PaperBLAST

PaperBLAST Hits for KEDOAH_12675 (47 a.a., MNAFKQLHQS...)

Show query sequence

>KEDOAH_12675
MNAFKQLHQSKDEVFERGVINVFRGPNGITKPIPPVNSAVKLSSTTW

Running BLASTp...

Found 7 similar proteins in the literature:

c3680 Conserved hypothetical protein from Escherichia coli CFT073
84% identity, 9% coverage

• Comparison of probe hybridization array typing to multilocus sequence typing for pathogenic Escherichia coli
  McNamara, Journal of clinical microbiology 2009
  • “...coli CFT073 included c0286, c0311, c0340, c1164, c1600, c3389, and c3680 (named after the gene locus tag for E. coli CFT073 in the NCBI database). The gene that...”
  • “...(c4836), c0286, c0311, c0340, c1164, c1600, c3386, c3389, and c3680. The primers for the following probes were designed from the S. flexneri 2457T locus number...”

ECs1409 hypothetical protein from Escherichia coli O157:H7 str. Sakai
Z1226 unknown from Escherichia coli O157:H7 EDL933
Z1664 unknown from Escherichia coli O157:H7 EDL933
78% identity, 10% coverage

• Association of the urease gene with enterohemorrhagic Escherichia coli strains irrespective of their serogroups
  Nakano, Journal of clinical microbiology 2001
  • “...(20-mer) 5-ACCAGTCTTCATCGCTGTCA-3 (20-mer) 883 60 1409-1 1409-2 ECs1409 L0010 7 5-ATATCACAATCTCCCGTCCG-3 (20-mer) 5-AGTCTGTCAACCAGTTCTGG-3 (20-mer) 790 63 a b c...”
• Duplication and diversification of a unique chromosomal virulence island hosting the subtilase cytotoxin in Escherichia coli ST58
  Wyrsch, Microbial genomics 2020
  • “...haemolysin expression-modulating protein. Both islands also have an IS Sfl8 -like element inserted into a Z1226 protein (putative RNA-directed DNA polymerase activity ), likely a once unique feature now shared by both PAI-1 and PAI-2, supporting the contention these islands were once a single element. Given...”
  • “...the acquired O-antigen lipopolysaccharide (see Fig. 1 ), but this copy did not include the Z1226 protein or the insertion, so the evolutionary relevance of its presence remains unresolved. A comparison of GC content of this potentially homologous region (Fig. S1, available in the online version...”
• Determination of virulence and fitness genes associated with the pheU, pheV and selC integration sites of LEE-negative food-borne Shiga toxin-producing Escherichia coli strains
  Saile, Gut pathogens 2018
  • “...protein x DUF2251 containing protein x DUF1705 containing protein x DUF2569 containing protein x Methyltransferases Z1226 a x x x x x DNA-cytosine methyltransferase x B12 uptake system TonB-dependent receptor a x x Outer membrane vitamin B12 receptor BtuB x x Hemolysin/hemagglutinin Putative member of ShlA/HecA/FhaA...”
  • “...described as being encoded in PAI II of UPEC strain 536. CDS 60, annotated as Z1226 with 99% identity to a restriction methylase, is also found in the mentioned strain encoded on PAI V and homologs are found in UPEC strain CFT073. Also CDS 4960 and...”
• A selC-associated genomic island of the extraintestinal avian pathogenic Escherichia coli strain BEN2908 is involved in carbohydrate uptake and virulence
  Chouikha, Journal of bacteriology 2006
  • “...coli RW1374 (5e-87) ORF104, E. coli RW1374 (1e-29) Z1226 protein, E. coli 536 (e-151) (Truncated ORF) Hypothetical protein c4580, E. coli CFT073 (5e-34)...”
• Global expression of prophage genes in Escherichia coli O157:H7 strain EDL933 in response to norfloxacin
  Herold, Antimicrobial agents and chemotherapy 2005
  • “...6068 5226 3495 4069 Z1120, Z1559a Z1180, Z1619a Z1226, Z1664a Z1555a Z2083, Z2152a Z2242 Z5070a Z5129a Z5136a Z5182a Z5906a Putative P4 family integrase,...”
• A mosaic pathogenicity island made up of the locus of enterocyte effacement and a pathogenicity island of Escherichia coli O157:H7 is frequently present in attaching and effacing E. coli
  Morabito, Infection and immunity 2003
  • “...Target gene Z0262 Z0260 Z0245 Z1214 terA Z1128 clpA Z1120 Z1226 serW ycdU Z1559 Z1664 serX Z4334 Z4336 Z4326 efa1 5 region efa1 3 region espF GenBank accession...”
• Catalytic efficiency and vitality of HIV-1 proteases from African viral subtypes
  Velazquez-Campoy, Proceedings of the National Academy of Sciences of the United States of America 2001
  • “...no. AF009410), C2220 (Ethiopia, GenBank no. U461016), Z1226 (Zimbabwe, GenBank no. AF083603), 96BW01 (Botswana, GenBank no. AF110959) and C11 (Zambia, GenBank...”
• Chromosomal instability in enterohaemorrhagic Escherichia coli O157:H7: impact on adherence, tellurite resistance and colony phenotype
  Bielaszewska, Molecular microbiology 2011
  • “...from ORF Z1638 (strain 134S) or Z1648 (strains 81S and 154S) to the last gene (Z1664) ( 26 and 16 kb, respectively) ( Fig. 2 ). Large ( 5362 kb) internal OI 48 regions were absent ( Fig. 2 ). Analysis of deletions in truncated OI...”
• A mosaic pathogenicity island made up of the locus of enterocyte effacement and a pathogenicity island of Escherichia coli O157:H7 is frequently present in attaching and effacing E. coli
  Morabito, Infection and immunity 2003
  • “...Z1214 terA Z1128 clpA Z1120 Z1226 serW ycdU Z1559 Z1664 serX Z4334 Z4336 Z4326 efa1 5 region efa1 3 region espF GenBank accession number (nucleotide position)...”

BI323_00080, CSF007_RS15805, DJ39_RS07890 DUF4942 domain-containing protein from Yersinia ruckeri ATCC 29473
76% identity, 9% coverage

• Comparative genome analysis reveals important genetic differences among serotype O1 and serotype O2 strains of Y. ruckeri and provides insights into host adaptation and virulence
  Cascales, MicrobiologyOpen 2017
  • “...Eco57I restrictionmodification methylase family protein BI323_06175 DJ39_RS04570 CSF007_RS05790 Type I restrictionmodification system, restriction subunit R BI323_00080 DJ39_RS07890 CSF007_RS15805 Type I restrictionmodification system, DNAmethyltransferase subunit M BI323_00010 DJ39_RS07820 CSF007_RS15875 Restriction methylase BI323_06275 DJ39_RS04465 CSF007_RS05895 Restriction methylase BI323_07120 DJ39_RS07795 CSF007_RS06135 Antirestriction family protein BI323_06250 DJ39_RS04490 CSF007_RS05870 Antirestriction family...”
  • “...methylase family protein BI323_06175 DJ39_RS04570 CSF007_RS05790 Type I restrictionmodification system, restriction subunit R BI323_00080 DJ39_RS07890 CSF007_RS15805 Type I restrictionmodification system, DNAmethyltransferase subunit M BI323_00010 DJ39_RS07820 CSF007_RS15875 Restriction methylase BI323_06275 DJ39_RS04465 CSF007_RS05895 Restriction methylase BI323_07120 DJ39_RS07795 CSF007_RS06135 Antirestriction family protein BI323_06250 DJ39_RS04490 CSF007_RS05870 Antirestriction family protein BI323_000601...”
  • “...restrictionmodification methylase family protein BI323_06175 DJ39_RS04570 CSF007_RS05790 Type I restrictionmodification system, restriction subunit R BI323_00080 DJ39_RS07890 CSF007_RS15805 Type I restrictionmodification system, DNAmethyltransferase subunit M BI323_00010 DJ39_RS07820 CSF007_RS15875 Restriction methylase BI323_06275 DJ39_RS04465 CSF007_RS05895 Restriction methylase BI323_07120 DJ39_RS07795 CSF007_RS06135 Antirestriction family protein BI323_06250 DJ39_RS04490 CSF007_RS05870 Antirestriction family protein...”

UTI89_C1152 hypothetical protein from Escherichia coli UTI89
76% identity, 9% coverage

• Cathelicidin Peptides Restrict Bacterial Growth via Membrane Perturbation and Induction of Reactive Oxygen Species
  Rowe-Magnus, mBio 2019
  • “...protein cspA UTI89_C2541 1.44 1.21E08 Undecaprenyl phosphate- l -ara4N flippase subunit arnF ( yfbJ ) UTI89_C1152 1.40 9.36E10 Hypothetical protein orf UTI89_C0130 1.39 2.93E05 Hypothetical protein yacH UTI89_C1870 1.34 5.84E05 Peptidoglycan d -transpeptidase ynhG UTI89_C0026 1.32 4.08E09 Hypothetical protein yaaY UTI89_C3182 1.31 4.40E09 Hypothetical protein ygdI...”

c1292 Conserved hypothetical protein from Escherichia coli CFT073
76% identity, 9% coverage

• Genomic islands of uropathogenic Escherichia coli contribute to virulence
  Lloyd, Journal of bacteriology 2009
  • “...ogrK Nucleotide 232 of c1165 to nucleotide 664 of c1292 Nucleotide 772 of c1400 to nucleotide 242 of c1506 172 nucleotides upstream of c2418 to nucleotide 657...”

S3207 hypothetical protein from Shigella flexneri 2a str. 2457T
SF3002 orf, conserved hypothetical protein from Shigella flexneri 2a str. 301
76% identity, 9% coverage

• Protection of bacteriophage-sensitive Escherichia coli by lysogens
  Brown, Proceedings of the National Academy of Sciences of the United States of America 2022
  • “...of Phage-Sensitive Bacteria. We infected a mixed population of sensitive bacteria, S3137, and immune bacteria, S3207, with cIb221 at a low initial multiplicity of infection (MOI = 0.003). We allowed the infected, mixed cultures to grow to saturation. Under these conditions in uninfected mixed cultures, S3137...”
  • “...in mixed cultures are summarized in Table1 . The majority of S3137 bacteria survived when S3207 as the immune strain represented 98% or more of the initial mixed population. There was low or no detectable survival of S3137 when S3207 represented 95% or less of the...”
• Extensive gene diversity in septicemic Escherichia coli strains
  Mokady, Journal of clinical microbiology 2005
  • “...of California, Berkeley Shigella flexneri 2a strain 301 SF3002 Function EXTENSIVE DIVERSITY OF SEPTICEMIC E. COLI VOL. 43, 2005 69 TABLE 1--Continued Sequence...”

BI323_06275, CSF007_RS05895, DJ39_RS04465 DUF4942 domain-containing protein from Yersinia ruckeri
72% identity, 9% coverage

• Comparative genome analysis reveals important genetic differences among serotype O1 and serotype O2 strains of Y. ruckeri and provides insights into host adaptation and virulence
  Cascales, MicrobiologyOpen 2017
  • “...BI323_00080 DJ39_RS07890 CSF007_RS15805 Type I restrictionmodification system, DNAmethyltransferase subunit M BI323_00010 DJ39_RS07820 CSF007_RS15875 Restriction methylase BI323_06275 DJ39_RS04465 CSF007_RS05895 Restriction methylase BI323_07120 DJ39_RS07795 CSF007_RS06135 Antirestriction family protein BI323_06250 DJ39_RS04490 CSF007_RS05870 Antirestriction family protein BI323_000601 DJ39_RS07870 CSF007_RS15825 Toxinantitoxin systems YfjZ protein (Antitoxin to YpjF) BI323_00070 DJ39_RS07880 CSF007_RS15815 Toxin...”
  • “...CSF007_RS15805 Type I restrictionmodification system, DNAmethyltransferase subunit M BI323_00010 DJ39_RS07820 CSF007_RS15875 Restriction methylase BI323_06275 DJ39_RS04465 CSF007_RS05895 Restriction methylase BI323_07120 DJ39_RS07795 CSF007_RS06135 Antirestriction family protein BI323_06250 DJ39_RS04490 CSF007_RS05870 Antirestriction family protein BI323_000601 DJ39_RS07870 CSF007_RS15825 Toxinantitoxin systems YfjZ protein (Antitoxin to YpjF) BI323_00070 DJ39_RS07880 CSF007_RS15815 Toxin YkfI BI323_00075...”
  • “...DJ39_RS07890 CSF007_RS15805 Type I restrictionmodification system, DNAmethyltransferase subunit M BI323_00010 DJ39_RS07820 CSF007_RS15875 Restriction methylase BI323_06275 DJ39_RS04465 CSF007_RS05895 Restriction methylase BI323_07120 DJ39_RS07795 CSF007_RS06135 Antirestriction family protein BI323_06250 DJ39_RS04490 CSF007_RS05870 Antirestriction family protein BI323_000601 DJ39_RS07870 CSF007_RS15825 Toxinantitoxin systems YfjZ protein (Antitoxin to YpjF) BI323_00070 DJ39_RS07880 CSF007_RS15815 Toxin YkfI...”

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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.