PaperBLAST

PaperBLAST Hits for KEDOAH_18880 (70 a.a., MLRDPQLLML...)

Show query sequence

>KEDOAH_18880
MLRDPQLLMLWLRLGDESVNASIDGAAFRVGAGVQADITKNMGAYASLDYTKGDDIENPL
QGVVGINVTW

Running BLASTp...

Found 8 similar proteins in the literature:

ECSE_0327 putative autotransporter from Escherichia coli SE11
98% identity, 8% coverage

• Complete genome sequence and comparative analysis of the wild-type commensal Escherichia coli strain SE11 isolated from a healthy adult
  Oshima, DNA research : an international journal for rapid publication of reports on genes and genomes 2008
  • “...strains (CTF073, UTI89 and 536) possess only four autotransporter genes homologous to four intact genes (ECSE_0327, ECSE_0393, ECSE_2494 and ECSE_3884) in SE11. Absence of orthologs of three genes (ECSE_1215, ECSE_1251 and ECSE_1600) is common in the three strains (CTF073, UTI89 and 536) belonging to phylogenetic group...”
  • “...SE11 Locus Length (aa) Presence in: a MG1655 E24377A HS O157 Sakai CFT073 UTI89 536 ECSE_0327 765 + (+) + + + ECSE_0393 968 (+) + (+) + + + + ECSE_1215 773 (+) + (+) ECSE_1251 961 + + + (+) ECSE_1600 1806 (+) (+)...”

c0426 Hypothetical protein from Escherichia coli CFT073
98% identity, 8% coverage

• Unique structural features of a bacterial autotransporter adhesin suggest mechanisms for interaction with host macromolecules
  Paxman, Nature communications 2019
  • “...purification of UpaB The coding sequence for the upaB alpha domain (residues 38500, locus tag c0426) was PCR-amplified from UPEC CFT073 genomic DNA using primers 4326-UpaB-F and 4327-UpaB-R containing ligation-independent cloning (LIC) overhangs (Supplementary Table 2 ). Using LIC cloning, the amplified gene was inserted into...”
• Evaluation of CpxRA as a Therapeutic Target for Uropathogenic Escherichia coli Infections
  Dbeibo, Infection and immunity 2018
  • “...2.02 3.28 59 60 60 60 60 61 Autotransporters, c0426 upaB Autotransporter 2.21 38 Iron transport and metabolism c1717 c4308 tonB chuA Transport protein TonB...”
• Molecular characterization of UpaB and UpaC, two new autotransporter proteins of uropathogenic Escherichia coli CFT073
  Allsopp, Infection and immunity 2012
  • “...of two closely related AT adhesins from CFT073: UpaB (c0426) and UpaC (c0478). PCR screening revealed that the upaB and upaC AT-encoding genes are common in E....”
  • “...following primers were used: for upaB (c0426), P1 (5=-CGCGCTCGAGATAATAA GGAATGGGAAATTGAAATTAGTTAC) and P2 (5=-CGGCGAAGCTT TTACCAGGTCACATTGATAC); and for upaC...”
• Transcriptome of Escherichia coli K1 bound to human brain microvascular endothelial cells
  Xie, Biochemical and biophysical research communications 2008
  • “...Endo- N -acylneuraminidase, endo- N 109 34 109 55 c0426 Unknown autotransporter protein 121 3 81 13 a HBMEC-association rate of E. coli RS218 was treated as...”
  • “...an unknown autotransporter protein (orthologue of E. coli CFT073 c0426) and deleted it from E. coli RS218 genome. Most of those genes (excepting frdA ) were...”
• Identification of candidates for a subunit vaccine against extraintestinal pathogenic Escherichia coli
  Durant, Infection and immunity 2007
  • “...c0021 c3398 c2525 c4209 c3794 c4776 c1174 c4424 c0345 c0426 c3153 c4849 c2482 c3389 c3391 c4204 c1266 c4423 c2524 c3198 ydeH c4775 Prevalence (%) of antigens in...”

EC958_0459 outer membrane autotransporter HyxB from Escherichia coli O25b:H4-ST131
98% identity, 8% coverage

• The serum resistome of a globally disseminated multidrug resistant uropathogenic Escherichia coli clone
  Phan, PLoS genetics 2013
  • “...hyxRAB ) as previously described in the UPEC strain UTI89 [70] . The hyxB gene (EC958_0459) has also been named upaB due to its function as an autotransporter [71] , and we prefer to maintain this nomenclature. This island is present (in several variations) in 24...”

NRG857_01490 outer membrane autotransporter HyxB from Escherichia coli O83:H1 str. NRG 857C
98% identity, 7% coverage

• Genome sequence of adherent-invasive Escherichia coli and comparative genomic analysis with other E. coli pathotypes
  Nash, BMC genomics 2010
  • “...with copper homeostasis and adhesion 99 0.62 NRG857_01440 putative adhesin S88 putative adhesin 95 0.91 NRG857_01490 putative autotransporter S88 Putative adhesin; putative outer membrane autotransporter barrel 82 0.91 NRG857_03200 hypothetical protein K-12 substr. W3110 predicted fimbrial-like adhesin protein 95 0.26 NRG857_04950 PgaD putative PGA biosynthesis protein...”

EbC_37340 autotransporter outer membrane beta-barrel domain-containing protein from Erwinia billingiae Eb661
47% identity, 10% coverage

• Genome comparison of the epiphytic bacteria Erwinia billingiae and E. tasmaniensis with the pear pathogen E. pyrifoliae
  Kube, BMC genomics 2010
  • “...non-pathogenic E. billingiae is the only species where we identified genes for corresponding autotransporters (EbC_25980, EbC_37340). They show similarities to the AidA domain family, which is mainly present in enteropathogenic bacteria, and pertactin, an autotransporter found in Bordetella sp., respectively. The primary role of the afore...”

STM0373 flagellar protein; similar to 3rd module of ATP-binding components of transporters from Salmonella typhimurium LT2
37% identity, 6% coverage

• Transcriptomic Responses of Salmonella enterica Serovars Enteritidis in Sodium Hypochlorite
  Wang, Frontiers in cellular and infection microbiology 2022
  • “...STM2172 yohG 1.6 multidrug resistance outer membrane protein MdtQ STM0570 apeE 1.2 outer membrane esterase STM0373 yaiU 1.1 autotransporter outer membrane beta-barrel domain-containing protein STM0196 stfC 2.0 fimbrial biogenesis outer membrane usher protein STM1460 ydgK 1.4 Inner membrane protein ydgK STM1571 yddG 2.4 inner membrane protein...”

SPA2350 putative flagellin structural protein from Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150
37% identity, 6% coverage

• Identification of Salmonella enterica serovar Dublin-specific sequences by subtractive hybridization and analysis of their role in intestinal colonization and systemic translocation in cattle
  Pullinger, Infection and immunity 2008
  • “...of the S. enterica serovar Paratyphi A gene product, SPA2350. Although the N-terminal region of this protein is unusual, the C terminus is highly conserved in a...”

SEN0356 puative autotransporter/virulence factor from Salmonella enterica subsp. enterica serovar Enteritidis str. P125109
37% identity, 5% coverage

• Genomic Comparison of the Closely Related Salmonella enterica Serovars Enteritidis and Dublin
  Betancor, The open microbiology journal 2012
  • “...fhuA , ferrichrome iron receptor Sing En2 SEN0281 NO safA , fimbrial subunit Sing En3 SEN0356 SGAL putative autotransporter Sing En4 SEN1515 CT18, TY2, LT2, DT104, SL1344, SBG, SPA, SGAL Ni/Fe-hydrogenase 1 b-type cytochrome subunit HyaC2 Sing En5 SEN1539 CT18, TY2, LT2, DT104, SL1344, SBG, SPA,...”

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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.