PaperBLAST

PaperBLAST Hits for BPHYT_RS20620 (78 a.a., MPIVTIQVTR...)

Show query sequence

>BPHYT_RS20620
MPIVTIQVTREGSKPGTNAVTADEKARLIAGVSQVLLDVLNKPLAATFVVIEEVDMENWG
WGGLPVEAYRKQLAQKPG

Running BLASTp...

Found 4 similar proteins in the literature:

SE37_07305 2-hydroxymuconate tautomerase family protein from Geobacter soli
51% identity, 91% coverage

• Genome sequence of a dissimilatory Fe(III)-reducing bacterium Geobacter soli type strain GSS01(T)
  Yang, Standards in genomic sciences 2015
  • “...acetyltransferase (SE37_11195, 83% similarity to Gmet_1719 in G. metallireducens ) , thiolase (SE37_13640), and tautomerase (SE37_07305) are predicted to be involved in the benzoate degradation; one 4Fe-4S ferredoxin (SE37_08830) and six hydrogenase (SE37_10910, SE37_13915, SE37_13920, SE37_10925, SE37_02470 and SE37_02475) are predicted to be involved in nitrotoluene...”

DDV75_06135 2-hydroxymuconate tautomerase family protein from Campylobacter jejuni
CJJ81176_1271 hypothetical protein from Campylobacter jejuni subsp. jejuni 81-176
Cj1255 putative isomerase from Campylobacter jejuni subsp. jejuni NCTC 11168
42% identity, 92% coverage

• Identification of Novel Phage Resistance Mechanisms in Campylobacter jejuni by Comparative Genomics
  Sørensen, Frontiers in microbiology 2021
  • “...significant similarity DDR89_05110 983.669987.490 N-6 DNA methylase DDV75_05120 980.543984.562 N-6 DNA methylase 84% 99.7% 0.0 DDV75_06135 1.187.1711.187.380 4-oxalocrotonate tautomerase family protein Not found in CAMSA2002 DDR89_06630 1.275.6811.276.898 DUF2920 family protein DDV75_06645 1.272.9611.273.551 DUF2920 family protein 37% 97.0% 0.0 1.496.3831.497.142 CRISPR region 1.492.4481.493.011 CRISPR region 100% 88.1%...”
• Long-term survival of Campylobacter jejuni at low temperatures is dependent on polynucleotide phosphorylase activity
  Haddad, Applied and environmental microbiology 2009
  • “...open reading frame (ORF) CJJ81176_1263 and ending in ORF CJJ81176_1271. There are six ORFs upstream and two ORFs downstream of pnp; among genes flanking pnp,...”
• Genomic Analysis of Chilean Strains of Campylobacter jejuni from Human Faeces
  Levican, BioMed research international 2019
  • “...distribution (18/25). The 7 genes, which were not detected in the latter strain, corresponded to Cj1255 (putative isomerase), Cj1122c (putative integral membrane), Cj0299 (putative periplasmic beta-lactamase), Cj0295 (putative acetyltransferase), and Cj0246c (Putative MCP-domain signal transduction protein), while Cj0055c and Cj0056c were hypothetical proteins [ 24 ]....”
• A Genome-Wide Association Study to Identify Diagnostic Markers for Human Pathogenic Campylobacter jejuni Strains
  Buchanan, Frontiers in microbiology 2017
  • “...Ferric enterobactin uptake receptor 11168_01072 4.90E-11 9.59E-08 Cj1122c Putative integral membrane protein. 11168_01201 6.12E-19 1.21E-15 Cj1255 Putative isomerase 11168_01309 5.30E-15 1.04E-11 Cj1365c Putative secreted serine protease 11168_01519 4.29E-10 8.39E-07 Cj1585c Putative oxidoreductase 11168_01610 4.29E-10 8.38E-07 Cj1679 Hypothetical protein 06_2866_00597 6.89E-28 1.36E-24 Di-/tripeptide transporter 06_7515_00723 4.19E-16 8.24E-13...”
• Phenotypic screening of a targeted mutant library reveals Campylobacter jejuni defenses against oxidative stress
  Flint, Infection and immunity 2014
  • “...cj0561c cj0672 cj0947c cj0949c cj1036c cj1167 cj1209 cj1241 cj1255 cj1340c cj1388 cj1406c cj1623 dprA folP pstC spoT Surface structures flaG flgD flgE 2268...”

HPB8_625 2-hydroxymuconate tautomerase family protein from Helicobacter pylori B8
D7FDC5 Tautomerase from Helicobacter pylori (strain B8)
HP0924 4-oxalocrotonate tautomerase (dmpI) from Helicobacter pylori 26695
39% identity, 92% coverage

• Alteration of the Helicobacter pylori membrane proteome in response to changes in environmental salt concentration
  Voss, Proteomics. Clinical applications 2015
  • “...2.26 Putative uncharacterized protein HP0467 HPB8_258 * & D7FCA8 heme binding 2.18 Cytochrome c553 HP1227 HPB8_625 D7FDC5 cellular aromatic compound metabolic process 2.15 4-oxalocrotonate tautomerase (DmpI) HP0924 HPB8_829 * D7FDX9 NA 2.1 Modulator of drug activity B (MDA66) HP0630 HPB8_958 * & D7FEA8 NA 2.07 Flagellar...”
• Alteration of the Helicobacter pylori membrane proteome in response to changes in environmental salt concentration
  Voss, Proteomics. Clinical applications 2015
  • “...Putative uncharacterized protein HP0467 HPB8_258 * & D7FCA8 heme binding 2.18 Cytochrome c553 HP1227 HPB8_625 D7FDC5 cellular aromatic compound metabolic process 2.15 4-oxalocrotonate tautomerase (DmpI) HP0924 HPB8_829 * D7FDX9 NA 2.1 Modulator of drug activity B (MDA66) HP0630 HPB8_958 * & D7FEA8 NA 2.07 Flagellar protein...”
• Delineation of the pH-Responsive Regulon Controlled by the Helicobacter pylori ArsRS Two-Component System
  Loh, Infection and immunity 2021 (secret)
• Alteration of the Helicobacter pylori membrane proteome in response to changes in environmental salt concentration
  Voss, Proteomics. Clinical applications 2015
  • “...2.18 Cytochrome c553 HP1227 HPB8_625 D7FDC5 cellular aromatic compound metabolic process 2.15 4-oxalocrotonate tautomerase (DmpI) HP0924 HPB8_829 * D7FDX9 NA 2.1 Modulator of drug activity B (MDA66) HP0630 HPB8_958 * & D7FEA8 NA 2.07 Flagellar protein FlaG HP0751 HPB8_844 * D7FDZ4 oxidation-reduction process 2.05 NAD(P)H-flavin oxidoreductase...”
• Identification of Helicobacter pylori genes that contribute to stomach colonization
  Baldwin, Infection and immunity 2007
  • “...into the urease enzyme, respectively. Interestingly, both amiE (HP0924) and amiF (HP1238), two amidases carried in the H. pylori genome, were identified as...”
• Characterization of the ArsRS regulon of Helicobacter pylori, involved in acid adaptation
  Pflock, Journal of bacteriology 2006
  • “...JHP0228 0.28 HP1022 JHP0402 0.30 HP0890 JHP0823 0.47 HP0924 JHP0858 0.44 HP0954 HP1104 JHP0888 JHP1030 0.45 0.34 JHP0585* 0.27 JHP1429 0.29 HP0891 JHP0824 0.41...”
• Chronic Helicobacter pylori infection with Sydney strain 1 and a newly identified mouse-adapted strain (Sydney strain 2000) in C57BL/6 and BALB/c mice
  Thompson, Infection and immunity 2004
  • “...HP0102 HP0105 HP0186 HP0720 HP0189 HP0408 HP1353 HP0594 HP0057 HP0924 HP0783 HP0311 HP0823 JHP0950 HP1097 infA thiB omp29 babB cag15 ftsZ tdhF hylB mod hsdR ung...”

jhp0858 putative from Helicobacter pylori J99
38% identity, 92% coverage

• Complexomics study of two Helicobacter pylori strains of two pathological origins: potential targets for vaccine development and new insight in bacteria metabolism
  Bernarde, Molecular & cellular proteomics : MCP 2010
  • “...et al. (31) (http://genolist.pasteur.fr/PyloriGene/genome.cgi). b a JHP0101 JHP0858 7,366 5 Da Chaperone protein dnaK (heat shock protein 70) (heat shock 70-kDa...”
• Characterization of the ArsRS regulon of Helicobacter pylori, involved in acid adaptation
  Pflock, Journal of bacteriology 2006
  • “...0.28 HP1022 JHP0402 0.30 HP0890 JHP0823 0.47 HP0924 JHP0858 0.44 HP0954 HP1104 JHP0888 JHP1030 0.45 0.34 JHP0585* 0.27 JHP1429 0.29 HP0891 JHP0824 0.41 Gene...”

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Statistics

How It Works

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.

Secrets

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.

Omissions from the PaperBLAST Database

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.