PaperBLAST

PaperBLAST Hits for OHPLBJKB_01937 (60 a.a., MGKATYTVTV...)

Show query sequence

>OHPLBJKB_01937
MGKATYTVTVTNNSNGVSVDYETETPMTLLVPEVAAEVIKDLVNTVRSYDTENEHDVCGW

Running BLASTp...

Found 2 similar proteins in the literature:

YoaG / b1796 DUF1869 domain-containing protein YoaG from Escherichia coli K-12 substr. MG1655 (see 4 papers)
YOAG_ECOLI / P64496 Protein YoaG from Escherichia coli (strain K12)
EC042_RS10415 DUF1869 domain-containing protein from Escherichia coli 042
UTI89_C1994 hypothetical protein YoaG from Escherichia coli UTI89
b1796 hypothetical protein from Escherichia coli str. K-12 substr. MG1655
c2202 Hypothetical protein yoaG from Escherichia coli CFT073
Z2838 orf, hypothetical protein from Escherichia coli O157:H7 EDL933
ECs2505 hypothetical protein from Escherichia coli O157:H7 str. Sakai
100% identity, 100% coverage

• subunit: Homodimer.
• Overexpression of the third H-NS paralogue H-NS2 compensates fitness loss in hns mutants of the enteroaggregative Escherichia coli strain 042
  Prieto, Scientific reports 2020
  • “...EC042_RS06755 (respiratory nitrate reductase subunit gamma NarI) 12.8 3.1 EC042_RS03510 (DUF1266 domain-containing protein) 8.2 5.0 EC042_RS10415 (DUF1869 domain-containing protein) 6.7 4.9 EC042_RS16380 (EscR/YscR/HrcR family type III secretion system export apparatus protein) 6.3 2.8 EC042_RS22730 (hypothetical protein) 5.4 5.0 EC042_RS19330 (nitrite reductase large subunit) 4.9 2.9 EC042_RS19990...”
• Metabolic Requirements of Escherichia coli in Intracellular Bacterial Communities during Urinary Tract Infection Pathogenesis
  Conover, mBio 2016
  • “...acid PA degradation in bacteria UTI89_C0587 3.658836126 MbtH-like protein (domain found in antibiotic synthesis proteins) UTI89_C1994 yoaG 3.380447626 Hypothetical protein UTI89_C5112 ybcS2 3.232487202 Bacteriophage lambda lysozyme-like protein UTI89_C3386 gspC 2.910385132 Putative type II secretion protein GspC UTI89_C1336 sitD 2.890235424 Transmembrane subunit, of PBP-dependent ABC transporters involved...”
• 18th Congress of the European Hematology Association, Stockholm, Sweden, June 13–16, 2013
  , Haematologica 2013
• Global gene expression profiling of the asymptomatic bacteriuria Escherichia coli strain 83972 in the human urinary tract
  Roos, Infection and immunity 2006
  • “...and in vitro urinea Gene Code c1686 b1476 b1226 b1796 b4209 b1223 ECs5443 b1797 Z2001 b1541 Z0893 b1227 b1225 b4013 b2941 b2552 c4141 b1475 b0873 b3240 b3556...”
  • “...be induced by nitrate, together with the yoaG gene (b1796) (15), which also showed significant up-regulation in all patients (Table 1). ahpC, the gene encoding...”
• YdgG (TqsA) controls biofilm formation in Escherichia coli K-12 through autoinducer 2 transport
  Herzberg, Journal of bacteriology 2006
  • “...4.9 4.9 4.6 4.6 4.6 4.6 4.3 b1228 ytfA yoaG yjgN b1228 b4205 b1796 b4257 4.3 4 4 4 yjcF yhaC ygfF yfdU yfaE b4066 b3121 b2902 b2373 b2236 4 4 4 4 4 yfaA yadS...”
• Hierarchical control of anaerobic gene expression in Escherichia coli K-12: the nitrate-responsive NarX-NarL regulatory system represses synthesis of the fumarate-responsive DcuS-DcuR regulatory system
  Goh, Journal of bacteriology 2005
  • “...These apparently activated genes were yeaR-yoaG (b1797 and b1796), and the apparently repressed genes were yegE (b2067) and yeiTA (b2146 and b2147). We did...”
• Genome-wide analysis of the response to nitric oxide in uropathogenic Escherichia coli CFT073
  Mehta, Microbial genomics 2015
  • “...Fold change * hlyC c3569 Haemolysin C 253.48 ndk c3041 Nucleoside diphosphate kinase 201.23 yoaG c2202 Hypothetical protein YoaG 167.79 yeaR c2204 Hypothetical protein YeaR 160.21 c2203 c2203 Hypothetical protein 147.10 c2201 c2201 Hypothetical protein 142.23 ytfE c5308 Hypothetical protein YtfE 69.63 hcp c1006 Prismane protein...”
• Disruption of rcsB by a duplicated sequence in a curli-producing Escherichia coli O157:H7 results in differential gene expression in relation to biofilm formation, stress responses and metabolism
  Sharma, BMC microbiology 2017
  • “...ydeH Z2292 Unknown +2.69 2.0E-04 ydeF Z2308 Unknown +2.83 2.7E-06 Z2421 Unknown +1.79 0.03 yoaG Z2838 Unknown +2.54 0.02 Z2839 Unknown +2.36 0.04 Z2893 Unknown 1.61 0.01 rcnB Z3275 Putative nickel/cobalt efflux protein 1.61 0.02 ypeC Z3656 Unknown 23.74 1.9E-17 ypfG Z3722 Unknown 4.58 9.0E-09 Z3965...”
• Gene expression induced in Escherichia coli O157:H7 upon exposure to model apple juice
  Bergholz, Applied and environmental microbiology 2009
  • “...ECs2281 ECs2283 ECs2289 ECs2292 ECs2303 ECs2392 ECs2449 ECs2505 ECs2506 ECs2536 ECs2544 ECs2558 ECs2581 ECs2614 ECs2622 ECs2623 ECs2692 ECs2714 ECs2737 ECs2758...”

STM1272 putative cytoplasmic protein from Salmonella typhimurium LT2
97% identity, 100% coverage

• Stress response, amino acid biosynthesis and pathogenesis genes expressed in Salmonella enterica colonizing tomato shoot and root surfaces
  Han, Heliyon 2020
  • “...synthetase associated 0.006 ygbA STM2860 Nitrous oxide-stimulated promoter; NsrR regulon 3.5 0.002 3.5 0.003 yoaG STM1272 DUF1869 domain-containing protein; NsrR regulon gene 0.004 0.006 ygbE STM2932 inner membrane protein 1.5 0.002 1.7 0.003 yhaK STM3236 pirin domain protein 2.1 0.002 1.4 0.003 yhcN STM3361 Putative outer...”

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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.