneidensis MR-1
100% identity, 100% coverage
- Transcriptome analysis reveals response regulator SO2426-mediated gene expression in Shewanella oneidensis MR-1 under chromate challenge
Chourey, BMC genomics 2008 - “...a zinc carboxypeptidase domain protein (SO2424), a hypothetical protein (SO2423), and a conserved hypothetical protein (SO2422) (Figure 2A ). The so2423 ORF overlaps so2422 by 3 bp based on the MR-1 genome annotation ( ). The so2426 region also includes a gene encoding a putative TonB-dependent...”
- “...upstream of so2426 . Putative -independent transcription terminators were identified downstream of the so2427 and so2422 ORFs ( ; [ 28 ]). Figure 2 Structural organization of the S. oneidensis MR-1 so2426 locus . (A) Schematic representation of the so2426 gene region. ORFs located upstream and...”
SF1446 hypothetical protein from Shigella flexneri 2a str. 301
46% identity, 94% coverage
- Virulence and Stress Responses of Shigella flexneri Regulated by PhoP/PhoQ
Lin, Frontiers in microbiology 2017 - “...homeobox protein ipgB1 2.03 0.0017 ND Chromosome IpgB1, secreted by the Mxi-Spa machinery, function unknown SF1446 2.09 0.0030 ND Chromosome Hypothetical protein SF0572 2.16 0.0447 ND Chromosome Hypothetical protein a WT, wild type; ND, not determined . b The differentially expressed genes of microarrays were defined...”
ECs2486 hypothetical protein from Escherichia coli O157:H7 str. Sakai
46% identity, 94% coverage
c2182 Hypothetical protein yeaC from Escherichia coli CFT073
46% identity, 83% coverage
YeaC / b1777 DUF1315 domain-containing protein YeaC from Escherichia coli K-12 substr. MG1655 (see paper)
b1777 orf, hypothetical protein from Escherichia coli str. K-12 substr. MG1655
46% identity, 94% coverage
YPO2159 conserved hypothetical protein from Yersinia pestis CO92
YPTB2085 hypothetical protein from Yersinia pseudotuberculosis IP 32953
42% identity, 96% coverage
- An integrated computational-experimental approach reveals Yersinia pestis genes essential across a narrow or a broad range of environmental conditions
Senior, BMC microbiology 2017 - “...protein YPO1102 ypo1102 hypothetical protein YPO1213 nrdB ribonucleotide-diphosphate reductase subunit beta YPO1391 cmk cytidylate kinase YPO2159 ypo2159 hypothetical protein YPO2327 ypo2327 lipoprotein YPO2350 pspB phage shock protein B YPO2883 ndk nucleoside diphosphate kinase YPO2894 iscA iron-sulfur cluster assembly protein YPO2907 glyA serine hydroxymethyltransferase YPO3173 thii thiamine...”
- “...four of these genes identified as essential at 37C but not at 28C (YPO0331, YPO1102, YPO2159 and YPO2327) could not be predicted on the basis of motif or homology matches, although YPO2327 is predicted to be a lipoprotein and is therefore likely to be surface located....”
- Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
Rosso, BMC microbiology 2008 - “...YPO1882 conserved hypothetical protein 1.552 (< 0.001) YPTB1941 YPO1943 putative membrane protein 2.118 (0.004) YPTB2085 YPO2159 conserved hypothetical protein 0.606 (0.032) YPTB2146 YPO2224 putative membrane protein 1.568 (0.018) YPTB2214 YPO2291 putative virulence factoR 0.638 (0.023) YPTB2234 YPO2315 putative exported protein 1.503 (0.008) YPTB2265 YPO2347 putative membrane...”
- Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
Rosso, BMC microbiology 2008 - “...YPTB1902 YPO1882 conserved hypothetical protein 1.552 (< 0.001) YPTB1941 YPO1943 putative membrane protein 2.118 (0.004) YPTB2085 YPO2159 conserved hypothetical protein 0.606 (0.032) YPTB2146 YPO2224 putative membrane protein 1.568 (0.018) YPTB2214 YPO2291 putative virulence factoR 0.638 (0.023) YPTB2234 YPO2315 putative exported protein 1.503 (0.008) YPTB2265 YPO2347 putative...”
STM1292 putative cytoplasmic protein from Salmonella typhimurium LT2
AEX15_08375, SL1344_1227, SeKA_A0714 YeaC family protein from Salmonella enterica subsp. enterica serovar Kentucky
44% identity, 94% coverage
- Genetic Determinants of Salmonella Resistance to the Biofilm-Inhibitory Effects of a Synthetic 4-Oxazolidinone Analog
Griewisch, Applied and environmental microbiology 2020 - “...of the major drug efflux pump AcrAB-TolC, and two genes of unknown function (STM0437 and STM1292). The results of this study suggest that JJM-ox-3-70 inhibits biofilm formation by indirect inhibition of extracellular matrix production that may be linked to disruption of flagellar motility. Further work is...”
- Repression of Salmonella enterica phoP expression by small molecules from physiological bile
Antunes, Journal of bacteriology 2012 - “...STM2141 STM0735 STM0738 STM1744 PSLT046 STM2190 STM2799 STM1292 STM0730 STM3321 STM1742 STM3033 STM4274 STM4126 ORF04918 Fold regulation cyoC cyoE dppA phoH...”
- speG Is Required for Intracellular Replication of Salmonella in Various Human Cells and Affects Its Polyamine Metabolism and Global Transcriptomes
Fang, Frontiers in microbiology 2017 - “...hutU SL1344_0767 Urocanate hydratase 1.237 SL1344_3732 SL1344_3732 Hypothetical protein 1.227 SL1344_0790 SL1344_0790 Hypothetical protein 1.163 SL1344_1227 SL1344_1227 Hypothetical protein 1.010 hutH SL1344_0768 Histidine ammonia-lyase 1.002 (B) DOWNREGULATED GENES Flagellar Genes flhA SL1344_1848 Flagellar biosynthetic protein FlhA 1.994 flhB SL1344_1849 Flagellar biosynthetic protein FlhB 1.918 fliP SL1344_1908...”
- Genomic and Evolutionary Analysis of Two Salmonella enterica Serovar Kentucky Sequence Types Isolated from Bovine and Poultry Sources in North America
Haley, PloS one 2016 - “...inner membrane metabolite transport protein, sorbitol dehydrogenase, fructose-bisphosphate aldolase, kinase. 9227 SeKA_A0714, SeKA_A0725 C AEX15_08380, AEX15_08375 C 16 putative membrane transport protein, mandelate racemase/muconate lactonizing enzyme, putative transcriptional regulator 3481 SeKA_A3461, SeKA_A3465 AEX15_14060, AEX15_14050 17 peroxisomal (S)-2-hydroxy-acid oxidase, putative glycolate oxidase 1202 SeKA_A1070, SeKA_A1073 AEX15_10030, AEX15_10060...”
- “...AEX15_20690, AEX15_20730 15 oxidoreductase, inner membrane metabolite transport protein, sorbitol dehydrogenase, fructose-bisphosphate aldolase, kinase. 9227 SeKA_A0714, SeKA_A0725 C AEX15_08380, AEX15_08375 C 16 putative membrane transport protein, mandelate racemase/muconate lactonizing enzyme, putative transcriptional regulator 3481 SeKA_A3461, SeKA_A3465 AEX15_14060, AEX15_14050 17 peroxisomal (S)-2-hydroxy-acid oxidase, putative glycolate oxidase 1202...”
- “...in glycolysis and gluconeogenesis, mannitol utilization) (SeKA_A2624, SeKA_A2631), and region 15 (sorbitol dehydrogenase, fructose-bisphosphate aldolase) (SeKA_A0714, SeKA_A0725). The presence of these operons in strains frequently isolated from dairy cows and poultry suggests their roles in these environments should be further investigated. In both STs ten homologous...”
PFLU2679 hypothetical protein from Pseudomonas fluorescens SBW25
34% identity, 60% coverage
EY04_RS12830 YeaC family protein from Pseudomonas chlororaphis
34% identity, 60% coverage
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 789,361 different protein sequences to 1,256,019 scientific articles. Searches against EuropePMC were last performed on January 10 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